Citations
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This panel provides information on past usage of this interatomic potential (IP) powered by the OpenKIM Deep Citation framework. The word cloud indicates typical applications of the potential. The bar chart shows citations per year of this IP (bars are divided into articles that used the IP (green) and those that did not (blue)). The complete list of articles that cited this IP is provided below along with the Deep Citation determination on usage. See the Deep Citation documentation for more information.
3660 Citations (800 used)
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USED (definite) Z. Fan, J. Ding, and E. Ma, “Making glassy solids ductile at room temperature by imparting flexibility into their amorphous structure,” Materials Research Letters. 2018. link Times cited: 15 Abstract: ABSTRACT Making glasses ductile at room temperature is a dau… read moreAbstract: ABSTRACT Making glasses ductile at room temperature is a daunting challenge, but has been shown to be feasible in recent years. We explain the plastic flow from the standpoint of the flexibility available in the amorphous structure: imparting flexibility into the structure facilitates bond switching needed to mediate shear transformations to carry strain. This structure–property correlation is demonstrated using molecular dynamics simulation data. The flexibility can be improved via ultrafast quench or rejuvenation. In particular, the flexibility volume parameter offers a quantitative metric to explain the flexibility and deformability, even for glasses where the commonly cited free volume is not applicable. GRAPHICAL ABSTRACT IMPACT STATEMENT This Perspective demonstrates using examples and models that it is the flexibility rather than the excess volume that can be tuned to facilitate plastic flow and ductility in glassy materials. read less USED (definite) B. A. Raubenolt, G. Gyawali, W. Tang, K. Wong, and S. Rick, “Coarse-Grained Simulations of Aqueous Thermoresponsive Polyethers,” Polymers. 2018. link Times cited: 13 Abstract: Thermoresponsive polymers can change structure or solubility… read moreAbstract: Thermoresponsive polymers can change structure or solubility as a function of temperature. Block co-polymers of polyethers have a response that depends on polymer molecular weight and co-polymer composition. A coarse-grained model for aqueous polyethers is developed and applied to polyethylene oxide and polyethylene oxide-polypropylene oxide-polyethylene oxide triblock co-polymers. In this model, no interaction sites on hydrogen atoms are included, no Coulombic interactions are present, and all interactions are short-ranged, treated with a combination of two- and three-body terms. Our simulations find that The triblock co-polymers tend to associate at temperatures above 350 K. The aggregation is stabilized by contact between The hydrophobic methyl groups on The propylene oxide monomers and involves a large, favorable change in entropy. read less USED (definite) M. Isaiev et al., “Gibbs Adsorption Impact on a Nanodroplet Shape: Modification of Young-Laplace Equation.,” The journal of physical chemistry. B. 2017. link Times cited: 13 Abstract: We present an efficient technique for the evaluation of the … read moreAbstract: We present an efficient technique for the evaluation of the Gibbs adsorption of a liquid on a solid substrate. The behavior of a water nanodroplet on a silicon surface is simulated with molecular dynamics. An external field with varying strength is applied on the system to tune the solid-liquid interfacial contact area. A linear dependence of droplet's volume as a function of the contact area is observed. We introduce a modified Young-Laplace equation to explain the influence of the Gibbs adsorption on the nanodroplet volume contraction. Fitting of the molecular dynamics results with the analytical approach allows us to evaluate the number of atoms per unit area adsorbed on the substrate, which quantifies the Gibbs adsorption. Thus, a threshold of a droplet size is obtained, for which the impact of the adsorption is crucial. For instance, a water droplet with 5 nm radius has 3% of its molecules adsorbed on silicon substrate, while for droplets less than 1 nm this amount is more than 10%. The presented results could be beneficial for the evaluation of the adsorption impact on the physical-chemical properties of nanohybrid systems with large surface-to-volume ration. read less USED (definite) G. P. P. Pun and Y. Mishin, “Optimized interatomic potential for silicon and its application to thermal stability of silicene,” Physical Review B. 2017. link Times cited: 35 Abstract: An optimized interatomic potential has been constructed for … read moreAbstract: An optimized interatomic potential has been constructed for silicon using a modified Tersoff model. The potential reproduces a wide range of properties of Si and improves over existing potentials with respect to point defect structures and energies, surface energies and reconstructions, thermal expansion, melting temperature, and other properties. The proposed potential is compared with three other potentials from the literature. The potentials demonstrate reasonable agreement with first-principles binding energies of small Si clusters as well as single-layer and bilayer silicenes. The four potentials are used to evaluate the thermal stability of free-standing silicenes in the form of nanoribbons, nanoflakes, and nanotubes. While single-layer silicene is found to be mechanically stable at zero Kelvin, it is predicted to become unstable and collapse at room temperature. By contrast, the bilayer silicene demonstrates a larger bending rigidity and remains stable at and even above room temperature. The results suggest that bilayer silicene might exist in a free-standing form at ambient conditions. read less USED (definite) T. Aoki, T. Seki, and J. Matsuo, “Molecular dynamics simulations study of nano particle migration by cluster impact,” Surface & Coatings Technology. 2016. link Times cited: 3 USED (definite) S. Chavoshi, S. Xu, and X. Luo, “Dislocation-mediated plasticity in silicon during nanometric cutting : a molecular dynamics simulation study materials science in semiconductor processing,” Materials Science in Semiconductor Processing. 2016. link Times cited: 50 USED (definite) R. Aghababaei, D. Warner, and J. Molinari, “Critical length scale controls adhesive wear mechanisms,” Nature Communications. 2016. link Times cited: 201 USED (definite) A. Bhowmik et al., “Classical molecular dynamics and quantum ab-initio studies on lithium-intercalation in interconnected hollow spherical nano-spheres of amorphous silicon,” Journal of Alloys and Compounds. 2016. link Times cited: 6 USED (definite) D. Varshney, S. Shriya, M. Varshney, N. Singh, and R. Khenata, “Elastic and thermodynamical properties of cubic (3C) silicon carbide under high pressure and high temperature,” Journal of Theoretical and Applied Physics. 2015. link Times cited: 27 USED (definite) N. Mousseau et al., “Following atomistic kinetics on experimental timescales with the kinetic Activation–Relaxation Technique,” Computational Materials Science. 2015. link Times cited: 27 USED (definite) J. Kermode, G. Peralta, Z. Li, and A. Vita, “Multiscale Modelling of Materials Chemomechanics: Brittle Fracture of Oxides and Semiconductors,” Procedia Materials Science. 2014. link Times cited: 3 USED (definite) K. Das, J. Freund, and H. T. Johnson, “A FIB induced boiling mechanism for rapid nanopore formation,” Nanotechnology. 2014. link Times cited: 7 Abstract: Focused ion beam (FIB) technology is widely used to fabricat… read moreAbstract: Focused ion beam (FIB) technology is widely used to fabricate nanopores in solid-state membranes. These nanopores have desirable thermomechanical properties for applications such as high-throughput DNA sequencing. Using large scale molecular dynamics simulations of the FIB nanopore formation process, we show that there is a threshold ion delivery rate above which the mechanism underlying nanopore formation changes. At low rates nanopore formation is slow, with the rate proportional to the ion flux and therefore limited by the sputter rate of the target material. However, at higher fluxes nanopores form via a thermally dominated process, consistent with an explosive boiling mechanism. In this case, mass is rapidly rearranged via bubble growth and coalescence, much more quickly than would occur during sputtering. This mechanism has the potential to greatly speed up nanopore formation. read less USED (definite) X. Zhang, M. Hu, K. Giapis, and D. Poulikakos, “Schemes for and Mechanisms of Reduction in Thermal Conductivity in Nanostructured Thermoelectrics,” Journal of Heat Transfer-transactions of The Asme. 2012. link Times cited: 20 Abstract: Nonequilibrium molecular dynamics (NEMD) simulations were pe… read moreAbstract: Nonequilibrium molecular dynamics (NEMD) simulations were performed to investigate schemes for enhancing the energy conversion efficiency of thermoelectric nanowires (NWs), including (1) roughening of the nanowire surface, (2) creating nanoparticle inclusions in the nanowires, and (3) coating the nanowire surface with other materials. The enhancement in energy conversion efficiency was inferred from the reduction in thermal conductivity of the nanowire, which was calculated by imposing a temperature gradient in the longitudinal direction. Compared to pristine nanowires, our simulation results show that the schemes proposed above lead to nanocomposite structures with considerably lower thermal conductivity (up to 82% reduction), implying ~5X enhancement in the ZT coefficient. This significant effect appears to have two origins: (1) increase in phonon-boundary scattering and (2) onset of interfacial interference. The results suggest new fundamental–yet realizable ways to improve markedly the energy conversion efficiency of nanostructured thermoelectrics. read less USED (definite) D. Demchenko, P. D. Heinz, and B. Lee, “Determining factors of thermoelectric properties of semiconductor nanowires,” Nanoscale Research Letters. 2011. link Times cited: 22 USED (definite) G. Zhang, “Nanowire Applications: Thermoelectric Cooling and Energy Harvesting.” 2011. link Times cited: 6 Abstract: Recently, thermoelectric materials have attracted extensive … read moreAbstract: Recently, thermoelectric materials have attracted extensive attention again. This is primarily due to the increasing awareness of the deleterious effect of global warming on the planet’s environment, a renewed requirement for long-life electrical power sources, and the increasing miniaturization of electronic circuits and sensors. Thermoelectrics is able to make a contribution to meet the requirements of all the above activities. Moreover, the advent of nanotechnology has had a dramatic effect on thermoelectric material development and has resulted in the syntheses of nanostructured materials whose thermoelectric properties surpass the best performance of its bulk counter, such as Silicon nanowires (SiNWs). (Boukai et al., 2008; Hochbaum et al., 2008) SiNWs are appealing choice in the novel nanoscale TE materials because of their small sizes and ideal interface compatibility with conventional Si-based technology. For a good thermoelectric material, the material must have a high figure of merit (ZT), which is proportional to the Seebeck coefficient (S), electrical conductivity, and absolute temperature, but inversely proportional to thermal conductivity. In order to make materials that are competitive for (commercial) thermoelectric application, the ZT of the material must be larger than three. There are several ways to do this. The first approach is to increase the Seebeck coefficient S. However, for general materials, simply increase S will lead to a simultaneous decrease in electrical conductivity. The second approach is to increase the electrical conductivity. This has also proven to be ineffective, because electrons are also carriers of heat and an increase in electrical conductivity will also lead to an increase in the thermal conductivity. The ideal case is to reduce the thermal conductivity without affecting the electrical conductivity. It is possible to achieve this in SiNWs. In SiNWs, the electrical conductivity and electron contribution to Seebeck coefficient are similar to those of bulk silicon, but exhibit 100-fold reduction in thermal conductivity, showing that the electrical and thermal conductivities are decoupled. Recent experiments have provided direct evidence that an approximately 100fold improvement of the ZT values over bulk Si are achieved in SiNW over a broad temperature range. (Boukai et al., 2008; Hochbaum et al., 2008) This large increase of ZT is contributed by the decrease of thermal conductivity. SiNWs have attracted broad interests in recently years due to their fascinating potential applications. Extensive investigations have been carried out on the synthesis, properties and applications of SiNWs. Experimental read less USED (definite) J. Samela, S. Norris, K. Nordlund, and M. Aziz, “Optimization of large amorphous silicon and silica structures for molecular dynamics simulations of energetic impacts,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2011. link Times cited: 10 USED (definite) J. Bai, H. Tanaka, and X. Zeng, “Graphene-like bilayer hexagonal silicon polymorph,” Nano Research. 2010. link Times cited: 42 USED (definite) N. Dugan and S. Erkoç, “Genetic Algorithms in Application to the Geometry Optimization of Nanoparticles,” Algorithms. 2009. link Times cited: 21 Abstract: Applications of genetic algorithms to the global geometry op… read moreAbstract: Applications of genetic algorithms to the global geometry optimization problem of nanoparticles are reviewed. Genetic operations are investigated and importance of phenotype genetic operations, considering the geometry of nanoparticles, are mentioned. Other efficiency improving developments such as floating point representation and local relaxation are described broadly. Parallelization issues are also considered and a recent parallel working single parent Lamarckian genetic algorithm is reviewed with applications on carbon clusters and SiGe core-shell structures. read less USED (definite) E. Silva, C. J. Först, J. Li, X. Lin, T. Zhu, and S. Yip, “MULTISCALE MATERIALS MODELLING: CASE STUDIES AT THE ATOMISTIC AND ELECTRONIC STRUCTURE LEVELS ∗,” Mathematical Modelling and Numerical Analysis. 2007. link Times cited: 4 Abstract: Although the intellectual merits of computational modelling … read moreAbstract: Although the intellectual merits of computational modelling across various length and time scales are generally well accepted, good illustrative examples are often lacking. One way to begin appreciating the benefits of the multiscale approach is to first gain experience in probing complex physical phenomena at one scale at a time. Here we discuss materials modelling at two characteris- tic scales separately, the atomistic level where interactions are specified through classical potentials and the electronic level where interactions are treated quantum mechanically. The former is generally sufficient for dealing with mechanical deformation at large strain, whereas the latter is necessary for treating chemical reactions or electronic transport. We will discuss simulations of defect nucleation using molecular dynamics, the study of water-silica reactions using a tight-binding approach, the design of a semiconductor-oxide interface using density functional theory, and the analysis of conjugated poly- mer in molecular actuation using Hartree-Fock calculations. The diversity of the problems discussed notwithstanding, our intent is to lay the groundwork for future problems in materials research, a few will be mentioned, where modelling at the electronic and atomistic scales are needed in an integrated fashion. It is in these problems that the full potential of multiscale modelling can be realized. read less USED (definite) T. Zhu, J. Li, and S. Yip, “Atomistic characterization of three-dimensional lattice trapping barriers to brittle fracture,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2006. link Times cited: 39 Abstract: We present a detailed account of an atomistic study of three… read moreAbstract: We present a detailed account of an atomistic study of three-dimensional lattice trapping barriers to brittle fracture in Si. By means of a prototypical interatomic potential model, we map out the molecular details of the evolution of atomically sharp cracks in the (111) cleavage plane with straight crack fronts along the and directions, respectively. The thermally activated processes of bond rupturing along the crack front are quantitatively characterized using a reaction pathway sampling scheme. The calculated minimum energy paths reveal a mechanism of kink-pair formation and migration in facilitating the crack front advancement. We show that the physical origin of directional anisotropy in cleavage crack propagation can be attributed to a difference in the kink-pair formation energy for different crack orientations. The effects of interatomic potentials are delineated by comparing the Stillinger–Weber model with an environment-dependent model. read less USED (definite) J. Li, M. Dao, C. T. Lim, and S. Suresh, “Spectrin-level modeling of the cytoskeleton and optical tweezers stretching of the erythrocyte.,” Biophysical journal. 2005. link Times cited: 411 Abstract: We present a three-dimensional computational study of whole-… read moreAbstract: We present a three-dimensional computational study of whole-cell equilibrium shape and deformation of human red blood cell (RBC) using spectrin-level energetics. Random network models consisting of degree-2, 3, ..., 9 junction complexes and spectrin links are used to populate spherical and biconcave surfaces and intermediate shapes, and coarse-grained molecular dynamics simulations are then performed with spectrin connectivities fixed. A sphere is first filled with cytosol and gradually deflated while preserving its total surface area, until cytosol volume consistent with the real RBC is reached. The equilibrium shape is determined through energy minimization by assuming that the spectrin tetramer links satisfy the worm-like chain free-energy model. Subsequently, direct stretching by optical tweezers of the initial equilibrium shape is simulated to extract the variation of axial and transverse diameters with the stretch force. At persistence length p = 7.5 nm for the spectrin tetramer molecule and corresponding in-plane shear modulus mu(0) approximately 8.3 microN/m, our models show reasonable agreement with recent experimental measurements on the large deformation of RBC with optical tweezers. We find that the choice of the reference state used for the in-plane elastic energy is critical for determining the equilibrium shape. If a position-independent material reference state such as a full sphere is used in defining the in-plane energy, then the bending modulus kappa needs to be at least a decade larger than the widely accepted value of 2 x 10(-19) J to stabilize the biconcave shape against the cup shape. We demonstrate through detailed computations that this paradox can be avoided by invoking the physical hypothesis that the spectrin network undergoes constant remodeling to always relax the in-plane shear elastic energy to zero at any macroscopic shape, at some slow characteristic timescale. We have devised and implemented a liquefied network structure evolution algorithm that relaxes shear stress everywhere in the network and generates cytoskeleton structures that mimic experimental observations. read less USED (definite) R. Rudd and J. Broughton, “Coupling of length scales and atomistic simulation of MEMS resonators,” Design, Test, Integration, and Packaging of MEMS/MOEMS. 1998. link Times cited: 2 Abstract: We present simulations of the dynamic and temperature depend… read moreAbstract: We present simulations of the dynamic and temperature dependent behavior of Micro-Electro-Mechanical Systems (MEMS) by utilizing recently developed parallel codes which enable a coupling of length scales. The novel techniques used in this simulation accurately model the behavior of the mechanical components of MEMS down to the atomic scale. We study the vibrational behavior of one class of MEMS devices: micron-scale resonators made of silicon and quartz. The algorithmic and computational avenue applied here represents a significant departure from the usual finite element approach based on continuum elastic theory. The approach is to use an atomistic simulation in regions of significantly anharmonic forces and large surface area to volume ratios or where internal friction due to defects using finite elements for efficiency. Thus, in central regions of the device, the motion of millions of individual atoms is simulated, while the relatively large peripheral regions are modeled with finite elements. The two techniques run concurrently and mesh seamlessly, passing information back and forth. We present novel simulations of the vibrational behavior of micro-scale silicon and quartz oscillators. Our result are contrasted with the predictions of continuum elastic theory as a function of size, and the failure of the continuum techniques is clear in the limit of small sizes. We also extract the Q value for the resonators and study the corresponding dissipative processes. read less USED (high confidence) S. Miyakawa et al., “Computational studies on defect chemistry and Li-ion conductivity of spinel-type LiAl5O8 as coating material for Li-metal electrode,” Scientific Reports. 2022. link Times cited: 3 USED (high confidence) J. Hu, H. Song, S. Sandfeld, X. Liu, and Y. Wei, “Breakdown of Archard law due to transition of wear mechanism from plasticity to fracture,” Tribology International. 2022. link Times cited: 10 USED (high confidence) Z. Zhang, Y. Guo, M. Bescond, J. Chen, M. Nomura, and S. Volz, “How coherence is governing diffuson heat transfer in amorphous solids,” npj Computational Materials. 2022. link Times cited: 15 USED (high confidence) K. Zongo, Béland, and O. ‐ Plamondon, “First-principles database for fitting a machine-learning silicon interatomic force field,” MRS Advances. 2022. link Times cited: 0 Abstract: Data-driven machine learning has emerged to address the limi… read moreAbstract: Data-driven machine learning has emerged to address the limitations of traditional methods when modeling interatomic interactions in materials, such as electronic density functional theory (DFT) and semi-empirical potentials. These machine-learning frameworks involve mathematical models coupled to quantum mechanical data. In the present article, we focus on the moment tensor potential (MTP) machine-learning framework. More specifically, we provide an account of the development of a preliminary MTP for silicon, including details pertaining to the construction of a DFT database. read less USED (high confidence) R. Ahmad and W. Cai, “Free energy calculation of crystalline solids using normalizing flows,” Modelling and Simulation in Materials Science and Engineering. 2021. link Times cited: 7 Abstract: Taking advantage of the advances in generative deep learning… read moreAbstract: Taking advantage of the advances in generative deep learning, particularly normalizing flow, a framework, called Boltzmann generator, has recently been proposed to generate equilibrium atomic configurations from the canonical ensemble and determining the associated free energy. In this work, we revisit Boltzmann generator to motivate the construction of the loss function from the statistical mechanical point of view and to cast the training of the normalizing flow model in a purely unsupervised manner that does not require any sample of the atomic configurations from the equilibrium ensemble. We further show that the normalizing flow framework furnishes a reference thermodynamic system, very close to the real thermodynamic system under consideration, that is suitable for the well-established free energy perturbation methods to determine accurate free energy of solids. We then apply the normalizing flow to two problems: temperature-dependent Gibbs free energy of perfect crystal and formation free energy of monovacancy defect in a model system of diamond cubic Si. The results obtained from the normalizing flow are shown to be in good agreement with that obtained from independent well-established free energy methods. read less USED (high confidence) K. Li et al., “Phonon resonant effect in silicon membranes with different crystallographic orientations,” International Journal of Heat and Mass Transfer. 2021. link Times cited: 9 USED (high confidence) D. Freeman, A. Kheifets, S. Yamada, A. Yamada, and K. Yabana, “High-order harmonic generation in semiconductors driven at near- and mid-infrared wavelengths,” Physical Review B. 2021. link Times cited: 2 Abstract: We study high order harmonics generation (HHG) in crystallin… read moreAbstract: We study high order harmonics generation (HHG) in crystalline silicon and diamond subjected to near and mid-infrared laser pulses. We employ time-dependent density functional theory and solve the time-dependent Kohn-Sham equation in the single-cell geometry. We demonstrate that clear and clean HHG spectra can be generated with careful selection of the pulse duration. In addition, we simulate dephasing effects in a large silicon super-cell through a displacement of atomic positions prepared by a molecular dynamics simulation. We compare our results with the previous calculations by Floss et al. [Phys. Rev. A 97 , 011401(R) (2018)] on Diamond at 800 nm and by Tancogne-Dejean et al. [Phys. Rev. Lett. 118 , 087403 (2017)] on Si at 3000 nm. read less USED (high confidence) L. Bonati, G. Piccini, and M. Parrinello, “Deep learning the slow modes for rare events sampling,” Proceedings of the National Academy of Sciences. 2021. link Times cited: 80 Abstract: Significance The use of enhanced sampling simulations is ess… read moreAbstract: Significance The use of enhanced sampling simulations is essential in the study of complex physical, chemical, and biological processes. We devise a procedure that, by combining machine learning and biased simulations, removes the bottlenecks that hinder convergence. This approach allows different types of challenging processes to be studied in a near-blind way, thus extending significantly the scope of atomistic simulations. The development of enhanced sampling methods has greatly extended the scope of atomistic simulations, allowing long-time phenomena to be studied with accessible computational resources. Many such methods rely on the identification of an appropriate set of collective variables. These are meant to describe the system’s modes that most slowly approach equilibrium under the action of the sampling algorithm. Once identified, the equilibration of these modes is accelerated by the enhanced sampling method of choice. An attractive way of determining the collective variables is to relate them to the eigenfunctions and eigenvalues of the transfer operator. Unfortunately, this requires knowing the long-term dynamics of the system beforehand, which is generally not available. However, we have recently shown that it is indeed possible to determine efficient collective variables starting from biased simulations. In this paper, we bring the power of machine learning and the efficiency of the recently developed on the fly probability-enhanced sampling method to bear on this approach. The result is a powerful and robust algorithm that, given an initial enhanced sampling simulation performed with trial collective variables or generalized ensembles, extracts transfer operator eigenfunctions using a neural network ansatz and then accelerates them to promote sampling of rare events. To illustrate the generality of this approach, we apply it to several systems, ranging from the conformational transition of a small molecule to the folding of a miniprotein and the study of materials crystallization. read less USED (high confidence) J. Moon, “Examining normal modes as fundamental heat carriers in amorphous solids: The case of amorphous silicon,” Journal of Applied Physics. 2021. link Times cited: 11 Abstract: Normal mode decomposition of atomic vibrations has been used… read moreAbstract: Normal mode decomposition of atomic vibrations has been used to provide microscopic understanding of thermal transport in amorphous solids for decades. In normal mode methods, it is naturally assumed that atoms vibrate around their equilibrium positions and that individual normal modes are the fundamental vibrational excitations transporting heat. With the abundance of predictions from normal mode methods and experimental measurements now available, we carefully analyze these calculations in amorphous silicon, a model amorphous solid. We find a number of discrepancies, suggesting that treating individual normal modes as fundamental heat carriers may not be accurate in amorphous solids. Further, our classical and ab-initio molecular dynamics simulations of amorphous silicon demonstrate a large degree of atomic diffusion, especially at high temperatures, leading to the conclusion that thermal transport in amorphous solids could be better described starting from the perspective of liquid dynamics rather than from crystalline solids. ∗ To whom correspondence should be addressed; E-mail: jmoon17@utk.edu 1 ar X iv :2 10 6. 08 45 9v 1 [ co nd -m at .m tr lsc i] 1 5 Ju n 20 21 read less USED (high confidence) S. Thaler and J. Zavadlav, “Learning neural network potentials from experimental data via Differentiable Trajectory Reweighting,” Nature Communications. 2021. link Times cited: 30 USED (high confidence) X. Chen, “Effect of phase interface atomic coherency on dynamics of dislocations,” Journal of Materials Research. 2021. link Times cited: 0 Abstract: Coarse-grained atomistic simulations are conducted to study … read moreAbstract: Coarse-grained atomistic simulations are conducted to study the effect of phase interface atomic coherency on the dynamics of dislocations in both metallic and non-metallic multilayers under compression. Results show that the Cu/Ni bimaterial with a coherent interface has a yield point of almost twice higher than the one with a semi-coherent interface. An increased number of semi-coherent interfaces provides richer sources for dislocation nucleation, giving rise to a lower yield point. The intersection of the deposited dislocations is shown as an effective facilitator of dislocation transmission and emission across the semi-coherent interfaces. In contrast to Cu/Ni, the Si/Ge bimaterial with coherent and semi-coherent interfaces exhibit yield strengths of only a 13% discrepancy. The dramatic difference is shown to be determined by the disparate deformation mechanisms of the interface dislocations. read less USED (high confidence) T. Reichenbach, G. Moras, L. Pastewka, and M. Moseler, “Solid-Phase Silicon Homoepitaxy via Shear-Induced Amorphization and Recrystallization.,” Physical review letters. 2021. link Times cited: 2 Abstract: We study mechanically induced phase transitions at tribologi… read moreAbstract: We study mechanically induced phase transitions at tribological interfaces between silicon crystals using reactive molecular dynamics. The simulations reveal that the interplay between shear-driven amorphization and recrystallization results in an amorphous shear interface with constant thickness. Different shear elastic responses of the two anisotropic crystals can lead to the migration of the amorphous interface normal to the sliding plane, causing the crystal with lowest elastic energy density to grow at the expense of the other one. This triboepitaxial growth can be achieved by crystal misorientation or exploiting elastic finite-size effects, enabling the direct deposition of homoepitaxial silicon nanofilms by a crystalline tip rubbing against a substrate. read less USED (high confidence) S. Mejía-Rosales, S. A. Sandoval-Salazar, A. Soria-Sánchez, and L. Y. Cantú-Sánchez, “Mechanical properties of MoS2 nanotubes under tension: a molecular dynamics study,” Molecular Simulation. 2021. link Times cited: 4 Abstract: ABSTRACT We investigate the tensile properties of MoS nanotu… read moreAbstract: ABSTRACT We investigate the tensile properties of MoS nanotubes by the implementation of a set of molecular dynamics runs, using a recently developed version of the Stillinger–Weber (SW) potential. The nanotubes considered are of the H and T polytypes, with zigzag and armchair chirality. We found that only nanotubes of diameter greater or equal than 30 Å are stable when modelled by the SW potential. Zigzag nanotubes have a larger elastic modulus than armchair nanotubes of the same polytype and diameter, and T nanotubes deform more easily than H nanotubes. We also found that elastic modulus, tensile strength, and point of rupture depend on diameter when the diameters are less than 60 Å. We investigate the role of defects on the mechanical response, finding that, while elastic modules is not appreciably affected by the presence of vacancies, tensile strength, and point of rupture value decrease significantly, in particular when the defect is a vacancy of a whole MoS unit. The presence of a defect also affects the nature of the rupture, with the fracture becoming brittle. Increasing the temperature makes Young's modulus and tensile strength decrease. The mechanical response of chiral nanotubes is also investigated. read less USED (high confidence) H. Wang et al., “Synergistic impeding of phonon transport through resonances and screw dislocations,” Physical Review B. 2021. link Times cited: 14 Abstract: Improving the control of heat flow at the nanoscale is essent… read moreAbstract: Improving the control of heat flow at the nanoscale is essential for promoting its applications in many fields, such as energy conversion, thermal informatics, and communication technologies. Here we perform a systematic study on the synergistic effect of screw dislocations and surface resonators on thermal transport of Si nanowires and the corresponding mechanisms based on molecular dynamics simulations. We uncover that screw dislocations reduce the thermal conductivity by enhancing the anharmonicity of nanowires due to the non-homogeneous stress field. For resonant structures, we demonstrate that the suppression of relaxation time is the main mechanism for thermal conductivity reduction. The suppression of relaxation time by more than two orders of magnitude below 4 THz dramatically reduces the resonant structure thermal conductivity, while the previously proposed group velocity reduction mechanism can only impede phonon transport beyond 4 THz slightly. By comparing the mechanisms produced by dislocations and resonators, we find that the resonators have a stronger effect over screw dislocations in impeding the phonon transport at low-frequencies while it becomes opposite at high-frequencies. As a result, they can be combined together to manipulate phonon transport synergistically at all frequencies. Our findings not only provide new insights on the mechanisms of thermal conductivity engineering by screw dislocations and surface resonators, but also illustrate a new paradigm for ultralow thermal conductivity design through the tailoring of the entire frequency range of phonon transport. read less USED (high confidence) V. On, N. T. Hung, D. T. K. Huyen, and L. T. D. Trinh, “Investigating the fast cooling process of silicene by MD simulation,” IOP Conference Series: Materials Science and Engineering. 2021. link Times cited: 0 Abstract: This paper presents the results of two-dimensional silicene … read moreAbstract: This paper presents the results of two-dimensional silicene cooling studies by MD simulation with a sample of 6400 atoms. Silicene after melting to 3500K, it is cooled at a rate of 1013K/s to a temperature of 300K. Investigation of the dependence of energy on temperature shows a jump in the average total energy of molten silicene at the temperature T = 1772K. Investigations on the radial distribution function g(r), coordinate number distribution, ring distribution, and angular distribution all show that the freezing temperature of silicene is about 1772K. When cooled to 300K, silicene is in crystalline form, but the ratio of the defects is quite high and approximately 37.5%. read less USED (high confidence) A. Sycheva, “Influence of Surface Curvature on Silicon Sputtering by Low-Energy Ar Ions,” Technical Physics Letters. 2020. link Times cited: 1 USED (high confidence) L. Li, R. Lin, and Y. Hu, “Cross-section effect on mechanics of nonlocal beams,” Archive of Applied Mechanics. 2020. link Times cited: 20 USED (high confidence) Y. Sun, L.-Y. Wang, C. Wang, and C. Tang, “Mechanical properties of 2D blue phosphorus and temperature effect,” Nanotechnology. 2020. link Times cited: 2 Abstract: Blue phosphorus is an emerging 2D material that exhibits fin… read moreAbstract: Blue phosphorus is an emerging 2D material that exhibits finite electronic band gap and may find promising applications in advanced semiconducting devices. Comparing to its allotrope, black phosphorus, mechanical properties of blue phosphorus have not been explored in detail. Here we report molecular dynamics simulations of mechanical responses of blue phosphorus under uniaxial tensile, biaxial tensile and shear loadings. It is found that blue phosphorus shows less anisotropic effect as compared to black phosphorus, the room temperature Young’s modulus is about 122.3 GPa and 121.6 GPa along armchair and zigzag directions, respectively, shear modulus is about 27.1 GPa and 28.6 GPa, respectively, along armchair and zigzag directions. Temperature effect on mechanical responses is also systematically studied within a range of 5–400 K. It is found that temperature reduces both Young’s modulus and fracture strain and fracture strength of blue phosphorus, owing to the interplay between thermal energy and strain energy applied to the models. Brittle fracture mode is found in blue phosphorus in all loading conditions, with varied crack nucleation and propagation modes. The role of strain rate on the mechanical properties is examined and found to systematically modify the ultimate stress and ultimate strain of BlueP. Structural details including bond length and bond angle variations to external strain are analyzed to gain deeper insights into the underlying mechanisms. read less USED (high confidence) A. Ghasemi and W. Gao, “A method to apply Piola-Kirchhoff stress in molecular statics simulation,” Computational Materials Science. 2020. link Times cited: 4 USED (high confidence) D. Dahal, H. Warren, and P. Biswas, “On the Origin and Structure of the First Sharp Diffraction Peak of Amorphous Silicon,” physica status solidi (b). 2020. link Times cited: 7 Abstract: The structure of the first sharp diffraction peak (FSDP) of … read moreAbstract: The structure of the first sharp diffraction peak (FSDP) of amorphous silicon (a‐Si) near 2 Å−1 is addressed with particular emphasis on the position, intensity, and width of the diffraction curve. By studying a number of continuous random network (CRN) models of a‐Si, it is shown that the position and intensity of the FSDP are primarily determined by radial atomic correlations in the amorphous network on the length scale of 15 Å. A shell‐by‐shell analysis of the contribution from different radial shells reveals that key contributions to the FSDP originate from the second and fourth radial shells in the network, which are accompanied by a background contribution from the first shell and small residual corrections from the distant radial shells. The results from numerical calculations are complemented by a phenomenological discussion of the relationship between the peaks in the structure factor in the wavevector space and the reduced pair‐correlation function in the real space. An approximate functional relation between the position of the FSDP and the average radial distance of Si atoms in the second radial shell in the network is derived, which is corroborated by numerical calculations. read less USED (high confidence) Y. Fu et al., “Stability, deformation and rupture of Janus oligomer enabled self-emulsifying water-in-oil microemulsion droplets.,” Physical chemistry chemical physics : PCCP. 2020. link Times cited: 2 Abstract: Microemulsions exist widely in nature, daily life and indust… read moreAbstract: Microemulsions exist widely in nature, daily life and industrial manufacturing processes, including petroleum production, food processing, drug delivery, new material fabrication, sewage treatment, etc. The mechanical properties of microemulsion droplets and a correlation to their molecular structures are of vital importance to those applications. Despite studies on their physicochemical determinants, there are lots of challenges of exploring the mechanical properties of microemulsions by experimental studies. Herein, atomistic modelling was utilized to study the stability, deformation, and rupture of Janus oligomer enabled water-in-oil microemulsion droplets, aiming at revealing their intrinsic relationship with Janus oligomer based surfactants and oil structures. The self-emulsifying process from a water, oil and surfactant mixture to a single microemulsion droplet was modulated by the amphiphilicity and structure of the surfactants. Four microemulsion systems with an interfacial thickness in the range of 7.4-17.3 Å were self-assembled to explore the effect of the surfactant on the droplet morphology. By applying counter forces on the water core and the surfactant shell, the mechanical stability of the microemulsion droplets was probed at different ambient temperatures. A strengthening response and a softening regime before and after a temperature-dependent peak force were identified followed by the final rupture. This work demonstrates a practical strategy to precisely tune the mechanical properties of a single microemulsion droplet, which can be applied in the formation, de-emulsification, and design of microemulsions in oil recovery and production, drug delivery and many other applications. read less USED (high confidence) L. Pizzagalli, J. Godet, S. Brochard, H. Gotsis, and T. Albaret, “Stacking fault formation created by plastic deformation at low temperature and small scales in silicon,” Physical Review Materials. 2020. link Times cited: 3 Abstract: Several studies have recently reported the formation of stac… read moreAbstract: Several studies have recently reported the formation of stacking faults in silicon compressed at low temperatures and high stresses. This observation contradicts the generally accepted framework for the plastic deformation of silicon. We propose here an original plasticity mechanism that could potentially explain stacking fault formation in these conditions: the nucleation and migration of a partial edge dislocation with Burgers vector 1 / 3 h 112 i . These results are obtained thanks to a multiscale approach combining three computational methods. Dislocation nucleation is determined by molecular dynamics in both a nanowire and a 2D slab. The latter results are used as inputs for hybrid MD/DFT “learn on the fly” calculations, allowing for studying the dynamical propagation of the dislocation. Selected configurations at different steps are next used for initiating nudged elastic band density functional theory calculations. These calculations revealed that the dislocation displacement mechanism depends on the compression strain. For low values, a dangling bond is temporarily created in the core, resulting in high activation energies. For compression strains larger than about 8%, the reduction of the interlayer distance allows for a more complex displacement mechanism with no dangling bonds in the dislocation core and a significant decrease of the activation energy. read less USED (high confidence) S. Xu, Y. Li, and Y. Chen, “Si/Ge (111) Semicoherent Interfaces: Responses to an In‐Plane Shear and Interactions with Lattice Dislocations,” physica status solidi (b). 2020. link Times cited: 8 Abstract: Concurrent atomistic–continuum simulations are employed to s… read moreAbstract: Concurrent atomistic–continuum simulations are employed to study Si/Ge (111) semicoherent interfaces in terms of their responses to an in‐plane shear and interactions with lattice dislocations. Three types of Si/Ge interfaces, differing in interfacial structures and energy, are considered. Type I interface coincides with the shuffle‐set slip plane and contains a hexagonal network of edge dislocations. Type II and Type III interfaces both coincide with the glide‐set slip plane, yet they contain, respectively, a triangular and a hexagonal network of Shockley partial dislocations. The simulations show that among the three types of interfaces, 1) Type I interface is the least stable subject to an in‐plane shear and 2) Type III interface impedes the gliding of lattice dislocations the most significantly. read less USED (high confidence) D. Wang, L. Liu, M. Chen, and H. Zhuang, “Electrical and thermal transport properties of medium-entropy Si Ge Sn alloys,” Acta Materialia. 2020. link Times cited: 10 USED (high confidence) X. Liu, J. Gao, G. Zhang, J. Zhao, and Y.-W. Zhang, “Remarkable Role of Grain Boundaries in the Thermal Transport Properties of Phosphorene,” ACS Omega. 2020. link Times cited: 10 Abstract: In this work, we study the effect of grain boundary (GB) on … read moreAbstract: In this work, we study the effect of grain boundary (GB) on the thermal transport of phosphorene by using molecular dynamics simulations. By exploring a total of 19 GBs with different GB defect types and densities, we find that there is a relatively high Kapitza thermal boundary resistance at these boundaries. By analyzing the spatial distributions of the heat flux, we find that this high thermal boundary resistance can be attributed to the strong phonon-boundary scattering at the GBs. With the same type of defect, the thermal boundary resistance is found to increase with the increase of the defect density along the GBs, which can be attributed to the nonuniform distribution of stress and lattice distortion. Finally, we investigate the anisotropy in the thermal conductivity of phosphorene with GBs and reveal a strikingly high anisotropy ratio of thermal conductivities, which is found to arise from the different influences of boundaries on the thermal transport along the zigzag and armchair directions. Our results highlight the importance of GBs in the transport behavior of phosphorene and the need to include their effects in the thermal management of phosphorene-based electronic devices. read less USED (high confidence) A. Sycheva and E. Voronina, “Molecular-Dynamics Simulation of Silicon Irradiation with Low-Energy Noble Gas Ions,” Journal of Surface Investigation: X-ray, Synchrotron and Neutron Techniques. 2020. link Times cited: 0 USED (high confidence) P. Gallo, “Some Considerations on Stress Intensity Factor at Atomic Scale.” 2020. link Times cited: 2 USED (high confidence) T. Mahadevan and J. Du, “Hydration and reaction mechanisms on sodium silicate glass surfaces from molecular dynamics simulations with reactive force fields,” Journal of the American Ceramic Society. 2020. link Times cited: 17 USED (high confidence) A. Sycheva and E. Voronina, “Features of Low-Energy He and Ar Ion Irradiation of Nanoporous Si/SiO2-Based Materials,” Technical Physics Letters. 2020. link Times cited: 0 USED (high confidence) T. Hao, T. Ahmed, R. J. Mou, J. Xu, S. Brown, and Z. Hossain, “Critical inter-defect distance that modulates strength and toughness in defective 2D sp2-lattice,” Journal of Applied Physics. 2020. link Times cited: 4 Abstract: This paper reveals the existence of a critical separation di… read moreAbstract: This paper reveals the existence of a critical separation distance ( d c) beyond which the elastic interactions between a pair of monovacancies in graphene or hexagonal boron nitride become inconsequential for the strength and toughness of the defective lattice. This distance is independent of the chirality of the lattice. For any inter-defect distance higher than d c, the lattice behaves mechanically as if there is a single defect. For a distance less than d c, the defect–defect elastic interactions produce distinctive mechanical behavior depending on the orientation ( θ) of the defect pair relative to the loading direction. Both strength and toughness of the lattice containing a pair of “interacting monovacancies (iMVs)” are either higher or smaller than that of the lattice containing a pair of “non-interacting monovacancies (nMVs),” suggesting the existence of a critical orientation angle θ c. For θ < θ c, the smaller the distance between the iMVs, the higher the toughness and strength compared to the lattice containing nMVs, whereas, for θ ≥ θ c, the smaller the separation distance between the iMVs, the smaller the toughness and strength compared to the lattice containing nMVs. The transitional behavior has a negligible dependence on the chirality of the lattice, which indicates that the crystallographic anisotropy has a much weaker influence on toughness and strength compared to the anisotropy induced by the orientation angle itself. These observations underline an important point that the elastic fields emanating from vacancy defects are highly localized and fully contained within a small region of around 1.5 nm radius. read less USED (high confidence) H. Zhang et al., “Novel phonon resonator based on surface screw thread for suppressing thermal transport of Si nanowires,” Physical Review B. 2020. link Times cited: 10 Abstract: We propose a novel phonon resonator for hindering the therma… read moreAbstract: We propose a novel phonon resonator for hindering the thermal transport of nanowires (NWs), based on a screw threadlike helical nanowall. Results from molecular dynamic simulations reveal that the thermal conductivity and phonon transmission of the screw threadlike Si NWs continuously decrease with an increase in the period density of the helical nanowall. The reduction can reach as high as 36% for the NW with six circles of the helical nanowall, which is much larger than in the case of NWs with straight nanowalls (12%) and nanopillars (15%). This phenomenon is due to that the helical nanowall has a larger contact area with the base structure, which leads to a larger volume of the resonating substructure with a constant height and width. Phonon dispersion relations show the formation of flat bands, which confirms the occurrence of phonon resonances due to the surface screw threadlike structures. The phonon spatial distribution reveals mode localization in the helical resonator at the resonant frequency. With regard to suppressing the phonon propagation, the helical nanowall as a phonon resonator exhibits superiority over the straight nanowalls or conventional nanopillars, because (1) it may be easier to fabricate a larger contact area with the base structure and (2) it avoids the problem of nanopillars or nanowalls touching each other, which maintains the ability of generating localized modes. The obtained results provide a novel design of efficient surface phonon resonators to realize nanowires with ultralow thermal conductivity. read less USED (high confidence) M. Isaiev, X. Wang, K. Termentzidis, and D. Lacroix, “Thermal transport enhancement due to confined water in hybrid nanocomposite,” arXiv: Mesoscale and Nanoscale Physics. 2020. link Times cited: 8 Abstract: The thermal transport properties of porous silicon and nano-… read moreAbstract: The thermal transport properties of porous silicon and nano-hybrid "porous silicon/water" systems are presented here. The thermal conductivity was evaluated with equilibrium molecular dynamics technique for porous systems made of spherical voids or water-filled cavities. We revealed large thermal conductivity enhancement in the nano-hybrid systems as compared to their dry porous counterparts, which cannot be captured by effective media theory. This rise of thermal conductivity is related to the increases of the specific surface of the liquid/solid interface. We demonstrated that significant difference for more than two folds of thermal conductivity of pristine porous silicon and "porous silicon liquid/composite" is due to the liquid density fluctuation close to "solid/liquid interface" (layering effect). This effect is getting more important for the high specific surface of the interfacial area. Specifically, the enhancement of the effective thermal conductivity is 50 % for specific surface area of 0.3 (1/nm), and it increases further upon the increase of the surface to volume ratio. Our study provides valuable insights into the thermal properties of hybrid liquid/solid nanocomposites and about the importance of confined liquids within nanoporous materials. read less USED (high confidence) B. S. Baboukani, Z. Ye, K. G. Reyes, and P. Nalam, “Prediction of Nanoscale Friction for Two-Dimensional Materials Using a Machine Learning Approach,” Tribology Letters. 2020. link Times cited: 37 USED (high confidence) V. V. Hoang, N. H. Giang, and V. Bubanja, “Hexa ↔ tetra silicene crystal–crystal phase transition,” Philosophical Magazine. 2020. link Times cited: 4 Abstract: ABSTRACT Formation of confined crystalline tetra-silicene (t… read moreAbstract: ABSTRACT Formation of confined crystalline tetra-silicene (t-silicene) from crystalline hexa-silicene (h-silicene) via compression, and the reverse transition from the obtained t-silicene to h-silicene via heating, are studied by molecular dynamics (MD) simulations. Models contain 6400 Si atoms interacted via the new version of the Stillinger-Weber potential. While t-silicene can be obtained via compression of the crystalline h-silicene at various temperatures, we find that the best quality samples (with the highest fraction of tetragons) are obtained at high temperatures but still well below the melting point. Such t-silicene is stable over a wide range of pressure and temperature. Evolution of the structural characteristics of samples and various thermodynamic quantities upon compression is studied. Detailed analysis of the structure of t-silicene at 300 K is presented via radial distribution function, coordination number and bond-angle distributions, ring statistics and interatomic distance distribution, as well as 2D visualisation of the atomic configurations. Various types of structural defects of t-silicene are found and discussed. In addition, heating of the obtained t-silicene is shown to lead first to the reverse tetra-to-hexa silicene phase transition, and then to the melting of h-silicene. Evolution of the structural characteristics of the samples and of the thermodynamic quantities upon heating are considered. Atomic mechanism underlaying the tetrahexa phase transitions is discussed. read less USED (high confidence) H. Moosavian and H. Shodja, “Mindlin–Eringen anisotropic micromorphic elasticity and lattice dynamics representation,” Philosophical Magazine. 2020. link Times cited: 9 Abstract: ABSTRACT To account for certain essential features of materi… read moreAbstract: ABSTRACT To account for certain essential features of material such as dispersive behaviour and optical branches in dispersion curves, a fundamental departure from classical elasticity to polar theories is required. Among the polar theories, micromorphic elasticity of appropriate grades and anisotropy is capable of capturing these physical phenomena completely. In the mathematical framework of micromorphic elasticity, in addition to the traditional elastic constants, some additional constants are introduced in the pertinent governing equations of motion. A precise evaluation of the numerical values of the aforementioned elastic constants in the realm of the experimentations poses serious difficulties. Thus this paper aims to provide a remedy as how to determine the micromorphic elastic constants theoretically in terms of the atomic force constants and lattice parameters of the crystalline solid with general anisotropy. In this treatment capture of the discrete nature of matter becomes an essential factor. To this end, the discrete lattice dynamics equations of a crystal are related to the pertinent anisotropic micromorphic equations of motion. This approach allows incorporating the symmetry groups of the crystals within lattice dynamics equations conveniently. For the illustration of the current theoretical developments, the micromorphic elastic constants of diamond and silicon crystals are computed in conjunction with ab initio density functional perturbation theory (DFPT). Moreover, the longitudinal and transverse optical and acoustic branches pertinent to [100] and [110] directions are presented. The accuracy of the results is verified by comparing the dispersion curves derived from the micromorphic theory, those of available experiments, and those directly obtained from DFPT calculations. read less USED (high confidence) S. Jiang, H. Wu, L. Kou, C. Tang, C. Wang, and C. Chen, “Buckling of blue phosphorus nanotubes under axial compression: Insights from molecular dynamics simulations,” Journal of Applied Physics. 2020. link Times cited: 4 Abstract: We report on mechanical properties of blue phosphorus nanotu… read moreAbstract: We report on mechanical properties of blue phosphorus nanotubes (BluePNTs) from systematic molecular dynamics simulations, adopting a Stillinger-Weber potential with parameters determined by fitting to energetic and structural data from first-principles calculations. Our results corroborate the previously reported bending poison effect and size-dependent buckling behaviors. Under axial compression, current simulations predict a shell-to-column buckling mode transition for BluePNTs with increasing aspect ratios; further compression of BluePNTs with large aspect ratios results in a column-to-shell buckling mode transition. Associated critical buckling strains can be described by the continuum mechanics theory. We also simulated buckling behavior of black phosphorus nanotubes (BlackPNTs) and found that the buckling modes of BluePNTs exhibit much less chirality dependence compared to BlackPNTs, stemming from subtle structural differences between these two closely related yet distinct systems. The present results offer insights into key structural and mechanical properties of BluePNTs for fundamental understanding and potential applications of this relatively new member of the large and diverse nanotube family of materials.We report on mechanical properties of blue phosphorus nanotubes (BluePNTs) from systematic molecular dynamics simulations, adopting a Stillinger-Weber potential with parameters determined by fitting to energetic and structural data from first-principles calculations. Our results corroborate the previously reported bending poison effect and size-dependent buckling behaviors. Under axial compression, current simulations predict a shell-to-column buckling mode transition for BluePNTs with increasing aspect ratios; further compression of BluePNTs with large aspect ratios results in a column-to-shell buckling mode transition. Associated critical buckling strains can be described by the continuum mechanics theory. We also simulated buckling behavior of black phosphorus nanotubes (BlackPNTs) and found that the buckling modes of BluePNTs exhibit much less chirality dependence compared to BlackPNTs, stemming from subtle structural differences between these two closely related yet distinct systems. The present resu... read less USED (high confidence) I. Talyzin and V. Samsonov, “Outlooks for development of silicon nanoparticle memory cells,” Modern Electronic Materials. 2019. link Times cited: 1 Abstract: Phase change memory is based on changes in the optical, elec… read moreAbstract: Phase change memory is based on changes in the optical, electrical or other properties of materials during phase transitions, e.g. an amorphous to crystalline transition. Currently existing and potential applications of this memory are primarily based on multicomponent alloys of metals and semiconductors. However single-component nanoparticles including Si ones are also of interest as promising nanosized memory cells. The potential for developing this type of memory cells is confirmed by the fact that the optical absorption index of bulk amorphous silicon is of the same order of magnitude as that of crystalline silicon. Certainly this phenomenon can hardly be implemented with a single nanoparticle the size of which is within light wavelength. Using molecular dynamics and the Stillinger-Weber potential we have studied the regularities of melting and the conditions of crystallization of silicon nanoparticles containing within 105 atoms. We have shown that cooling of nanosized silicon drops at a 0.2 TK/s rate or higher rates causes their amorphous transition whereas single-component nanosized metallic drops crystallize in molecular dynamics experiments even at a 1 TK/s rate. Further heating of amorphous silicon nanoparticles containing above 5 ∙ 104 atoms causes their crystallization in a specific temperature range from 1300 to 1400 K. We have concluded that there is a possibility of developing phase change memory cells on the basis of the above phase transitions. An amorphous transition of a nanoparticle can be achieved by its melting and further cooling to room temperature at a 0.2 TK/s rate whereas a crystalline transition, by its heating to 1300–1400 K at a 0.2 TK/s rate followed by cooling. Results of molecular dynamics experiments suggest there is a minimum silicon nanoparticle size for which the development of phase change memory cells becomes theoretically impossible at a given temperature change rate. For a 0.2 TK/s temperature change rate this minimum size is 12.4 nm (number of atoms approx. 5 ∙ 104). read less USED (high confidence) C. Qian and J. Wang, “Dodecagonal quasicrystal silicene: preparation, mechanical property, and friction behaviour.,” Physical chemistry chemical physics : PCCP. 2019. link Times cited: 1 Abstract: In this study, we obtained dodecagonal monolayer silicene wi… read moreAbstract: In this study, we obtained dodecagonal monolayer silicene with three-fold and four-fold coordination by melt quenching via molecular dynamics (MD) simulations. Stretching simulation of the pre-strained dodecagonal silicene showed lower critical stress than the honeycomb silicene and resulted in an increase in six-fold rings during the plastic deformation since the four-coordinated atom sites are less mechanically favoured than the three-coordinated sites. The friction behaviours with an AFM tip sliding on the dodecagonal and honeycomb surfaces under different loads and tip sizes were simulated and compared. For all the investigated cases, the dodecagonal surface always showed a lower mean friction force than the honeycomb surface. The lower friction of the quasicrystal was observed, and the mechanism was illuminated successfully for the first time by MD simulations. The reduced friction of dodecagonal silicene can be explained by the morphology of the one-dimensional potential energy surface (PES). The 1D PES of dodecagonal silicene has longer potential corrugation lengths than honeycomb silicene, which induce mild motion of the tip in the stick process and lower friction force. Considering the close density of the employed dodecagonal and honeycomb structure, the longer potential corrugation length is a consequence of the quasiperiodic morphology rather than the interspace between atoms. Besides, with a larger tip size, the 1D PES on the dodecagonal surface has a flatter area, which contributes further to the reduced friction force on the dodecagonal surface. read less USED (high confidence) P. Biswas, D. Paudel, R. Atta-Fynn, and S. Elliott, “Temperature-induced nanostructural evolution of hydrogen-rich voids in amorphous silicon: a first-principles study.,” Nanoscale. 2019. link Times cited: 2 Abstract: The paper presents an ab initio study of temperature-induced… read moreAbstract: The paper presents an ab initio study of temperature-induced nanostructural evolution of hydrogen-rich voids in amorphous silicon. By using large a-Si models, obtained from classical molecular-dynamics simulations, with a realistic void-volume density of 0.2%, the dynamics of Si and H atoms on the surface of the nanometer-size cavities were studied and their effects on the shape and size of the voids were examined using first-principles density-functional simulations. The results from ab initio calculations were compared with those obtained from using the modified Stillinger-Weber potential. The temperature-induced nanostructural evolution of the voids was examined by analyzing the three-dimensional distribution of Si and H atoms on/near void surfaces using the convex-hull approximation, and computing the radius of gyration of the corresponding convex hulls. A comparison of the results with those from the simulated values of the intensity in small-angle X-ray scattering of a-Si/a-Si:H in the Guinier approximation is also provided, along with a discussion on the dynamics of bonded and non-bonded hydrogen in the vicinity of voids. read less USED (high confidence) A. Tlili, V. Giordano, Y. Beltukov, P. Desmarchelier, S. Merabia, and A. Tanguy, “Enhancement and anticipation of the Ioffe-Regel crossover in amorphous/nanocrystalline composites.,” Nanoscale. 2019. link Times cited: 13 Abstract: Nanocomposites made of crystalline nanoinclusions embedded i… read moreAbstract: Nanocomposites made of crystalline nanoinclusions embedded in an amorphous matrix are at the forefront of current research for energy harvesting applications. However, the microscopic mechanisms leading alternatively to an effectively reduced or enhanced thermal transport still escape understanding. In this work, we present a molecular dynamics simulation study of model systems, where for the first time we combine a microscopic investigation of phonon dynamics with the macroscopic thermal conductivity calculation, to shed light on thermal transport in these materials. We clearly show that crystalline nanoinclusions represent a novel scattering source for vibrational waves, modifying the nature of low energy vibrations and significantly anticipating the propagative-to-diffusive crossover (Ioffe-Regel), usually located at energies of few THz in amorphous materials. Moreover, this crossover position can be tuned by changing the elastic contrast between nanoinclusions and the matrix, and anticipated by a factor as large as 10 for a harder inclusion. While the propagative contribution to thermal transport is drastically reduced, the calculated thermal conductivity is not significantly affected in the chosen system, as the diffusive contribution dominates heat transport when all phonons are thermally populated. These findings allow finally to understand the panoply of contradictory results reported on thermal transport in nanocomposites and give clear indications to the characteristics that the parent phases should have for efficiently reducing heat transport in a nanocomposite. read less USED (high confidence) M. Hussein, C. Tsai, and H. Honarvar, “Thermal Conductivity Reduction in a Nanophononic Metamaterial versus a Nanophononic Crystal: A Review and Comparative Analysis,” Advanced Functional Materials. 2019. link Times cited: 44 Abstract: The notion of a locally resonant metamaterial—widely applied… read moreAbstract: The notion of a locally resonant metamaterial—widely applied to light and sound—has recently been introduced to heat, whereby the thermal conductivity is reduced primarily by intrinsic localized atomic vibrations rather than scattering mechanisms. This article reviews and analyzes this new emerging concept, termed nanophononic metamaterial (NPM), and contrasts it with the competing concept of a nanophononic crystal (NPC) in which thermal conductivity reduction is realized primarily via nanoscale Bragg scattering. Both the NPM and NPC core mechanisms require the presence of a sufficient level of wave behavior, which is possible when there is a relatively wide distribution of the phonon mean free path (MFP). Silicon serves as a perfect material to form NPMs and NPCs given its relatively large average phonon MFP. This offers a unique opportunity considering silicon's abundance and mature fabrication technology. It is shown in this comparative study that while both the NPM and NPC nanosystems may be rendered to serve as extreme insulators of heat, an NPM may do so without excessive reduction in the minimum feature size–which is key to keeping the electrical properties intact. This trait makes a silicon‐based NPM poised to serve as a low‐cost thermoelectric material with exceptional performance. read less USED (high confidence) M. Verdier, D. Lacroix, and K. Termentzidis, “Roughness and amorphization impact on thermal conductivity of nanofilms and nanowires: Making atomistic modeling more realistic,” Journal of Applied Physics. 2019. link Times cited: 6 Abstract: In this work, the impact of roughness and amorphization on t… read moreAbstract: In this work, the impact of roughness and amorphization on the effective thermal conductivity of silicon nanofilms and nanowires is studied with atomistic simulations. The discrepancy between simulations and experimental measurements shows that it is necessary to consider realistic roughness and amorphization to reach an agreement. We show that subnanometric roughness and specific correlation length can reduce thermal transport by a factor of two in both nanofilms and nanowires; in addition, this reduction is even more pronounced than the one related to the existence of native oxides or amorphous phases on nanostructure edges. Furthermore, an interfacial thermal resistance parallel to the heat flux is observed. This thermal resistance is increasing upon the increase of the amorphous shell thickness, reaching a maximum value for thickness of 6 nm. Our findings could improve the strategy to elaborate nanomaterials with enhanced thermoelectric efficiency by tuning thermal conductivity through the engineering of surfaces. read less USED (high confidence) A. Sycheva, E. Voronina, and T. Rakhimova, “Structural Changes in Nanoporous Silicon-Based Materials under Low-Energy Ion Impact,” Journal of Surface Investigation: X-ray, Synchrotron and Neutron Techniques. 2019. link Times cited: 0 USED (high confidence) T. Morishita and A. Ito, “Traveling without dwelling: Extending the timescale accessible to molecular dynamics simulation,” Physical Review Research. 2019. link Times cited: 1 USED (high confidence) P. Gallo, Y. Hagiwara, T. Shimada, and T. Kitamura, “Strain energy density approach for brittle fracture from nano to macroscale and breakdown of continuum theory,” Theoretical and Applied Fracture Mechanics. 2019. link Times cited: 16 USED (high confidence) M. Chen, R. Baer, D. Neuhauser, and E. Rabani, “Energy window stochastic density functional theory.,” The Journal of chemical physics. 2019. link Times cited: 10 Abstract: Linear scaling density functional theory is important for un… read moreAbstract: Linear scaling density functional theory is important for understanding electronic structure properties of nanometer scale systems. Recently developed stochastic density functional theory can achieve linear or even sublinear scaling for various electronic properties without relying on the sparsity of the density matrix. The basic idea relies on projecting stochastic orbitals onto the occupied space by expanding the Fermi-Dirac operator and repeating this for Nχ stochastic orbitals. Often, a large number of stochastic orbitals are required to reduce the statistical fluctuations (which scale as Nχ -1/2) below a tolerable threshold. In this work, we introduce a new stochastic density functional theory that can efficiently reduce the statistical fluctuations for certain observable and can also be integrated with an embedded fragmentation scheme. The approach is based on dividing the occupied space into energy windows and projecting the stochastic orbitals with a single expansion onto all windows simultaneously. This allows for a significant reduction of the noise as illustrated for bulk silicon with a large supercell. We also provide theoretical analysis to rationalize why the noise can be reduced only for a certain class of ground state properties, such as the forces and electron density. read less USED (high confidence) R. Freitas and E. Reed, “Uncovering the effects of interface-induced ordering of liquid on crystal growth using machine learning,” Nature Communications. 2019. link Times cited: 28 USED (high confidence) C. Zhang and Q. Sun, “Gaussian approximation potential for studying the thermal conductivity of silicene,” Journal of Applied Physics. 2019. link Times cited: 22 Abstract: Due to the compatibility with the well-developed Si-based se… read moreAbstract: Due to the compatibility with the well-developed Si-based semiconductor technology, the properties of silicene and silicene-based materials have attracted tremendous attention. Among them, the thermal conductivity (TC) is of special importance for electronic devices. However, unlike graphene, the poor quality of empirical potentials hinders the reliable evaluation of TC for silicene using molecular dynamics (MD). Here, we present a Gaussian approximation potential (GAP) for silicene based on ab initio derived training data. The potential can precisely describe the geometries, mechanical properties, as well as phonon dispersion of free-standing sheet, outperforming any other empirical ones. Using sinusoidal approach-to-equilibrium MD simulations based on the GAP potential, the TC of silicene is found to be 32.4 ± 2.9 W / m K at room temperature. Importantly, our result achieves a good agreement with Boltzmann transport equation (BTE) based first-principles predictions ( ∼ 30 W / m K), such that the TC value of silicene is confirmed via both MD and BTE; thus, we prove that the accuracy of machine learning potentials, like GAP, can enable a faithful prediction of TC at a density functional theory (DFT) level.Due to the compatibility with the well-developed Si-based semiconductor technology, the properties of silicene and silicene-based materials have attracted tremendous attention. Among them, the thermal conductivity (TC) is of special importance for electronic devices. However, unlike graphene, the poor quality of empirical potentials hinders the reliable evaluation of TC for silicene using molecular dynamics (MD). Here, we present a Gaussian approximation potential (GAP) for silicene based on ab initio derived training data. The potential can precisely describe the geometries, mechanical properties, as well as phonon dispersion of free-standing sheet, outperforming any other empirical ones. Using sinusoidal approach-to-equilibrium MD simulations based on the GAP potential, the TC of silicene is found to be 32.4 ± 2.9 W / m K at room temperature. Importantly, our result achieves a good agreement with Boltzmann transport equation (BTE) based first-principles predictions ( ∼ 30 W / m K), such that ... read less USED (high confidence) F. Lançon, N. Gunkelmann, D. Caliste, and J. Rouviere, “Incommensurate grain boundary in silicon and the silver-ratio sequence,” Physical Review B. 2019. link Times cited: 0 Abstract: A scheme is proposed to solve the structure of incommensurat… read moreAbstract: A scheme is proposed to solve the structure of incommensurate interfaces, starting from high-resolution images of electron microscopy, supplemented by adapted simulation techniques and com-plemented by theoretical tools. Direct silicon bonding is a way to produce artificial interfaces, in particular incommensurate ones. We focus on a technology-driven tilt grain boundary in silicon. While the Fibonacci sequence, linked to the golden ratio, is a prototype of the quasicrystalline structures, a silver-ratio sequence allows us to analyze this incommensurate interface. The four-fold coordination of the Si atoms is kept at the interface. read less USED (high confidence) A. Ciani, R. Pimpinella, J. S. Feldman, and C. Grein, “Improving the Quantum Efficiency of GA-Free Type-II Superlattices,” 2019 IEEE Photonics Conference (IPC). 2019. link Times cited: 0 Abstract: Molecular dynamics modeling of epitaxial growth provides ins… read moreAbstract: Molecular dynamics modeling of epitaxial growth provides insights relating growth processes to the spectral absorption and charge carrier lifetimes of Ga-free Type-II superlattices. Guided by the growth modeling, epitaxial process modifications were implemented that resulted in Type-II superlattices with improved spectral and carrier transport characteristics. read less USED (high confidence) M. H. Naik, S. Kundu, I. Maity, and M. Jain, “Origin and evolution of ultraflat bands in twisted bilayer transition metal dichalcogenides: Realization of triangular quantum dots,” Physical Review B. 2019. link Times cited: 40 Abstract: Using a multiscale computational approach, we probe the orig… read moreAbstract: Using a multiscale computational approach, we probe the origin and evolution of ultraflat bands in moir\'e superlattices of twisted bilayer $\mathrm{Mo}{\mathrm{S}}_{2}$, a prototypical transition metal dichalcogenide. Unlike twisted bilayer graphene, we find no unique magic angles in twisted bilayer $\mathrm{Mo}{\mathrm{S}}_{2}$ for flat-band formation. Ultraflat bands form at the valence band edge for twist angles ($\ensuremath{\theta}$) close to ${0}^{\ensuremath{\circ}}$ and at both the valence and conduction band edges for $\ensuremath{\theta}$ close to ${60}^{\ensuremath{\circ}}$, and have distinct origins. For $\ensuremath{\theta}$ close to ${0}^{\ensuremath{\circ}}$, inhomogeneous hybridization in the reconstructed moir\'e superlattice is sufficient to explain the formation of flat bands. For $\ensuremath{\theta}$ close to ${60}^{\ensuremath{\circ}}$, additionally, local strains cause the formation of modulating triangular potential wells such that electrons and holes are spatially separated. This leads to multiple energy-separated ultraflat bands at the band edges closely resembling eigenfunctions of a quantum particle in an equilateral triangle well. Twisted bilayer transition metal dichalcogenides are thus suitable candidates for the realization of ordered quantum dot array. read less USED (high confidence) J. Gu’enol’e et al., “Assessment and optimization of the fast inertial relaxation engine (fire) for energy minimization in atomistic simulations and its implementation in lammps,” Computational Materials Science. 2019. link Times cited: 89 USED (high confidence) O. Yenigun and M. Barisik, “Effect of Electric Field on Interfacial Thermal Resistance Between Silicon and Water at Nanoscales,” Proceedings of the 5th World Congress on Mechanical, Chemical, and Material Engineering. 2019. link Times cited: 0 Abstract: In this study, heat transfer rate of a nano-confined liquid … read moreAbstract: In this study, heat transfer rate of a nano-confined liquid is controlled by applying an electric field parallel to the heat transfer direction. Molecular Dynamics simulations are performed for deionized water confined between silicon slabs, where their surfaces oppositely charged to create an electric field perpendicular to the silicon wall to promote the electrowetting. Electric field strengths used in this study are 0, 0.18 and 0.35 V/nm. To investigate the effect of electric field on heat transfer, first water density profiles near the silicon walls are examined. Results shows that by applying electric field, water molecules near the silicon walls develop layering, which indicates the increased solid/liquid coupling. With the increasing electric field strength, an increase in the peak of the density layering is observed. Furthermore, heat transfer at the solid/liquid interface is characterized with the Kapitza length values. The results show that applying electric field reduces the interfacial thermal resistance between water and silicon due to the increased solid/liquid coupling and doubles the total heat flux. read less USED (high confidence) E. Villanueva-Bonay and M. Gamero-Castaño, “Molecular dynamics of nanodroplet impact: The effect of particle resolution in the projectile model,” AIP Advances. 2019. link Times cited: 4 Abstract: The energetic impact of projectiles with diameters between a… read moreAbstract: The energetic impact of projectiles with diameters between a few nanometers and microns can now be investigated with electrospays operating in the cone-jet mode, a particle source that produces beams of highly charged and monodisperse droplets with average diameters down to a few nanometers. The hypervelocity impact of these nanodroplets on ceramic targets cause sputtering, amorphization and cratering. This experimental phenomenology has been reproduced with molecular dynamics modeling the molecules of the projectile as large pseudo atoms. This model can be over simplistic, especially for liquids made of large molecules, and the goal of this article is to evaluate this uncertainty by comparing the impacts resulting from this coarse model with those of a full atomic model of the molecules. Impact simulations for projectiles of two liquids with dissimilar molecular complexity, formamide and 1-ethyl-3-methylimidazolium bis (trifluoro-methylsulfonyl) imide, show that sufficient resolution of the projectile is needed to reproduce the impact zone, which has a depth of the order of the diameter of the projectile.The energetic impact of projectiles with diameters between a few nanometers and microns can now be investigated with electrospays operating in the cone-jet mode, a particle source that produces beams of highly charged and monodisperse droplets with average diameters down to a few nanometers. The hypervelocity impact of these nanodroplets on ceramic targets cause sputtering, amorphization and cratering. This experimental phenomenology has been reproduced with molecular dynamics modeling the molecules of the projectile as large pseudo atoms. This model can be over simplistic, especially for liquids made of large molecules, and the goal of this article is to evaluate this uncertainty by comparing the impacts resulting from this coarse model with those of a full atomic model of the molecules. Impact simulations for projectiles of two liquids with dissimilar molecular complexity, formamide and 1-ethyl-3-methylimidazolium bis (trifluoro-methylsulfonyl) imide, show that sufficient resolution of the projectile is... read less USED (high confidence) Y. A. P. Sirkin, E. D. Gadea, D. Scherlis, and V. Molinero, “Mechanisms of Nucleation and Stationary States of Electrochemically Generated Nanobubbles.,” Journal of the American Chemical Society. 2019. link Times cited: 56 Abstract: Gas evolving reactions are ubiquitous in the operation of el… read moreAbstract: Gas evolving reactions are ubiquitous in the operation of electrochemical devices. Recent studies of individual gas bubbles on nanoelectrodes have resulted in unprecedented control and insights on their formation. The experiments, however, lack the spatial resolution to elucidate the molecular pathway of nucleation of nanobubbles and their stationary size and shape. Here we use molecular simulations with an algorithm that mimics the electrochemical formation of gas, to investigate the mechanisms of nucleation of gas bubbles on nanoelectrodes, and characterize their stationary states. The simulations reproduce the experimental currents in the induction and stationary stages, and indicate that surface nanobubbles nucleate through a classical mechanism. We identify three distinct regimes for bubble nucleation, depending on the binding free energy per area of bubble to the electrode, Δγbind. If Δγbind is negative, the nucleation is heterogeneous and the nanobubble remains bound to the electrode, resulting in a low-current stationary state. For very negative Δγ, the bubble fully wets the electrode, forming a one-layer-thick micropancake that nucleates without supersaturation. On the other hand, when Δγbind >0 the nanobubble nucleates homogeneously close to the electrode, but never attaches to it. We conclude that all surface nanobubbles must nucleate heterogeneously. The simulations reveal that the size and contact angle of stationary nanobubbles increase with the reaction driving force, although their residual current is invariant. The myriad of driven non-equilibrium stationary states with the same rate of produc-tion of gas, but distinct bubble properties, suggests that these dissipative systems have attractors that control the stationary current. read less USED (high confidence) C. Melis, R. Rurali, X. Cartoixà, and F. X. Alvarez, “Indications of Phonon Hydrodynamics in Telescopic Silicon Nanowires,” Physical Review Applied. 2019. link Times cited: 9 Abstract: Heat flow at the nanoscale is still a topic full of unsolved… read moreAbstract: Heat flow at the nanoscale is still a topic full of unsolved questions. This lack of understanding is one of the main reasons for the persistence of the ``thermal wall'' that impedes the downsizing of electronic devices. This work shows that phonon hydrodynamics could be behind this unexplained behavior. Generalizing Fourier's law by incorporating hydrodynamic terms reveals that phenomena like viscosity and vorticity appear as important aspects for describing heat at this scale, such that agreement between theory and simulations improves significantly. read less USED (high confidence) L. Yang, Y. Zhao, Q. Zhang, J. Yang, and D. Li, “Thermal transport through fishbone silicon nanoribbons: unraveling the role of Sharvin resistance.,” Nanoscale. 2019. link Times cited: 15 Abstract: Heat conduction has been shown to be greatly suppressed in S… read moreAbstract: Heat conduction has been shown to be greatly suppressed in Si nanomeshes, which has attracted extensive attention for potential thermoelectric applications, yet the precise suppression mechanism remains to be fully understood. Attempting to further disclose the underlying mechanisms, we report on the thermal conductivity of the building block for nanomeshes, i.e., Si nanoribbons with fins attached to the two opposite sides. By expanding only the fin width while keeping both the period length and the backbone size constant, we observed an unexpected non-monotonic trend of the effective thermal conductivity normalized with the backbone cross-section. Further analysis showed that the corrected thermal conductivity extracted with appropriate consideration of the geometrical effect on diffusion followed a monotonically decreasing trend, reaching a maximum thermal conductivity reduction of 18% at 300 K for a ribbon with the maximum explored fin width of 430 nm, as compared to that of the straight ribbon of 66 nm backbone width. We attribute the thermal conductivity reduction to the thermal constriction resistance induced by the cross-section reduction between the fin and backbone sections. For ribbons with a larger fin width, the effective phonon mean free path is longer for phonons arriving at the constriction, which boosts the ballistic constriction resistance, i.e., Sharvin resistance, and leads to a lower thermal conductivity. read less USED (high confidence) N. Zhou, X. Sui, X. He, S. Huang, and L. Zhou, “Nucleation of self-growth dislocations on growth front during the solidification process of silicon,” Journal of Applied Physics. 2019. link Times cited: 2 Abstract: Molecular dynamics simulation of the nucleation of dislocati… read moreAbstract: Molecular dynamics simulation of the nucleation of dislocations in the solidification of silicon has been carried out. The self-growth dislocations could be generated on growth front of grains with the reduction of local energy during homogenous nucleation and growth of silicon. The nucleation mechanism of the self-growth dislocation has been discussed; the essence of it is the mismatch of two atomic islands with different twin stacking sequences in the rough interface. Temperature could affect the interface morphology and then the generation of self-growth dislocation. In addition, some dislocations move along twin boundaries in the grain and even are absorbed by grain boundaries in the course of crystal growth.Molecular dynamics simulation of the nucleation of dislocations in the solidification of silicon has been carried out. The self-growth dislocations could be generated on growth front of grains with the reduction of local energy during homogenous nucleation and growth of silicon. The nucleation mechanism of the self-growth dislocation has been discussed; the essence of it is the mismatch of two atomic islands with different twin stacking sequences in the rough interface. Temperature could affect the interface morphology and then the generation of self-growth dislocation. In addition, some dislocations move along twin boundaries in the grain and even are absorbed by grain boundaries in the course of crystal growth. read less USED (high confidence) T. Kunikiyo, S. Hattori, R. Shirasawa, and S. Tomiya, “First-principles calculations of carrier localization in fluctuated InGaN quantum wells,” Japanese Journal of Applied Physics. 2019. link Times cited: 1 Abstract: The carrier localizations in c-plane and (20 2 ¯ 1) plane In… read moreAbstract: The carrier localizations in c-plane and (20 2 ¯ 1) plane InGaN/GaN quantum wells (QWs) with structure fluctuations are investigated using first-principles calculations. The conduction band minimum (CBM) and valence band maximum (VBM) tend to localize in the region of high indium composition about both the c-plane QW and (20 2 ¯ 1) plane QW. In the case of the (20 2 ¯ 1) plane QW, the CBM and VBM can separate from each other in the in-plane direction as well as in the perpendicular direction, when fluctuations in indium composition or well width exist. The origin of the in-plane separation is the polarization charge generated by non-uniform piezoelectric polarization due to structure fluctuation in the InGaN QWs. Our results imply that the carrier separation in the in-plane direction originating from the structure fluctuation may contribute to lowering the light emission efficiency in semi-polar plane QWs. read less USED (high confidence) L. Bonati, Y.-Y. Zhang, and M. Parrinello, “Neural networks-based variationally enhanced sampling,” Proceedings of the National Academy of Sciences. 2019. link Times cited: 92 Abstract: Significance Atomistic-based simulations are one of the most… read moreAbstract: Significance Atomistic-based simulations are one of the most widely used tools in contemporary science. However, in the presence of kinetic bottlenecks, their power is severely curtailed. In order to mitigate this problem, many enhanced sampling techniques have been proposed. Here, we show that by combining a variational approach with deep learning, much progress can be made in extending the scope of such simulations. Our development bridges the fields of enhanced sampling and machine learning and allows us to benefit from the rapidly growing advances in this area. Sampling complex free-energy surfaces is one of the main challenges of modern atomistic simulation methods. The presence of kinetic bottlenecks in such surfaces often renders a direct approach useless. A popular strategy is to identify a small number of key collective variables and to introduce a bias potential that is able to favor their fluctuations in order to accelerate sampling. Here, we propose to use machine-learning techniques in conjunction with the recent variationally enhanced sampling method [O. Valsson, M. Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] in order to determine such potential. This is achieved by expressing the bias as a neural network. The parameters are determined in a variational learning scheme aimed at minimizing an appropriate functional. This required the development of a more efficient minimization technique. The expressivity of neural networks allows representing rapidly varying free-energy surfaces, removes boundary effects artifacts, and allows several collective variables to be handled. read less USED (high confidence) M. H. Naik, I. Maity, P. Maiti, and M. Jain, “Kolmogorov–Crespi Potential For Multilayer Transition-Metal Dichalcogenides: Capturing Structural Transformations in Moiré Superlattices,” The Journal of Physical Chemistry C. 2019. link Times cited: 57 Abstract: We develop parameters for the interlayer Kolmogorov–Crespi (… read moreAbstract: We develop parameters for the interlayer Kolmogorov–Crespi (KC) potential to study structural features of four transition-metal dichalcogenides (TMDs): MoS2, WS2, MoSe2, and WSe2. We also propose a... read less USED (high confidence) S. Susarla et al., “Strain‐Induced Structural Deformation Study of 2D MoxW(1‐x) S2,” Advanced Materials Interfaces. 2019. link Times cited: 12 Abstract: The possibility of tuning properties and its potential appli… read moreAbstract: The possibility of tuning properties and its potential applications in the fields of optoelectronics and/or flexible electronics, has increased the demand for 2D alloys in recent times. Understanding the mechanical performance of 2D materials under extreme conditions, such as strain, stress, and fracture is essential for the reliable electronic devices based on these structures. In this study, combined molecular dynamics (MD) simulations and in situ Raman spectroscopic techniques are used to study the mechanical performance of a 2D alloy system, MoxW(1‐x) S2. It is observed that W substitution in MoS2 causes solid‐solution strengthening and increase in the Young's modulus values. Higher W content decreases failure strain for MoS2. Based on spatially resolved Raman spectroscopy and MD simulations results, a detailed model to explain failure mechanisms in MoxW(1‐x) S2 alloys is proposed. read less USED (high confidence) H. A. Huy et al., “Novel pressure-induced topological phase transitions of supercooled liquid and amorphous silicene,” Journal of Physics: Condensed Matter. 2019. link Times cited: 6 Abstract: This molecular dynamics (MD) simulation carries a detailed a… read moreAbstract: This molecular dynamics (MD) simulation carries a detailed analysis of a pressure-induced structural transition supercooled liquid and amorphous silicene (a-silicene). Low-density models of supercooled liquid and a-silicene containing 10 000 atoms are obtained by rapid cooling processes from the melts. Then, an a-silicene model at T = 1000 K, a supercooled liquid model at T = 1500 K and a liquid silicon model at T = 2000 K have been isothermally compressed step by step up to a high density in order to observe the pressure-induced structural changes. Specifically ‘Cairo tiling’ pentagonal and square lattices of silicene are discovered in our calculations. Structural properties of those penta-silicene and tetra-silicene models have been carefully analyzed through the radial distribution functions, interatomic distances, bond-angle distributions under high-pressure condition. The dependence of pressure on formation behaviors is calculated via pressure–volume and energy–density relationships. The first order transition from low-density supercooled liquid/amorphous silicene to high-density penta-silicene and continuous transition from low-density liquid to high-density tetra-silicene are discussed. Atomic mechanism and sp3/sp2 hybridization evolution are inspected whereas the role of low-membered ring defects/boundary promises remarkable application and advanced research in future. read less USED (high confidence) I. Santos, M. Aboy, L. Marqués, P. López, and L. Pelaz, “Generation of amorphous Si structurally compatible with experimental samples through the quenching process: A systematic molecular dynamics simulation study,” Journal of Non-Crystalline Solids. 2019. link Times cited: 3 USED (high confidence) Y. Chen and A. Diaz, “Physical foundation and consistent formulation of atomic-level fluxes in transport processes,” Physical Review E. 2018. link Times cited: 26 Abstract: Irving and Kirkwood derived the transport equations from the… read moreAbstract: Irving and Kirkwood derived the transport equations from the principles of classical statistical mechanics using the Dirac delta to define local densities. Thereby, formulas for fluxes were obtained in terms of molecular variables. The Irving and Kirkwood formalism has inspired numerous formulations. Many of the later developments, however, considered it more rigorous to replace the Dirac delta with a continuous volume-weighted averaging function and subsequently defined fluxes as a volume density. Although these volume-averaged flux formulas have dominated the literature for decades and are widely implemented in popular molecular dynamics (MD) software, they are a departure from the well-established physical concept of fluxes. In this work, we review the historical developments that led to the unified physical concept of fluxes for transport phenomena. We then use MD simulations to show that these popular flux formulas conserve neither momentum nor energy; nor do they produce fluxes that are consistent with their physical definitions. We also use two different approaches to derive fluxes for general many-body potentials. The results of the formulation show that atomistic formulas for fluxes can be fully consistent with the physical definitions of fluxes and conservation laws. read less USED (high confidence) Z. Wei, Y. Kan, Y. Zhang, and Y. Chen, “The frictional energy dissipation and interfacial heat conduction in the sliding interface,” AIP Advances. 2018. link Times cited: 8 Abstract: The energy dissipation rate and interfacial thermal conducta… read moreAbstract: The energy dissipation rate and interfacial thermal conductance between two sliding surfaces are important to accurately predict the interface temperature rise, while their physical mechanism is not well understood. In this study the energy dissipation and interfacial thermal transport between a sliding silicon film and a fixed silicon substrate are investigated by molecular dynamics simulations. The results show that the mean friction force first increases with increasing normal load. However, when the normal load exceeds the critical value of about 60 eV/A, the interface atoms begin to collapse, causing the mean friction force to drop with the further increase of the normal load. Our study also shows that the energy dissipated during the friction process is quantitatively equal to the conducted heat. By extracting the interfacial temperature difference, it is found that the interfacial thermal conductance in sliding state is 2∼4 times higher than that in static state with the same normal load from 10 to 60 eV/A. This is because the interfacial atoms suffer great dynamic impacts during the friction process, which excites more non-equilibrium phonons and helps to enhance the phonon interfacial transmission coefficient. The present investigation demonstrates that the dynamic excitation induced by the friction process can modify the interfacial thermal conductance, which would be of great significance to accurately predict the temperature rise of the sliding interface. read less USED (high confidence) Y. Zhang and L. Wang, “Thermally stimulated nonlinear vibration of rectangular single-layered black phosphorus,” Journal of Applied Physics. 2018. link Times cited: 6 Abstract: Black phosphorus (BP), a novel material with wide potential … read moreAbstract: Black phosphorus (BP), a novel material with wide potential applications, has recently attracted considerable attention. In this study, the nonlinear thermal vibrational behavior of single-layered BP (SLBP) is investigated using a nonlinear orthotropic plate model (OPM) and molecular dynamics (MD) simulations. The dynamic equation for the nonlinear orthotropic plate considering large deflections and thermal stress is obtained. The stationary probability density of the nonlinear thermally stimulated vibrational behavior of SLBP is presented based on the nonlinear OPM for both the pre-buckling and post-buckling cases. For the post-buckling case, the time histories of SLBP with different damping ratios are obtained by nonlinear OPM using the fourth-order Runge–Kutta algorithm. As the damping ratio increases, one equilibrium position jumps to the other more frequently. The time histories of the SLBP at different temperatures are gotten by nonlinear OPM and MD simulations. The MD results indicate that the nonlinear OPM can predict the nonlinear thermally stimulated vibrational behavior of SLBP well.Black phosphorus (BP), a novel material with wide potential applications, has recently attracted considerable attention. In this study, the nonlinear thermal vibrational behavior of single-layered BP (SLBP) is investigated using a nonlinear orthotropic plate model (OPM) and molecular dynamics (MD) simulations. The dynamic equation for the nonlinear orthotropic plate considering large deflections and thermal stress is obtained. The stationary probability density of the nonlinear thermally stimulated vibrational behavior of SLBP is presented based on the nonlinear OPM for both the pre-buckling and post-buckling cases. For the post-buckling case, the time histories of SLBP with different damping ratios are obtained by nonlinear OPM using the fourth-order Runge–Kutta algorithm. As the damping ratio increases, one equilibrium position jumps to the other more frequently. The time histories of the SLBP at different temperatures are gotten by nonlinear OPM and MD simulations. The MD results indicate that the nonl... read less USED (high confidence) C. Chen, P. Song, F. Meng, P. Ou, X. Liu, and J. Song, “Predictive modeling of misfit dislocation induced strain relaxation effect on self-rolling of strain-engineered nanomembranes,” Applied Physics Letters. 2018. link Times cited: 2 Abstract: Combining atomistic simulations and continuum modeling, the … read moreAbstract: Combining atomistic simulations and continuum modeling, the effects of misfit dislocations on strain relaxation and subsequently self-rolling of strain-engineered nanomembranes have been investigated. Two representative material systems including (GaN/In0.5Ga0.5N) of wurtzite lattice and II–VI materials (CdTe/CdTe0.5S0.5) of zinc-blend lattice were considered. The atomistic characteristics of dislocation and the resulting lattice distorting were first determined by generalized-stacking-fault energy profile and disregistry function obtained through Peierls-Nabarro model. Those properties were then used to calculate the accurate mismatch strain of those nanomembranes with the presence of dislocations, and as inputs into von-Karman shell theory to quantitatively evaluate the effects on self-rolling curvature and anisotropy. The theoretical results were further confirmed by atomistic simulations of different crystal geometries and dislocation configurations. Our results provide essential theoretical insights ... read less USED (high confidence) X. Sui, Y. Cheng, N. Zhou, B.-bing Tang, and L. Zhou, “Molecular dynamics simulation of the solidification process of multicrystalline silicon from homogeneous nucleation to grain coarsening,” CrystEngComm. 2018. link Times cited: 15 Abstract: Based on the Stillinger–Weber potential, molecular dynamics … read moreAbstract: Based on the Stillinger–Weber potential, molecular dynamics simulations of the solidification processes of multicrystalline silicon were carried out. Every stage of the whole solidification process, including homogeneous nucleation, grain growth, grain coarsening and defect characterization, was investigated. In the nucleation stage, it showed two typical nucleation models (spontaneous nucleation and sporadic nucleation) at high and low temperatures. Local heterogeneity was occasionally observed during homogeneous nucleation. The simulated nucleation rates at different temperatures were measured, whose trends were in agreement with the results of theoretical calculations, and both of them reached the maximum nucleation rate at a critical temperature of ∼0.65Tm. In the growth stage, the nuclei showed the maximum growth exponent at ∼0.65Tm. The evolution of the grain number at different temperatures exhibited three different patterns. Furthermore, the grains showed modest anisotropic growth before the growth was influenced by other grains. In the grain coarsening stage, the grain size distribution could be described suitably by the log-normal distribution. The grain coarsening exponent was approximately one order of magnitude lower than the nuclei growth exponent. The analyses of crystal defects showed that the dislocation density is about 105 m−2, twin percentages are above 40%, and the percentage of CSL grain boundaries is about 30.30% in mc-Si of the simulations. The statistics of crystal defects are similar to experimental results. read less USED (high confidence) K. Xu, Z. Fan, J. Zhang, N. Wei, and T. Ala‐Nissila, “Thermal transport properties of single-layer black phosphorus from extensive molecular dynamics simulations,” Modelling and Simulation in Materials Science and Engineering. 2018. link Times cited: 17 Abstract: We compute the anisotropic in-plane thermal conductivity of … read moreAbstract: We compute the anisotropic in-plane thermal conductivity of suspended single-layer black phosphorus (SLBP) using three molecular dynamics (MD) based methods, including the equilibrium MD method, the nonequilibrium MD (NEMD) method, and the homogeneous NEMD (HNEMD) method. Two existing parameterizations of the Stillinger–Weber (SW) potential for SLBP are used. Consistent results are obtained for all the three methods and conflicting results from previous MD simulations are critically assessed. Among the three methods, the HNEMD method is the most and the NEMD method the least efficient. The thermal conductivity values from our MD simulations are about an order of magnitude larger than the most recent predictions obtained using the Boltzmann transport equation approach considering long-range interactions in density functional theory calculations, suggesting that the short-range SW potential might be inadequate for describing the phonon anharmonicity in SLBP. read less USED (high confidence) M. Khaled, L. Zhang, and W. Liu, “Some critical issues in the characterization of nanoscale thermal conductivity by molecular dynamics analysis,” Modelling and Simulation in Materials Science and Engineering. 2018. link Times cited: 4 Abstract: The nanoscale thermal conductivity of a material can be sign… read moreAbstract: The nanoscale thermal conductivity of a material can be significantly different from its value at the macroscale. Although a number of studies using the equilibrium molecular dynamics (EMD) with Green–Kubo (GK) formula have been conducted for nano-conductivity predictions, there are many problems in the analysis that have made the EMD results unreliable or misleading. This paper aims to clarify such critical issues through a thorough investigation on the effect and determination of the vital physical variables in the EMD-GK analysis, using the prediction of the nanoscale thermal conductivity of Si as an example. The study concluded that to have a reliable prediction, quantum correction, time step, simulation time, correlation time and system size are all crucial. read less USED (high confidence) D. Paudel, R. Atta-Fynn, D. A. Drabold, S. Elliott, and P. Biswas, “Small-Angle X-Ray Scattering in Amorphous Silicon: A Computational Study,” Physical Review B. 2018. link Times cited: 8 Abstract: We present a computational study of small-angle X-ray scatte… read moreAbstract: We present a computational study of small-angle X-ray scattering (SAXS) in amorphous silicon ($a$-Si) with particular emphasis on the morphology and microstructure of voids. The relationship between the scattering intensity in SAXS and the three-dimensional structure of nanoscale inhomogeneities or voids is addressed by generating ultra-large high-quality $a$-Si networks with 0.1-0.3% volume concentration of voids, as observed in experiments using SAXS and positron annihilation spectroscopy. A systematic study of the variation of the scattering intensity in the small-angle scattering region with the size, shape, number density, and the spatial distribution of the voids in the networks is presented. Our results suggest that the scattering intensity in the small-angle region is particularly sensitive to the size and the total volume-fraction of the voids, but the effect of the geometry or shape of the voids is less pronounced in the intensity profiles. A comparison of the average size of the voids obtained from the simulated values of the intensity, using the Guinier approximation and Kratky plots, with those from the spatial distribution of the atoms in the vicinity of void surfaces is presented. read less USED (high confidence) H. Sun, L. Chen, S. Sun, and T.-Y. Zhang, “Size- and temperature-dependent Young’s modulus and size-dependent thermal expansion coefficient of nanowires,” Science China Technological Sciences. 2018. link Times cited: 17 USED (high confidence) H. Sun, L. Chen, S. Sun, and T.-Y. Zhang, “Size- and temperature-dependent Young’s modulus and size-dependent thermal expansion coefficient of nanowires,” Science China Technological Sciences. 2018. link Times cited: 0 USED (high confidence) R. Aguirre et al., “Crystal Growth and Atom Diffusion in (Cu)ZnTe/CdTe via Molecular Dynamics,” IEEE Journal of Photovoltaics. 2018. link Times cited: 4 Abstract: Molecular dynamics (MD) simulations and experimental evapora… read moreAbstract: Molecular dynamics (MD) simulations and experimental evaporation were applied to study the growth of evaporated (Cu)ZnTe on mono- and polycrystalline CdTe. The simulated structures show polytypism and polycrystallinity, including texturing and grain boundaries, diffusion, and other phenomena in excellent qualitative agreement with experimental atomic probe tomography, transmission electron microscope, and secondary ion mass spectrometry. Results show formation of Cu clusters in nonstoichiometric growths even at early stages of deposition. Results also show significantly faster diffusion along defected regions (uncorrelated CdTe grain boundaries) as compared with more highly crystalline areas (high-symmetry grain boundaries and pristine regions). Activation energies and pre-exponential factors of Cu, Zn, and Te diffusion were determined using simulation. The MD model captures crystal growth phenomena with a high degree of fidelity. read less USED (high confidence) Y. Zhang, L. Wang, and J. Jiang, “Thermal vibration of rectangular single-layered black phosphorus predicted by orthotropic plate model,” Journal of Applied Physics. 2018. link Times cited: 13 Abstract: Vibrational behavior is very important for nanostructure-bas… read moreAbstract: Vibrational behavior is very important for nanostructure-based resonators. In this work, an orthotropic plate model together with a molecular dynamics (MD) simulation is used to investigate the thermal vibration of rectangular single-layered black phosphorus (SLBP). Two bending stiffness, two Poisson's ratios, and one shear modulus of SLBP are calculated using the MD simulation. The natural frequency of the SLBP predicted by the orthotropic plate model agrees with the one obtained from the MD simulation very well. The root of mean squared (RMS) amplitude of the SLBP is obtained by MD simulation and the orthotropic plate model considering the law of energy equipartition. The RMS amplitude of the thermal vibration of the SLBP is predicted well by the orthotropic plate model compared to the MD results. Furthermore, the thermal vibration of the SLBP with an initial stress is also well-described by the orthotropic plate model. read less USED (high confidence) J.-D. He, J.-S. Sun, and J.-W. Jiang, “Nanomechanical resonators based on group IV element monolayers,” Nanotechnology. 2018. link Times cited: 3 Abstract: We perform molecular dynamics simulations to investigate the… read moreAbstract: We perform molecular dynamics simulations to investigate the energy dissipation of the resonant oscillation for the group IV monolayers of puckered configuration, in which the oscillation is driven with different actuation velocities. We find that, in the moderate actuation velocity regime, the nonlinear coupling between the resonant oscillation mode and other high-frequency modes will lead to the non-resonant motion of the system. For the larger actuation velocity, the effective strain generated during the resonant oscillating causes a structural transition from the puckered configuration into the planar configuration, which is a characteristic energy dissipation mechanism for the resonant oscillation of these group IV puckered monolayers. Our findings shed light on mechanical applications of the group IV monolayers in the nanomechanical resonator field. read less USED (high confidence) M. Verdier, D. Lacroix, and K. Termentzidis, “Thermal transport in two- and three-dimensional nanowire networks,” Physical Review B. 2018. link Times cited: 14 Abstract: We report on thermal transport properties in 2 and 3 dimensi… read moreAbstract: We report on thermal transport properties in 2 and 3 dimensions interconnected nanowire networks (strings and nodes). The thermal conductivity of these nanostructures decreases in increasing the distance of the nodes, reaching ultra-low values. This effect is much more pronounced in 3D networks due to increased porosity, surface to volume ratio and the enhanced backscattering at 3D nodes compared to 2D nodes. We propose a model to estimate the thermal resistance related to the 2D and 3D interconnections in order to provide an analytic description of thermal conductivity of such nanowire networks; the latter is in good agreement with Molecular Dynamic results. read less USED (high confidence) K. Termentzidis, M. Isaiev, A. Salnikova, I. Belabbas, D. Lacroix, and J. Kioseoglou, “Impact of screw and edge dislocations on the thermal conductivity of individual nanowires and bulk GaN: a molecular dynamics study.,” Physical chemistry chemical physics : PCCP. 2018. link Times cited: 22 Abstract: We report the thermal transport properties of wurtzite GaN i… read moreAbstract: We report the thermal transport properties of wurtzite GaN in the presence of dislocations using molecular dynamics simulations. A variety of isolated dislocations in a nanowire configuration are analyzed and found to considerably reduce the thermal conductivity while impacting its temperature dependence in a different manner. Isolated screw dislocations reduce the thermal conductivity by a factor of two, while the influence of edge dislocations is less pronounced. The relative reduction of thermal conductivity is correlated with the strain energy of each of the five studied types of dislocations and the nature of the bonds around the dislocation core. The temperature dependence of the thermal conductivity follows a physical law described by a T-1 variation in combination with an exponent factor that depends on the material's nature, type and the structural characteristics of the dislocation core. Furthermore, the impact of the dislocation density on the thermal conductivity of bulk GaN is examined. The variation and absolute values of the total thermal conductivity as a function of the dislocation density are similar for defected systems with both screw and edge dislocations. Nevertheless, we reveal that the thermal conductivity tensors along the parallel and perpendicular directions to the dislocation lines are different. The discrepancy of the anisotropy of the thermal conductivity grows with increasing density of dislocations and it is more pronounced for the systems with edge dislocations. Besides the fundamental insights of the presented results, these could also be used for the identification of the type of dislocations when one experimentally obtains the evolution of thermal conductivity with temperature since each type of dislocation has a different signature, or one could extract the density of dislocations with a simple measurement of thermal anisotropy. read less USED (high confidence) K. Termentzidis, “Thermal conductivity anisotropy in nanostructures and nanostructured materials,” Journal of Physics D: Applied Physics. 2018. link Times cited: 13 Abstract: Thermal conductivity anisotropy is a subject for both fundam… read moreAbstract: Thermal conductivity anisotropy is a subject for both fundamental and application interests. The anisotropy can be induced either by van der Waals forces in bulk systems or by nanostructuration. Here, we will examine four cases in which thermal anisotropy has been observed: (i) Si/Ge superlattices which exhibit higher thermal anisotropy between in-plane and cross-plane directions for the case of smooth interfaces, (ii) amorphous/crystalline superlattices with much higher anisotropy than the crystalline/crystalline superlattices and which can reach a factor of six when the amorphous fraction increases, (iii) the impact of the density of edge and screw dislocations on the thermal anisotropy of defected GaN, and (iv) the influence of the growth direction of Bi2Te3 nanowires on thermal conductivity. read less USED (high confidence) J. Cao and K. Cai, “Thermal expansion producing easier formation of a black phosphorus nanotube from nanoribbon on carbon nanotube,” Nanotechnology. 2018. link Times cited: 6 Abstract: As a novel one-dimensional material having excellent electri… read moreAbstract: As a novel one-dimensional material having excellent electrical properties, a black phosphorus (BP) nanotube has wide potential applications in nanodevices. A BP nanotube has not yet, however, been discovered in experiments or fabricated via chemical synthesis. In this study, the feasibility of forming a nanotube from a parallelogram nanoribbon upon a carbon nanotube (CNT) at different temperatures is discussed through the use of molecular dynamics simulations. Results obtained demonstrate that an ideal BP nanotube from the same nanoribbon can be obtained via self-assembly on a CNT at 50 K or lower temperature. At temperatures between 50–100 K, the BP nanotube formed from a single ribbon has defects at both ends. When the temperature is higher than 100 K, it is difficult to obtain a BP nanotube of high quality. It is discovered that when the ribbon can only wind upon the same CNT at low temperature, it may form into an ideal nanotube by increasing the temperature of the system. The reason is that the BP ribbon has a higher thermal expansion than the CNT under the same temperature difference. read less USED (high confidence) Y. Qiu, L. Lupi, and V. Molinero, “Is Water at the Graphite Interface Vapor-like or Ice-like?,” The journal of physical chemistry. B. 2018. link Times cited: 23 Abstract: Graphitic surfaces are the main component of soot, a major c… read moreAbstract: Graphitic surfaces are the main component of soot, a major constituent of atmospheric aerosols. Experiments indicate that soots of different origins display a wide range of abilities to heterogeneously nucleate ice. The ability of pure graphite to nucleate ice in experiments, however, seems to be almost negligible. Nevertheless, molecular simulations with the monatomic water model mW with water-carbon interactions parameterized to reproduce the experimental contact angle of water on graphite predict that pure graphite nucleates ice. According to classical nucleation theory, the ability of a surface to nucleate ice is controlled by the binding free energy between ice immersed in liquid water and the surface. To establish whether the discrepancy in freezing efficiencies of graphite in mW simulations and experiments arises from the coarse resolution of the model or can be fixed by reparameterization, it is important to elucidate the contributions of the water-graphite, water-ice, and ice-water interfaces to the free energy, enthalpy, and entropy of binding for both water and the model. Here we use thermodynamic analysis and free energy calculations to determine these interfacial properties. We demonstrate that liquid water at the graphite interface is not ice-like or vapor-like: it has similar free energy, entropy, and enthalpy as water in the bulk. The thermodynamics of the water-graphite interface is well reproduced by the mW model. We find that the entropy of binding between graphite and ice is positive and dominated, in both experiments and simulations, by the favorable entropy of reducing the ice-water interface. Our analysis indicates that the discrepancy in freezing efficiencies of graphite in experiments and the simulations with mW arises from the inability of the model to simultaneously reproduce the contact angle of liquid water on graphite and the free energy of the ice-graphite interface. This transferability issue is intrinsic to the resolution of the model, and arises from its lack of rotational degrees of freedom. read less USED (high confidence) Z. Zhang and H. Urbassek, “Dislocations penetrating an Al/Si interface,” AIP Advances. 2017. link Times cited: 8 Abstract: We study indentation of a nanolayered material consisting of… read moreAbstract: We study indentation of a nanolayered material consisting of a Si top layer above an Al substrate, using molecular dynamics simulation. We focus on the activity of Si dislocations upon reaching the interface. We find that passage of the dislocations through the interface is possible, if the slip systems of the two crystals are aligned. Upon absorption at the interface, the Si dislocations generate slip which leads to 1-monolayer deep interface pits with well-defined steps; on the Al side dislocations and stacking fault planes are generated, which are pinned to the interface pit. For interfaces with not well aligned slip systems, the passage of dislocations is strongly suppressed. However, still interface pits, albeit with less well defined contours, and stacking fault planes aligned with the interface are created. read less USED (high confidence) Y. Lee and G. Hwang, “Molecular dynamics investigation of the thermal conductivity of ternary silicon–germanium–tin alloys,” Journal of Physics D: Applied Physics. 2017. link Times cited: 9 Abstract: A further reduction of the thermal conductivity (κ) of silic… read moreAbstract: A further reduction of the thermal conductivity (κ) of silicon-germanium (SiGe) alloys is indispensable for their use as thermoelectric materials. Thus far, heteroatom-doped and nanostructured SiGe systems have been mainly synthesized and tested. This work presents a possibility of reducing the κ of SiGe by alloying with tin (Sn). Our molecular dynamics simulations predict that the κ of ternary SiGeSn alloys can be 40% lower than those of binary SiGe and GeSn alloys due mainly to increased mass disorder scattering of phonons. Our findings provide insight into the mechanism of κ suppression in multielement alloys and guidance on how to design them for thermoelectric applications. read less USED (high confidence) X. Liu, J. Gao, G. Zhang, and Y.-W. Zhang, “Unusual Twisting Phonons and Breathing Modes in Tube‐Terminated Phosphorene Nanoribbons and Their Effects on Thermal Conductivity,” Advanced Functional Materials. 2017. link Times cited: 19 Abstract: By studying tube‐terminated phosphorene nanoribbons (PNRs), … read moreAbstract: By studying tube‐terminated phosphorene nanoribbons (PNRs), it is found that unusual phonon and thermal properties can emerge from topologically new edges. The lattice dynamics calculations show that in tube‐terminated PNRs, the breaking of rotation symmetry suppresses the degeneracy of phonon modes, causing the emergence of twisting mode. An anomalous change of an out‐of‐plane acoustic mode to breathing modes with nonzero energy at the center of Brillouin zone occurs when the phosphorene sheet is converted into a tube‐terminated PNR. These unusual twisting and breathing modes provide a larger phase space for scattering phonons, thus explaining the low thermal conductivity of tube‐terminated PNRs revealed by molecular dynamics calculations. Due to the change in the stress field distribution caused by the tube edge, a nearly strain‐independent thermal conductivity in tube‐terminated PNRs is observed, which is in contrast to the apparent enhancement of thermal conductivity in pristine and dimer‐terminated PNRs under tensile strain. The work reveals intriguing phononic and thermal behaviors of tube‐terminated 2D materials. read less USED (high confidence) X. Wang et al., “Molecular dynamics simulation of the surface tension of aqueous sodium chloride: from dilute to highly supersaturated solutions and molten salt,” Atmospheric Chemistry and Physics. 2017. link Times cited: 27 Abstract: Abstract. Sodium chloride (NaCl) is one of the key component… read moreAbstract: Abstract. Sodium chloride (NaCl) is one of the key components of atmospheric
aerosols. The surface tension of aqueous NaCl solution (σNaCl,sol)
and its concentration dependence are essential to determine the equilibrium water vapor
pressure of aqueous NaCl droplets. Supersaturated NaCl solution droplets are observed in
laboratory experiments and under atmospheric conditions, but the experimental data for
σNaCl,sol are mostly limited up to subsaturated solutions. In this
study, the surface tension of aqueous NaCl is investigated by molecular dynamics (MD)
simulations and the pressure tensor method from dilute to highly supersaturated
solutions. We show that the linear approximation of concentration dependence of σNaCl,sol at molality scale can be extended to the supersaturated NaCl
solution until a molality of ∼10.7 mol kg−1 (i.e., solute mass fraction
(xNaCl) of ∼0.39). Energetic analyses show that this monotonic
increase in surface tension is driven by the increase in excess surface enthalpy (ΔH) as the solution becomes concentrated. After that, the simulated σNaCl,sol remains almost unchanged until xNaCl of ∼0.47
(near the concentration upon efflorescence). The existence of the “inflection point” at
xNaCl of ∼0.39 and the stable surface tension of xNaCl
between ∼0.39 and ∼0.47 can be attributed to the nearly unchanged excess
surface entropy term (T⋅ΔS) and the excess surface enthalpy term (ΔH). After a “second inflection point” at xNaCl of ∼0.47, the
simulated σNaCl,sol gradually regains the growing momentum with a
tendency to approach the surface tension of molten NaCl (∼175.58 mN m−1
at 298.15 K, MD simulation-based extrapolation). This fast increase in σNaCl,sol at xNaCl>0.47 is a process driven by excess surface
enthalpy and excess surface entropy. Our results reveal different regimes of
concentration dependence of the surface tension of aqueous NaCl at 298.15 K: a
water-dominated regime (xNaCl from 0 to ∼0.39), a transition regime
(xNaCl from ∼0.39 to ∼0.47) and a molten NaCl-dominated regime
(xNaCl from ∼0.47 to 1).
read less USED (high confidence) M. Verdier, D. Lacroix, and K. Termentzidis, “Heat transport in phononic-like membranes: Modeling and comparison with modulated nano-wires,” International Journal of Heat and Mass Transfer. 2017. link Times cited: 14 USED (high confidence) J. Burg and R. Dauskardt, “The Effects of Terminal Groups on Elastic Asymmetries in Hybrid Molecular Materials.,” The journal of physical chemistry. B. 2017. link Times cited: 3 Abstract: An asymmetric elastic modulus is a recently discovered and u… read moreAbstract: An asymmetric elastic modulus is a recently discovered and unexpected property of hybrid molecular materials that has significant implications for their underlying thermomechanical reliability. Elastic asymmetries are inherently related to terminal groups in the molecular structure, which limit network connectivity. Terminal groups sterically interact to stiffen the network in compression, while they disconnect the network and interact significantly less in tension. Here we study the importance of terminal group molecular weight and size (OH, methyl, vinyl, and phenyl) on the resulting elastic asymmetries and find that increasing the terminal group size actually leads to even larger degrees of asymmetry. As a result, we develop a molecular design criterion to predict how molecular structure affects the mechanical properties, a vital step toward integrating hybrid molecular materials into emerging nanotechnologies. read less USED (high confidence) K. Cai, J. Shi, L. Liu, and Q. Qin, “Self-assembly of a nanotube from a black phosphorus nanoribbon on a string of fullerenes at low temperature.,” Physical chemistry chemical physics : PCCP. 2017. link Times cited: 8 Abstract: A string of fullerenes is used for generating a nanotube by … read moreAbstract: A string of fullerenes is used for generating a nanotube by self-assembly of a black phosphorus (BP) nanoribbon at a temperature of 8 K. Among the fullerenes in the string, there are at least two fixed fullerenes placed along the edge of the BP ribbon for keeping its configuration stability during winding. By way of molecular dynamics simulations, it is found that successful generation of a BP nanotube depends on the bending stiffness of the ribbon and the attraction between the fullerenes and the ribbon. When the attraction is strong enough, the two edges (along the zigzag direction) of the BP ribbon will be able to bond covalently to form a nanotube. By the molecular dynamics approach, the maximum width of the BP ribbon capable of forming a nanotube with a perfect length is investigated in three typical models. The maximum width of the BP ribbon becomes larger with the string containing more fullerenes. This finding reveals a way to control the width of the BP ribbon which forms a nanotube. It provides guidance for fabricating a BP nanotube with a specified length, the same as to the width of the ribbon. read less USED (high confidence) Z. Zhang and H. Urbassek, “Comparative Study of Interatomic Interaction Potentials for Describing Indentation into Si Using Molecular Dynamics Simulation,” Applied Mechanics and Materials. 2017. link Times cited: 5 Abstract: We compare the performance of three interatomic interaction … read moreAbstract: We compare the performance of three interatomic interaction potentials for describing the evolution of plasticity and phase transformations in Si: the well established Stillinger-Weber potential, a recent modification used in the description of Al/Si composites, and a modification of the well known Tersoff potential. We show that the generation of dislocations and the evolution of plasticity are well described by the Stillinger-Weber potential and its modification, while the phase transformation to the high-pressure bct5 modification and the subsequent amorphization are better included in the modified Tersoff potential. read less USED (high confidence) Z. Wei, W. Chen, Z. Chen, K. Bi, J. Yang, and Y. Chen, “Phonon filtering for reduced thermal conductance in unconventional superlattices,” Applied Physics Express. 2017. link Times cited: 2 Abstract: The thermal transport of an unconventional superlattice is i… read moreAbstract: The thermal transport of an unconventional superlattice is investigated by nonequilibrium molecular dynamics simulation. It is shown that the thermal conductance of a two-order superlattice decreases by 15–29% as compared with that of a conventional superlattice. This result is unambiguously explained by the phonon transmission functions of similar one-dimensional superlattice atomic chains calculated by Green’s function method. It is demonstrated that the multiscale structure introduces additional phonon bandgaps, leading to the reduction in thermal conductance due to phonon filtering effects. The proposed unconventional superlattice may find potential applications in phonon engineering, such as thermoelectrics and thermal isolation. read less USED (high confidence) A. Mokshin and B. N. Galimzyanov, “Calculation of the Nucleation Barrier and Interfacial Free Energy of New-Phase nuclei by the thermodynamic integration method using molecular dynamics simulation data,” Russian Journal of Physical Chemistry B. 2017. link Times cited: 1 USED (high confidence) H. Xie, X. Gu, and H. Bao, “Effect of the accuracy of interatomic force constants on the prediction of lattice thermal conductivity,” Computational Materials Science. 2017. link Times cited: 16 USED (high confidence) F. Ricci and P. Debenedetti, “A free energy study of the liquid-liquid phase transition of the Jagla two-scale potential,” Journal of Chemical Sciences. 2017. link Times cited: 10 USED (high confidence) L. Dorf et al., “Etching with atomic precision by using low electron temperature plasma,” Journal of Physics D: Applied Physics. 2017. link Times cited: 23 Abstract: There has been a steady increase in sub-nm precision require… read moreAbstract: There has been a steady increase in sub-nm precision requirement for many critical plasma etching processes in the semiconductor industry. In addition to high selectivity and low controllable etch rate, an important requirement of atomic precision etch processes is no (or minimal) damage to the remaining material surface. It has traditionally not been possible to avoid damage in conventional radio-frequency (RF) plasma processing systems, even during layer-by-layer or ‘atomic layer’ etch. To meet these increasingly stringent requirements, it is necessary to have an accurate control over ion energy and ion/radical composition during plasma processing. In this work, a new plasma etch system designed to facilitate atomic precision plasma processing is presented. An electron sheet beam parallel to the substrate surface is used to produce a plasma in this system. This plasma has a significantly lower electron temperature Te ~ 0.3 eV and ion energy Ei < 3 eV (without applied bias) compared to inductively and capacitively coupled RF plasmas. Electron beam plasmas also have a higher ion–to–radical ratio compared to RF plasmas, so this plasma etch system employs an independent radical source for accurate control over relative ion and radical concentrations. A low frequency RF bias capability that allows control of ion energy in the 2–50 eV range is another important component of this plasma etch system. The results of etching of a variety of materials and structures in this low-electron temperature plasma system are presented in this study: (1) layer-by-layer etching of p-Si at Ei ~ 25–50 eV using electrical and gas cycling is demonstrated; (2) continuous etching of epi-grown µ-Si in Cl2-based plasmas is performed, showing that surface damage can be minimized by keeping Ei < 10 eV. Also presented are the results of molecular dynamics modeling of atomic precision etching at low Ei. read less USED (high confidence) A. Galashev, K. Ivanichkina, A. Vorob’ev, and O. Rakhmanova, “Structure and stability of defective silicene on Ag(001) and Ag(111) substrates: A computer experiment,” Physics of the Solid State. 2017. link Times cited: 30 USED (high confidence) K. Eriguchi, “Defect generation in electronic devices under plasma exposure: Plasma-induced damage,” Japanese Journal of Applied Physics. 2017. link Times cited: 30 Abstract: The increasing demand for higher performance of ULSI circuit… read moreAbstract: The increasing demand for higher performance of ULSI circuits requires aggressive shrinkage of device feature sizes in accordance with Moore’s law. Plasma processing plays an important role in achieving fine patterns with anisotropic features in metal–oxide–semiconductor field-effect transistors (MOSFETs). This article comprehensively addresses the negative aspect of plasma processing — plasma-induced damage (PID). PID naturally not only modifies the surface morphology of materials but also degrades the performance and reliability of MOSFETs as a result of defect generation in the materials. Three key mechanisms of PID, i.e., physical, electrical, and photon-irradiation interactions, are overviewed in terms of modeling, characterization techniques, and experimental evidence reported so far. In addition, some of the emerging topics — control of parameter variability in ULSI circuits caused by PID and recovery of PID — are discussed as future perspectives. read less USED (high confidence) W. Deng and H. Kesari, “Molecular statics study of depth-dependent hysteresis in nano-scale adhesive elastic contacts,” Modelling and Simulation in Materials Science and Engineering. 2017. link Times cited: 9 Abstract: The contact force—indentation-depth (P–h) measurements in ad… read moreAbstract: The contact force—indentation-depth (P–h) measurements in adhesive contact experiments, such as atomic force microscopy, display hysteresis. In some cases, the amount of hysteretic energy loss is found to depend on the maximum indentation-depth. This depth-dependent hysteresis (DDH) is not explained by classical contact theories, such as Johnson–Kendall–Roberts and Derjaguin–Muller–Toporov, and is often attributed to surface moisture, material viscoelasticity, and plasticity. We present molecular statics simulations that are devoid of these mechanisms, yet still capture DDH. In our simulations, DDH is due to a series of surface mechanical instabilities. Surface features, such as depressions or protrusions, can temporarily arrest the growth or recession of the contact area. With a sufficiently large change of indentation-depth, the contact area grows or recedes abruptly by a finite amount and dissipates energy. This is similar to the pull-in and pull-off instabilities in classical contact theories, except that in this case the number of instabilities depends on the roughness of the contact surface. Larger maximum indentation-depths result in more surface features participating in the load–unload process, resulting in larger hysteretic energy losses. This mechanism is similar to the one recently proposed by one of the authors using a continuum mechanics-based model. However, that model predicts that the hysteretic energy loss always increases with roughness, whereas experimentally it is found that the hysteretic energy loss initially increases but then later decreases with roughness. Our simulations capture this non-monotonic dependence of hysteretic energy loss on roughness. read less USED (high confidence) D. Chrobak and R. Nowak, “Influence of Phase Transformations on Incipient Plasticity of Si-Nanospheres,” Acta Physica Polonica A. 2017. link Times cited: 0 Abstract: Powered by TCPDF (www.tcpdf.org) This material is protected … read moreAbstract: Powered by TCPDF (www.tcpdf.org) This material is protected by copyright and other intellectual property rights, and duplication or sale of all or part of any of the repository collections is not permitted, except that material may be duplicated by you for your research use or educational purposes in electronic or print form. You must obtain permission for any other use. Electronic or print copies may not be offered, whether for sale or otherwise to anyone who is not an authorised user. Chrobak, D.; Nowak, R. read less USED (high confidence) K. Cai, L. Liu, J. Shi, and Q. Qin, “Self-Assembly of a Jammed Black Phosphorus Nanoribbon on a Fixed Carbon Nanotube,” Journal of Physical Chemistry C. 2017. link Times cited: 17 Abstract: Nanotube synthesizing from black phosphorus (BP) is still ch… read moreAbstract: Nanotube synthesizing from black phosphorus (BP) is still challenging in laboratory. Fabricating a BP nanotube by self-assembling of a BP nanoribbon seems promising. To estimate the feasibility of such fabrication method, this study performs numerical experiments of self-assembling a jammed BP ribbon on a fixed carbon nanotube using molecular dynamics simulation. The study is based on the following two facts: The phosphorus–phosphorus (P–P) bond is weaker than the bond of carbon–carbon (C–C) and the van der Waals interaction among nonbonding phosphorus atoms is stronger than that between phosphorus atoms and carbon atoms. The results show that when a longer BP ribbon is jammed by a shorter BP ribbon the self-assembling result depends on the relative positions of carbon nanotube (CNT) and the two BP ribbons. Only when the shorter BP ribbon is on the outside of the longer ribbon can the longer BP ribbon be wound on the CNT to form an ideal BP nanotube. The finding is helpful for practical applications of BP... read less USED (high confidence) J. Moon, B. Latour, and A. Minnich, “Propagating elastic vibrations dominate thermal conduction in amorphous silicon,” Physical Review B. 2017. link Times cited: 47 Abstract: The thermal atomic vibrations of amorphous solids can be dis… read moreAbstract: The thermal atomic vibrations of amorphous solids can be distinguished by whether they propagate as elastic waves or do not propagate due to lack of atomic periodicity. In
a-Si, prior works concluded that nonpropagating waves are the dominant contributors to heat transport, with propagating waves being restricted to frequencies less than a few THz and scattered by anharmonicity. Here, we present a lattice and molecular dynamics analysis of vibrations in
a-Si that supports a qualitatively different picture in which propagating elastic waves dominate the thermal conduction and are scattered by local fluctuations of elastic modulus rather than anharmonicity. We explicitly demonstrate the propagating nature of waves up to around 10 THz, and further show that pseudoperiodic structures with homogeneous elastic properties exhibit a marked temperature dependence characteristic of anharmonic interactions. Our work suggests that most heat is carried by propagating elastic waves in a-Si and demonstrates that manipulating local elastic modulus variations is a promising route to realize amorphous materials with extreme thermal properties. read less USED (high confidence) K. Termentzidis, M. Isaiev, A. Salnikova, I. Belabbas, D. Lacroix, and J. Kioseoglou, “Impact of Screw and Edge Dislocation on the Thermal Conductivity of Nanowires and Bulk GaN.” 2017. link Times cited: 2 Abstract: We report on thermal transport properties of wurtzite GaN in… read moreAbstract: We report on thermal transport properties of wurtzite GaN in the presence of dislocations, by using molecular dynamics simulations. A variety of isolated dislocations in a nanowire configuration were analyzed and found to reduce considerably the thermal conductivity while impacting its temperature dependence in a different manner. We demonstrate that isolated screw dislocations reduce the thermal conductivity by a factor of two, while the influence of edge dislocations is less pronounced. The relative reduction of thermal conductivity is correlated with the strain energy of each of the five studied types of dislocations and the nature of the bonds around the dislocation core. The temperature dependence of the thermal conductivity follows a physical law described by a T$^{-1}$ variation in combination with an exponent factor which depends on the material's nature, the type and the structural characteristics of the dislocation's core. Furthermore, the impact of the dislocations density on the thermal conductivity of bulk GaN is examined. The variation and even the absolute values of the total thermal conductivity as a function of the dislocation density is similar for both types of dislocations. The thermal conductivity tensors along the parallel and perpendicular directions to the dislocation lines are analyzed. The discrepancy of the anisotropy of the thermal conductivity grows in increasing the density of dislocations and it is more pronounced for the systems with edge dislocations. read less USED (high confidence) A. Singh and E. Tadmor, “Simulating the superheating of nanomaterials due to latent heat release in surface reconstruction,” International Journal of Heat and Mass Transfer. 2017. link Times cited: 0 USED (high confidence) B. Dongre, T. Wang, and G. K. H. Madsen, “Comparison of the Green–Kubo and homogeneous non-equilibrium molecular dynamics methods for calculating thermal conductivity,” Modelling and Simulation in Materials Science and Engineering. 2017. link Times cited: 17 Abstract: Different molecular dynamics methods like the direct method,… read moreAbstract: Different molecular dynamics methods like the direct method, the Green–Kubo (GK) method and homogeneous non-equilibrium molecular dynamics (HNEMD) method have been widely used to calculate lattice thermal conductivity ( κ ℓ ). While the first two methods have been used and compared quite extensively, there is a lack of comparison of these methods with the HNEMD method. Focusing on the underlying computational parameters, we present a detailed comparison of the GK and HNEMD methods for both bulk and vacancy Si using the Stillinger–Weber potential. For the bulk calculations, we find both methods to perform well and yield κ ℓ within acceptable uncertainties. In case of the vacancy calculations, HNEMD method has a slight advantage over the GK method as it becomes computationally cheaper for lower κ ℓ values. This study could promote the application of HNEMD method in κ ℓ calculations involving other lattice defects like nanovoids, dislocations, interfaces. read less USED (high confidence) N. Winter, M. Becton, L. Zhang, and X. Wang, “Effects of pore design on mechanical properties of nanoporous silicon,” Acta Materialia. 2017. link Times cited: 23 USED (high confidence) Y. Zhou, X. Zhang, and M. Hu, “Nonmonotonic Diameter Dependence of Thermal Conductivity of Extremely Thin Si Nanowires: Competition between Hydrodynamic Phonon Flow and Boundary Scattering.,” Nano letters. 2017. link Times cited: 50 Abstract: By carefully and systematically performing Green-Kubo equili… read moreAbstract: By carefully and systematically performing Green-Kubo equilibrium molecular dynamics simulations, we report that the thermal conductivity (κ) of Si nanowires (NWs) does not diverge but converges and increases steeply when NW diameter (D) becomes extremely small (dκ/dD < 0), a long debate of one-dimensional heat conduction in history. The κ of the thinnest possible Si NWs reaches a superhigh level that is as large as more than 1 order of magnitude higher than its bulk counterpart. The abnormality is explained in terms of the dominant normal (N) process (energy and momentum conservation) of low frequency acoustic phonons that induces hydrodynamic phonon flow in the Si NWs without being scattered. With D increasing, the downward shift of optical phonons triggers strong Umklapp (U) scattering with acoustic phonons and attenuates the N process, leading to the regime of phonon boundary scattering (dκ/dD < 0). The two competing mechanisms result in nonmonotonic diameter dependence of κ with minima at critical diameter of 2-3 nm. Our results unambiguously demonstrate the converged κ and the clear trend of κ ∼ D for extremely thin Si NWs by fully elucidating the competition between the hydrodynamic phonon flow and phonon boundary scattering. read less USED (high confidence) J. Li, H. Wang, Y. Li, and K.-zhen Han, “The impact of the number of layers of the graphene nanopores and the electrical field on ssDNA translocation,” Molecular Simulation. 2017. link Times cited: 11 Abstract: Graphene-based nanopore devices hold great promise for the n… read moreAbstract: Graphene-based nanopore devices hold great promise for the next generation DNA sequencing because graphene is atomically thin which is extremely important for single base recognition. To understand the fundamental details of DNA translocation through a graphene nanopore, in this work, molecular dynamics simulations of ssDNA translocation through the nanopore were performed to trace the nucleobase trajectories and to investigate the impact of the number of layers of the graphene membrane and the electrical field on ssDNA translocation. We found that the velocity of ssDNA translocation was speeded up with the higher bias voltage, and the two-layered and five-layered graphene membrane with 1.0-nm diameter circular nanopore could discern different DNA strand by the translocation time. read less USED (high confidence) J. Dunn, E. Antillon, J. Maassen, M. Lundstrom, and A. Strachan, “Role of energy distribution in contacts on thermal transport in Si: A molecular dynamics study,” Journal of Applied Physics. 2016. link Times cited: 13 Abstract: We use molecular dynamics simulations to investigate how the… read moreAbstract: We use molecular dynamics simulations to investigate how the energy input and distribution in contacts affect the thermal transport in silicon as described by the Stillinger-Webber potential. We create a temperature difference across a Si specimen by maintaining the temperature of two contacts (also made of Si) using widely used thermostats: the deterministic Nose-Hoover approach and a stochastic Langevin bath. Quite surprisingly, the phonon thermal conductivity of the channel obtained using the two thermostats but under otherwise identical conditions can differ by a factor of up to three. The discrepancy between the two methods vanishes as the coupling strength between the thermostat and material is reduced and for long channels. A spectral analysis of the contacts and channel shows that increasing the coupling of the stochastic Langevin thermostat affects the spectral energy distribution in the contacts away from that based on the vibrational density of states, broadening peaks and smoothening the distr... read less USED (high confidence) L. Wu, Q. Li, B. Xu, and W. Liu, “Calculation of solid–liquid interfacial free energy of silicon based on classical nucleation theory,” Journal of Materials Research. 2016. link Times cited: 7 Abstract: The solid–liquid interfacial free energy of silicon was calc… read moreAbstract: The solid–liquid interfacial free energy of silicon was calculated by the method based on classical nucleation theory (CNT), where the molecular dynamic (MD) simulations were carried out, and a series of cylindrical solid nuclei were equilibrated with undercooled liquid phase to create an ideal model of a homogeneous nucleation. The interfacial free energy was extracted from the relationship between the critical nuclei radii and their corresponding equilibrium temperatures. The influence of the interfacial curvature on its free energy was for the first time considered in our work, the influence can be measured by a Tolman length which was introduced to modify the traditional CNT; therefore, more accurate results were obtained. The averaged melting point and Tolman length extracted from simulations were 1678.27 K and 2.82 Å, respectively, which are consistent with the expected results. The averaged interfacial free energy is 401.92 mJ/m^2, which is in good agreement with the results from experiments. read less USED (high confidence) S. Li et al., “The evolving quality of frictional contact with graphene,” Nature. 2016. link Times cited: 361 USED (high confidence) R. P. Leite, R. Freitas, R. Azevedo, and M. de Koning, “The Uhlenbeck-Ford model: Exact virial coefficients and application as a reference system in fluid-phase free-energy calculations.,” The Journal of chemical physics. 2016. link Times cited: 14 Abstract: The Uhlenbeck-Ford (UF) model was originally proposed for th… read moreAbstract: The Uhlenbeck-Ford (UF) model was originally proposed for the theoretical study of imperfect gases, given that all its virial coefficients can be evaluated exactly, in principle. Here, in addition to computing the previously unknown coefficients B11 through B13, we assess its applicability as a reference system in fluid-phase free-energy calculations using molecular simulation techniques. Our results demonstrate that, although the UF model itself is too soft, appropriately scaled Uhlenbeck-Ford (sUF) models provide robust reference systems that allow accurate fluid-phase free-energy calculations without the need for an intermediate reference model. Indeed, in addition to the accuracy with which their free energies are known and their convenient scaling properties, the fluid is the only thermodynamically stable phase for a wide range of sUF models. This set of favorable properties may potentially put the sUF fluid-phase reference systems on par with the standard role that harmonic and Einstein solids play as reference systems for solid-phase free-energy calculations. read less USED (high confidence) S. Numazawa, K. Machida, M. Isobe, and S. Hamaguchi, “Molecular dynamics study on fluorine radical multilayer adsorption mechanism during Si, SiO2, and Si3N4 etching processes,” Japanese Journal of Applied Physics. 2016. link Times cited: 4 Abstract: The surface adsorption processes of fluorine (F) radicals on… read moreAbstract: The surface adsorption processes of fluorine (F) radicals on silicon (Si), silicon dioxide (SiO2), and silicon nitride (Si3N4) substrates during reactive ion etching (RIE) with F incident flux have been studied by molecular dynamics (MD) simulation with bond-order potential functions. In such processes, F radicals are trapped on adsorption sites and thin mixing layers are formed. The radicals break existing bonds near the surface and new trapping sites are generated with specific probabilities. By introducing an extended Langmuir adsorption model, the multilayer adsorption mechanism during etching has been elucidated. The newly proposed Langmuir model takes into account this dynamical site generation by considering two different states of the F mixing layer. The adsorption–desorption processes predicted by the extended Langmuir model are compared with MD simulation results. read less USED (high confidence) J. Moon and A. Minnich, “Sub-amorphous thermal conductivity in amorphous heterogeneous nanocomposites,” RSC Advances. 2016. link Times cited: 20 Abstract: Pure amorphous solids are traditionally considered to set th… read moreAbstract: Pure amorphous solids are traditionally considered to set the lower bound of thermal conductivity due to their disordered atomic structure that impedes vibrational energy transport. However, the lower limits for thermal conductivity in heterogeneous amorphous solids and the physical mechanisms underlying these limits remain unclear. Here, we use equilibrium molecular dynamics to show that an amorphous SiGe nanocomposite can possess thermal conductivity substantially lower than those of the amorphous Si and Ge constituents. Normal mode analysis indicates that the presence of the Ge inclusion localizes vibrational modes with frequency above the Ge cutoff in the Si host, drastically reducing their ability to transport heat. This observation suggests a general route to achieve exceptionally low thermal conductivity in fully dense solids by restricting the vibrational density of states available for transport in heterogeneous amorphous nanocomposites. read less USED (high confidence) Z. Wei, G. Wehmeyer, C. Dames, and Y. Chen, “Geometric tuning of thermal conductivity in three-dimensional anisotropic phononic crystals.,” Nanoscale. 2016. link Times cited: 19 Abstract: Molecular dynamics simulations are performed to investigate … read moreAbstract: Molecular dynamics simulations are performed to investigate the thermal transport properties of a three-dimensional (3D) anisotropic phononic crystal consisting of silicon nanowires and films. The calculation shows that the in-plane thermal conductivity is negatively correlated with the out-of-plane thermal conductivity upon making geometric changes, whether varying the nanowire diameter or the film thickness. This enables the anisotropy ratio of thermal conductivity to be tailored over a wide range, in some cases by more than a factor of 20. Similar trends in thermal conductivity are also observed from an independent phonon ray tracing simulation considering only diffuse boundary scattering effects, though the range of anisotropy ratios is smaller than that obtained in MD simulation. By analyzing the phonon dispersion relation with varied geometric parameters, it is found that increasing the nanowire diameter increases the out-of-plane acoustic phonon group velocities, but reduces the in-plane longitudinal and fast transverse acoustic phonon group velocities. The calculated phonon irradiation further verified the negative correlation between the in-plane and the out-of-plane thermal conductivity. The proposed 3D phononic crystal may find potential application in thermoelectrics, energy storage, catalysis and sensing applications owing to its widely tailorable thermal conductivity. read less USED (high confidence) A. Nassour, “Embedded atom approach for gold–silicon system from ab initio molecular dynamics simulations using the force matching method,” Bulletin of Materials Science. 2016. link Times cited: 2 USED (high confidence) H. Han et al., “Effects of phonon interference through long range interatomic bonds on thermal interface conductance,” Journal of Low Temperature Physics. 2016. link Times cited: 10 Abstract: We investigate the role of two-path destructive phonon inter… read moreAbstract: We investigate the role of two-path destructive phonon interference induced by interatomic bonds beyond the nearest neighbor in the thermal conductance of a silicon-germanium-like metasurface. Controlled by the ratio between the second and first nearest-neighbor harmonic force constants, the thermal conductance across a germanium atomic plane in the silicon lattice exhibits a trend switch induced by the destructive interference of the nearest-neighbor phonon path with a direct path bypassing the defect atoms. We show that bypassing of the heavy isotope impurity is crucial to the realization of the local minimum in the thermal conductance. We highlight the effect of the second phonon path on the distinct behaviors of the dependence of the thermal conductance on the impurity mass ratio. All our conclusions are confirmed both by Green's Function calculations for the equivalent quasi-1D lattice models and by molecular dynamics simulations. read less USED (high confidence) J. Yang, A. Hatano, S. Izumi, and S. Sakai, “Reaction pathway analysis for shuffle-set 60° perfect dislocation in Si,” Philosophical Magazine. 2016. link Times cited: 2 Abstract: In this work, the EDIP potential is employed for representin… read moreAbstract: In this work, the EDIP potential is employed for representing silicon and the shuffle-set 60° perfect dislocation motion is investigated by reaction pathway analysis. There are three possible shuffle-set 60° perfect dislocation core structures named as S1, S2 and S3. The activation energy barriers of the kink migration and nucleation in S1and S2 types are calculated by CI-NEB method. The simulation results show that the critical resolved shear strain of the shuffle-set dislocation in S1 type is around 5%, and the S1 type is the dominate one in the shear strain region of 0 to 5%. During the shear strain from 5to 11.81%, the dislocation moves as the S1 core kink nucleation and migration, meanwhile the S1 dislocation core is in process of transforming into S2. More interestingly, both S1 and S2 dislocation core structures is observed along the dislocation line in this shear strain regime, which could response to the missing observation of long segment dislocation line in the experiment. read less USED (high confidence) Z. Zhang, J. Zhong, H. Ye, Z. Liu, G. Cheng, and J. Ding, “A novel nanopin model based on a Y-junction carbon nanotube,” Journal of Applied Physics. 2016. link Times cited: 2 Abstract: A prototype of nanopin based on a Y-junction carbon nanotube… read moreAbstract: A prototype of nanopin based on a Y-junction carbon nanotube (CNT) is first proposed. The loading and unloading processes are investigated by using classical molecular dynamics, considering the influences of the fit dimension, positioning error, thermal effect, and the loading/unloading velocity on the performance of the proposed nanopin. The optimum size of the gap between the nanopin and the through hole in a silicon component is obtained, which is responsible for a desired fixity with the acceptable install resistance. It is found that a proper positioning error in a certain direction associated with the branched structure of the nanopin will facilitate the installation process. The performance of the proposed nanopin is not sensitive to thermal and normal axial velocity of the nanopin, while the unloading direction affects appreciably on the service performance of the nanopin attributed to the orientation of the branched CNT. Particularly, the service performance of the proposed nanopin considerably d... read less USED (high confidence) W. M. Brown, A. Semin, M. Hebenstreit, S. Khvostov, K. Raman, and S. Plimpton, “Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency,” SC16: International Conference for High Performance Computing, Networking, Storage and Analysis. 2016. link Times cited: 6 Abstract: Electrical power efficiency is a primary concern in designin… read moreAbstract: Electrical power efficiency is a primary concern in designing modern HPC systems. Common strategies to improve CPU power efficiency rely on increased parallelism within a processor that is enabled both by an increase in the vector capabilities within the core and also the number of cores within a processor. Although many-core processors have been available for some time, achieving power-efficient performance has been challenging due to the offload model. Here, we evaluate performance of the molecular dynamics code LAMMPS on two new Intel® processors including the second generation many-core Intel® Xeon Phi™ processor that is available as a bootable CPU. We describe our approach to measure power consumption out-of-band and software optimizations necessary to achieve energy efficiency. We analyze benefits from Intel® Advanced Vector Extensions 512 instructions and demonstrate increased simulations rates with over 9X the CPU+DRAM power efficiency when compared to the unoptimized code on previous generation processors. read less USED (high confidence) X. Yuan, G. Lin, and Y. Wang, “Mechanical properties of armchair silicene nanoribbons with edge cracks: a molecular dynamics study,” Molecular Simulation. 2016. link Times cited: 13 Abstract: Silicene has been proven to be a promising material with att… read moreAbstract: Silicene has been proven to be a promising material with attractive electronic properties. During the synthesis of silicene, structural defects such as edge crack are likely to be generated and such defects in silicene have impacts on its properties. Herein, molecular dynamics simulations were performed to investigate the mechanical properties of the armchair silicene nanoribbons (ASiNRs) with edge cracks. Our results showed that the mechanical properties of the ASiNRs decrease because of the existence of edge crack. Both the pristine ASiNRs and the ASiNRs with edge cracks show brittle fracture behaviours. The crack length plays an important role in determining the critical strain and fracture strength of the ASiNRs. Moreover, we investigated the effects of strain rate and temperature on the mechanical properties of the ASiNRs with edge cracks. We observed that the increasing strain rate increases the critical strain and fracture strength while decreasing the Young’s modulus. Low-strain rates also changes the expanded directions of cracks in the ASiNRs. We also found that the increasing temperature could significantly decrease the mechanical properties of the ASiNRs with edge cracks. read less USED (high confidence) H. Honarvar and M. Hussein, “Two orders of magnitude reduction in silicon membrane thermal conductivity by resonance hybridizations,” Physical Review B. 2016. link Times cited: 39 Abstract: The thermal conductivity of a freestanding single-crystal si… read moreAbstract: The thermal conductivity of a freestanding single-crystal silicon membrane may be reduced significantly by attaching nanoscale pillars on one or both surfaces. Atomic resonances of the nanopillars locally and intrinsically couple with the base membrane phonon modes causing these modes to hybridize and flatten at each coupling location in the phonon band structure. The ensuing group velocity reductions, which in principle may be tuned to take place across silicon's full spectrum, lead to a lowering of the in-plane thermal conductivity in the base membrane. Using equilibrium molecular dynamics simulations, we report a staggering two orders of magnitude reduction in the thermal conductivity at room temperature by this mechanism. read less USED (high confidence) G. Hobler, M. L. Nietiadi, R. M. Bradley, and H. Urbassek, “Sputtering of silicon membranes with nanoscale thickness,” Journal of Applied Physics. 2016. link Times cited: 5 Abstract: A theoretical study of forward and backward sputtering produ… read moreAbstract: A theoretical study of forward and backward sputtering produced by the impact of single 20 keV Ar ions on freestanding amorphous Si membranes is carried out. We use three techniques: Monte Carlo (MC) and molecular dynamics (MD) simulations, as well as analytical theory based on the Sigmund model of sputtering. We find that the analytical model provides a fair description of the simulation results if the film thickness d exceeds about 10%–30% of the mean depth of energy deposition a. In this regime, backward sputtering is nearly independent of the membrane thickness and forward sputtering shows a maximum for thicknesses d≈a. The dependence of forward sputtering on the ion's incidence angle shows a qualitative change as a function of d: while for d≲a, the forward sputter yield has a maximum at oblique incidence angles, the maximum occurs at normal incidence for d≳a. As the membrane thickness is reduced below 0.1– 0.3a, the theory's predictions increasingly deviate from the MC results. For example, the predi... read less USED (high confidence) Y. Lü, Q. Bi, and X. Yan, “Density-wave-modulated crystallization in nanoscale silicon films and droplets.,” The Journal of chemical physics. 2016. link Times cited: 4 Abstract: Free surfaces have been known to significantly influence the… read moreAbstract: Free surfaces have been known to significantly influence the crystallization of tetrahedral liquids. However, a comprehensive understanding of the influence mechanism is still lacking at present. By employing molecular dynamics simulations, we find that the nucleation probability in nanoscale silicon films and droplets exhibits a ripple-like distribution spatially. This phenomenon is closely related to the structural order wave, which is induced by the density fluctuations arisen from the volume expansion in a confinement environment defined by free surfaces. By the aid of the intrinsic relation between the tetrahedral order and the density, the analytic results based on the density wave equation well account for the nucleation probability distributions in both films and droplets. Our findings reveal the underlying mechanism of the surface-assisted nucleation in tetrahedral liquids and provide an overall description of crystallization in liquid films and droplets. read less USED (high confidence) S. Mukherjee, J. Song, and S. Vengallatore, “Atomistic simulations of material damping in amorphous silicon nanoresonators,” Modelling and Simulation in Materials Science and Engineering. 2016. link Times cited: 1 Abstract: Atomistic simulations using molecular dynamics (MD) are emer… read moreAbstract: Atomistic simulations using molecular dynamics (MD) are emerging as a valuable tool for exploring dissipation and material damping in nanomechanical resonators. In this study, we used isothermal MD to simulate the dynamics of the longitudinal-mode oscillations of an amorphous silicon nanoresonator as a function of frequency (2 GHz–50 GHz) and temperature (15 K–300 K). Damping was characterized by computing the loss tangent with an estimated uncertainty of 7%. The dissipation spectrum displays a sharp peak at 50 K and a broad peak at around 160 K. Damping is a weak function of frequency at room temperature, and the loss tangent has a remarkably high value of ~0.01. In contrast, at low temperatures (15 K), the loss tangent increases monotonically from 4×10−4 to 4×10−3 as the frequency increases from 2 GHz to 50 GHz. The mechanisms of dissipation are discussed. read less USED (high confidence) R. Aguirre, J. J. Chavez, X. W. Zhou, S. Almeida, and D. Zubia, “Molecular dynamics simulations of ZnTe/Cu back contacts for CdTe solar cells,” 2016 IEEE 43rd Photovoltaic Specialists Conference (PVSC). 2016. link Times cited: 2 Abstract: Molecular dynamics (MD) simulations have been applied to stu… read moreAbstract: Molecular dynamics (MD) simulations have been applied to study the growth of ZnTe/Cu/CdTe layers on CdTe substrates. Our studies show that Cu forms pure clusters and ejects Cd atoms within the CdTe layer out towards the film's surface. Elemental concentration plots indicate that the amount of Cu added to the growth plays an important role on the intermixing between ZnTe and CdTe layers and the doping of CdTe. These results provide useful insight to the development of effective and reliable back contacts used in CdTe solar cells. read less USED (high confidence) K. Sääskilahti, K. Sääskilahti, J. Oksanen, J. Tulkki, A. McGaughey, and S. Volz, “Vibrational mean free paths and thermal conductivity of amorphous silicon from non-equilibrium molecular dynamics simulations,” arXiv: Computational Physics. 2016. link Times cited: 39 Abstract: The frequency-dependent mean free paths (MFPs) of vibrationa… read moreAbstract: The frequency-dependent mean free paths (MFPs) of vibrational heat carriers in amorphous silicon are predicted from the length dependence of the spectrally decomposed heat current (SDHC) obtained from non-equilibrium molecular dynamics simulations. The results suggest a (frequency)$^{-2}$ scaling of the room-temperature MFPs below 5 THz. The MFPs exhibit a local maximum at a frequency of 8 THz and fall below 1 nm at frequencies greater than 10 THz, indicating localized vibrations. The MFPs extracted from sub-10 nm system-size simulations are used to predict the length-dependence of thermal conductivity up to system sizes of 100 nm and good agreement is found with separate molecular dynamics simulations. Weighting the SDHC by the frequency-dependent quantum occupation function provides a simple and convenient method to account for quantum statistics and provides reasonable agreement with the experimentally-measured trend and magnitude. read less USED (high confidence) H. Honarvar, L. Yang, and M. Hussein, “Thermal transport size effects in silicon membranes featuring nanopillars as local resonators,” arXiv: Mesoscale and Nanoscale Physics. 2016. link Times cited: 44 Abstract: Silicon membranes patterned by nanometer-scale pillars stand… read moreAbstract: Silicon membranes patterned by nanometer-scale pillars standing on the surface provide a practical platform for thermal conductivity reduction by resonance hybridization. Using molecular simulations, we investigate the effect of nanopillar size, unit-cell size, and finite-structure size on the net capacity of the local resonators in reducing the thermal conductivity of the base membrane. The results indicate that the thermal conductivity reduction increases as the ratio of the volumetric size of a unit nanopillar to that of the base membrane is increased, and the intensity of this reduction varies with unit-cell size at a rate dependent on the volumetric ratio. Considering sample size, the resonance-induced thermal conductivity drop is shown to increase slightly with the number of unit cells until it would eventually level off. read less USED (high confidence) T. Aschenbrenner et al., “Composition analysis of coaxially grown InGaN multi quantum wells using scanning transmission electron microscopy,” Journal of Applied Physics. 2016. link Times cited: 0 Abstract: GaN nanotubes with coaxial InGaN quantum wells were analyzed… read moreAbstract: GaN nanotubes with coaxial InGaN quantum wells were analyzed by scanning transmission electron microscopy in order to determine their structural properties as well as the indium distribution across the InGaN quantum wells. For the latter, two process steps are necessary. First, a technique to prepare cross-sectional slices out of the nanotubes has been developed. Second, an existing scanning transmission electron microscopy analysis technique has been extended with respect to the special crystallographic orientation of this type of specimen. In particular, the shape of the nanotubes, their defect structure, and the incorporation of indium on different facets were investigated. The quantum wells preferentially grow on m-planes of the dodecagonally shaped nanotubes and on semipolar top facets while no significant indium signal was found on a-planes. An averaged indium concentration of 6% to 7% was found by scanning transmission electron microscopy analysis and could be confirmed by cathodoluminescence measu... read less USED (high confidence) J. Zhang and C. Wang, “Size-dependent pyroelectric properties of gallium nitride nanowires,” Journal of Applied Physics. 2016. link Times cited: 14 Abstract: The size scale effect on the pyroelectricproperties is studi… read moreAbstract: The size scale effect on the pyroelectricproperties is studied for gallium nitride(GaN) nanowires (NWs) based on molecular dynamics simulations and the theoretical analysis. Due to the significant influence of the surface thermoelasticity and piezoelectricity at the nanoscale, the pyroelectric coefficient of GaN NWs is found to depend on the cross-sectional size. This size-dependent pyroelectric coefficient of GaN NWs together with the size-dependent dielectric constant reported in our previous study is employed to study the pyroelectric potential of GaN NWs subjected to heating. The results show that the size scale effect is significant for thin NWs (cross-sectional size in nanometers) and may raise the pyroelectric potential of GaN NWs by over 10 times. Such a size scale effect on the pyroelectricproperties of NWs originates from the influence of thermoelasticity, piezoelectricity, and dielectricity at the nanoscale and decreases with increasing cross-section of GaN NWs. It is expected that the present study may have strong implication in the field of energy harvesting at the nanoscale, as pyroelectricity offers a new avenue to the design of novel nanogenerators. read less USED (high confidence) D. Packwood et al., “A universal preconditioner for simulating condensed phase materials.,” The Journal of chemical physics. 2016. link Times cited: 38 Abstract: We introduce a universal sparse preconditioner that accelera… read moreAbstract: We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes. read less USED (high confidence) R. Khusnutdinoff, “Microscopic collective dynamics of water,” Colloid Journal. 2016. link Times cited: 2 USED (high confidence) Z. Zhang, Y. Chen, Y. Xie, and S. Zhang, “Transition of thermal rectification in silicon nanocones,” arXiv: Mesoscale and Nanoscale Physics. 2016. link Times cited: 24 USED (high confidence) K. Park, P. N. Martin, and U. Ravaioli, “Electronic and thermal transport study of sinusoidally corrugated nanowires aiming to improve thermoelectric efficiency,” Nanotechnology. 2016. link Times cited: 18 Abstract: Improvement of thermoelectric efficiency has been very chall… read moreAbstract: Improvement of thermoelectric efficiency has been very challenging in the solid-state industry due to the interplay among transport coefficients which measure the efficiency. In this work, we modulate the geometry of nanowires to interrupt thermal transport with causing only a minimal impact on electronic transport properties, thereby maximizing the thermoelectric power generation. As it is essential to scrutinize comprehensively both electronic and thermal transport behaviors for nano-scale thermoelectric devices, we investigate the Seebeck coefficient, the electrical conductance, and the thermal conductivity of sinusoidally corrugated silicon nanowires and eventually look into an enhancement of the thermoelectric figure-of-merit Z T ?> from the modulated nanowires over typical straight nanowires. A loss in the electronic transport coefficient is calculated with the recursive Green function along with the Landauer formalism, and the thermal transport is simulated with the molecular dynamics. In contrast to a small influence on the thermopower and the electrical conductance of the geometry-modulated nanowires, a large reduction of the thermal conductivity yields an enhancement of the efficiency by 10% to 35% from the typical nanowires. We find that this approach can be easily extended to various structures and materials as we consider the geometrical modulation as a sole source of perturbation to the system. read less USED (high confidence) A. Porter, C. Tran, and F. Sansoz, “Intrinsic nanotwin effect on thermal boundary conductance in bulk and single-nanowire twinning superlattices,” Physical Review B. 2015. link Times cited: 19 Abstract: Coherent twin boundaries form periodic lamellar twinning in … read moreAbstract: Coherent twin boundaries form periodic lamellar twinning in a wide variety of semiconductor nanowires, and they are often viewed as near-perfect interfaces with reduced phonon and electron scattering behaviors. Such unique characteristics are of practical interest for high-performance thermoelectrics and optoelectronics; however, insufficient understanding of twin-size effects on thermal boundary resistance poses significant limitations for potential applications. Here, using atomistic simulations and ab initio calculations, we report direct computational observations showing a crossover from diffuse interface scattering to superlatticelike behavior for thermal transport across nanoscale twin boundaries present in prototypical bulk and nanowire Si examples. Intrinsic interface scattering is identified for twin periods $\ensuremath{\ge}22.6$ nm, but it also vanishes below this size to be replaced by ultrahigh Kapitza thermal conductances. Detailed analysis of vibrational modes shows that modeling twin boundaries as atomically thin $6H\text{\ensuremath{-}}\mathrm{Si}$ layers, rather than phonon scattering interfaces, provides an accurate description of effective cross-plane and in-plane thermal conductivities in twinning superlattices, as a function of the twin period thickness. read less USED (high confidence) C. Miao, G. Tai, J. Zhou, and W. Guo, “Phonon Trapping in Pearl-Necklace-Shaped Silicon Nanowires.,” Small. 2015. link Times cited: 3 Abstract: A pearl-necklace-shaped silicon nanowire, in contrast to a s… read moreAbstract: A pearl-necklace-shaped silicon nanowire, in contrast to a smooth nanowire, presents a much lower thermal conductivity due to the phonon trapping effect. By precisely controlling the pearl size and density, this reduction can be more than 70% for the structures designed in the study, which provides a unique approach for designing high-performance nanoscale thermoelectric devices. read less USED (high confidence) J.-W. Jiang, “Intrinsic twisting instability of kinked silicon nanowires for intracellular recording.,” Physical chemistry chemical physics : PCCP. 2015. link Times cited: 2 Abstract: A kinked silicon nanowire (KSiNW) is a zigzag-shaped nanowir… read moreAbstract: A kinked silicon nanowire (KSiNW) is a zigzag-shaped nanowire with its growth direction changing regularly at the kinking joints, resulting in a quasi-two-dimensional structure. An intrinsic tendency for the two-dimensional system is to generate some out-of-plane vibrations to withstand the mechanical instability in the third dimension. In the present work, we report a lattice dynamical study of the intrinsic out-of-plane twisting vibration of KSiNWs. We derive the dynamical matrix analytically, and explore the kinking effect on the phonon spectrum of the KSiNWs. Based on lattice dynamical analysis, we obtain an analytical formula for the geometrical dependence of the twisting amplitude of the KSiNWs. The analytical formula provides valuable information on the kinking induced twisting stability of KSiNWs serving as bio-probes for intracellular recording application. read less USED (high confidence) Z. Wei, J. Yang, K. Bi, and Y. Chen, “Phonon transport properties in pillared silicon film,” Journal of Applied Physics. 2015. link Times cited: 33 Abstract: The phonon transport property of pillared silicon film is sy… read moreAbstract: The phonon transport property of pillared silicon film is systematically investigated by molecular dynamics simulation and lattice dynamics calculation. It is found that the thermal conductivity can be reduced to as low as 28.6% of the conductivity of plain ones. Although the reduced thermal conductivity can be explained qualitatively by increased surface roughness, our calculations show that the pillars modify the phonon dispersion relation and reduce the phonon group velocity due to the local resonance effects. Furthermore, by analyzing the participation ratio spectra, it is shown that the pillars reduce the mode participation ratio over the whole range of frequency. We found that the mode localization around the pillars is another important factor to reduce the thermal conductivity of pillared film. The present investigations indicate that the pillared film may have potential application in thermoelectric energy conversion. read less USED (high confidence) X. Chen, A. Chernatynskiy, L. Xiong, and Y. Chen, “A coherent phonon pulse model for transient phonon thermal transport,” Comput. Phys. Commun. 2015. link Times cited: 15 USED (high confidence) L. Sang, V. V. Hoang, and D. T. N. Tranh, “Melting of crystalline Si nanoparticle investigated by simulation,” The European Physical Journal D. 2015. link Times cited: 6 USED (high confidence) T. Damart, V. Giordano, and A. Tanguy, “Nano-crystalline inclusions as a low-pass filter for thermal transport in a-Si,” Physical Review B. 2015. link Times cited: 20 Abstract: We use atomistic simulations to study the resonant acoustic … read moreAbstract: We use atomistic simulations to study the resonant acoustic modes and compare different calculations of the acoustic mean-free path in amorphous systems with nanometric crystalline spherical inclusions. We show that the resonant acoustic properties are not a simple combination of the vibrations in the inclusions and in the amorphous matrix. The presence of the inclusion affects the transport properties mainly in the frequency range separating simple scattering from multiple scattering processes. However, propagation of acoustic wavepackets is spatially heterogeneous and shows that the amorphous/crystalline interface acts as a low energy pass filter slowing down the high kinetic energy motion whatever the vibration frequency. These heterogeneities cannot be catched by the mean free path, but still they must play an important role in thermal transport, thus raising the question of the correct modeling of thermal transport in composite systems. read less USED (high confidence) T. Vo and B. H. Kim, “Interface thermal resistance between liquid water and various metallic surfaces,” International Journal of Precision Engineering and Manufacturing. 2015. link Times cited: 57 USED (high confidence) L. Zhang, W. Wu, H. Ren, J. Dong, Y. Liu, and H. Li, “Structural evolution of a Si melt in nanoscale confined space,” RSC Advances. 2015. link Times cited: 2 Abstract: Molecular dynamics (MD) simulations are performed to systema… read moreAbstract: Molecular dynamics (MD) simulations are performed to systematically study the structural evolution of a Si melt confined in nanoscale space. The freezing Si structure at 300 K is stratification which is composed of a stable crystalline shell and a metastable glassy core. Due to the spatial restriction effect, the confined structure consists of higher-coordinated clusters compared to the bulk Si. It is revealed that the statistical average of the ordered shell and the disordered core gives rise to the split of the second peak of the pair distribution function curves of the Si melt. Moreover, increasing the cavity size is detrimental to the stability of the layered configuration of the confined melt and increasing the cooling rate mainly influences the arrangement of Si atoms adjacent to the SWCNT wall. Interestingly, we also find that the cylindric cavity is more beneficial than the square one in inducing the formation of long-range crystalline order in nanoscale space. read less USED (high confidence) Y. Okada, K. Eriguchi, and K. Ono, “Surface orientation dependence of ion bombardment damage during plasma processing,” 2015 International Conference on IC Design & Technology (ICICDT). 2015. link Times cited: 4 Abstract: Geometrical transition to three dimensional (3D) or Si nanow… read moreAbstract: Geometrical transition to three dimensional (3D) or Si nanowire (SNW) MOSFETs imposes critical issues regarding process technologies. High energy ion bombardment damage in 3D MOSFETs has been considered inevitable because of the fundamental nature of plasma process. In this study, we further investigated plasma-induced physical damage (PPD) on Si substrates with different surface orientations - (100), (111), and (110) to emulate PPD of future 3D and SNW devices. A classical molecular dynamics simulation implies that the channeling of incident ions is expected in a substrate with the (110) plane. However, spectroscopic ellipsometry identified thinner damaged layers in the case of (110) plane for higher ion energies (> 500 eV) and the pseudo-extinction coefficient k was smaller for the (110) plane. A capacitance-voltage measurement confirmed that the damaged layer consisted of SiO2. Thus, the same Si loss leading to Si recess that degrades device performance is presumable on both of the planes. The present findings provide key guidelines for designing future SNW devices exposed to plasma. read less USED (high confidence) J. Luo and Y. Shi, “The local stress state of a running shear band in amorphous solids,” Journal of Materials Research. 2015. link Times cited: 7 Abstract: In molecular dynamics simulations, the local stress state in… read moreAbstract: In molecular dynamics simulations, the local stress state in the shear band is examined in six different model metallic glasses and one amorphous Si system (also has been perceived as a metallic glass analog) under different loading conditions. For all but the FeP and the amorphous Si systems, the running shear band (RSB) exhibits a liquid-like hydrostatic plus shear stress state. Our results suggest that the liquid feature of a RSB is not due to temperature rise or plastic confinement but due to the disorder driven by flow, which can be offset by strong directionality in bonding, phase segregation, or aging. The knowledge of the liquid-like stress state can be conveniently utilized in experiments to infer the local stress state of the RSB from the global tensile stress for metallic glasses. read less USED (high confidence) T. Vo and B. H. Kim, “Interface thermal resistance between liquid water and various metallic surfaces,” International Journal of Precision Engineering and Manufacturing. 2015. link Times cited: 0 USED (high confidence) S.-C. Chien, S. Auerbach, and P. A. Monson, “Modeling the self-assembly of silica-templated nanoparticles in the initial stages of zeolite formation.,” Langmuir : the ACS journal of surfaces and colloids. 2015. link Times cited: 16 Abstract: The reaction ensemble Monte Carlo method was used to model t… read moreAbstract: The reaction ensemble Monte Carlo method was used to model the self-assembly and structure of silica nanoparticles found in the initial stages of the clear-solution synthesis of the silicalite-1 zeolite. Such nanoparticles, which comprise both silica and organic structure-directing agents (OSDAs), are believed to play a crucial role in the formation of silica nanoporous materials, yet very limited atomic-level structural information is available for these nanoparticles. We have modeled silica monomers as flexible tetrahedra with spring constants fitted in previous work to silica bulk moduli and OSDAs as spheres attracted to anionic silica monomers. We have studied one-step and two-step formation mechanisms, the latter involving the initial association of silica species and OSDAs driven by physical solution forces, followed by silica condensation/hydrolysis reactions simulated with reaction ensemble Monte Carlo. The two-step process with preassociation was found to be crucial for generating nearly spherical nanoparticles; otherwise, without preassociation they exhibited jagged, ramified structures. The two-step nanoparticles were found to exhibit a core-shell structure with mostly silica in the core surrounded by a diffuse shell of OSDAs, in agreement with SANS and SAXS data. The Qn distribution, quantifying silicon atoms bound to n bridging oxygens, found in the simulated nanoparticles is in broad agreement with (29)Si solid-state NMR data on smaller, 2 nm nanoparticle populations. Ring-size distributions from the simulated nanoparticles show that five-membered rings are prevalent when considering OSDA/silica mole fractions (∼0.2) that lead to silicalite-1, in agreement with a previous IR and modeling study. Nanoparticles simulated with higher OSDA concentrations show ring-size distributions shifted to smaller rings, with three-membered silica rings dominating at an OSDA/silica mole fraction of 0.8. Our simulations show no evidence of long-range silicalite-1 order in these nanoparticles. read less USED (high confidence) T. Zhan, S. Minamoto, Y. Xu, Y. Tanaka, and Y. Kagawa, “Thermal boundary resistance at Si/Ge interfaces by molecular dynamics simulation,” AIP Advances. 2015. link Times cited: 25 Abstract: In this study, we investigated the temperature dependence an… read moreAbstract: In this study, we investigated the temperature dependence and size effect of the thermal boundary resistance at Si/Ge interfaces by non-equilibrium molecular dynamics (MD) simulations using the direct method with the Stillinger-Weber potential. The simulations were performed at four temperatures for two simulation cells of different sizes. The resulting thermal boundary resistance decreased with increasing temperature. The thermal boundary resistance was smaller for the large cell than for the small cell. Furthermore, the MD-predicted values were lower than the diffusion mismatch model (DMM)-predicted values. The phonon density of states (DOS) was calculated for all the cases to examine the underlying nature of the temperature dependence and size effect of thermal boundary resistance. We found that the phonon DOS was modified in the interface regions. The phonon DOS better matched between Si and Ge in the interface region than in the bulk region. Furthermore, in interface Si, the population of low-frequen... read less USED (high confidence) Z. Nourmohammadi, S. Mukherjee, S. Joshi, J. Song, and S. Vengallatore, “Methods for Atomistic Simulations of Linear and Nonlinear Damping in Nanomechanical Resonators,” Journal of Microelectromechanical Systems. 2015. link Times cited: 6 Abstract: Atomistic simulations can be used to compute damping from fi… read moreAbstract: Atomistic simulations can be used to compute damping from first principles and gain unprecedented insights into the mechanisms of dissipation. However, the technique is still in its infancy and many foundational aspects remain unexplored. As a step toward addressing these issues, we present here a comparative study of five different methods for estimating damping under isothermal conditions. Classical molecular dynamics was used to simulate the fundamental longitudinal-mode oscillations of nanowires and nanofilms of silicon and nickel at room temperature (300 K) in the canonical ensemble using the Nosé-Hoover thermostat. In the subresonant regime, damping was quantified using the loss tangent and loss factor during steady-state harmonic vibration. The quality factor was obtained by analyzing the spectrum of thermomechanical noise and also from the Duffing-like nonlinearity in the frequency response under harmonic excitation. In addition, the nonlinear logarithmic decrement was obtained from the Hilbert transform of freely decaying oscillations. We discuss the factors that must be considered while selecting simulation parameters, establish criteria for convergence and linearity, and highlight the relative merits and limitations of each method. read less USED (high confidence) F. van Swol, X. W. Zhou, S. R. Challa, and J. E. Martin, “Heterojunctions of model CdTe/CdSe mixtures,” Modelling and Simulation in Materials Science and Engineering. 2015. link Times cited: 0 Abstract: We report on the strain behavior of compound mixtures of mod… read moreAbstract: We report on the strain behavior of compound mixtures of model group II–VI semiconductors. We use the Stillinger–Weber Hamiltonian that we recently introduced, specifically developed to model binary mixtures of group II–VI compounds such as CdTe and CdSe. We employ molecular dynamics simulations to examine the behavior of thin sheets of material, bilayers of CdTe and CdSe. The lattice mismatch between the two compounds leads to a strong bending of the entire sheet, with about a 0.5 to 1° deflection between neighboring planes. To analyze bilayer bending, we introduce a simple one-dimensional model and use energy minimization to find the angle of deflection. The analysis is equivalent to a least-squares straight line fit. We consider the effects of bilayers which are asymmetric with respect to the thickness of the CdTe and CdSe parts. From this we learn that the bending can be subdivided into four kinds depending on the compressive/tensile nature of each outer plane of the sheet. We use this approach to directly compare our findings with experimental results on the bending of CdTe/CdSe rods. To reduce the effects of the lattice mismatch we explore diffuse interfaces, where we mix (i.e. alloy) Te and Se, and estimate the strain response. read less USED (high confidence) R. Borrajo-Pelaez, F. Saiz, and M. Gamero-Castaño, “The Effect of the Molecular Mass on the Sputtering of Si, SiC, Ge, and GaAs by Electrosprayed Nanodroplets at Impact Velocities up to 17 km/s,” Aerosol Science and Technology. 2015. link Times cited: 9 Abstract: Electrosprayed nanodroplets impacting on covalently bonded m… read moreAbstract: Electrosprayed nanodroplets impacting on covalently bonded materials at velocities of a few kilometers per second strongly modify their surfaces by sputtering atoms, amorphizing the region surrounding the impact, and carving craters of comparable size. This article investigates the effects of the projectile's molecular mass on the phenomenology of the impact on Si, SiC, Ge, and GaAs at impact velocities significantly higher than previously studied. An appropriate range of molecular mass is covered by electrospraying the ionic liquids ethylammonium nitrate, EAN, and 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide, EMI-Im, which have molecular masses of 108 and 391 amu, respectively. The beamlets are characterized with the time-of-flight technique to determine the impact velocity, stagnation pressure, and molecular kinetic energy of the projectiles, and to estimate their average diameters. The ranges of these parameters are 7–17 km/s, 40–190 GPa, 50–420 eV, and 10–14 nm. Under these conditions, we find that the molecular mass has a strong effect on sputtering: the sputtering yield for the heavier EMI-Im molecule is always higher than for EAN, with maximum values for Si, SiC, Ge, and GaAs of 4.3, 11.5, 10.9, and 9.4 atoms per EMI-Im molecule, and 1.1, 3.9, 3.3, and 2.9 in the case of EAN. More importantly, droplets of the same diameter (10 nm) and kinetic energy eject significantly different numbers of atoms, with average ratios between the EMI-Im and EAN droplets of 1.8, 1.5, 1.7, and 1.5 for Si, SiC, Ge, and GaAs. Molecular dynamics simulations reproduce the observed enhancement of the sputtering at increasing molecular mass. Copyright 2015 American Association for Aerosol Research read less USED (high confidence) F. Wang and Y.-pu Zhao, “Structural evolution of the silicon nanowire via molecular dynamics simulations: the double-strand atomic chain and the monatomic chain,” Archive of Applied Mechanics. 2015. link Times cited: 21 USED (high confidence) Y. Lü, “Homogeneous two-dimensional nucleation of guest-free silicon clathrates,” Philosophical Magazine. 2015. link Times cited: 1 Abstract: The difficulty in synthesizing guest-free semiconductor clat… read moreAbstract: The difficulty in synthesizing guest-free semiconductor clathrates complicates the process of determining how these cage-like structures form. This work studies the microscopic mechanism of the nucleation of guest-free Si136 clathrate using molecular dynamics simulations with the Stillinger–Weber potential. The homogeneous nucleation of Si136, which is realized in a narrow negative pressure range before liquid cavitation, exhibits the characteristic feature of the two-dimensional (2D) mode. The critical nucleus is composed of one to two five-membered rings, and the nucleation barrier is close to 1 kBT. According to a thermodynamic model based on atomistic nucleation theory, the effective binding energy associated with the formation of 2D critical nuclei is significantly low, which is responsible for the low nucleation barrier of Si136 clathrate. In the post-nucleation period, the critical nucleus preferentially grows into a dodecahedron, and the latter continuously grows with sharing face along 〈1 1 0〉. read less USED (high confidence) X. Chen, L. Xiong, A. Chernatynskiy, and Y. Chen, “A molecular dynamics study of tilt grain boundary resistance to slip and heat transfer in nanocrystalline silicon,” Journal of Applied Physics. 2014. link Times cited: 17 Abstract: We present a molecular dynamics study of grain boundary (GB)… read moreAbstract: We present a molecular dynamics study of grain boundary (GB) resistance to dislocation-mediated slip transfer and phonon-mediated heat transfer in nanocrystalline silicon bicrystal. Three most stable ⟨110⟩ tilt GBs in silicon are investigated. Under mechanical loading, the nucleation and growth of hexagonal-shaped shuffle dislocation loops are reproduced. The resistances of different GBs to slip transfer are quantified through their constitutive responses. Results show that the Σ3 coherent twin boundary (CTB) in silicon exhibits significantly higher resistance to dislocation motion than the Σ9 GB in glide symmetry and the Σ19 GB in mirror symmetry. The distinct GB strengths are explained by the atomistic details of the dislocation-GB interaction. Under thermal loading, based on a thermostat-induced heat pulse model, the resistances of the GBs to transient heat conduction in ballistic-diffusive regime are characterized. In contrast to the trend found in the dislocation-GB interaction in bicrystal models with different GBs, the resistances of the same three GBs to heat transfer are strikingly different. The strongest dislocation barrier Σ3 CTB is almost transparent to heat conduction, while the dislocation-permeable Σ9 and Σ19 GBs exhibit larger resistance to heat transfer. In addition, simulation results suggest that the GB thermal resistance not only depends on the GB energy but also on the detailed atomic structure along the GBs. read less USED (high confidence) C.-ying Wang et al., “Multi-scale simulation of the stability and diffusion of lithium in the presence of a 90° partial dislocation in silicon,” Journal of Applied Physics. 2014. link Times cited: 5 Abstract: The stable positions, binding energies, and dynamic properti… read moreAbstract: The stable positions, binding energies, and dynamic properties of Li impurity in the presence of a 90° partial dislocation in Si have been studied by using the multi-scale simulation method. The corresponding results are compared with the defect-free Si crystal in order to reflect how the dislocation defect affects the performances of Li-ion batteries (LIBs) at the atomic level. It is found that the inserted Li atom in the dislocation core and nearest regions is more stable, since the binding energies are 0.13 eV to 0.52 eV larger than the bulk Si. Moreover, it is easier for Li atom to diffuse into those defect areas and harder to diffuse out. Thus, Li dopant may tend to congregate in the dislocation core and nearest regions. On the other side, the 90° partial dislocation can glide in the {111} plane accompanied by the diffusion of Li impurity along the pentagon ring of core. In addition, the spacious heptagon ring of dislocation core can lower the migration barrier of Li atom from 0.63 eV to 0.34 eV, whi... read less USED (high confidence) K. M. Bal and E. Neyts, “On the time scale associated with Monte Carlo simulations.,” The Journal of chemical physics. 2014. link Times cited: 44 Abstract: Uniform-acceptance force-bias Monte Carlo (fbMC) methods hav… read moreAbstract: Uniform-acceptance force-bias Monte Carlo (fbMC) methods have been shown to be a powerful technique to access longer timescales in atomistic simulations allowing, for example, phase transitions and growth. Recently, a new fbMC method, the time-stamped force-bias Monte Carlo (tfMC) method, was derived with inclusion of an estimated effective timescale; this timescale, however, does not seem able to explain some of the successes the method. In this contribution, we therefore explicitly quantify the effective timescale tfMC is able to access for a variety of systems, namely a simple single-particle, one-dimensional model system, the Lennard-Jones liquid, an adatom on the Cu(100) surface, a silicon crystal with point defects and a highly defected graphene sheet, in order to gain new insights into the mechanisms by which tfMC operates. It is found that considerable boosts, up to three orders of magnitude compared to molecular dynamics, can be achieved for solid state systems by lowering of the apparent activation barrier of occurring processes, while not requiring any system-specific input or modifications of the method. We furthermore address the pitfalls of using the method as a replacement or complement of molecular dynamics simulations, its ability to explicitly describe correct dynamics and reaction mechanisms, and the association of timescales to MC simulations in general. read less USED (high confidence) V. V. Hoang and H. T. C. Mi, “Free-standing silicene obtained by cooling from 2D liquid Si: structure and thermodynamic properties,” Journal of Physics D: Applied Physics. 2014. link Times cited: 20 Abstract: The structure and various thermodynamic properties of free-s… read moreAbstract: The structure and various thermodynamic properties of free-standing silicene have been studied by computer simulation. Models are obtained by cooling from buckling two-dimensional (2D) liquid Si via molecular dynamics (MD) simulation with Stillinger–Weber interatomic potential. The temperature dependence of total energy, heat capacity, mean ring size and mean coordination number shows that silicenization of 2D liquid Si exhibits a first-order-like behavior. The evolution of radial distribution function upon cooling from the melt also shows that solidification occurs in the system. The final configuration of silicene is analyzed via coordination, bond-angle, interatomic distance and ring distributions or distribution of buckling in the system. 2D visualization of atomic configurations clearly demonstrated that silicene obtained ‘naturally’ by cooling from the melt exhibits various structural previously unreported behaviors. We find the formation of polycrystalline silicene with clear grain boundaries containing various defects including various vacancies, Stone–Wales defects or skew rings and multimembered rings unlike those proposed in the literature. However, atoms in the obtained silicene are mostly involved in six-fold rings, forming a buckling honeycomb structure like that found in practice. We find that buckling is not unique for all atoms in the models although the majority of atoms reveal buckling of the most stable low-buckling silicene found in the literature. The buckling distribution is broad and symmetric. Our comprehensive MD simulation of a relatively large silicene model containing 104 atoms and obtained ‘naturally’ by cooling from the melt provides original insights into the structure and thermodynamics of this important 2D material. read less USED (high confidence) Z. Wei, J. Yang, K. Bi, and Y. Chen, “Mode dependent lattice thermal conductivity of single layer graphene,” Journal of Applied Physics. 2014. link Times cited: 63 Abstract: Molecular dynamics simulation is performed to extract the ph… read moreAbstract: Molecular dynamics simulation is performed to extract the phonon dispersion and phonon lifetime of single layer graphene. The mode dependent thermal conductivity is calculated from the phonon kinetic theory. The predicted thermal conductivity at room temperature exhibits important quantum effects due to the high Debye temperature of graphene. But the quantum effects are reduced significantly when the simulated temperature is as high as 1000 K. Our calculations show that out-of-plane modes contribute about 41.1% to the total thermal conductivity at room temperature. The relative contribution of out-of-plane modes has a little decrease with the increase of temperature. Contact with substrate can reduce both the total thermal conductivity of graphene and the relative contribution of out-of-plane modes, in agreement with previous experiments and theories. Increasing the coupling strength between graphene and substrate can further reduce the relative contribution of out-of-plane modes. The present investigations also show that the relative contribution of different mode phonons is not sensitive to the grain size of graphene. The obtained phonon relaxation time provides useful insight for understanding the phonon mean free path and the size effects in graphene. read less USED (high confidence) B. Liu et al., “Interfacial thermal conductance of a silicene/graphene bilayer heterostructure and the effect of hydrogenation.,” ACS applied materials & interfaces. 2014. link Times cited: 113 Abstract: van der Waals heterostructures, obtained by stacking layers … read moreAbstract: van der Waals heterostructures, obtained by stacking layers of isolated two-dimensional atomic crystals like graphene (GE) and silicene (SE), are one of emerging nanomaterials for the development of future multifunctional devices. Thermal transport behaviors at the interface of these heterostructures play a pivotal role in determining their thermal properties and functional performance. Using molecular dynamics simulations, the interfacial thermal conductance G of an SE/GE bilayer heterostructure is studied. Simulations show that G of a pristine SE/GE bilayer at room temperature is 11.74 MW/m(2)K when heat transfers from GE to SE, and is 9.52 MW/m(2)K for a reverse heat transfer, showing apparent thermal rectification effects. In addition, G increases monotonically with both the temperature and the interface coupling strength. Furthermore, hydrogenation of GE is efficient in enhancing G if an optimum hydrogenation pattern is adopted. By changing the hydrogen coverage f, G can be controllably manipulated and maximized up to five times larger than that of pristine SE/GE. This study is helpful for understanding the interface thermal transport behaviors of novel van der Waals heterostructures and provides guidance for the design and control of their thermal properties. read less USED (high confidence) R. Frieling, M. Radek, S. Eon, H. Bracht, and D. Wolf, “Phonon coherence in isotopic silicon superlattices,” Applied Physics Letters. 2014. link Times cited: 10 Abstract: Recent experimental and theoretical investigations have conf… read moreAbstract: Recent experimental and theoretical investigations have confirmed that a reduction in thermal conductivity of silicon is achieved by isotopic silicon superlattices. In the present study, non-equilibrium molecular dynamics simulations are performed to identify the isotope doping and isotope layer ordering with minimum thermal conductivity. Furthermore, the impact of isotopic intermixing at the superlattice interfaces on phonon transport is investigated. Our results reveal that the coherence of phonons in isotopic Si superlattices is prevented if interfacial mixing of isotopes is considered. read less USED (high confidence) K. Zhang, H. Li, and Y. Y. Jiang, “Liquid-liquid phase transition in quasi-two-dimensional supercooled silicon.,” Physical chemistry chemical physics : PCCP. 2014. link Times cited: 13 Abstract: Anomalies of the local structural order in quasi-two-dimensi… read moreAbstract: Anomalies of the local structural order in quasi-two-dimensional liquid silicon upon cooling are investigated. Results show that the appearance of the left subpeak in pair correlation functions is the signature of the liquid-liquid phase transition (LLPT). The structural origin of the LLPT is the formation of a crystal-like ordered structure with a short-range scale, which in turn forms the local well-organized paracrystalline region. Unlike in the bulk liquid silicon, the stages of the LLPT and liquid-solid phase transition (LSPT) in the quasi-two-dimensional liquid silicon do not overlap. The crystal-like ordered structures formed in the LLPT are precursors which are prepared for the subsequent LSPT. Also observed was a strong interconnection between the local well-organized paracrystalline region and the transition from the typical metal to the semimetal in the two-dimensional silicon. This study will aid in better understanding of the essential phase change in two-dimensional liquid silicon. read less USED (high confidence) G. K. N’Tsouaglo, L. Béland, J. Joly, P. Brommer, N. Mousseau, and P. Pochet, “Probing Potential Energy Surface Exploration Strategies for Complex Systems.,” Journal of chemical theory and computation. 2014. link Times cited: 4 Abstract: The efficiency of minimum-energy configuration searching alg… read moreAbstract: The efficiency of minimum-energy configuration searching algorithms is closely linked to the energy landscape structure of complex systems, yet these algorithms often include a number of steps of which the effect is not always clear. Decoupling these steps and their impacts can allow us to better understand both their role and the nature of complex energy landscape. Here, we consider a family of minimum-energy algorithms based, directly or indirectly, on the well-known Bell-Evans-Polanyi (BEP) principle. Comparing trajectories generated with BEP-based algorithms to kinetically correct off-lattice kinetic Monte Carlo schemes allow us to confirm that the BEP principle does not hold for complex systems since forward and reverse energy barriers are completely uncorrelated. As would be expected, following the lowest available energy barrier leads to rapid trapping. This is why BEP-based methods require also a direct handling of visited basins or barriers. Comparing the efficiency of these methods with a thermodynamical handling of low-energy barriers, we show that most of the efficiency of the BEP-like methods lie first and foremost in the basin management rather than in the BEP-like step. read less USED (high confidence) M. Park, I. Lee, and Y.-S. Kim, “Lattice thermal conductivity of crystalline and amorphous silicon with and without isotopic effects from the ballistic to diffusive thermal transport regime,” Journal of Applied Physics. 2014. link Times cited: 23 Abstract: Thermal conductivity of a material is an important physical … read moreAbstract: Thermal conductivity of a material is an important physical parameter in electronic and thermal devices, and as the device size shrinks down, its length-dependence becomes unable to be neglected. Even in micrometer scale devices, materials having a long mean free path of phonons, such as crystalline silicon (Si), exhibit a strong length dependence of the thermal conductivities that spans from the ballistic to diffusive thermal transport regime. In this work, through non-equilibrium molecular-dynamics (NEMD) simulations up to 17 μm in length, the lattice thermal conductivities are explicitly calculated for crystalline Si and up to 2 μm for amorphous Si. The Boltzmann transport equation (BTE) is solved within a frequency-dependent relaxation time approximation, and the calculated lattice thermal conductivities in the BTE are found to be in good agreement with the values obtained in the NEMD. The isotopic effects on the length-dependent lattice thermal conductivities are also investigated both in the crystalline and amorphous Si. read less USED (high confidence) G. Singh, J. Kermode, A. Vita, and R. Zimmerman, “Validity of linear elasticity in the crack-tip region of ideal brittle solids,” International Journal of Fracture. 2014. link Times cited: 20 USED (high confidence) Y. Bi and T. Li, “Probing methane hydrate nucleation through the forward flux sampling method.,” The journal of physical chemistry. B. 2014. link Times cited: 77 Abstract: Understanding the nucleation of hydrate is the key to develo… read moreAbstract: Understanding the nucleation of hydrate is the key to developing effective strategies for controlling methane hydrate formation. Here we present a computational study of methane hydrate nucleation, by combining the forward flux sampling (FFS) method and the coarse-grained water model mW. To facilitate the application of FFS in studying the formation of methane hydrate, we developed an effective order parameter λ on the basis of the topological analysis of the tetrahedral network. The order parameter capitalizes the signature of hydrate structure, i.e., polyhedral cages, and is capable of efficiently distinguishing hydrate from ice and liquid water while allowing the formation of different hydrate phases, i.e., sI, sII, and amorphous. Integration of the order parameter λ with FFS allows explicitly computing hydrate nucleation rates and obtaining an ensemble of nucleation trajectories under conditions where spontaneous hydrate nucleation becomes too slow to occur in direct simulation. The convergence of the obtained hydrate nucleation rate was found to depend crucially on the convergence of the spatial distribution for the spontaneously formed hydrate seeds obtained from the initial sampling of FFS. The validity of the approach is also verified by the agreement between the calculated nucleation rate and that inferred from the direct simulation. Analyzing the obtained large ensemble of hydrate nucleation trajectories, we show hydrate formation at 220 K and 500 bar is initiated by the nucleation events occurring in the vicinity of water-methane interface, and facilitated by a gradual transition from amorphous to crystalline structure. The latter provides the direct support to the proposed two-step nucleation mechanism of methane hydrate. read less USED (high confidence) K. Eriguchi, Y. Takao, and K. Ono, “A new aspect of plasma-induced physical damage in three-dimensional scaled structures — Sidewall damage by stochastic straggling and sputtering,” 2014 IEEE International Conference on IC Design & Technology. 2014. link Times cited: 14 Abstract: Increasing demands for higher performance LSIs require three… read moreAbstract: Increasing demands for higher performance LSIs require three dimensional (3D) structures such as a FinFET and 3D integration package, and a 3D NAND flash memory. We focused on damage creation mechanism in such structures during plasma etching-plasma-induced physical damage (PPD). Compared to PPD in planar FETs (e.g. Si recess), atomistic simulations predicted that, during etching of FinFETs, both “straggling” of impinging ions in the bulk and “sputtering” of species at the reacting surface created defects in the bulk fin. The damage layer formation in the fin structure was modeled on the basis of range theory. A molecular dynamics simulation was performed in a Si fin structure to verify the proposed mechanism. Created defect structures by these mechanisms were confirmed to play the role of a carrier trap site by a quantum mechanical calculation. The obtained results showed that ions with lighter masses and higher incident energies induced a larger amount of damage in the bulk fin. Since they are the intrinsic nature of plasma etching, both stochastic straggling and sputtering should be implemented in the PPD evaluation of 3D devices. read less USED (high confidence) A. Hudait and V. Molinero, “Ice crystallization in ultrafine water-salt aerosols: nucleation, ice-solution equilibrium, and internal structure.,” Journal of the American Chemical Society. 2014. link Times cited: 50 Abstract: Atmospheric aerosols have a strong influence on Earth's… read moreAbstract: Atmospheric aerosols have a strong influence on Earth's climate. Elucidating the physical state and internal structure of atmospheric aqueous aerosols is essential to predict their gas and water uptake, and the locus and rate of atmospherically important heterogeneous reactions. Ultrafine aerosols with sizes between 3 and 15 nm have been detected in large numbers in the troposphere and tropopause. Nanoscopic aerosols arising from bubble bursting of natural and artificial seawater have been identified in laboratory and field experiments. The internal structure and phase state of these aerosols, however, cannot yet be determined in experiments. Here we use molecular simulations to investigate the phase behavior and internal structure of liquid, vitrified, and crystallized water-salt ultrafine aerosols with radii from 2.5 to 9.5 nm and with up to 10% moles of ions. We find that both ice crystallization and vitrification of the nanodroplets lead to demixing of pure water from the solutions. Vitrification of aqueous nanodroplets yields nanodomains of pure low-density amorphous ice in coexistence with vitrified solute rich aqueous glass. The melting temperature of ice in the aerosols decreases monotonically with an increase of solute fraction and decrease of radius. The simulations reveal that nucleation of ice occurs homogeneously at the subsurface of the water-salt nanoparticles. Subsequent ice growth yields phase-segregated, internally mixed, aerosols with two phases in equilibrium: a concentrated water-salt amorphous mixture and a spherical cap-like ice nanophase. The surface of the crystallized aerosols is heterogeneous, with ice and solution exposed to the vapor. Free energy calculations indicate that as the concentration of salt in the particles, the advance of the crystallization, or the size of the particles increase, the stability of the spherical cap structure increases with respect to the alternative structure in which a core of ice is fully surrounded by solution. We predict that micrometer-sized particles and nanoparticles have the same equilibrium internal structure. The variation of liquid-vapor surface tension with solute concentration is a key factor in determining whether a solution-embedded ice core or vapor-exposed ice cap is the equilibrium structure of the aerosols. In agreement with experiments, we predict that the structure of mixed-phase HNO3-water particles, representative of polar stratospheric clouds, consists of an ice core surrounded by freeze-concentrated solution. The results of this work are important to determine the phase state and internal structure of sea spray ultrafine aerosols and other mixed-phase particles under atmospherically relevant conditions. read less USED (high confidence) J. Zhang, C. Wang, and S. Adhikari, “Surface Effects on the Electrostatic Potential Generated in a Bent Gallium Nitride Nanowire,” IEEE Transactions on Nanotechnology. 2014. link Times cited: 6 Abstract: The aim of this paper is to conduct the first study of the s… read moreAbstract: The aim of this paper is to conduct the first study of the surface effects on the voltage output of bent gallium nitride (GaN) nanowires (NWs), which are promising for nanogenerators. To reach this goal, a 3-D composite beam model was developed and the corresponding theoretical framework was established for the structural responses of piezoelectric NWs. In this study molecular dynamics simulations (MDS) were first carried out to determine the exact material properties for several small NW samples. The MDS-derived size-dependence of parameters provide fitting points for the 3-D composite beam with a core-shell geometry. With the aid of the finite element techniques the equivalent material properties obtained from above fitting procedure enable the use of the core-shell model for larger structures where MDS were not feasible. The obtained results showed that the influence of the surface layer greatly modifies the potential distribution on the cross section and raises the voltage output of bent GaN NWs by up to 120%. In particular, the contribution from the surface piezoelectricity to the surface effect is found to be predominant over that of the surface elasticity and surface stresses. read less USED (high confidence) B. Liu et al., “Thermal conductivity of silicene nanosheets and the effect of isotopic doping,” Journal of Physics D: Applied Physics. 2014. link Times cited: 62 Abstract: This paper investigates the thermal conductivity of silicene… read moreAbstract: This paper investigates the thermal conductivity of silicene nanosheets (SiNSs) via molecular dynamic simulation. It shows that the thermal conductivity of pristine SiNSs is about 25–30 W mK−1 and exhibits anisotropic behaviour. Moreover, it is found that isotopic doping is efficient in reducing the thermal conductivity of SiNSs. When SiNSs are randomly doped with 30Si at the doping percentage of 50%, a maximum reduction of about 20% is obtained. This reduction can be increased when the dopants are arranged into a superlattice pattern. The thermal conductivity of these superlattice-structured SiNSs changes non-monotonically as the thickness of their lattice layers decreases. Detailed analysis of the phonon spectra demonstrates that the competing mechanism between the interface scattering and confinement effects of the phonon modes is responsible for this non-monotonical behaviour. read less USED (high confidence) C. Fusco, T. Albaret, and A. Tanguy, “Rheological properties vs. local dynamics in model disordered materials at low temperature,” The European Physical Journal E. 2014. link Times cited: 11 USED (high confidence) T. Wang, G. Madsen, and A. Hartmaier, “Atomistic study of the influence of lattice defects on the thermal conductivity of silicon,” Modelling and Simulation in Materials Science and Engineering. 2014. link Times cited: 22 Abstract: Lattice defects such as vacancies, voids and dislocations ar… read moreAbstract: Lattice defects such as vacancies, voids and dislocations are inevitably present in any material of technological interest. In this work, non-equilibrium molecular dynamics simulations are conducted to investigate how the monatomic vacancies and nanovoids influence the lattice thermal conductivity of silicon. The results show a clear non-linear decrease of the thermal conductivity with increasing defect volume fraction. Furthermore, it is found that for a given volume fraction of defects, a random distribution shows a lower lattice thermal conductivity. To develop a fundamental understanding of these observations, the spectral energy densities for all phonon branches obtained from 2D Fourier transformations of the atomic trajectories are analyzed. This yields the mean phonon group velocities and relaxation times, which are the main physical quantities contributing to the lattice thermal conductivity. Our analysis reveals that the phonon relaxation time is the most important parameter for describing the degrading of the thermal transport behavior in the defected structures. read less USED (high confidence) K. Eriguchi, A. Matsuda, Y. Takao, and K. Ono, “Effects of straggling of incident ions on plasma-induced damage creation in ‘fin’-type field-effect transistors,” Japanese Journal of Applied Physics. 2014. link Times cited: 26 Abstract: We investigated the plasma-induced physical damage (PPD) mec… read moreAbstract: We investigated the plasma-induced physical damage (PPD) mechanism in a field-effect transistor (FET) with a fin-type channel, called FinFET. Compared to PPD in planar metal–oxide–semiconductor field-effect transistors (MOSFETs), such as Si loss or Si recess formed by energetic ion bombardment during plasma processing followed by the subsequent wet-etch stripping, it was predicted that PPD in FinFETs are generated primarily by a stochastic process called straggling of incident ions. During the etching of a fin structure in a FinFET, an impinging ion penetrates into the crystalline Si region to be etched, not only in the vertical direction but also in the lateral direction, resulting in lateral damage in the sidewall region, that is, the bulk fin. The damage layer generation mechanism in the fin structure was modeled on the basis of range theory. A molecular dynamics simulation was performed for noble and halogen species impacting on a Si fin structure to verify the proposed mechanism. The calculated results showed that ions with lighter masses and higher incident energies induced a larger amount of damage in the bulk fin owing to the nature of straggling phenomena. It should be noted that the PPD in the bulk fin may lead to latent defect sites in the channel region, and hence to operating speed degradation, which is a problematic concern for high-performance FinFETs. read less USED (high confidence) M. Barisik and A. Beskok, “Temperature dependence of thermal resistance at the water/silicon interface,” International Journal of Thermal Sciences. 2014. link Times cited: 86 USED (high confidence) S. Cea et al., “Process modeling for advanced device technologies,” Journal of Computational Electronics. 2014. link Times cited: 8 USED (high confidence) A. Pham, M. Barisik, and B. H. Kim, “Molecular dynamics simulations of Kapitza length for argon-silicon and water-silicon interfaces,” International Journal of Precision Engineering and Manufacturing. 2014. link Times cited: 46 USED (high confidence) C.-ying Wang et al., “Multi-scale simulation of lithium diffusion in the presence of a 30° partial dislocation and stacking fault in Si,” Journal of Applied Physics. 2014. link Times cited: 6 Abstract: The multi-scale simulation method is employed to investigate… read moreAbstract: The multi-scale simulation method is employed to investigate how defects affect the performances of Li-ion batteries (LIBs). The stable positions, binding energies and dynamics properties of Li impurity in Si with a 30° partial dislocation and stacking fault (SF) have been studied in comparison with the ideal crystal. It is found that the most table position is the tetrahedral (Td) site and the diffusion barrier is 0.63 eV in bulk Si. In the 30° partial dislocation core and SF region, the most stable positions are at the centers of the octagons (Oct-A and Oct-B) and pentahedron (site S), respectively. In addition, Li dopant may tend to congregate in these defects. The motion of Li along the dislocation core are carried out by the transport among the Oct-A (Oct-B) sites with the barrier of 1.93 eV (1.12 eV). In the SF region, the diffusion barrier of Li is 0.91 eV. These two types of defects may retard the fast migration of Li dopant that is finally trapped by them. Thus, the presence of the 30° partial di... read less USED (high confidence) H. Zhan, Y. Zhang, J. Bell, and Y. Gu, “Thermal conductivity of Si nanowires with faulted stacking layers,” Journal of Physics D: Applied Physics. 2014. link Times cited: 27 Abstract: Faulted stacking layers are ubiquitously observed during the… read moreAbstract: Faulted stacking layers are ubiquitously observed during the crystal growth of semiconducting nanowires (NWs). In this paper, we employ the reverse non-equilibrium molecular dynamics simulation to elucidate the effect of various faulted stacking layers on the thermal conductivity (TC) of silicon (Si) NWs. We find that the stacking faults can greatly reduce the TC of the Si NW. Among the different stacking faults that are parallel to the NW's axis, the 9R polytype structure, the intrinsic and extrinsic stacking faults (iSFs and eSFs) exert more pronounced effects in the reduction of TC than the twin boundary (TB). However, for the perpendicularly aligned faulted stacking layers, the eSFs and 9R polytype structures are observed to induce a larger reduction to the TC of the NW than the TB and iSFs. For all considered NWs, the TC does not show a strong relation with the increasing number of faulted stacking layers. Our studies suggest the possibility of tuning the thermal properties of Si NWs by altering the crystal structure via the different faulted stacking layers. read less USED (high confidence) Y. Qiu, Q. Tan, W. Si, and Y. Chen, “Ion specificity in NaCl solution confined in silicon nanochannels,” Science China Technological Sciences. 2013. link Times cited: 0 USED (high confidence) Y. Wang, B. Li, and G. Xie, “Significant reduction of thermal conductivity in silicon nanowires by shell doping,” RSC Advances. 2013. link Times cited: 11 Abstract: Reducing the thermal conductivity of silicon nanowires (SiNW… read moreAbstract: Reducing the thermal conductivity of silicon nanowires (SiNWs) can enhance the thermoelectric figure of merit. Applying non-equilibrium molecular dynamics simulation, we demonstrate that the thermal conductivity of SiNWs can be reduced remarkably by shell doping due to both impurity scattering and interface scattering associated with the peculiar structure of shell-doped SiNWs. In order to reveal the origin of the reduction of thermal conductivity, we perform the vibrational eigenmodes analysis and find the strong localization of phonon modes from 9.0 THz to 16.0 THz in shell-doped SiNWs. Furthermore, we evaluate the spatial distribution of localized modes and demonstrate that the strong localization of phonons in the shell-doped region suppresses thermal transport in shell-doped SiNWs greatly and is responsible for the significant reduction of thermal conductivity. read less USED (high confidence) J. Zhang, C. Wang, and S. Adhikari, “Fracture and buckling of piezoelectric nanowires subject to an electric field,” Journal of Applied Physics. 2013. link Times cited: 14 Abstract: Fracture and buckling are major failure modes of thin and lo… read moreAbstract: Fracture and buckling are major failure modes of thin and long nanowires (NWs), which could be affected significantly by an electric field when piezoelectricity is involved in the NWs. This paper aims to examine the issue based on the molecular dynamics simulations, where the gallium nitride (GaN) NWs are taken as an example. The results show that the influence of the electric field is strong for the fracture and the critical buckling strains, detectable for the fracture strength but almost negligible for the critical buckling stress. In addition, the reversed effects are achieved for the fracture and the critical buckling strains. Subsequently, the Timoshenko beam model is utilized to account for the effect of the electric field on the axial buckling of the GaN NWs, where nonlocal effect is observed and characterized by the nonlocal coefficient e0a=1.1 nm. The results show that the fracture and buckling of piezoelectric NWs can be controlled by applying an electric field. read less USED (high confidence) Y. Lee and G. Hwang, “Microsegregation effects on the thermal conductivity of silicon-germanium alloys,” Journal of Applied Physics. 2013. link Times cited: 12 Abstract: A silicon-germanium (SiGe) alloy is a promising candidate fo… read moreAbstract: A silicon-germanium (SiGe) alloy is a promising candidate for thermoelectric materials; while it shows a significantly reduced thermal conductivity (κ) as compared to pure Si and Ge, the κ values obtained from previous experiments and computations tend to be widely scattered. We present here a computational analysis of thermal transport in SiGe, particularly the effects of the local segregation (microsegregation) of alloying elements. Our nonequilibrium molecular dynamics simulations confirm the strong dependence of κ on the Si:Ge ratio and the occurrence of the minimum κ around Si0.8Ge0.2, consistent with existing experimental observations. Moreover, our study clearly demonstrates that the κ of Si0.8Ge0.2 increases substantially and monotonically as Ge atoms undergo segregation; that is, the magnitude of alloy scattering is found to be sensitive to homogeneity in the distribution of alloying elements. Nonequilibrium Green's function analysis also shows that such microsegregation enhances phonon transmiss... read less USED (high confidence) C. Cassidy, D. V. Singh, P. Grammatikopoulos, F. Djurabekova, K. Nordlund, and M. Sowwan, “Inoculation of silicon nanoparticles with silver atoms,” Scientific Reports. 2013. link Times cited: 37 USED (high confidence) A. Argon, “Strain avalanches in plasticity,” Philosophical Magazine. 2013. link Times cited: 39 Abstract: Plastic deformation at the mechanism level in all solids occ… read moreAbstract: Plastic deformation at the mechanism level in all solids occurs in the form of discrete thermally activated individual stress relaxation events. While there are clear differences in mechanisms between dislocation mediated events in crystalline solids and by individual shear transformations in amorphous metals and semiconductors, such relaxation events interact strongly to form avalanches of strain bursts. In all cases the attendant distributions of released energy as amplitudes of acoustic emissions, or in serration amplitudes in flow stress, the levels of strain bursts are of fractal character with fractal exponents in the range from −1.5 to −2.0, having the character of phenomena of self-organized criticality, SOC. Here we examine strain avalanches in single crystals of ice, hcp metals, the jerky plastic deformations of nano-pillars of fcc and bcc metals deforming in compression, those in the plastic flow of bulk metallic glasses, all demonstrating the remarkable universality of character of plastic relaxation events. read less USED (high confidence) Z. Yuan, K. Shimamura, F. Shimojo, and A. Nakano, “Critical size for the generation of misfit dislocations and their effects on electronic properties in GaAs nanosheets on Si substrate,” Journal of Applied Physics. 2013. link Times cited: 3 Abstract: While nanowires and nanosheets (NSs) grown on lattice-mismat… read moreAbstract: While nanowires and nanosheets (NSs) grown on lattice-mismatched substrates have a number of promising technological applications such as solar cells, generation of misfit dislocations (MFDs) at their interfaces is a major concern for the efficiency of these devices. Here, combined molecular-dynamics and quantum-mechanical simulations are used to study MFDs at the interface between a GaAs NS and a Si substrate. Simulation results show the existence of a critical NS thickness, below which NSs are grown free of MFDs. The calculated critical thickness value is consistent with available experimental observations. Charge transfer at the MFD core is found to modify the electronic band profile at the GaAs/Si interface significantly. These effects should have profound impacts on the efficiency of lattice-mismatched NS devices. read less USED (high confidence) S. Cea et al., “Process modeling for advanced device technologies,” Journal of Computational Electronics. 2013. link Times cited: 0 USED (high confidence) Y. Qiu, J. Ma, W. Guo, W. Si, Q. Tan, and Y. Chen, “Ionic current investigation in silicon nanochannels with molecular dynamics simulations,” 2013 International Conference on Manipulation, Manufacturing and Measurement on the Nanoscale. 2013. link Times cited: 0 Abstract: Through the molecular dynamics simulations, the ionic curren… read moreAbstract: Through the molecular dynamics simulations, the ionic currents in physically realistic nanochannels with consideration of the thermal motion of channel walls are observed. It is found that the ionic current changes a little as the surface charge density increases from 0 to -0.3C/m2 with a huge decrease at -0.3C/m2 when the electric filed strength is 0.25V/nm. The Cl-ion current shows a decrease-increase profile as the surface charge density increases, while there is an increase-decrease trend in the Na+ ion current with the turning point at -0.075C/m2. By the statistic of the concentration and velocity distributions, the location of Na+ ions which provide main contribution to the current moves from the center of the channel to the charged surface as surface charge density increases from 0 to -0.225C/m2. The two parts included in current carriers have different concentrations and mobility. So the different contributions of the two parts Na+ ions and Cl-ions cause the feature of ionic current. read less USED (high confidence) Y. Jing, Y. Sun, H. Niu, and J. Shen, “Atomistic simulations on the mechanical properties of silicene nanoribbons under uniaxial tension,” physica status solidi (b). 2013. link Times cited: 37 Abstract: The mechanical properties of silicene are investigated using… read moreAbstract: The mechanical properties of silicene are investigated using ab initio calculation and molecular dynamics simulations with different empirical potentials. The simulation results show that the calculated Young's modulus of bulk silicene with EDIP model is consistent with the ab initio calculations. The chirality has a significant effect on the critical strain and stress of bulk silicene under uniaxial tension. In addition, the Young's modulus depends strongly on the chirality and size of the silicene nanoribbon due to the edge effects. The fracture process of a silicene nanoribbon is also studied. read less USED (high confidence) Y. Chalopin and S. Volz, “A microscopic formulation of the phonon transmission at the nanoscale,” Applied Physics Letters. 2013. link Times cited: 71 Abstract: We present a microscopic approach for estimating the frequen… read moreAbstract: We present a microscopic approach for estimating the frequency vs. wave-vector dependent phonon transmission across a solid-solid interface. We show that the spectral properties of the heat flux can be generally deduced from the equilibrium displacements fluctuations of the contact atoms. We have applied and demonstrated our formalism with molecular dynamics simulations to predict the angular and mode dependent phonon transport in silicon and germanium thin films. This notably unveils the existence of confined interface mode at the thermal contacts. read less USED (high confidence) F. Saiz, R. Borrajo-Pelaez, and M. Gamero-Castaño, “The influence of the projectile’s velocity and diameter on the amorphization of silicon by electrosprayed nanodroplets,” Journal of Applied Physics. 2013. link Times cited: 12 Abstract: The hypervelocity impact of electrosprayed nanodroplets on s… read moreAbstract: The hypervelocity impact of electrosprayed nanodroplets on single-crystal silicon amorphizes a thin layer of the target. Molecular Dynamics simulations have shown that the amorphization results from the melting of the material surrounding the impact interface, followed by an ultrafast quenching that prevents recrystallization. This article extends this previous work to study the role of the projectile's diameter and velocity on the amorphization phenomena and compares the simulation results with experimental measurements of a bombarded silicon target. In the range of projectile diameter and impact velocity studied (diameter between 5 and 30 nm, and velocity between 1 and 6 km/s), the projectile velocity plays a more relevant role than its diameter. A significant amorphous layer begins to develop at a velocity near 3 km/s, its thickness rapidly increasing with velocity until it plateaus at about 4 km/s. The reduction of the melting temperature with pressure combined with the conversion of kinetic energy in... read less USED (high confidence) M. Barisik and A. Beskok, “Wetting characterisation of silicon (1,0,0) surface,” Molecular Simulation. 2013. link Times cited: 76 Abstract: Water droplets on bare silicon surfaces are studied to exami… read moreAbstract: Water droplets on bare silicon surfaces are studied to examine the wetting behaviour as a function of the surface energy and to parameterise water–silicon interactions in order to recover the hydrophobic behaviour measured by experiments. Two different wetting regimes characterised by a critical interaction strength value are observed. At a threshold value of the water–silicon interaction parameter, water molecules start penetrating into the first layer of silicon surface under thermally vibrating walls, resulting in two distinct wetting behaviours. Fixed (cold) silicon walls do not exhibit the two different wetting characteristics. Size effects are studied for nano-scale droplets, and line tension influence is observed depending on the surface wettability. Decrease in the droplet size increases the contact angle values for the low wetting cases, while contact angles decrease for smaller droplets on the high wetting surfaces. Considering the line tension effects and droplet size, ϵSi–O for water–silicon interactions to recover the hydrophobic behaviour of silicon surfaces is estimated to be 12.5% of the value predicted using the Lorentz–Berthelot mixing rule. read less USED (high confidence) J. N. Sarma, R. Chowdhury, and R. Jayaganthan, “Molecular dynamics investigation of the thermomechanical behavior of monolayer GaN,” Journal of Applied Physics. 2013. link Times cited: 8 Abstract: Molecular dynamics simulations are performed on monolayer ga… read moreAbstract: Molecular dynamics simulations are performed on monolayer gallium nitride to study their mechanical behavior at various temperatures in the range of 10 to 1700 K. The transition from brittle to ductile nature has been illustrated from the evolution of fracture at two different temperatures of 700 and 1300 K. Brittle to ductile transition temperatures TBDT are obtained from the plots of logarithm of yield stress and inverse temperature at different strain rates and compared qualitatively with the same system in the presence of single and diatomic vacancies. Logarithm of strain rate against inverse of TBDT thus obtained represents an Arrhenius plot, the slope of which corresponds to the activation energy of dislocation glide that is found to be approximately 2.0 ± 0.05 eV for the present case. This suggests that the brittle to ductile transition is controlled by the dislocation mobility as in the case of other semiconductors like silicon and germanium. This behavior is found to be consistent with the presen... read less USED (high confidence) J. Xie, A. Frachioni, D. Williams, and B. White, “Thermal conductivity of a ZnO nanowire/silica aerogel nanocomposite,” Applied Physics Letters. 2013. link Times cited: 10 Abstract: The thermal conductivity of 100 nm zinc oxide nanowires embe… read moreAbstract: The thermal conductivity of 100 nm zinc oxide nanowires embedded in silica aerogel was measured using the 3ω method over a temperature range of 150 K to 300 K. Compared to 100 nm ZnO nanowires alone, the thermal conductivity of the nanocomposite was reduced by over an order of magnitude throughout this temperature range. We attribute this reduction to the scattering of ballistic phonons at the nanowire surface and the subsequent emission of and transport of energy by the scattered phonon into the silica aerogel, as predicted by the diffuse mismatch model. read less USED (high confidence) T. Mehrtens et al., “Measurement of the indium concentration in high indium content InGaN layers by scanning transmission electron microscopy and atom probe tomography,” Applied Physics Letters. 2013. link Times cited: 37 Abstract: A method for determining concentrations from high-angle annu… read moreAbstract: A method for determining concentrations from high-angle annular dark field-scanning transmission electron microscopy images is presented. The method is applied to an InGaN/GaN multi-quantum well structure with high In content, as used for the fabrication of light emitting diodes and laser diodes emitting in the green spectral range. Information on specimen thickness and In concentration is extracted by comparison with multislice calculations. Resulting concentration profiles are in good agreement with a comparative atom probe tomography analysis. Indium concentrations in the quantum wells ranging from 26 at. % to 33 at. % are measured in both cases. read less USED (high confidence) J. Rouviere, F. Lançon, and O. H. H. Duparc, “Atomic structures of Si and Ge Σ = 13 [0 0 1] tilt grain boundaries studied by high-resolution electron microscopy and atomistic simulations,” Philosophical Magazine. 2013. link Times cited: 5 Abstract: By combining high-resolution electron microscopy and atomist… read moreAbstract: By combining high-resolution electron microscopy and atomistic simulations, the atomic structures of several interfaces, {5 1 0}, {2 3 0} and {8 1 0}/{7 4 0}, in germanium and in silicon Σ = 13 [0 0 1] tilt grain boundaries (TGBs) are studied using bicrystals prepared in two different ways from the melt. The interfaces are characterized by either transmission electron microscopy or scanning transmission electron microscopy (STEM). The Si TGB shows only one interface, {1 5 0} with one interfacial structure. The Ge TGB contains many facets. In Ge, observations performed in two perpendicular directions, [0 0 1] and [ 5 0], confirm that the {5 1 0} interface has two different structures. One structure, called M-structure, is periodic along [0 0 1] and has tetracoordinated atoms. The other structure, called U-structure, is more peculiar as it contains a fixed part surrounding a variable complex core. High-resolution STEM, realised in modern microscopes equipped with a probe Cs-corrector, is a very effective technique for structure determination of grain boundaries (GBs). However, current limitations for high-resolution study of GBs are the structural changes under the electron beam and the limited number of crystallographic axes suitable for atomic-resolution imaging. The structures of GB atomistic models can be ordered according to their calculated energies. It appears that energies calculated using empirical potentials, like Tersoff or Stillinger-Weber potentials, do not give the same classification as ab initio calculations and cannot be used to determine the structure of lowest energy. This structure is the M-structure, the structure observed in the Si bicrystal. read less USED (high confidence) J.-W. Jiang and T. Rabczuk, “Mechanical oscillation of kinked silicon nanowires: A natural nanoscale spring,” Applied Physics Letters. 2013. link Times cited: 12 Abstract: We perform classical molecular dynamics simulations to demon… read moreAbstract: We perform classical molecular dynamics simulations to demonstrate the application of kinked silicon nanowires (KSiNWs) as nanoscale springs. The spring-like oscillation in gigahertz frequency range is successfully actuated using a similar procedure as the actuation of a classical mass spring oscillator. We detect the spring-like mechanical oscillation and some other low-frequency oscillations by the energy spectrum analysis, where a dimensional crossover phenomenon is observed for the transverse mode in KSiNWs with decreasing aspect ratio. Our findings shed light on the elastic properties of the KSiNW and open a way for its application in nanomechanical devices. read less USED (high confidence) Q. Zhang, Q. Li, and M. Li, “Melting and superheating in solids with volume shrinkage at melting: a molecular dynamics study of silicon.,” The Journal of chemical physics. 2013. link Times cited: 12 Abstract: The thermodynamics of homogeneous melting in superheated cry… read moreAbstract: The thermodynamics of homogeneous melting in superheated crystalline solids with volume shrinkage at melting is investigated using extensive molecular dynamics simulation in conjunction with a classical nucleation theory. A liquid-solid co-existing model is established to overcome the difficult in observing liquid phase formation in a superheated Si crystal. We found that melting is governed by two major factors, the volume change induced strain energy and the curvature of the interface between the liquid and the solid phases. The driving force for melting in superheating regime is lowered by the additional strain energy that restricts homogeneous nucleation of a liquid phase till temperature rises above the normal melting point, thus causing superheating. However, due to the abnormal behavior in the compressibility of the silicon liquid in the superheating regime, the degree of superheating in terms of the liquid nucleation gap becomes significantly reduced. More potential complications caused by the change of the atomic bonding in Si at melting are discussed. read less USED (high confidence) L. Yang, N. Yang, and B. Li, “Reduction of Thermal Conductivity by Nanoscale 3D Phononic Crystal,” Scientific Reports. 2013. link Times cited: 50 USED (high confidence) N. Mori, M. Tomita, H. Minari, T. Watanabe, and N. Koshida, “Disorder-Induced Enhancement of Avalanche Multiplication in a Silicon Nanodot Array,” Japanese Journal of Applied Physics. 2012. link Times cited: 0 Abstract: Impacts of atomic disorder on avalanche multiplication in a … read moreAbstract: Impacts of atomic disorder on avalanche multiplication in a one-dimensional silicon nanodot (SiND) array have been theoretically studied. The disorder lifts the degeneracy of the energy levels and reduces the impact-ionization threshold. This leads to a larger carrier multiplication factor in the disordered SiND array compared to an ideal SiND array without disorder or strain. read less USED (high confidence) C. H. Baker, D. Jordan, and P. Norris, “Application of the wavelet transform to nanoscale thermal transport,” Physical Review B. 2012. link Times cited: 27 Abstract: The continuous wavelet transform is employed to analyze the … read moreAbstract: The continuous wavelet transform is employed to analyze the dynamics and time-dependent energy distribution of phonon wave-packet propagation and scattering in molecular dynamics simulations. The equations of the one-dimensional continuous wavelet transform are presented and then discretized for implementation. Practical aspects and limitations of the transform are discussed, with attention to its application in the analysis of molecular dynamics simulations. The transform is demonstrated using three examples that are relevant to nanoscale thermal transport. First, a system of wave packets that interfere in both the spatial and Fourier domains are separated by the wavelet transform, allowing the measurement of each packet’s contribution to the system energy. Second, the wavelet transform is applied to a multiple wave-packet simulation of a silicon, heavy-silicon interface. The wavelet-based calculation of mode-dependent transmission is validated through comparison to literature results and theoretical predictions. Third, the dynamic scattering of a large amplitude wave packet is studied using the wavelet transform. The transform reveals a transition in the structure of the energy distribution. Unlike current techniques, the wavelet transform can be used to determine how the energy of a simulated system is distributed in time, in space, and among wave numbers, simultaneously. The ability to resolve phonon motion and energy from a vibrating ensemble of atoms in a molecular dynamics simulation makes the wavelet transform a promising technique for probing the physical mechanisms of nanoscale thermal transport. read less USED (high confidence) S. Ju and X.-gang Liang, “Thermal rectification and phonon scattering in silicon nanofilm with cone cavity,” Journal of Applied Physics. 2012. link Times cited: 16 Abstract: The thermal rectification has potential application in the t… read moreAbstract: The thermal rectification has potential application in the thermal management of electronics and energy saving. This paper investigates the thermal rectification in silicon nanofilm with cone cavity by the non-equilibrium molecular dynamics simulation. The results show that the thermal resistance caused by the cone cavity is on the order of 10−9 m2 KW−1. The thermal resistance of cone cavity differs averagely by about 11% from 300 K to 1100 K when the heat flow direction is turned over. The phonon wave packet dynamic simulations indicate that transverse phonons are generated by the cavity scattering of longitudinal phonon. When the phonon transport direction is reversed, the average transmission coefficient is changed by about 14% in all the frequency range and is regarded as the main reason for the thermal rectification in silicon film with cone cavity. The thermal rectification depends on the aspect ratio of the cone cavity. read less USED (high confidence) F. Saiz and M. Gamero-Castaño, “Amorphization of silicon induced by nanodroplet impact: A molecular dynamics study,” Journal of Applied Physics. 2012. link Times cited: 16 Abstract: The hypervelocity impact of electrosprayed nanodroplets on c… read moreAbstract: The hypervelocity impact of electrosprayed nanodroplets on crystalline silicon produces an amorphous layer with a thickness comparable to the droplet diameters. The phase transition is puzzling considering that amorphization has not been observed in macroscopic shock compression of silicon, the only apparent difference being the several orders of magnitude disparity between the sizes of the macroscopic and nanodroplet projectiles. This article investigates the physics of the amorphization by modeling the impact of a nanodrop on single-crystal silicon via molecular dynamics. The simulation shows that the amorphization results from the heating and subsequent melting of a thin layer of silicon surrounding the impact area, followed by an ultrafast quenching with cooling rates surpassing 1013 K/s. These conditions impede crystalline growth in the supercooled liquid phase, which finally undergoes a glass transition to render a disordered solid phase. The high temperature field near the impact interface is a loc... read less USED (high confidence) C. Knight, G. Lindberg, and G. Voth, “Multiscale reactive molecular dynamics.,” The Journal of chemical physics. 2012. link Times cited: 64 Abstract: Many processes important to chemistry, materials science, an… read moreAbstract: Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. read less USED (high confidence) Z. Li, R. C. Picu, R. Muralidhar, and P. Oldiges, “Effect of Ge on dislocation nucleation from surface imperfections in Si-Ge,” Journal of Applied Physics. 2012. link Times cited: 5 Abstract: Nucleation of dislocation loops from sharp corners playing t… read moreAbstract: Nucleation of dislocation loops from sharp corners playing the role of stress concentrators located on the surface of Si1−xGex strained layers is studied. The surface is of {100} type and the concentrator is oriented such as to increase the applied resolved shear stress in one of the {111} glide planes. The mean stress in the structure is controlled through the boundary conditions, independent of the Ge concentration. Shuffle dislocations are considered throughout, as appropriate for low temperature-high stress conditions. The effect of Ge atoms located in the glide plane, in the vicinity of the glide plane and at larger distances is studied separately. It is observed that Ge located in the glide plane leads to the reduction of the activation energy for dislocation nucleation. The activation volume in presence of Ge is identical to that in pure Si. Ge located in {111} planes three interplanar distances away from the active glide plane has little effect on nucleation parameters. The far-field Ge contribute... read less USED (high confidence) S. Ju and X.-gang Liang, “Thermal rectification and phonon scattering in asymmetric silicon nanoribbons,” Journal of Applied Physics. 2012. link Times cited: 17 Abstract: Thermal rectification is an interesting phenomenon and has i… read moreAbstract: Thermal rectification is an interesting phenomenon and has important potential applications in improving the thermal management of electronics and saving energy. Exploring thermal rectification phenomena and understanding the mechanism are very necessary and important. This paper reports the investigation of the thermal conductivity and thermal rectification of asymmetric silicon nanoribbons by the non-equilibrium molecular dynamics simulation. The results indicate that the thermal conductivity of the nanoribbon is only on the order of 100 Wm−1K−1. Thermal rectification is observed in silicon nanoribbons at different temperatures, geometry aspects, and ribbon length. The thermal conductivity is apparently larger when heat flows from the thin end to the thick end. The larger the aspect ratio of the thick end to thin end is, the larger the thermal rectification. The rectification coefficient does not change much in the ribbon length ranges from 8.1 nm to 21.7 nm. The longitudinal phonon scattering in the si... read less USED (high confidence) T. Morishita, “Compressed exponential relaxation in liquid silicon: universal feature of the crossover from ballistic to diffusive behavior in single-particle dynamics.,” The Journal of chemical physics. 2012. link Times cited: 5 Abstract: We report a first-principles molecular-dynamics study of the… read moreAbstract: We report a first-principles molecular-dynamics study of the relaxation dynamics in liquid silicon (l-Si) over a wide temperature range (1000-2200 K). We find that the intermediate scattering function for l-Si exhibits a compressed exponential decay above 1200 K including the supercooled regime, which is in stark contrast to that for normal "dense" liquids which typically show stretched exponential decay in the supercooled regime. The coexistence of particles having ballistic-like motion and those having diffusive-like motion is demonstrated, which accounts for the compressed exponential decay in l-Si. An attempt to elucidate the crossover from the ballistic to the diffusive regime in the "time-dependent" diffusion coefficient is made and the temperature-independent universal feature of the crossover is disclosed. read less USED (high confidence) A. Frachioni and B. White, “Simulated thermal conductivity of silicon-based random multilayer thin films,” Journal of Applied Physics. 2012. link Times cited: 17 Abstract: Reverse nonequilibrium molecular dynamics simulations have b… read moreAbstract: Reverse nonequilibrium molecular dynamics simulations have been used to quantify the impact of randomly placed mass-altered atomic planes, such as those produced in pseudomorphically grown heterostructures, on the thermal conductivity of silicon. The results indicate that the room temperature thermal conductivity of these silicon-based structures can be reduced to values below 0.050 W/m-K. These values are significantly less than those found in random alloy or superlattice structures containing the same percentage of mass-altered atoms and are attributed to Anderson localization of phonons. Such low lattice thermal conductivity in these silicon-based structures could dramatically improve the thermoelectric efficiency of this earth abundant material. read less USED (high confidence) P. Marepalli, J. Murthy, B. Qiu, and X. Ruan, “Quantifying Uncertainty in Multiscale Heat Conduction Calculations,” Journal of Heat Transfer-transactions of The Asme. 2012. link Times cited: 17 Abstract: In recent years, there has been interest in employing atomis… read moreAbstract: In recent years, there has been interest in employing atomistic computations to inform macroscale thermal transport analyses. In heat conduction simulations in semiconductors and dielectrics, for example, classical molecular dynamics (MD) is used to compute phonon relaxation times, from which material thermal conductivity may be inferred and used at the macroscale. A drawback of this method is the noise associated with MD simulation (here after referred to as MD noise), which is generated due to the possibility of multiple initial configurations corresponding to the same system temperature. When MD is used to compute phonon relaxation times, the spread may be as high as 20%. In this work, we propose a method to quantify the uncertainty in thermal conductivity computations due to MD noise, and its effect on the computation of the temperature distribution in heat conduction simulations. Bayesian inference is used to construct a probabilistic surrogate model for thermal conductivity as a function of temperature, accounting for the statistical spread in MD relaxation times. The surrogate model is used in probabilistic computations of the temperature field in macroscale Fourier conduction simulations. These simulations yield probability density functions (PDFs) of the spatial temperature distribution resulting from the PDFs of thermal conductivity. To allay the cost of probabilistic computations, a stochastic collocation technique based on generalized polynomial chaos (gPC) is used to construct a response surface for the variation of temperature (at each physical location in the domain) as a function of the random variables in the thermal conductivity model. Results are presented for the spatial variation of the probability density function of temperature as a function of spatial location in a typical heat conduction problem to establish the viability of the method. read less USED (high confidence) Y. Wang et al., “Mechanism of formation of the misfit dislocations at the cubic materials interfaces,” Applied Physics Letters. 2012. link Times cited: 21 Abstract: High-angle annular dark-field scanning transmission electron… read moreAbstract: High-angle annular dark-field scanning transmission electron microscopy and molecular dynamic simulation are applied to study the misfit dislocations at the GaSb/GaAs interface. In the investigated samples, three types of misfit dislocations have been observed: shuffle and glide set Lomer dislocations and 60° dislocation pairs. The dislocation density tensor analysis is next used to quantify the Burgers vector of misfit dislocations and investigate the misfit dislocation formation mechanism. This work demonstrates that, in these hetero-structures, the dominant mechanism underlying the formation of misfit dislocations is the glide and reaction of 60° dislocations. It is shown that the final structure of each misfit dislocation depends on the Burgers vectors of the initial 60° dislocations. Finally, this analysis points out an approach to determine the local rotation at interface due to mixed type dislocations. read less USED (high confidence) R. Baron and V. Molinero, “Water-Driven Cavity-Ligand Binding: Comparison of Thermodynamic Signatures from Coarse-Grained and Atomic-Level Simulations.,” Journal of chemical theory and computation. 2012. link Times cited: 43 Abstract: The role of water (thermo)dynamics is crucial in molecular r… read moreAbstract: The role of water (thermo)dynamics is crucial in molecular recognition and self-assembly. Here, we study a prototype cavity-ligand system as a model for hydrophobic noncovalent binding. Two alternative molecular dynamics simulation resolutions are employed and the resulting structural, dynamic, and thermodynamic properties compared: first, a coarse-grained (CG) resolution based on the previously reported and validated methane-like M solute and mW water models; second, an atomic-level (AL) resolution based on the popular OPLS united atom methane and the TIP4P water models. The CG model reproduces, as a function of the cavity-ligand distance, (1) the water occupancy of the cavity, (2) the cavity-ligand potential of mean force (free energy) and its temperature dependence, and (3) some of the major qualitative features of the thermodynamic signatures (free energy, enthalpy, and entropy) for cavity-ligand association of the AL model. The limits of the CG and AL models in this context are also discussed with comparison to experimental data. Our study suggests that CG simulation with models that include the translational contribution of water and anisotropic "hydrogen-bond"-like interactions could reproduce the thermodynamics of molecular recognition and water-driven assembly in complex macromolecular systems and nanoscale processes with convenient computational time savings. read less USED (high confidence) M. Z. Hossain, J. Freund, and H. Johnson, “Ion impact energy distribution and sputtering of Si and Ge,” Journal of Applied Physics. 2012. link Times cited: 27 Abstract: The spatial distribution of ion deposited energy is often as… read moreAbstract: The spatial distribution of ion deposited energy is often assumed to linearly relate to the local ion-induced sputtering of atoms from a solid surface. This—along with the assumption of an ellipsoidal region of energy deposition—is the central mechanism used in the Bradley and Harper [J. Vac. Sci. Technol. A 6, 2390 (1988)] explanation of ion-induced surface instabilities, but it has never been assessed directly. To do this, we use molecular dynamics to compute the actual distribution of deposited energy and relate this to the source of sputtered atoms for a range of ion energies (250 eV and 1500 eV), ion species (Ar, Kr, Xe, and Rn), targets (Si and Ge), and incidence angles (0°, 10°, 20°, 30°, 40°, 50°, 60°, 70°, and 80°). It is found that the energy deposition profile is remarkably ellipsoidal but that the relation between local deposited energy and local sputtering is not simple. It depends significantly upon the incidence angle, and the relation between energy and local sputter yield is nonlinear, though with a nearly uniform power-law relation. These results will affect, in particular, surface instability models based upon simpler approximations. read less USED (high confidence) N. Le, J. Duda, T. English, P. Hopkins, T. Beechem, and P. Norris, “Strategies for tuning phonon transport in multilayered structures using a mismatch-based particle model,” Journal of Applied Physics. 2012. link Times cited: 16 Abstract: The performance of many micro- and nanoscale devices depends… read moreAbstract: The performance of many micro- and nanoscale devices depends on the ability to control interfacial thermal transport, which is predominantly mediated by phonons in semiconductor systems. The phonon transmissivity at an interface is therefore a quantity of interest. In this work, an empirical model, termed the thermal mismatch model, is developed to predict transmissivity at ideal interfaces between semiconductor materials, producing an excellent agreement with molecular dynamics simulations of wave packets. To investigate propagation through multilayered structures, this thermal mismatch model is then incorporated into a simulation scheme that represents wave packets as particles, showing a good agreement with a similar scheme that used molecular dynamics simulations as input [P. K. Schelling and S. R. Phillpot, J. Appl. Phys. 93, 5377 (2003)]. With these techniques validated for both single interfaces and superlattices, they are further used to identify ways to tune the transmissivity of multilayered str... read less USED (high confidence) Y. Gan and J. K. Chen, “A hybrid method for integrated atomistic-continuum simulation of ultrashort-pulsed laser interaction with semiconductors,” Comput. Phys. Commun. 2012. link Times cited: 18 USED (high confidence) Y. Shen and Y. Gan, “Numerical simulations of germanium nanofilm under femtosecond pulse laser heating,” 2011 Symposium on Piezoelectricity, Acoustic Waves and Device Applications (SPAWDA). 2011. link Times cited: 0 Abstract: Femtosecond pulse laser heating of a germanium nanofilm is s… read moreAbstract: Femtosecond pulse laser heating of a germanium nanofilm is simulated by a method coupling the molecular dynamics and an energy transfer model for ultrafast laser interaction with semiconductors. Simulations demonstrate that the carrier temperature and density drastically evolve at the early heating time, while the lattice temperature gradually rises until the carrier-lattice thermal equilibrium is reached. The surface reflectivity dynamically changes as the carrier density evolves. The femtosecond laser heating can cause a strong thermal stress wave in the film. Initially, a compressive wave is yielded with the peak compression near the irradiated surface. Then, the compression wave transforms into a two-fold wave including compression and tension. At the rear film side, a strong tensile wave occurs with the maximum tension near the back surface. It is also found that shorter laser wavelength brings not only higher carrier temperature and density but also higher lattice temperature and larger thermal stresses. read less USED (high confidence) J. Guénolé, J. Godet, and S. Brochard, “Deformation of silicon nanowires studied by molecular dynamics simulations,” Modelling and Simulation in Materials Science and Engineering. 2011. link Times cited: 29 Abstract: The effect of various parameters such as temperature or surf… read moreAbstract: The effect of various parameters such as temperature or surface state on the very first stages of plasticity in semiconductor nanowires has been investigated by molecular dynamics simulations. In particular, the role of edge and surface reconstructions has been analyzed and discussed in detail. To this end, square nanowires with the [0 0 1] and [1 2 3] axis and various side surfaces have been considered. In general, the onset of plasticity appears from the NW edges at very high stresses. However, when surface reconstructions make surface steps at the intersection of the slip plane and the NW surface, the step can favor the dislocation nucleation from surfaces. This study raises the role of the detailed geometry of the surfaces and edges on the onset of plasticity in nanostructures. read less USED (high confidence) J. Fang and L. Pilon, “Scaling laws for thermal conductivity of crystalline nanoporous silicon based on molecular dynamics simulations,” Journal of Applied Physics. 2011. link Times cited: 38 Abstract: This study establishes that the effective thermal conductivi… read moreAbstract: This study establishes that the effective thermal conductivity keff of crystalline nanoporous silicon is strongly affected not only by the porosity f ν and the system’s length Lz but also by the pore interfacial area concentration Ai. The thermal conductivity of crystalline nanoporous silicon was predicted using non-equilibrium molecular dynamics simulations. The Stillinger-Weber potential for silicon was used to simulate the interatomic interactions. Spherical pores organized in a simple cubic lattice were introduced in a crystalline silicon matrix by removing atoms within selected regions of the simulation cell. Effects of the (i) system length ranging from 13 to 130 nm, (ii) pore diameter varying between 1.74 and 5.86 nm, and (iii) porosity ranging from 8% to 38%, on thermal conductivity were investigated. A physics-based model was also developed by combining kinetic theory and the coherent potential approximation. The effective thermal conductivity was proportional to (1 − 1.5f ν) and inversely propor... read less USED (high confidence) J. Chen, G. Zhang, and B. Li, “Phonon coherent resonance and its effect on thermal transport in core-shell nanowires.,” The Journal of chemical physics. 2011. link Times cited: 88 Abstract: We study heat current autocorrelation function and thermal c… read moreAbstract: We study heat current autocorrelation function and thermal conductivity in core-shell nanowires by using molecular dynamics simulations. Interestingly, a remarkable oscillation effect in heat current autocorrelation function is observed in core-shell NWs, while the same effect is absent in pure silicon nanowires, nanotube structures, and random doped nanowires. Detailed characterizations of the oscillation signal reveal that this intriguing oscillation is caused by the coherent resonance effect of the transverse and longitudinal phonon modes. This phonon resonance results in the localization of the longitudinal modes, which leads to the reduction of thermal conductivity in core-shell nanowires. Our study reveals that a coherent mechanism can be used to tune thermal conductivity in core-shell nanowires. read less USED (high confidence) Y. Gan and J. Chen, “Combined continuum-atomistic modeling of ultrashort-pulsed laser irradiation of silicon,” Applied Physics A. 2011. link Times cited: 37 USED (high confidence) H. Tsuda, Y. Takao, K. Eriguchi, and K. Ono, “Molecular Dynamics Analysis of the Formation of Surface Roughness during Si Etching in Chlorine-Based Plasmas,” Japanese Journal of Applied Physics. 2011. link Times cited: 5 Abstract: Addition of oxygen to Cl2 discharge is widely used in Si etc… read moreAbstract: Addition of oxygen to Cl2 discharge is widely used in Si etching for the fabrication of gate electrodes and shallow trench isolation. As the control of etching processes becomes more critical, a deeper understanding of plasma-surface interactions is required for the formation of roughened surfaces during etching. In particular, a small amount of O2 often leads to profile anomalies such as residues, micropillars, and roughened surfaces. In this study, we focus on the mechanism underlying local surface oxidation during Si etching in Cl2/O2 plasmas, and analyze the relationship between local surface oxidation and surface roughness on the nanometer scale, by a classical molecular dynamics (MD) simulation. The numerical results indicated that O radicals tend to break Si–Si bonds and distort the Si lattice structure; thus, nanometer-scale micromasks tend to be formed on convex roughened surfaces, owing to the reactivity of O radicals with substrate Si atoms and Cl atoms. The results also imply that the nanometer-scale micromasks significantly affect the formation of roughened surfaces and evolution of micropillars. read less USED (high confidence) T. Ishida et al., “Exceptional plasticity of silicon nanobridges,” Nanotechnology. 2011. link Times cited: 12 Abstract: The plasticity of covalently bonded materials is a subject a… read moreAbstract: The plasticity of covalently bonded materials is a subject at the forefront of materials science, bearing on a wide range of technological and fundamental aspects. However, covalent materials fracture in a brittle manner when the deformation exceeds just a few per cent. It is predicted that a macroscopically brittle material like silicon can show nanoscale plasticity. Here we report the exceptional plasticity observed in silicon nanocontacts (‘nanobridges’) at room temperature using a special experimental setup combining a transmission electron microscope and a microelectromechanical system. When accounting for surface diffusion, we succeeded in elongating the nanocontact into a wire-like structure, with a fivefold increase in volume, up to more than twenty times the original length. Such a large plasticity was caused by the stress-assisted diffusion and the sliding of the intergranular, amorphous-like material among the nanocrystals. read less USED (high confidence) Y. Mu, J.-rong Li, J. Wan, F. Song, and G. Wang, “Structures and polarizabilities of medium-sized GanAsm clusters,” Chemical Physics Letters. 2011. link Times cited: 2 USED (high confidence) J. Delaye, S. Peuget, G. Bureau, and G. Calas, “Molecular dynamics simulation of radiation damage in glasses,” Journal of Non-crystalline Solids. 2011. link Times cited: 85 USED (high confidence) C. Krzeminski and E. Lampin, “Solid phase epitaxy amorphous silicon re-growth: some insight from empirical molecular dynamics simulation,” The European Physical Journal B. 2011. link Times cited: 9 USED (high confidence) O. Stein, Z. Lin, L. Zhigilei, and M. Asscher, “Selective ablation of Xe from silicon surfaces: molecular dynamics simulations and experimental laser patterning.,” The journal of physical chemistry. A. 2011. link Times cited: 9 Abstract: The mechanism of laser-induced removal of Xe overlayers from… read moreAbstract: The mechanism of laser-induced removal of Xe overlayers from a Si substrate has been investigated employing MD simulations and evaluated by buffer layer assisted laser patterning experiments. Two distinct regimes of overlayer removal are identified in the simulations of a uniform heating of the Si substrate by a 5 ns laser pulse: The intensive evaporation from the surface of the Xe overlayer and the detachment of the entire Xe overlayer driven by explosive boiling in the vicinity of the hot substrate. Simulations of selective heating of only a fraction of the silicon substrate suggest that the lateral heat transfer and bonding to the unheated, colder regions of the Xe overlayer is very efficient and suppresses the separation of a fraction of the overlayer from the substrate. Interaction with surrounding cold Xe is responsible for significant increase in the substrate temperature required for achieving the spatially selective ablation of the overlayer. The predictions of the MD simulations are found to be in a qualitative agreement with the results of experimental measurements of the threshold laser power required for the removal of Xe overlayers of different thickness and the shapes of metallic stripes generated by buffer-assisted laser patterning. read less USED (high confidence) A. Silverman, A. Hoffman, and J. Adler, “Computational Study of Interstitial Hydrogen Atoms in Nano-Diamond Grains Embedded in an Amorphous Carbon Shell,” Communications in Computational Physics. 2011. link Times cited: 3 Abstract: The properties of hydrogen atoms in a nano-diamond grain sur… read moreAbstract: The properties of hydrogen atoms in a nano-diamond grain surrounded by an amorphous carbon shell are studied with Tight Binding computer simulations. Our samples model nano-diamond grains, of a few nanometers in size, that nucleate within an amorphous carbon matrix, as observed in deposition from a hydrocarbon rich plasma. The calculations show that the average hydrogen interstitial formation energy in the amorphous region is lower than in the nano-diamond core, therefore hydrogen interstitial sites in the in the amorphous region are more stable than in the nano-diamond core. This formation energy difference is the driving force for the diffusion of hydrogen atoms from nano-diamond grains into amorphous carbon regions. An energy well was observed on the amorphous side of the nano-diamond amorphous carbon interface: hydrogen atoms are expected to be trapped here. This scenario agrees with experimental results which show that hydrogen retention of diamond films increases with decreasing grain size, and suggest that hydrogen is bonded and trapped in nano-diamond grain boundaries and on internal grain surfaces. read less USED (high confidence) Z. H. Wang and M. Ni, “Thermal conductivity and its anisotropy research of germanium thin film,” Heat and Mass Transfer. 2011. link Times cited: 9 USED (high confidence) J. Timoshenko, A. Kuzmin, and J. Purāns, “Molecular dynamics simulations of EXAFS in germanium,” Central European Journal of Physics. 2011. link Times cited: 15 Abstract: Classical molecular dynamics simulations have been performed… read moreAbstract: Classical molecular dynamics simulations have been performed for crystalline germanium with the aim to estimate the thermal effects within the first three coordination shells and their influence on the single-scattering and multiple-scattering contributions to the Ge K-edge extended x-ray absorption fine structure (EXAFS). read less USED (high confidence) J. Wang et al., “Surface stress effect in mechanics of nanostructured materials,” Acta Mechanica Solida Sinica. 2011. link Times cited: 308 USED (high confidence) Y. Kamakura, T. Zushi, T. Watanabe, N. Mori, and K. Taniguchi, “Numerical simulation of transient heat conduction in nanoscale Si devices,” 2010 10th IEEE International Conference on Solid-State and Integrated Circuit Technology. 2010. link Times cited: 0 Abstract: Two numerical simulation techniques are presented to investi… read moreAbstract: Two numerical simulation techniques are presented to investigate the heating issues in nanoscale Si devices. The first one is the Monte Carlo simulation for both electron and phonon transport, and the transient electrothermal analysis is carrier out in n+-n-n+ device with the n-layer length of 10 nm. The second is the molecular dynamics approach for simulating the atomic thermal vibration in the nanoscale Si/SiO2 systems. It is shown that the lattice temperature at the drain edge is raised by the hot electron injection from the source after turning on the device, and the impact of this phenomenon becomes more significant in the smaller devices due to the worse heat conductivity. read less USED (high confidence) L. C. Jacobson, W. Hujo, and V. Molinero, “Nucleation pathways of clathrate hydrates: effect of guest size and solubility.,” The journal of physical chemistry. B. 2010. link Times cited: 180 Abstract: Understanding the microscopic mechanism of nucleation of cla… read moreAbstract: Understanding the microscopic mechanism of nucleation of clathrate hydrates is important for their use in hydrogen storage, CO(2) sequestration, storage and transport of natural gas, and the prevention of the formation of hydrate plugs in oil and gas pipelines. These applications involve hydrate guests of varied sizes and solubility in water that form different hydrate crystal structures. Nevertheless, molecular studies of the mechanism of nucleation of hydrates have focused on the single class of small hydrophobic guests that stabilize the sI crystal. In this work, we use molecular dynamics simulations with a very efficient coarse-grained model to elucidate the mechanisms of nucleation of clathrate hydrates of four model guests that span a 2 orders of magnitude range in solubility in water and that encompass sizes which stabilize each one a different hydrate structure (sI and sII, with and without occupancy of the dodecahedral cages). We find that the overall mechanism of clathrate nucleation is similar for all guests and involves a first step of formation of blobs, dense clusters of solvent-separated guest molecules that are the birthplace of the clathrate cages. Blobs of hydrophobic guests are rarer and longer-lived than those for soluble guests. For each guest, we find multiple competing channels to form the critical nuclei, filled dodecahedral (5(12)) cages, empty 5(12) cages, and a variety of filled large (5(12)6(n) with n = 2, 3, and 4) clathrate cages. Formation of empty dodecahedra is an important nucleation channel for all but the smallest guest. The empty 5(12) cages are stabilized by the presence of guests from the blob in their first solvation shell. Under conditions of high supercooling, the structure of the critical and subcritical nuclei is mainly determined by the size of the guest and does not reflect the cage composition or ordering of the stable or metastable clathrate crystals. read less USED (high confidence) T. Saegusa, K. Eriguchi, K. Ono, and H. Ohta, “Molecular Dynamics Evaluation of Thermal Transport in Naked and Oxide-Coated Silicon Nanowires,” Japanese Journal of Applied Physics. 2010. link Times cited: 3 Abstract: The thermal conductivities (κ) of Si nanowires (SiNWs) with … read moreAbstract: The thermal conductivities (κ) of Si nanowires (SiNWs) with naked and sub-nm-oxidized surfaces have been evaluated by nonequilibrium classical molecular dynamics simulations. For the naked SiNWs, the dependence of κ on the cross-sectional area qualitatively agreed with previous Monte Carlo simulations and experiments. It was confirmed that κ was not sensitive to cross-sectional shape or crystalline orientation. The κ of the SiOx-coated SiNWs was decreased compared with that of the naked SiNWs when both types of NW had the same crosssection. However, the κ corresponding to the core part of Si (including the interfacial layer between the Si core and surface SiOx) was equivalent to the κ of the naked SiNWs. The presence of a surface oxide does not modulate the internal thermal conduction of the SiNWs. read less USED (high confidence) K. Shima, S. Izumi, and S. Sakai, “Reaction pathway analysis for dislocation nucleation from a sharp corner in silicon: Glide set versus shuffle set,” Journal of Applied Physics. 2010. link Times cited: 33 Abstract: Using reaction pathway sampling, we have investigated the sh… read moreAbstract: Using reaction pathway sampling, we have investigated the shear stress dependences of the activation energies of shuffle-set and glide-set dislocation nucleation from a sharp corner in silicon. The gradient of the glide-set dislocation curve is lower than that of the shuffle-set dislocation, and the athermal stress of glide-set dislocation is largely higher than that of shuffle-set dislocation. As a result, the two curves have a cross point, which means that shuffle-set dislocation is likely nucleated at high stress and low temperature and glide-set dislocation is likely nucleated at low stress and high temperature. Our result clearly explains the mechanism of recent molecular dynamics on these two types of dislocation nucleation at different temperatures and stress regimes. With increased compressive stress on the slip plane, the activation energy of the shuffle-set dislocation nucleation is greatly decreased, while that of glide-set dislocation nucleation is slightly increased. That would explain why shuffle-set dislocations were found under compressive stress fields. read less USED (high confidence) T. Zhu and J. Li, “Ultra-strength materials,” Progress in Materials Science. 2010. link Times cited: 684 USED (high confidence) H. Tsuda, M. Mori, Y. Takao, K. Eriguchi, and K. Ono, “Atomic-Scale Cellular Model and Profile Simulation of Si Etching: Analysis of Profile Anomalies and Microscopic Uniformity,” Japanese Journal of Applied Physics. 2010. link Times cited: 11 Abstract: Reactive ion etching (RIE) has been used in the manufacture … read moreAbstract: Reactive ion etching (RIE) has been used in the manufacture of semiconductor integrated circuit devices. However, the formation mechanisms of profile anomalies and microscopic uniformity have been poorly understood until now. In this paper, we focus on the analysis of formation mechanisms of profile anomalies and microscopic uniformity during plasma etching of Si in Cl2 plasmas, using our own atomic-scale cellular model (ASCeM). The numerical results indicated that high neutral-to-ion flux ratios result in microtrench formation. Moreover, RIE lag tends to occur at low neutral-to-ion flux ratios (<50), whereas inverse RIE lag occurs at high neutral-to-ion flux ratios in typical low-pressure and high-density plasmas. In particular, the etch rates for narrow patterns (<70 nm) increase significantly with increasing neutral-to-ion flux ratio. The synergistic effects between ion-enhanced etching and neutral shadowing in microstructural features play a significant role in the formation of profile anomalies. read less USED (high confidence) Z. Li and R. C. Picu, “Dislocation nucleation from interacting surface corners in silicon,” Journal of Applied Physics. 2010. link Times cited: 4 Abstract: The nucleation of dislocations from sharp corners acting as … read moreAbstract: The nucleation of dislocations from sharp corners acting as stress concentration sites on a silicon (100) surface is studied by a combination of atomistic and continuum modeling. Ledges of various heights, similar to those found in microelectronic devices, are considered. In this work we focus on the effect of ledge height and of ledge-ledge elastic interaction on the activation energy for dislocation nucleation. The activation energy decreases slightly with increasing the height of the ledge and has a more pronounced, nonmonotonic variation with the distance between stress concentration sites. The effect of introducing a radius of curvature at the root of the ledge is also studied. It is concluded that even a small radius of curvature renders the nucleation process similar to that from a flat surface of same crystallographic orientation. read less USED (high confidence) V. Polukhin and A. Galashev, “Structure and thermal stability of noncrystalline silicon nanoparticles during heating and melting,” Russian Metallurgy (Metally). 2010. link Times cited: 0 USED (high confidence) R. K. F. Lee, B. Cox, and J. M. Hill, “The geometric structure of single-walled nanotubes.,” Nanoscale. 2010. link Times cited: 31 Abstract: In this paper, we survey a number of existing geometric stru… read moreAbstract: In this paper, we survey a number of existing geometric structures which have been proposed by the authors as possible models for various nanotubes. Atoms assemble into molecules following the laws of quantum mechanics, and in general computational approaches to predicting the molecular structure can be arduous and involve considerable computing time. Fortunately, nature favours minimum energy structures which tend to be either very symmetric or very unsymmetric, and which therefore can be analyzed from a geometrical perspective. The conventional rolled-up model of nanotubes completely ignores any effects due to curvature and the present authors have proposed a number of exact geometric models. Here we review a number of these recent developments relating to the geometry of nanotubes, including both the traditional rolled-up models and some exact polyhedral constructions. We review a number of formulae for four materials, carbon, silicon, boron and boron nitride, and we also include results for the case when the bond lengths may take on distinct values. read less USED (high confidence) S. Tardif et al., “Strain and correlation of self-organized Ge1 xMnx nanocolumns embedded in Ge (001),” Physical Review B. 2010. link Times cited: 18 Abstract: We report on the structural properties of Ge_(1-x)Mn_x layer… read moreAbstract: We report on the structural properties of Ge_(1-x)Mn_x layers grown by molecular beam epitaxy. In these layers, nanocolumns with a high Mn content are embedded in an almost-pure Ge matrix. We have used grazing-incidence X-ray scattering, atomic force and transmission electron microscopy to study the structural properties of the columns. We demonstrate how the elastic deformation of the matrix (as calculated using atomistic simulations) around the columns, as well as the average inter-column distance can account for the shape of the diffusion around Bragg peaks. read less USED (high confidence) J. Chen, G. Zhang, and B. Li, “Molecular Dynamics Simulations of Heat Conduction in Nanostructures: Effect of Heat Bath,” Journal of the Physical Society of Japan. 2010. link Times cited: 85 Abstract: We investigate systematically the impacts of heat bath used … read moreAbstract: We investigate systematically the impacts of heat bath used in molecular dynamics simulations on heat conduction in nanostructures exemplified by silicon nanowires (SiNWs) and silicon/germanium nano junction. It is found that multiple layers of Nose–Hoover heat bath are required to reduce the temperature jump at the boundary, while only a single layer of Langevin heat bath is sufficient to generate a linear temperature profile with small boundary temperature jump. Moreover, an intermediate value of heat bath parameter is recommended for both Nose–Hoover and Langevin heat bath in order to achieve correct temperature profile and thermal conductivity in homogeneous materials. Furthermore, the thermal rectification ratio in Si/Ge thermal diode depends on the choice of Nose–Hoover heat bath parameter remarkably, which may lead to non-physical results. In contrast, Langevin heat bath is recommended because it can produce consistent results with experiment in large heat bath parameter range. read less USED (high confidence) T.-M. Chang, C. Weng, and M.-J. Huang, “A Nonequilibrium Molecular Dynamics Study of In-Plane Thermal Conductivity of Silicon Thin Films,” Journal of Electronic Materials. 2010. link Times cited: 7 USED (high confidence) S.-jin Kim, J.-H. Choi, S.-C. Lee, and C. Park, “Effects of temperature and tilt angle on the grain boundary structure in silicon oxide: Molecular dynamics study,” Metals and Materials International. 2010. link Times cited: 4 USED (high confidence) X. Yang, A. To, and R. Tian, “Anomalous heat conduction behavior in thin finite-size silicon nanowires,” Nanotechnology. 2010. link Times cited: 39 Abstract: Anomalous heat conduction behavior is observed for the first… read moreAbstract: Anomalous heat conduction behavior is observed for the first time using non-equilibrium molecular dynamics (NEMD) simulations to obtain the thermal conductivity of thin finite-size silicon nanowires (NWs) in the ⟨001⟩ lattice direction. In the series of simulations, the length dependence of thermal conductivity of thin silicon nanowires (NWs) ranging from 6 to 434 nm is analyzed. It is found that a transition occurs in the thermal conductivity versus length curve after the initial convergence trend appears near the mean free path of bulk silicon. Because no experimental measurements of thermal conductivity are available for sub-10 nm diameter silicon NWs, different NEMD methods are used to test and analyze this anomalous thermal behavior of thin Si NWs with different boundary conditions. The underlying mechanism of the observed behavior is inferred from MD simulations with different boundary conditions so that the anomalous behavior is mainly caused by border restriction and boundary scattering of the thin silicon NWs. read less USED (high confidence) T. Aoki, T. Seki, and J. Matsuo, “Molecular dynamics simulations for gas cluster ion beam processes,” Vacuum. 2010. link Times cited: 41 USED (high confidence) E. Holmström, K. Nordlund, and A. Kuronen, “Threshold defect production in germanium determined by density functional theory molecular dynamics simulations,” Physica Scripta. 2010. link Times cited: 34 Abstract: We studied the threshold displacement energy in germanium us… read moreAbstract: We studied the threshold displacement energy in germanium using density functional theory molecular dynamics simulations. The average threshold energy over all lattice directions for creating stable Frenkel pairs was found to be (23±2stat±3syst) eV. In the lattice directions ⟨111⟩ and ⟨100⟩, the threshold energy was found to be (11.5±1.5syst) eV and (19.5±1.5syst) eV, respectively. In a notable fraction of all the studied directions, a bond defect was created with a lower threshold than a Frenkel pair. The average threshold energy for creating either a bond defect or a Frenkel pair was found to be (21±1stat±3syst) eV. read less USED (high confidence) J. Samela and K. Nordlund, “Classical molecular dynamics simulations of hypervelocity nanoparticle impacts on amorphous silica,” Physical Review B. 2010. link Times cited: 21 Abstract: We have investigated the transition from the atomistic to th… read moreAbstract: We have investigated the transition from the atomistic to the macroscopic impact mechanism by simulating large Argon cluster impacts on amorphous silica. The transition occurs at cluster sizes less than $50\text{ }000$ atoms at hypervelocity regime (22 km/s). After that, the crater volume increases linearly with the cluster size opposite to the nonlinear scaling typical of small cluster impacts. The simulations demonstrate that the molecular dynamics method can be used to explore atomistic mechanisms that lead to damage formation in small particle impacts, for example, in impacts of micrometeorites on spacecraft. read less USED (high confidence) R. K. F. Lee, B. Cox, and J. M. Hill, “Geometric model of silicon nanotubes,” 2010 International Conference on Nanoscience and Nanotechnology. 2010. link Times cited: 0 Abstract: In this paper, we extend both the rolled-up and the polyhedr… read moreAbstract: In this paper, we extend both the rolled-up and the polyhedral models for single-walled silicon nanotubes with equal bond lengths to models having distinct bond lengths. The silicon nanotubes considered here are assumed to be formed by sp3 hybridization with different bond lengths so that the nanotube lattice is assumed to comprise only skew rhombi. Beginning with the three postulates that (i) all bonds lying on the same helix are equal, (ii) all adjacent bond angles are equal, and (iii) all atoms are equidistant from a common axis of symmetry, we derive exact formulae for the polyhedral geometric parameters such as chiral angles, adjacent bond angles and radius. Finally, some molecular dynamics simulations are undertaken for comparison with the geometric model. These simulations start with equal bond lengths and then stabilize in such a way that two distinct bond lengths emerge. read less USED (high confidence) R. K. F. Lee, B. Cox, and J. M. Hill, “Silicon nanotubes with distinct bond lengths,” Journal of Mathematical Chemistry. 2010. link Times cited: 7 USED (high confidence) L. Liu and X. Chen, “Effect of surface roughness on thermal conductivity of silicon nanowires,” Journal of Applied Physics. 2010. link Times cited: 84 Abstract: Reducing the thermal conductivity of nanowires may enhance t… read moreAbstract: Reducing the thermal conductivity of nanowires may enhance their already exciting efficiency of thermoelectric energy conversion. Using molecular dynamics simulations, we demonstrate that the thermal conductivity of silicon nanowires could be significantly decreased by patterning (or etching) induced roughness of the nanowire surfaces. The type, amplitude, and wavelength of the surface roughness all have profound effects, and the thermal conductivity could be reduced more when the wavelength is smaller or the amplitude is larger. Such an effect of roughness on the thermal conductivity is furthermore found to be coupled with the effects of nanowire cross-sectional size and length. Typically, the roughness effect is more prominent in longer and larger nanowires. read less USED (high confidence) E. Landry and A. McGaughey, “Effect of film thickness on the thermal resistance of confined semiconductor thin films,” Journal of Applied Physics. 2010. link Times cited: 55 Abstract: The thermal resistance of semiconductor thin films is predic… read moreAbstract: The thermal resistance of semiconductor thin films is predicted using lattice dynamics (LD) calculations and molecular dynamics (MD) simulations. We consider Si and Ge films with thicknesses, LF, between 0.2 and 30 nm that are confined between larger extents of the other species (i.e., Ge/Si/Ge and Si/Ge/Si structures). The LD predictions are made in the classical limit for comparison to the classical MD simulations, which are performed at a temperature of 500 K. For structures with LF 2 nm, the MD-predicted thermal resistances are independent of the film thickness for the Ge/Si/Ge structures and increase with increasing film thickness for the Si/Ge/Si st... read less USED (high confidence) A. Harjunmaa and K. Nordlund, “Molecular dynamics simulations of Si/Ge cluster condensation,” Computational Materials Science. 2009. link Times cited: 19 USED (high confidence) G. Makov, C. Gattinoni, and A. D. Vita, “Ab initio based multiscale modelling for materials science,” Modelling and Simulation in Materials Science and Engineering. 2009. link Times cited: 15 Abstract: Materials modelling of extended defects in semiconductors (a… read moreAbstract: Materials modelling of extended defects in semiconductors (and many other systems) requires both detailed electronic models of matter to account for bond breaking and formation at the atomic scale and the representation of material systems at large scales, in the micrometre–microsecond range. These twin demands, if implemented directly by ab initio calculations, are unachievable with potentially available computational resources for the foreseeable future. An alternative approach is to develop multiscale simulations, where the level of simulation detail can vary in time and space, thus saving on computational cost without sacrificing the necessary detailed modelling. This paper introduces the basic concepts and reviews some progress in this field, and the related challenges along two main strands: (i) sequential multiscale modelling to construct larger-scale material models from first principles and (ii) hybrid multiscale modelling for the description of unitary systems which are too large for monoscale modelling at the desired accuracy. read less USED (high confidence) A. Thompson, S. Plimpton, and W. Mattson, “General formulation of pressure and stress tensor for arbitrary many-body interaction potentials under periodic boundary conditions.,” The Journal of chemical physics. 2009. link Times cited: 711 Abstract: Three distinct forms are derived for the force virial contri… read moreAbstract: Three distinct forms are derived for the force virial contribution to the pressure and stress tensor of a collection of atoms interacting under periodic boundary conditions. All three forms are written in terms of forces acting on atoms, and so are valid for arbitrary many-body interatomic potentials. All three forms are mathematically equivalent. In the special case of atoms interacting with pair potentials, they reduce to previously published forms. (i) The atom-cell form is similar to the standard expression for the virial for a finite nonperiodic system, but with an explicit correction for interactions with periodic images. (ii) The atom form is particularly suited to implementation in modern molecular dynamics simulation codes using spatial decomposition parallel algorithms. (iii) The group form of the virial allows the contributions to the virial to be assigned to individual atoms. read less USED (high confidence) E. Landry and A. McGaughey, “Thermal boundary resistance predictions from molecular dynamics simulations and theoretical calculations,” Physical Review B. 2009. link Times cited: 247 Abstract: The accuracies of two theoretical expressions for thermal bo… read moreAbstract: The accuracies of two theoretical expressions for thermal boundary resistance are assessed by comparing their predictions to independent predictions from molecular dynamics MD simulations. In one expression RE, the phonon distributions are assumed to follow the equilibrium, Bose-Einstein distribution, while in the other expression RNE, the phonons are assumed to have nonequilibrium, but bulk-like distributions. The phonon properties are obtained using lattice dynamics-based methods, which assume that the phonon interface scattering is specular and elastic. We consider i a symmetrically strained Si/Ge interface, and ii a series of interfaces between Si and “heavy-Si,” which differs from Si only in mass. All of the interfaces are perfect, justifying the assumption of specular scattering. The MD-predicted Si/Ge thermal boundary resistance is temperature independent and equal to 3.1 10 �9 m 2 -K/ W below a temperature of 500 K, indicating that the phonon scattering is elastic, as required for the validity of the theoretical calculations. At higher-temperatures, the MD-predicted Si/Ge thermal boundary resistance decreases with increasing temperature, a trend we attribute to inelastic scattering. For the Si/Ge interface and the Si/heavy-Si interfaces with mass ratios greater than two, RE is in good agreement with the corresponding MD-predicted values at temperatures where the interface scattering is elastic. When applied to a system containing no interface, RE is erroneously nonzero due to the assumption of equilibrium phonon distributions on either side of the interface. While RNE is zero for a system containing no interface, it is 40%–60% less than the corresponding MD-predicted values for the Si/Ge interface and the Si/heavy-Si interfaces at temperatures where the interface scattering is elastic. This inaccuracy is attributed to the assumption of bulk-like phonon distributions on either side of the interface. read less USED (high confidence) Z. Yang, Z.-X. Lu, and Y.-pu Zhao, “Shape effects on the yield stress and deformation of silicon nanowires: A molecular dynamics simulation,” Journal of Applied Physics. 2009. link Times cited: 49 Abstract: The tension and compression of single-crystalline silicon na… read moreAbstract: The tension and compression of single-crystalline silicon nanowires (SiNWs) with different cross-sectional shapes are studied systematically using molecular dynamics simulation. The shape effects on the yield stresses are characterized. For the same surface to volume ratio, the circular cross-sectional SiNWs are stronger than the square cross-sectional ones under tensile loading, but reverse happens in compressive loading. With the atoms colored by least-squares atomic local shear strain, the deformation processes reveal that the failure modes of incipient yielding are dependent on the loading directions. The SiNWs under tensile loading slip in {111} surfaces, while the compressive loading leads the SiNWs to slip in the {110} surfaces. The present results are expected to contribute to the design of the silicon devices in nanosystems. read less USED (high confidence) T. Morishita, “Structural, electronic, and vibrational properties of high-density amorphous silicon: a first-principles molecular-dynamics study.,” The Journal of chemical physics. 2009. link Times cited: 14 Abstract: We report a first-principles study of the structural, electr… read moreAbstract: We report a first-principles study of the structural, electronic, and dynamical properties of high-density amorphous (HDA) silicon, which was found to be formed by pressurizing low-density amorphous (LDA) silicon (a normal amorphous Si) [T. Morishita, Phys. Rev. Lett. 93, 055503 (2004); P. F. McMillan, M. Wilson, D. Daisenberger, and D. Machon, Nature Mater. 4, 680 (2005)]. Striking structural differences between HDA and LDA are revealed. The LDA structure holds a tetrahedral network, while the HDA structure contains a highly distorted tetrahedral network. The fifth neighboring atom in HDA tends to be located at an interstitial position of a distorted tetrahedron composed of the first four neighboring atoms. Consequently, the coordination number of HDA is calculated to be approximately 5 unlike that of LDA. The electronic density of state (EDOS) shows that HDA is metallic, which is consistent with a recent experimental measurement of the electronic resistance of HDA Si. We find from local EDOS that highly distorted tetrahedral configurations enhance the metallic nature of HDA. The vibrational density of state (VDOS) also reflects the structural differences between HDA and LDA. Some of the characteristic vibrational modes of LDA are dematerialized in HDA, indicating the degradation of covalent bonds. The overall profile of the VDOS for HDA is found to be an intermediate between that for LDA and liquid Si under pressure (high-density liquid Si). read less USED (high confidence) A. Matsuda, Y. Nakakubo, R. Ogino, H. Ohta, K. Eriguchi, and K. Ono, “Simulation and experimental study on the characteristics of plasma-induced damage and methodology for accurate damage analysis,” 2009 IEEE International Conference on IC Design and Technology. 2009. link Times cited: 0 Abstract: Physical damages to Si substrate induced by energetic ions f… read moreAbstract: Physical damages to Si substrate induced by energetic ions from plasma, associated with Si recess, is studied. By using molecular dynamics (MD) simulation, we clarified the structural picture of the damage. By spectroscopic ellipsometry (SE) measurements, we experimentally analyzed damaged layer thickness and energy band structure. Comprehensive analysis of the damage suggests device performance degradation related to basic plasma parameters. The methodology described in this work is necessary in accurate understanding and prediction of plasma-induced damage, e.g., Si recess. read less USED (high confidence) K.-C. Fang, C. Weng, and S. Ju, “An investigation into the mechanical properties of silicon nanoparticles using molecular dynamics simulations with parallel computing,” Journal of Nanoparticle Research. 2009. link Times cited: 12 USED (high confidence) B. Yildiz, A. Nikiforova, and S. Yip, “METALLIC INTERFACES IN HARSH CHEMO-MECHANICAL ENVIRONMENTS,” Nuclear Engineering and Technology. 2009. link Times cited: 1 Abstract: The use of multiscale modeling concepts and simulation techn… read moreAbstract: The use of multiscale modeling concepts and simulation techniques to study the destabilization of an ultrathin layer of oxide interface between a metal substrate and the surrounding environment is considered. Of particular interest are chemomechanical behavior of this interface in the context of a molecular-level description of stress corrosion cracking. Motivated by our previous molecular dynamics simulations of unit processes in materials strength and toughness, we examine the challenges of dealing with chemical reactivity on an equal footing with mechanical deformation, (a) understanding electron transfer processes using first-principles methods, (b) modeling cation transport and associated charged defect migration kinetics, and (c) simulation of pit nucleation and intergranular deformation to initiate the breakdown of the oxide interlayer. These problems illustrate a level of multi-scale complexity that would be practically impossible to attack by other means; they also point to a perspective framework that could guide future research in the broad computational science community. read less USED (high confidence) S. Ketharanathan, S. Sinha, J. Shumway, and J. Drucker, “Electron charging in epitaxial Ge quantum dots on Si(100),” Journal of Applied Physics. 2009. link Times cited: 6 Abstract: Electron confinement to heteroepitaxial Ge/Si(100) quantum d… read moreAbstract: Electron confinement to heteroepitaxial Ge/Si(100) quantum dots encapsulated in a Si matrix was investigated using capacitance-voltage measurements. Optimized growth conditions produced dot ensembles comprised of either huts and pyramids or dome clusters allowing investigation of electron confinement to these distinct dot morphologies. At room temperature, 20–40 nm diameter hut and pyramid clusters confine ∼0.7 electrons, while 60–80 nm diameter dome clusters confine ∼6 electrons. The greater capacity of dome clusters may be attributed to the four distinct conduction band minima that are deeper than the single minimum found for pyramid clusters using a simple band structure model. read less USED (high confidence) Q. Meng and Q. Wang, “Molecular dynamics simulation of annihilation of 60° dislocations in Si crystals,” physica status solidi (b). 2009. link Times cited: 1 Abstract: The annihilation of two 60° shuffle dislocations is studied … read moreAbstract: The annihilation of two 60° shuffle dislocations is studied via the molecular dynamics method. The Stillinger–Weber (SW) potential and environment‐dependent interatomic potential (EDIP) are used to describe the atomic interactions. The simulation results show that the complete annihilation of the 60° dislocations takes place only when the two dislocations lie on the same slip plane. The annihilation process may occur without external shear stress when the temperature is higher than a critical value. It is found that the critical temperature increases exponentially as a function of distance between the two dislocations. Also revealed in this simulation is an incomplete annihilation occurring when the distance between the slip planes of the two dislocations is less than about 1 nm. If the distance between the two slip planes is larger than about 1 nm, the dislocations will glide on their own slip planes as if no interaction exists between them. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) read less USED (high confidence) S. Wang, X.-gang Liang, X. Xu, and T. Ohara, “Thermal conductivity of silicon nanowire by nonequilibrium molecular dynamics simulations,” Journal of Applied Physics. 2009. link Times cited: 101 Abstract: The thermal conductivity of silicon nanowires was predicted … read moreAbstract: The thermal conductivity of silicon nanowires was predicted using the nonequilibrium molecular dynamics method using the Stillinger–Weber potential model and the Nose–Hoover thermostat. The dependence of the thermal conductivity on the wire length, cross-sectional area, and temperature was investigated. The surface along the longitudinal direction was set as a free boundary with potential boundaries in the other directions. The cross-sectional areas of the nanowires ranged from about 5 to 19 nm2 with lengths ranging from 6 to 54 nm. The thermal conductivity dependence on temperature agrees well with the experimental results. The reciprocal of the thermal conductivity was found to be linearly related to the nanowire length. These results quantitatively show that decreasing the cross-sectional area reduces the phonon mean free path in nanowires. read less USED (high confidence) R. K. F. Lee, B. Cox, and J. M. Hill, “An idealized polyhedral model and geometric structure for silicon nanotubes,” Journal of Physics: Condensed Matter. 2009. link Times cited: 9 Abstract: In this paper, we introduce an idealized model of silicon na… read moreAbstract: In this paper, we introduce an idealized model of silicon nanotubes comprising an exact polyhedral geometric structure for single-walled silicon nanotubes. The silicon nanotubes considered here are assumed to be formed by sp3 hybridization and thus the nanotube lattice is assumed to comprise only squares or skew rhombi. Beginning with the three postulates that all bond lengths are equal, all adjacent bond angles are equal, and all atoms are equidistant from a common axis of symmetry, we derive exact formulae for the geometric parameters such as radii, bond angles and unit cell length. We present asymptotic expansions for these quantities to the first two orders of magnitude. Because of the faceted nature of the polyhedral model we may determine a perceived inner radius for the nanotube, from which an expression for the wall thickness emerges. We also describe the geometric properties of some ultra-small silicon nanotubes. Finally, the values of the diameters for the polyhedral model are compared with results obtained from molecular dynamics simulations and some limited numerical calculations are undertaken to confirm the meta-stability of the proposed structures. read less USED (high confidence) J. Kermode et al., “Low-speed fracture instabilities in a brittle crystal,” Nature. 2008. link Times cited: 190 USED (high confidence) S. Michaelson, R. Akhvlediani, A. Hoffman, A. Silverman, and J. Adler, “Hydrogen in nano‐diamond films: experimental and computational studies,” physica status solidi (a). 2008. link Times cited: 10 Abstract: We present studies related to the incorporation of hydrogen … read moreAbstract: We present studies related to the incorporation of hydrogen and its bonding configuration in diamond films composed of diamond grains of varying size which were deposited by three different methods: hot filament (HF), micro wave (MW) and direct current glow discharge (dc GD) chemical vapor deposition. The size of the diamond grains which constitute the films varies in the following way: hundreds of nm in the case of HF CVD (“sub‐micron size”, ∼300 nm), tens of nm in the case of MW CVD (3–30 nm) and a few nm in the case of dc GD CVD (“ultra nano‐crystalline diamond”, ∼5 nm). Secondary ion mass spectroscopy (SIMS) and high resolution electron energy loss spectroscopy (HR‐EELS) were applied to investigate the hydrogen trapping in the films. The hydrogen retention of the diamond films increases with decreasing grain size, indicating that most likely hydrogen is bonded and trapped in grain boundaries as well as on the internal grain surfaces. HR‐EELS analysis shows that at least part of this hydrogen is bonded to sp2‐ and sp3‐hybridized carbon, thus giving rise to typical C–H vibration modes. The vibrational spectroscopies show the increase of sp2 C–H modes in transition from sub‐micron to ultra nano‐crystalline grain size. These conclusions are supported by preliminary results of computer simulations which show that hydrogen atoms at the boundary between a nano‐diamond particle and an amorphous shell have lower energy than hydrogen atoms within either the nano‐diamond or the amorphous region. These results suggest that hydrogen is expected to be localized at the nano‐diamond/amorphous carbon interface as experimentally found. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) read less USED (high confidence) K. Yan and A. Soh, “Effects of grain boundary cavities on the thermal resistance under ultrashort laser pulse,” Journal of Physics D: Applied Physics. 2008. link Times cited: 2 Abstract: Molecular dynamics simulations were carried out for nonequil… read moreAbstract: Molecular dynamics simulations were carried out for nonequilibrium phonon heat transport across the Si Σ = 5, (3 1 0) symmetric tilt grain boundaries subjected to an ultrashort laser pulse. It has been found that the existence of cavities at the grain boundary will increase the grain boundary potential energy and decrease the heat dissipation, which is evident from the approximately 20% longer relaxation time required for the system to reach thermodynamic equilibrium. Thus, the existence of grain boundary cavities is one of the main hindrances in the thermal management of nanostructures. read less USED (high confidence) H. Zhao and J. Freund, “Full-spectrum phonon relaxation times in crystalline Si from molecular dynamics simulations,” Journal of Applied Physics. 2008. link Times cited: 18 Abstract: The lattice vibrations of a periodic silicon crystal are sim… read moreAbstract: The lattice vibrations of a periodic silicon crystal are simulated by a molecular dynamics simulation. The history of atomic displacements and velocities obtained is used to compute the amplitudes of all phonon modes supported by the lattice. The phonon amplitude autocorrelation coefficients are found to decay exponentially in time, in agreement with single-mode relaxation timemodels for phonon scattering. However, the relaxation times extracted from the correlation curves are found to differ significantly from the empirical formulas currently used in models for microscale thermal transport, suggesting that improved relaxation timemodels are needed for accurate predictions in complex small-scale heat transfer systems. read less USED (high confidence) S. Izumi and S. Yip, “Dislocation nucleation from a sharp corner in silicon,” Journal of Applied Physics. 2008. link Times cited: 51 Abstract: By combining molecular dynamics simulation with reaction pat… read moreAbstract: By combining molecular dynamics simulation with reaction pathway sampling, we have observed the nucleation of a three-dimensional dislocation loop from a sharp corner in silicon and investigated the shear stress dependence of the activation energy and saddle-point configuration. The nucleated shuffle-set half-loop consisted of two 60° segments and one screw segment, each lying along a Peierls valley. The half-hexagonal shape is in good agreement with experiments at low temperature. Under high stress (90%–95% of athermal shear stress), the dislocation embryo is far from perfect, with half-size Burgers vector (about 0.2 nm) and a 0.4–0.7 nm radius forming a diffuse core region. A consequence is that the Rice–Thompson theory gives incorrect predictions regarding the activation energy and saddle-point configuration. With decreasing applied stress (less than 70%), the embryo approaches that of a perfect dislocation. read less USED (high confidence) X.-peng Huang and H. Xiulan, “Molecular Dynamics Simulation of Thermal Conductivity in Si–Ge Nanocomposites,” Chinese Physics Letters. 2008. link Times cited: 7 Abstract: Thermal conductivity of nanocomposites is calculated by mole… read moreAbstract: Thermal conductivity of nanocomposites is calculated by molecular dynamics (MD) simulation. The effect of size on thermal conductivity of nanowire composites and the temperature profiles are studied. The results indicate that the thermal conductivity of nanowire composites could be much lower than alloy value; the thermal conductivity is slightly dependent on temperature except at very low temperature. read less USED (high confidence) T. Ohchi et al., “Reducing Damage to Si Substrates during Gate Etching Processes,” Japanese Journal of Applied Physics. 2008. link Times cited: 87 Abstract: The mechanism of formation of a “Si recess” that appears dur… read moreAbstract: The mechanism of formation of a “Si recess” that appears during gate poly-Si etching was studied. Hydrogen in HBr plasma penetrates through a thin gate oxide film and generates dislocated sites in the Si substrate. We developed a molecular dynamics (MD) simulation to clarify both the penetration depth of H and O and the dislocation of Si. The damage was successfully minimized by controlling the high energy peak in the ion energy distribution function (IEDF) to be lower than the threshold energy of ion penetration. read less USED (high confidence) R. Kobayashi and T. Nakayama, “Atomic and Electronic Structures of Stair-Rod Dislocations in Si and GaAs,” Japanese Journal of Applied Physics. 2008. link Times cited: 5 Abstract: Atomic and electronic structures of stair-rod dislocations i… read moreAbstract: Atomic and electronic structures of stair-rod dislocations in Si and GaAs films are studied using the first-principles calculations. It is shown that the stair-rod dislocation shows the dimer-bond reconstruction in the core region and that there are two types of dimer-array configurations, parallel and zigzag dimer structures. The bonding and antibonding states originating from these dimer bonds are embedded in valence and conduction bands in the case of Si, while they appear as partially occupied midgap bands and act as carrier traps in the case of GaAs. We found that the adjacent dimer bonds in GaAs have different lengths on different partial dislocation lines in order to stabilize the electronic band energy. read less USED (high confidence) A. Galashev, “Thermal instability of silicon fullerenes stabilized with hydrogen: Computer simulation,” Semiconductors. 2008. link Times cited: 4 USED (high confidence) Y. Petrov et al., “Equation of state of matter irradiated by short laser pulse and geometry of spalled cupola,” High-Power Laser Ablation. 2008. link Times cited: 8 Abstract: The motion of both Lennard-Jones solids and metals induced b… read moreAbstract: The motion of both Lennard-Jones solids and metals induced by ultrashort laser irradiation near the ablation threshold is investigated by molecular dynamics simulation. The universality of the ablation threshold fluence with respect to the cohesion energy of solids irradiated by femtosecond laser pulses is demonstrated for Lennard-Jones solid and metals simulated by many-body EAM potentials. read less USED (high confidence) M. Z. Hossain, J. Freund, and H. Johnson, “Differential sputter yields in Si1−xGex,” Journal of Applied Physics. 2008. link Times cited: 13 Abstract: Sputter yields for ion bombardment of Si1−xGex alloys are co… read moreAbstract: Sputter yields for ion bombardment of Si1−xGex alloys are computed using molecular dynamics simulations with the target material modeled using the Stillinger–Weber empirical potential. The results show that Si atoms are preferentially sputtered relative to Ge atoms for all x. The parameters of the Stillinger–Weber potential are altered to investigate the relative importance of atomic mass, bonding energy, atomic number, and atomic density leading to the observed differential sputter yields. The results explain an experimentally observed nonlinear dependence of total sputter yields on composition in Si1−xGex [Tuboltsev et al., Phys. Rev. B 72, 205434 (2005)]. read less USED (high confidence) J. Samela, K. Nordlund, V. Popok, and E. Campbell, “Origin of complex impact craters on native oxide coated silicon surfaces,” Physical Review B. 2008. link Times cited: 55 Abstract: Crater structures induced by impact of keV-energy ${\mathrm{… read moreAbstract: Crater structures induced by impact of keV-energy ${\mathrm{Ar}}_{n}^{+}$ cluster ions on silicon surfaces are measured with atomic force microscopy. Complex crater structures consisting of a central hillock and outer rim are observed more often on targets covered with a native silicon oxide layer than on targets without the oxide layer. To explain the formation of these complex crater structures, classical molecular dynamics simulations of Ar cluster impacts on oxide coated silicon surfaces, as well as on bulk amorphous silica, amorphous Si, and crystalline Si substrates, are carried out. The diameter of the simulated hillock structures in the silicon oxide layer is in agreement with the experimental results, but the simulations cannot directly explain the height of hillocks and the outer rim structures when the oxide coated silicon substrate is free of defects. However, in simulations of $5\phantom{\rule{0.3em}{0ex}}\mathrm{keV}$/atom ${\mathrm{Ar}}_{12}$ cluster impacts, transient displacements of the amorphous silicon or silicon oxide substrate surfaces are induced in an approximately $50\phantom{\rule{0.3em}{0ex}}\mathrm{nm}$ wide area surrounding the impact point. In silicon oxide, the transient displacements induce small topographical changes on the surface in the vicinity of the central hillock. The comparison of cluster stopping mechanisms in the various silicon oxide and silicon structures shows that the largest lateral momentum is induced in the silicon oxide layer during the impact; thus, the transient displacements on the surface are stronger than in the other substrates. This can be a reason for the higher frequency of occurrence of the complex craters on oxide coated silicon. read less USED (high confidence) A. Argon and M. Demkowicz, “What Can Plasticity of Amorphous Silicon Tell Us about Plasticity of Metallic Glasses?,” Metallurgical and Materials Transactions A. 2008. link Times cited: 55 USED (high confidence) Z. Wang, X. Zu, F. Gao, and W. J. Weber, “Mechanical behavior of gallium nitride nanotubes under combined tension-torsion: An atomistic simulation,” Journal of Applied Physics. 2008. link Times cited: 11 Abstract: The tensile mechanical behavior of single crystalline galliu… read moreAbstract: The tensile mechanical behavior of single crystalline gallium nitride (GaN) nanotubes under combined tension-torsion is investigated using molecular dynamics simulations with an empirical potential. The simulation results show that a small torsion rate (<0.010degps−1) does not affect the tensile behavior of GaN nanotube, i.e., the nanotubes show brittle properties at low temperatures; whereas at high temperatures, they behave as ductile materials. However, the failure stress decreases with increasing rate of torsion above 0.010degps−1, and the nanotube fails in a different manner. The torsion rate has no effect on the elastic properties of GaN nanotubes. read less USED (high confidence) Y. Zhang, J. Cao, Y. Xiao, and X. H. Yan, “Phonon spectrum and specific heat of silicon nanowires,” Journal of Applied Physics. 2007. link Times cited: 37 Abstract: Based on lattice dynamics theory and molecular dynamics simu… read moreAbstract: Based on lattice dynamics theory and molecular dynamics simulations, we have investigated the geometrical structures, phonon dispersion relations, and specific heat of silicon nanowires with Stillinger-Weber potential. It was shown that the original Stillinger-Weber potential can reproduce the well-established four acoustical branches. With the calculated spectra, we calculated specific heats of silicon nanowires. It is found that the specific heats of thin nanowires are much higher than those of bulk silicon. According to the partial density of states of surface atoms, the enhancement of specific heats of silicon nanowires can be attributed to the surface effect and phonon confinement effect. read less USED (high confidence) N. Pradeep, D.-in Kim, J. Grobelny, T. Hawa, B. Henz, and M. Zachariah, “Ductility at the nanoscale: Deformation and fracture of adhesive contacts using atomic force microscopy,” Applied Physics Letters. 2007. link Times cited: 16 Abstract: Fracture of nanosize contacts formed between spherical probe… read moreAbstract: Fracture of nanosize contacts formed between spherical probes and flat surfaces is studied using an atomic force microscope in an ultrahigh vacuum environment. Analysis of the observed deformation during the fracture process indicates significant material extensions for both gold and silica contacts. The separation process begins with an elastic deformation followed by plastic flow of material with atomic rearrangements close to the separation. Classical molecular dynamics studies show similarity between gold and silicon, materials that exhibit entirely different fracture behavior at macroscopic scale. This direct experimental evidence suggests that fracture at nanoscale occurs through a ductile process. read less USED (high confidence) I. Zsoldos and G. Kakuk, “New formations of carbon nanotube junctions,” Modelling and Simulation in Materials Science and Engineering. 2007. link Times cited: 10 Abstract: A method is demonstrated for constructing models on which we… read moreAbstract: A method is demonstrated for constructing models on which we show that carbon nanotubes with optional type and diameter can be connected to different three-dimensional surfaces. Basic examples (zigzag and armchair-type junctions and holes) are studied in this paper. read less USED (high confidence) D. Humbird, D. Graves, A. Stevens, and W. Kessels, “Molecular dynamics simulations of Ar + bombardment of Si with comparison to experiment,” Journal of Vacuum Science and Technology. 2007. link Times cited: 14 Abstract: The authors present molecular dynamics (MD) simulations of e… read moreAbstract: The authors present molecular dynamics (MD) simulations of energetic Ar+ ions (20–200eV) interacting with initially crystalline silicon, with quantitative comparison to experiment. Ar+ bombardment creates a damaged or amorphous region at the surface, which reaches a steady-state thickness that is a function of the impacting ion energy. Real-time spectroscopic ellipsometry data of the same phenomenon match the MD simulation well, as do analogous SRIM simulations. They define positional order parameters that detect a sharp interface between the amorphous and crystalline regions. They discuss the formation of this interesting feature in the simulation, and show that it provides insight into some assumptions made in the analysis of experimental data obtained by interface-sensitive surface spectroscopy techniques. read less USED (high confidence) M. H. Bhat et al., “Vitrification of a monatomic metallic liquid,” Nature. 2007. link Times cited: 181 USED (high confidence) T. Hawa and M. Zachariah, “Molecular dynamics simulation and continuum modeling of straight-chain aggregate sintering : Development of a phenomenological scaling law,” Physical Review B. 2007. link Times cited: 27 Abstract: Atomistic molecular dynamics simulation and a simple continu… read moreAbstract: Atomistic molecular dynamics simulation and a simple continuum viscous flow model are employed to investigate the sintering of straight-chain nanoparticle aggregates. The results are used to develop a phenomenological sintering scaling law. The chain aggregates investigated consist of up to 80 primary particles of silicon, with primary particles of 2.5–7 nm in diameter. We found that sintering of chain aggregates consists of three steps. In step a , reaction between particles to minimize surface defects and development of a cylindrical like shape comprised an induction period. Step b consisted of contraction of the cylinder, which actually consisted of two contraction stages. The first stage was the local contraction stage where sintering occurs only at the ends of the particle chain, and the second stage involved the global contraction. The last step was the nominal sintering process from an oval to spherical shape. As expected, sintering time increases with increasing chain length, with the exception that very long chains fragmented. The sintering times normalized by the primary particle diameter showed a universal relationship which only depends on chain length. These results were found to be consistent with a mathematical model we develop based on continuum viscous flow. The model was able to predict the sintering time in excellent agreement with results obtained from molecular dynamics simulation for any chain length and any primary particle size for straight nanoparticle chain aggregates. The results for sintering times for aggregate chains could be summarized with a power law modification of the Frenkel viscous flow equation, to include a dependence on the number of particle connections in a chain aggregate: t= tFrenkel * N−1 0.68. read less USED (high confidence) K. Kang and W. Cai, “Brittle and ductile fracture of semiconductor nanowires – molecular dynamics simulations,” Philosophical Magazine. 2007. link Times cited: 135 Abstract: Fracture of silicon and germanium nanowires in tension at ro… read moreAbstract: Fracture of silicon and germanium nanowires in tension at room temperature is studied by molecular dynamics simulations using several interatomic potential models. While some potentials predict brittle fracture initiated by crack nucleation from the surface, most potentials predict ductile fracture initiated by dislocation nucleation and slip. A simple parameter based on the ratio between the ideal tensile strength and the ideal shear strength is found to correlate very well with the observed brittle versus ductile behaviours for all the potentials used in this study. This parameter is then computed by ab initio methods, which predict brittle fracture at room temperature. A brittle-to-ductile transition (BDT) is observed in MD simulations at higher temperature. The BDT mechanism in semiconductor nanowires is different from that in the bulk, due to the lack of a pre-existing macrocrack that is always assumed in bulk BDT models. read less USED (high confidence) V. Hugouvieux, E. Farhi, M. R. Johnson, F. Jurányi, P. Bourges, and W. Kob, “Structure and dynamics of l − Ge : Neutron scattering experiments and ab initio molecular dynamics simulations,” Physical Review B. 2007. link Times cited: 22 Abstract: We report the first measurements of the dynamics of liquid g… read moreAbstract: We report the first measurements of the dynamics of liquid germanium (l-Ge) by quasielastic neutron scattering on time-of-flight and triple-axis spectrometers. These results are compared with simulation data of the structure and dynamics of l-Ge which have been obtained with ab initio density functional theory methods. The simulations accurately reproduce previous results from elastic and inelastic scattering experiments, as well as the q dependence of the width of the quasielastic signal of the new experimental data. In order to understand some special features of the structure of the liquid we have also simulated amorphous Ge. Overall we find that the atomistic model represents accurately the average structure of real l-Ge as well as the time dependent structural fluctuations. The quasielastic neutron scattering data allows us to investigate to what extent simple theoretical models can be used to describe diffusion in l-Ge. read less USED (high confidence) L. Sun, C. Le, F. Saied, and J. Murthy, “Performance of a Parallel Molecular Dynamics Program for Computation of Thermal Properties,” Numerical Heat Transfer, Part B: Fundamentals. 2007. link Times cited: 5 Abstract: The parallel performance of classical molecular dynamics sim… read moreAbstract: The parallel performance of classical molecular dynamics simulations of the thermal properties of solid-state materials is evaluated. Computations are validated by predicting the bulk silicon thermal conductivity as a function of temperature. The performance of the computational algorithm and software are tested on three different architectures, including the IBM BlueGene, the IBM Power 4 +, and an Intel Xeon Linux cluster, corresponding to different combinations of processor speeds, communications bandwidth, and latency. Two popular three-body potentials used for silicon simulation are evaluated and compared. In addition, the popular Lennard-Jones potential is used to investigate to role of cutoff distance on parallel performance. read less USED (high confidence) A. Galashev, I. A. Izmodenov, A. N. Novruzov, and O. Novruzova, “Computer study of physical properties of silicon nanostructures,” Semiconductors. 2007. link Times cited: 9 USED (high confidence) Z. Wang, X. Zu, F. Gao, and W. J. Weber, “Atomistic simulation of brittle to ductile transition in GaN nanotubes,” Applied Physics Letters. 2006. link Times cited: 26 Abstract: Molecular dynamics methods with a Stillinger-Weber [Phys. Re… read moreAbstract: Molecular dynamics methods with a Stillinger-Weber [Phys. Rev. B 31, 5262 (1985)] potential have been used to investigate the mechanical properties of wurtzite-type single-crystalline GaN nanotubes under applied tensile strains. At low temperatures, the nanotubes show brittle properties, whereas at high temperatures, they behave as ductile materials. The brittle to ductile transition (BDT) is systematically investigated and the corresponding transition temperatures have been determined in GaN nanotubes. The BDT temperature generally increases with increasing thickness of nanotubes and strain rate. read less USED (high confidence) K. Sugio, H. Fukushima, and O. Yanagisawa, “Molecular Dynamics Simulation of Grain Boundary Formation and Migration in Silicon,” Materials Transactions. 2006. link Times cited: 5 Abstract: Molecular dynamics simulation using Tersoff potential was ca… read moreAbstract: Molecular dynamics simulation using Tersoff potential was carried out to investigate the formation and the migration of (010) E5 twist boundary in silicon. Effects of carbon atoms on the grain boundary formation and the grain boundary migration were also investigated. Amorphous thin layers remained at the twist boundary even after crystallization, and changes in the thickness of this layers caused grain boundary migration. When carbon atoms were segregated at the twist boundary, these atoms prevented shrinkage of an amorphous thin layer, and the grain boundary migration was retarded. Precipitated carbon atoms within the grain produces a strain field and this strain field possibly became driving force for the grain boundary migration. read less USED (high confidence) V. Astapenko and N. Nasonov, “Suppression of the polarization bremsstrahlung from a fast charged particle in an amorphous medium,” Journal of Experimental and Theoretical Physics. 2006. link Times cited: 3 USED (high confidence) N. Lazarev, C. Abromeit, R. Schäublin, and R. Gotthardt, “Temperature-controlled martensitic phase transformations in a model NiAl alloy,” Journal of Applied Physics. 2006. link Times cited: 12 Abstract: Reversible martensitic phase transformations in a partially … read moreAbstract: Reversible martensitic phase transformations in a partially disordered Ni–Al alloy within the composition range from 60to65at.% of Ni are investigated using molecular dynamics simulation. During a complete temperature cycle a wide hysteresis in enthalpy, volume, and shape of the simulated crystals is observed. The temperature T0 of the phase transformation is found from the calculated free energy evolution. To investigate the atomic-scale development during the phase transformation a local order parameter is defined which is based on a combined method of Voronoy tessellation [J. Reine Angew. Math. 134, 198 (1908)] with common-neighbor analysis. This local order parameter allows us to get a detailed localized picture of nucleation and growth of the new phases. Both homogeneous formation of the new phase and heterogeneous nucleation are observed. The velocity of new phase growth front is estimated. read less USED (high confidence) J. Goicochea, M. Madrid, and C. Amon, “Phonon relaxation rates in silicon thin films determined by molecular dynamics,” Thermal and Thermomechanical Proceedings 10th Intersociety Conference on Phenomena in Electronics Systems, 2006. ITHERM 2006. 2006. link Times cited: 7 Abstract: Silicon thin films with nanometer dimensions are increasingl… read moreAbstract: Silicon thin films with nanometer dimensions are increasingly being used in the electronic and nanotechnology industries. At such small scales, the continuum assumption is no longer valid and the interactions of the energy carriers (phonons) with the boundaries affect the thermal conductivity of the films. For semiconductors and dielectric thin films, understanding phonon properties in the nanometer scale is important not only to predict their thermal transport behavior, but also to propose solutions to a broad range of thermally induced problems, such as self-heating, sub-continuum localized heating effects and thermally induced reliability. In this work, we estimate, by means of molecular dynamics, the phonon relaxation times in silicon thin films, in the out-of-plane direction, at different temperatures and thin film thicknesses. The relaxation times are determined from the temporal decay of the autocorrelation function of the energy components of the phonons allowed in the crystal. The results are compared with the relaxation times obtained from perturbation theory and Mathiessen's rule. Two major trends were observed, the relaxation rates for transversal acoustic modes are lower than those for the longitudinal acoustic mode for all thickness and temperatures studied, and the longitudinal acoustic modes do not follow the theoretical predictions read less USED (high confidence) B. Becker, P. Schelling, and S. Phillpot, “Interfacial phonon scattering in semiconductor nanowires by molecular-dynamics simulation,” Journal of Applied Physics. 2006. link Times cited: 34 Abstract: We use molecular-dynamics simulations of vibrational wave pa… read moreAbstract: We use molecular-dynamics simulations of vibrational wave packets to study the scattering of longitudinal-acoustic modes from interfaces in semiconductor nanowires of varying diameters. The energy transmission coefficient at the interface is found to depend strongly on both the nanowire diameter and the frequency of the incident wave. By analyzing the scattering events, we determine the selection rules for nanowire scattering that can be understood in terms of the representations of the point-group symmetry of the nanowire. Using such symmetry arguments, we predict that the presence of gaps in the phonon spectrum of thin high-symmetry nanowires will result in a complete reflection of phonons at the interfaces. We discuss the implications of our results for interfacial scattering in real systems, including Si∕Ge superlattice nanowires. read less USED (high confidence) R. Kobayashi and T. Nakayama, “Thermal annihilation process of stacking-fault tetrahedron defect in Si-film epitaxy,” Thin Solid Films. 2006. link Times cited: 1 USED (high confidence) M. Mckay, J. Shumway, and J. Drucker, “Real-time coarsening dynamics of Ge∕Si(100) nanostructures,” Journal of Applied Physics. 2006. link Times cited: 13 Abstract: The coarsening dynamics of Ge∕Si(100) nanostructures were mo… read moreAbstract: The coarsening dynamics of Ge∕Si(100) nanostructures were monitored using real-time, elevated temperature scanning tunneling microscopy (STM). Gas-source molecular beam epitaxy from digermane onto Si(100) was used to produce mixed hut and pyramid cluster ensembles. The width of the most elongated rectangular-based hut clusters was always less than the side length of square-based pyramid clusters for the growth conditions employed. This suggests that pyramid elongation to form hut clusters occurred at early growth stages for some smaller clusters. A previously unidentified coarsening mechanism was characterized during growth temperature annealing and was interpreted using atomistic elastic modeling. Pyramid clusters were more stable than narrow hut clusters with larger volumes. These larger volume huts decayed by reducing their length at a constant width, finally becoming small pyramids. These small pyramids are less stable than those that never elongated to form huts and consequently dissolve. The decreas... read less USED (high confidence) M. Haran, J. Catherwood, and P. Clancy, “Effects of Ge content on the diffusion of group-V dopants in SiGe alloys,” Applied Physics Letters. 2006. link Times cited: 16 Abstract: Density functional theory calculations and molecular dynamic… read moreAbstract: Density functional theory calculations and molecular dynamics simulations are used to decouple the influence of strain and the effect of germanium content on the diffusivity of intrinsic defects and group-V dopants in strained Si and SiGe materials. Vacancy diffusivities increase with increasing germanium content. In contrast, interstitial diffusivities in SiGe remain roughly constant until the germanium content reaches 25% and then decrease. Tensile strain increases interstitial-assisted dopant diffusivity and decreases vacancy-assisted diffusivity. Germanium reduces interstitial diffusivity in a manner controlled by dopant V size but assists vacancy diffusivity (lowering formation energies by ∼0.2eV). read less USED (high confidence) A. Bodapati, P. Keblinski, P. Schelling, and S. Phillpot, “Crossover in Thermal Transport Mechanism in Nanocrystalline Silicon,” Bulletin of the American Physical Society. 2006. link Times cited: 8 Abstract: Using vibrational mode analysis, we demonstrate that lattice… read moreAbstract: Using vibrational mode analysis, we demonstrate that lattice vibrations in small grain (≲3nm) structurally inhomogeneous nanocrystalline silicon are almost identical to those in homogeneous amorphous structures with the majority of the vibrations delocalized and unpolarized. As a consequence the principal thermal conductivity mechanism in such a nanocrystalline material is the same as in the amorphous material. With increasing grain size the ability of vibrations to homogenize over the nanocrystalline structure is gradually lost and the phonon spectrum becomes progressively more like that of a crystalline material; this is reflected in a crossover in the mechanism of thermal transport. read less USED (high confidence) P. Krasnochtchekov, K. Albe, Y. Ashkenazy, and R. Averback, “Molecular-dynamics study of the density scaling of inert gas condensation.,” The Journal of chemical physics. 2005. link Times cited: 11 Abstract: The initial stages of vapor condensation of Ge in the presen… read moreAbstract: The initial stages of vapor condensation of Ge in the presence of a cold Ar atmosphere were studied by molecular-dynamics simulations. The state variables of interest included the densities of condensing vapor and gas, the density of clusters, and the average cluster size, while the temperatures of the vapor and the clusters were separately monitored with time. Three condensation processes were explicitly identified: nucleation, monomeric growth, and cluster aggregation. Our principal finding is that both the average cluster size and the number of clusters scale with the linear dimension of the computation cell, L, and Ln, with the scaling parameter n approximately 4, corresponding to a reaction order of nu approximately 2.33. This small value of n is explained by an unexpected nucleation path involving the formation of Ge dimers via two-body collisions. read less USED (high confidence) V. Molinero, S. Sastry, and C. A. Angell, “Tuning of tetrahedrality in a silicon potential yields a series of monatomic (metal-like) glass formers of very high fragility.,” Physical review letters. 2005. link Times cited: 101 Abstract: We obtain monatomic glass formers in simulations by modifyin… read moreAbstract: We obtain monatomic glass formers in simulations by modifying the tetrahedral character in a silicon potential to explore a triple point zone between potentials favoring diamond (dc) and bcc crystals. dc crystallization is always preceded by a polyamorphic transformation of the liquid, and is frustrated when the Kauzmann temperature of the high temperature liquid intersects the liquid-liquid coexistence line. The glass forming liquids are extraordinarily fragile. Our results suggest that Si and Ge liquids may be vitrified at a pressure close to the diamond-beta-tin-liquid triple point. read less USED (high confidence) G. Csányi, T. Albaret, G. Moras, M. Payne, and A. Vita, “Multiscale hybrid simulation methods for material systems,” Journal of Physics: Condensed Matter. 2005. link Times cited: 40 Abstract: We review recent progress in the field of multiscale hybrid … read moreAbstract: We review recent progress in the field of multiscale hybrid computer simulations of materials, and present an overview of a novel scheme that links arbitrary atomistic simulation techniques together in a truly seamless manner. Rather than constructing a new hybrid Hamiltonian that combines different models, we use a unique short range classical potential and continuously tune its parameters to reproduce the atomic trajectories at the prescribed level of accuracy throughout the system. read less USED (high confidence) S. Phillpot, P. Schelling, and P. Keblinski, “Interfacial thermal conductivity: Insights from atomic level simulation,” Journal of Materials Science. 2005. link Times cited: 22 USED (high confidence) D. Choudhary and P. Clancy, “Application of accelerated molecular dynamics schemes to the production of amorphous silicon.,” The Journal of chemical physics. 2005. link Times cited: 8 Abstract: The evolving nature of a Stillinger-Weber modeled silicon gl… read moreAbstract: The evolving nature of a Stillinger-Weber modeled silicon glass is studied using two accelerated molecular dynamics scheme, specifically, hyperdynamics and self-guided algorithms due to Voter and due to Wu and Wang, respectively. We obtain an acceleration of the dynamics, a "boost," on the order of 20 without incurring any significant computational overhead. The validity of the results using accelerated methods is provided by comparison to a conventional molecular dynamics (MD) algorithm simulated under constant temperature conditions for more than 100 ns. We found that performing a sensitivity analysis of the effect of the parameters lambda and t1 before applying the self-guided MD scheme was important. Values of lambda greater than 0.1 and t1 equal to 1 ps were found to give improved structural evolution as compared to a conventional MD scheme. The hyperdynamics approximation scheme was found to be effective in obtaining boosts in the range of 4-12 for a small system without changing the dynamics of the evolution. However, for a large system size such an approach introduces significant perturbations to the pertinent equations of motion. read less USED (high confidence) J. Kioseoglou et al., “Atomic simulations and HRTEM observations of a Σ 18 tilt grain boundary in GaN,” physica status solidi (a). 2005. link Times cited: 2 Abstract: The crystalline quality of GaN thin films grown on foreign s… read moreAbstract: The crystalline quality of GaN thin films grown on foreign substrates for opto‐ and micro‐electronics applications depends strongly on the growth conditions. Among a variety of microstructural defects that appear in GaN epilayers, grain boundaries (GBs) are extended defects that may be formed during the growth process under certain circumstances. In this work, the atomic structures of a ‘symmetric' and an ‘asymmetric' 70.53° 〈$ 1 \bar 2 10$〉 Σ18 tilt boundaries are investigated by combining large scale energetic calculations, using a modified Stillinger–Weber interatomic potential, with high resolution transmission electron microscopy observations. The energetically favourable short‐period asymmetric interface is matched to the experimental observations. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) read less USED (high confidence) Y. Jeng, P. Tsai, and T. Fang, “Molecular dynamics studies of atomic-scale tribological characteristics for different sliding systems,” Tribology Letters. 2005. link Times cited: 27 USED (high confidence) T. Kawahara, N. Tabuchi, T. Arai, Y. Sato, J. Morimoto, and H. Matsumura, “Coordination number constraint models for hydrogenated amorphous Si deposited by catalytic chemical vapour deposition,” Journal of Physics: Condensed Matter. 2005. link Times cited: 3 Abstract: We measured structure factors of hydrogenated amorphous Si b… read moreAbstract: We measured structure factors of hydrogenated amorphous Si by x-ray diffraction and analysed the obtained structures using a reverse Monte Carlo (RMC) technique. A small shoulder in the measured structure factor S(Q) was observed on the larger Q side of the first peak. The RMC results with an unconstrained model did not clearly show the small shoulder. Adding constraints for coordination numbers 2 and 3, the small shoulder was reproduced and the agreement with the experimental data became better. The ratio of the constrained coordination numbers was consistent with the ratio of Si–H and Si–H2 bonds which was estimated by the Fourier transformed infrared spectra of the same sample. This shoulder and the oscillation of the corresponding pair distribution function g(r) at large r seem to be related to the low randomness of cat-CVD deposited a-Si:H. read less USED (high confidence) K.-C. Fang and C. Weng, “An investigation into the melting of silicon nanoclusters using molecular dynamics simulations,” Nanotechnology. 2005. link Times cited: 26 Abstract: Using the Stillinger–Weber (SW) potential model, we have per… read moreAbstract: Using the Stillinger–Weber (SW) potential model, we have performed molecular dynamics (MD) simulations to investigate the melting of silicon nanoclusters comprising a maximum of 9041 atoms. This study investigates the size, surface energy and root mean square displacement (RMSD) characteristics of the silicon nanoclusters as they undergo a heating process. The numerical results reveal that an intermediate nanocrystal regime exists for clusters with more than 357 atoms. Within this regime, a linear relationship exists between the cluster size and its melting temperature. It is found that melting of the silicon nanoclusters commences at the surface and that Tm,N = Tm,Bulk−αN−1/3. Therefore, the extrapolated melting temperature of the bulk with a surface decreases from Tm,Bulk = 1821 K to a value of Tm,357 = 1380 K at the lower limit of the intermediate nanocrystal regime. read less USED (high confidence) P. Krasnochtchekov and R. Averback, “Molecular dynamics simulations of cluster nucleation during inert gas condensation.,” The Journal of chemical physics. 2005. link Times cited: 19 Abstract: Molecular dynamics simulations of vapor-phase nucleation of … read moreAbstract: Molecular dynamics simulations of vapor-phase nucleation of germanium in an argon atmosphere were performed and a unexpected channel of nucleation was observed. This channel, vapor-induced cluster splitting, is important for more refractory materials since the critical nucleus size can fall below the size of a dimer. As opposed to conventional direct vapor nucleation of the dimer, which occurs by three-body collisions, cluster-splitting nucleation is a second-order reaction. The most important cluster-splitting reaction is the collision of a vapor atom and a trimer that leads to the formation of two dimers. The importance of the cluster-splitting nucleation channel relative to the direct vapor nucleation channel is observed to increase with decreasing vapor density and increasing ratio of vapor to carrier gas atoms. read less USED (high confidence) T. Zhu, J. Li, and S. Yip, “Atomistic configurations and energetics of crack extension in silicon.,” Physical review letters. 2004. link Times cited: 59 Abstract: We report the first atomistic determination of the minimum e… read moreAbstract: We report the first atomistic determination of the minimum energy path for a series of bond ruptures to advance a crack front. Saddle-point configurations on (111) cleavage planes in Si reveal a steplike distribution of atomic displacements, implying a kink mechanism which is known to control dislocation mobility. Manifestations of lattice trapping and directional cleavage anisotropy are further elucidated. read less USED (high confidence) P. Beaucage and N. Mousseau, “Nucleation and crystallization process of silicon using the Stillinger-Weber potential,” Physical Review B. 2004. link Times cited: 28 Abstract: We study the homogeneous nucleation process in Stillinger-We… read moreAbstract: We study the homogeneous nucleation process in Stillinger-Weber silicon in the canonical ensemble. A clear first-order transition from the liquid to crystal phase is observed thermodynamically with kinetic and structural evidence of the transformation. At 0.75Tm, the critical cluster size is about 175 atoms. The lifetime distribution of clusters as a function of the maximum size they reach follows an inverse Gaussian distribution as was predicted recently from the classical theory of nucleation ! CNT" . However, while there is a qualitative agreement with the CNT, the free-energy curve obtained from the simulations differs significantly from the theoretical predictions, suggesting that the low-density liquid phase found recently could play a role at the interface between the crystallite and the surrounding liquid during the nucleation process. read less USED (high confidence) M. Okuniewski, Y. Ashkenazy, B. Heuser, and R. Averback, “Molecular dynamics simulations of void and helium bubble stability in amorphous silicon during heavy-ion bombardment,” Journal of Applied Physics. 2004. link Times cited: 13 Abstract: A study of void and helium (He) bubble stability in amorphou… read moreAbstract: A study of void and helium (He) bubble stability in amorphous silicon (a-Si) subjected to heavy-ion bombardment was conducted with molecular dynamics simulations. The effects of incident ion energy, incident ion direction, and He pressure were investigated. He bubbles with pressures equal to or greater than 0.1kbar were found to be stable during isotropic 2keV xenon (Xe) irradiation. Bubbles with pressures below this limit collapsed completely. On the other hand, voids and bubbles of all pressures were stable following unidirectional 2keV Xe bombardment. In this case, the voids and bubbles became elongated and resisted closure, a phenomenon attributed to the inability of liquid Si to wet the flat, low-curvature internal surfaces of the open-volume defect. The void closure rates varied from 55 to 180A∕dpa as the Xe projectile energy increased from 0.2keV to 2keV, respectively. An analytical model based on a viscous flow mechanism is presented to describe the behavior associated with the slowest closure rat... read less USED (high confidence) P. Lorazo, D. Perez, L. J. Lewis, and M. Meunier, “Thermodynamics of absorbing solids during short-pulse laser ablation,” SPIE High-Power Laser Ablation. 2004. link Times cited: 4 Abstract: The fundamental mechanisms of matter removal involved in the… read moreAbstract: The fundamental mechanisms of matter removal involved in the interaction of short laser pulses with absorbing solids have been investigated using molecular-dynamics/Monte~Carlo simulations. This is accomplished under the two following assumptions: (i) the elementary thermodynamic properties of targets (metals and semiconductors) are adequately described by empirical potentials; (ii) in the regime where ablation is thermal, the complete time evolution of the system can be followed in p-T-P space and the result mapped onto the equilibrium phase diagram of the material. We find remarkable similarities in the physical pathways to ablation in metals and semiconductors for pulse durations ranging from 200 fs to 400 ps: (i) under conditions of isochoric heating and rapid adiabatic cooling with femtosecond pulses, several mechanisms can simultaneously account for matter removal in the target: spallation, phase explosion, vaporization, and fragmentation; the latter is identified for the first time in the context of laser ablation. (ii) Under nonadiabatic cooling with picosecond pulses, ablation is driven by a "trivial" fragmentation process in the metallic, supercritical fluid; this suggests a pulse duration upper limit for phase explosion of ~ 10-11 s. read less USED (high confidence) J. K. Christie, S. Taraskin, and S. Elliott, “Atomic vibrations in disordered systems: Comparison of disordered diamond lattices and a realistic amorphous silicon model,” Physica Status Solidi (c). 2004. link Times cited: 1 Abstract: Force-constant and positional disorder have been introduced … read moreAbstract: Force-constant and positional disorder have been introduced into diamond lattice models in an attempt to mimic the vibrational properties of a realistic amorphous silicon model. Neither type of disorder is sufficient on its own to mimic the realistic model. By comparing the spectral densities of these models, it is shown that a combination of both disorders is a better representation, but still not completely satisfactory. Topological disorder in these models was investigated by renumbering the atoms and examining the dynamical matrix graphically. The dynamical matrix of the realistic model is similar to that of a positionally-disordered lattice model, implying that the short-range order in both systems is similar. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) read less USED (high confidence) E. Reed, L. Fried, M. Manaa, and J. Joannopoulos, “A multi-scale approach to molecular dynamics simulations of shock waves.” 2004. link Times cited: 22 USED (high confidence) P. Beaucage and N. Mousseau, “Liquid–liquid phase transition in Stillinger–Weber silicon,” Journal of Physics: Condensed Matter. 2004. link Times cited: 39 Abstract: It was recently demonstrated that Stillinger–Weber silicon u… read moreAbstract: It was recently demonstrated that Stillinger–Weber silicon undergoes a liquid–liquid first-order phase transition deep into the supercooled region (Sastry and Angell 2003 Nat. Mater. 2 739). Here we study the effects of perturbations on this phase transition. We show that the order of the liquid–liquid transition changes with negative pressure. We also find that the liquid–liquid transition disappears when the three-body term of the potential is strengthened by as little as 5%. This implies that the details of the potential could affect strongly the nature and even the existence of the liquid–liquid phase. read less USED (high confidence) P. Schelling, S. Phillpot, and P. Keblinski, “Kapitza conductance and phonon scattering at grain boundaries by simulation,” Journal of Applied Physics. 2004. link Times cited: 225 Abstract: We use a nonequilibrium molecular-dynamics method to compute… read moreAbstract: We use a nonequilibrium molecular-dynamics method to compute the Kapitza resistance of three twist grain boundaries in silicon, which we find to increase significantly with increasing grain boundary energy, i.e., with increasing structural disorder at the grain boundary. The origin of this Kapitza resistance is analyzed directly by studying the scattering of packets of lattice vibrations of well-defined polarization and frequency from the grain boundaries. We find that scattering depends strongly on the wavelength of the incident wave packet. In the case of a high-energy grain boundary, the scattering approaches the prediction of the diffuse mismatch theory at high frequencies, i.e., as the wavelength becomes comparable to the lattice parameter of the bulk crystal. We discuss the implications of our results in terms of developing a general model of scattering probabilities that can be applied to mesoscale models of heat transport in polycrystalline systems. read less USED (high confidence) S. Ogata, F. Shimojo, R. Kalia, A. Nakano, and P. Vashishta, “Environmental effects of H2O on fracture initiation in silicon: A hybrid electronic-density-functional/molecular-dynamics study,” Journal of Applied Physics. 2004. link Times cited: 45 Abstract: A hybrid quantum-mechanical/molecular-dynamics simulation is… read moreAbstract: A hybrid quantum-mechanical/molecular-dynamics simulation is performed to study the effects of environmental molecules on fracture initiation in silicon. A (110) crack under tension (mode-I opening) is simulated with multiple H2O molecules around the crack front. Electronic structure near the crack front is calculated with density functional theory. To accurately model the long-range stress field, the quantum-mechanical description is embedded in a large classical molecular-dynamics simulation. The hybrid simulation results show that the reaction of H2O molecules at a silicon crack tip is sensitive to the stress intensity factor K. For K=0.4 MPa⋅m, an H2O molecule either decomposes and adheres to dangling-bond sites on the crack surface or oxidizes Si, resulting in the formation of a Si–O–Si structure. For a higher K value of 0.5 MPa⋅m, an H2O molecule either oxidizes or breaks a Si–Si bond. read less USED (high confidence) J. Bai, X. Zeng, H. Tanaka, and J. Zeng, “Metallic single-walled silicon nanotubes.,” Proceedings of the National Academy of Sciences of the United States of America. 2004. link Times cited: 117 Abstract: Atomistic computer-simulation evidences are presented for th… read moreAbstract: Atomistic computer-simulation evidences are presented for the possible existence of one-dimensional silicon nanostructures: the square, pentagonal, and hexagonal single-walled silicon nanotubes (SWSNTs). The local geometric structure of the SWSNTs differs from the local tetrahedral structure of cubic diamond silicon, although the coordination number of atoms of the SWSNTs is still fourfold. Ab initio calculations show that the SWSNTs are locally stable in vacuum and have zero band gap, suggesting that the SWSNTs are possibly metals rather than wide-gap semiconductors. read less USED (high confidence) K. Tatsumura, T. Watanabe, D. Yamasaki, T. Shimura, M. Umeno, and I. Ohdomari, “Residual order within thermally grown amorphous SiO2 on crystalline silicon,” Physical Review B. 2004. link Times cited: 34 Abstract: The origin of x-ray diffraction peaks observed on the crysta… read moreAbstract: The origin of x-ray diffraction peaks observed on the crystal truncation rods (CTR's) in reciprocal space for thermally grown ${\mathrm{SiO}}_{2}$ films has been investigated by large-scale atomistic simulation of silicon oxidation. Three models of ${\mathrm{SiO}}_{2}$ on Si(001), Si(111), and Si(113) were formed by introducing oxygen atoms in crystalline Si from the surfaces in an atom-by-atom manner. The ${\mathrm{SiO}}_{2}$ structures are classified as being amorphous in conventional characterizations, but retain the residual order originating from the {111} atomic planes in their parent crystals. The calculated diffraction patterns exhibit intensity peaks with Laue-function-like fringe profiles along the CTR's, at positions depending on the substrate orientations, agreeing quite well with experimental results. read less USED (high confidence) S. Yoo, X. Zeng, and J. R. Morris, “The melting lines of model silicon calculated from coexisting solid-liquid phases.,” The Journal of chemical physics. 2004. link Times cited: 76 Abstract: The molecular-dynamics simulation approach [Morris and Song,… read moreAbstract: The molecular-dynamics simulation approach [Morris and Song, J. Chem. Phys. 116, 9352 (2002)] is employed to calculate the melting lines for two model systems of silicon: the Stillinger–Weber (SW) model and the Tersoff-89 model. To address the anisotropic stress problem indicated in the previous paper, a slightly improved simulation procedure is used to prepare the coexisting solid and liquid phases at the thermodynamic equilibrium. For the SW silicon, the calculated melting temperature Tm at zero pressure agrees with that based on the free-energy calculation [Broughton and Li, Phys. Rev. B 35, 9120 (1987)]. The dependence of Tm at zero pressure on the selected solid surface orientation is also examined. The relative difference between Tm calculated based on the sharp Si (111)/liquid interface and the faceted Si (100)/liquid interface is less than 1%. Both models predict that the melting line exhibits a negative slope, which is consistent with the fact that the molar volume of the solid is larger than tha... read less USED (high confidence) X. Su, R. Kalia, A. Nakano, P. Vashishta, and A. Madhukar, “InAs/GaAs square nanomesas: Multimillion-atom molecular dynamics simulations on parallel computers,” Journal of Applied Physics. 2003. link Times cited: 11 Abstract: A model potential for GaAs(100) and InAs(100) surface atoms … read moreAbstract: A model potential for GaAs(100) and InAs(100) surface atoms is developed and surface reconstructions on GaAs(100) and InAs(100) are studied with the conjugate gradient (CG) method. Not only does this model reproduce well surface energies for the (100) orientation, it also yields (1×2) dimer lengths in accordance with ab initio calculations. Large-scale molecular dynamics (MD) simulations are performed to investigate mechanical stresses in InAs/GaAs nanomesas with {101}-type sidewalls. The in-plane lattice constant of InAs layers parallel to the InAs/GaAs(001) interface are found to exceed the InAs bulk value at the twelfth monolayer (ML) and the hydrostatic stresses in InAs layers become tensile above 12 ML. Hence, it is energetically unfavorable for InAs overlayers to exceed 12 ML. This may explain the experimental finding that the growth of flat InAs overlayers is self-limiting to ∼11 ML on GaAs nanomesas. MD simulations are also used to investigate the lateral size effects on the stress distribution an... read less USED (high confidence) L. Nurminen, F. Tavazza, D. Landau, A. Kuronen, and K. Kaski, “Reconstruction and intermixing in thin Ge layers on Si(001),” Physical Review B. 2003. link Times cited: 16 Abstract: In this work the Monte Carlo method with an empirical potent… read moreAbstract: In this work the Monte Carlo method with an empirical potential model for atomic interactions is applied to study reconstruction and intermixing at a Ge-covered Si(001) surface. We investigate the structure and energetics of the $2\ifmmode\times\else\texttimes\fi{}n$ reconstruction which serves as a strain-relief mechanism. The optimal value of n is found to be strongly dependent on the thickness of the Ge overlayer. Si-Ge intermixing is studied using a direct simulation method which includes entropic effects. Ge occupation probabilities in subsurface layers are evaluated as a function of Ge coverage at different temperatures. The results show that strain-relief driven intermixing has a pronounced effect on the surface reconstruction once the Ge coverage reaches a full layer. We also evaluate the effect of temperature on the distribution of Ge in subsurface layers and discuss effects due to kinetic limitations. In agreement with experiments, the study provides a description of the interplay between reconstruction and intermixing at Ge-covered Si(001). read less USED (high confidence) T. Aoki, J. Matsuo, G. Takaoka, N. Toyoda, and I. Yamada, “Defect characteristics by boron cluster ion implantation,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2003. link Times cited: 13 USED (high confidence) P. Schelling and S. Phillpot, “Multiscale simulation of phonon transport in superlattices,” Journal of Applied Physics. 2003. link Times cited: 55 Abstract: A particle-based model for phonon transport and the scatteri… read moreAbstract: A particle-based model for phonon transport and the scattering of phonon wave packets at interfaces is developed. The model, which incorporates the interference effects associated with the wave nature of phonons, is parametrized with frequency-dependent scattering rates obtained from molecular-dynamics simulations of the interaction of phonon wave packets with a single interface. From simulations of scattering of phonon wave packets from superlattices, we find that when the interference effects are not included there is qualitative disagreement between the molecular-dynamics and particle simulations. Moreover, we show that such interference effects tend to result in a larger amount of energy being transmitted through a superlattice. read less USED (high confidence) T. Aoki, J. Matsuo, and G. Takaoka, “Molecular dynamics study of damage formation characteristics by large cluster ion impacts,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2003. link Times cited: 45 USED (high confidence) A. Kubota et al., “Threats to ICF reactor materials: computational simulations of radiation damage induced topological changes in fused silica,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2003. link Times cited: 11 USED (high confidence) L. Pizzagalli, P. Beauchamp, and J. Rabier, “Stability and core structure of undissociated screw dislocations in group IV materials investigated by means of atomistic calculations,” Journal of Physics: Condensed Matter. 2002. link Times cited: 11 Abstract: We have examined the various possible configurations for an … read moreAbstract: We have examined the various possible configurations for an undissociated screw dislocation in group IV materials (Ge, Si, 3C-SiC, diamond) by means of semi-empirical atomistic calculations. A complete structural characterization and a determination of the relative stability are performed. We found that, in contrast to the case for Ge and Si, a geometry with the presence of sp 2 atoms in th ec ore is the most stable structure for 3C-SiC and diamond. This yields a stable screw dislocation configuration i nt he ‘shuffle’ set for Si and Ge, and in th e‘ glide’ set for 3C-SiC and diamond. read less USED (high confidence) S. Ogata, F. Shimojo, R. Kalia, A. Nakano, and P. Vashishta, “Hybrid quantum mechanical/molecular dynamics simulation on parallel computers: density functional theory on real-space multigrids,” Computer Physics Communications. 2002. link Times cited: 56 USED (high confidence) I. Markov and J. Prieto, “Dislocation-Free 3D Islands in Highly Mismatched Epitaxy: An Equilibrium Study With Anharmonic Interactions,” arXiv: Materials Science. 2002. link Times cited: 2 USED (high confidence) R. Shetty, F. Escobedo, D. Choudhary, and P. Clancy, “A novel algorithm for characterization of order in materials,” Journal of Chemical Physics. 2002. link Times cited: 14 Abstract: In this work, we present a simple approach for devising orde… read moreAbstract: In this work, we present a simple approach for devising order parameters (OPs) for atomic systems based on pattern recognition techniques. It exploits the fact that all crystalline substances are characterized by a unique “signature” cell (SC) which is constructed using a central atom and its nearest NSC neighbors in a given crystal. The algorithm measures the local degree of similarity between a SC and the system to be analyzed. The best fit of a SC to NSC atoms surrounding a given atom in the system is determined by maximizing a fictitious energy of binding among those atoms and the SC atoms. The fictitious potential energy is designed to give maximum attractive energy for maximum overlap. The maximum binding energy of interaction attained in this process is used as a measure of similarity between the crystal structure and the system (i.e., as an OP). The proposed method provides a unified and intuitive approach for constructing relevant OPs for a given system. We used these OPs to characterize the orde... read less USED (high confidence) D. Humbird and D. Graves, “Controlling surfaces in plasma processing: role of ions via molecular dynamics simulations of surface chemistry,” Plasma Sources Science and Technology. 2002. link Times cited: 13 Abstract: A study of the interactions of energetic ions with various s… read moreAbstract: A study of the interactions of energetic ions with various surfaces using molecular dynamics simulations is reported. Silicon atoms in the amorphous region are readily mixed by argon ions. Limited mixing in the crystalline layer is observed. Fluorine adsorbed on the silicon surface does not mix into the layer with argon ion impact. When an energetic F+ impacts a silicon surface, the uptake and apparent sub-surface mixing of F is much greater than Ar+-induced mixing. However, a closer examination shows that the F impacts have primarily increased the Si surface area by creating crevices and cracks, and that the F remains mainly on the surface of this layer. read less USED (high confidence) K. A. Jackson, “The Interface Kinetics of Crystal Growth Processes,” Interface Science. 2002. link Times cited: 124 USED (high confidence) P. Schelling, S. Phillpot, and P. Keblinski, “Phonon wave-packet dynamics at semiconductor interfaces by molecular-dynamics simulation,” Applied Physics Letters. 2002. link Times cited: 285 Abstract: We directly observe phonon wave packets of well-defined freq… read moreAbstract: We directly observe phonon wave packets of well-defined frequency and polarization scattering at a coherent semiconductor interface using molecular-dynamics simulations. We find that in the low-frequency limit the transmission coefficients of both longitudinal and transverse acoustic phonons agree well with those predicted by the continuum-level based acoustic mismatch model. However, the transmission coefficients rapidly decrease close to the cutoff frequency, a result that can be understood within a simple one-dimensional discrete atomic-chain model. We also find that the transmission coefficient for transverse acoustic phonons depends strongly on the relative orientation of the polarization and the Si-Si bonds in the diamond lattice structure. read less USED (high confidence) K. Nordlund, “Diffuse x-ray scattering from 311 defects in Si,” Journal of Applied Physics. 2002. link Times cited: 5 Abstract: 311 defects are extended, rodlike defects that play a centra… read moreAbstract: 311 defects are extended, rodlike defects that play a central role in the processing of Si during integrated circuit manufacturing. Diffuse x-ray scattering techniques provide a nondestructive means to detect defects in solids. However, to date there has been no knowledge of what the x-ray scattering pattern from 311 defects looks like. Using a recently introduced fully atomistic modeling scheme, the diffuse x-ray scattering patterns were calculated from 311 defects. The results demonstrate how 311 defects can be detected, how the main varieties of 311 defect can be distinguished, and how both the defect width and length can be derived from the scattering. read less USED (high confidence) A. Charaï et al., “Structural change induced on an atomie scale by equilibrium sulphur segregation in tilt germanium grain boundaries,” Philosophical Magazine B. 2001. link Times cited: 1 Abstract: In the present study, structural modifications induced by ea… read moreAbstract: In the present study, structural modifications induced by eauilibrium sulphur segregation in pure tilt germanium {710}<001>, ∑=25 (θ=16.26°) and {551}<011>, ∑=51 (θ=16.10°) grain boundaries (GBs) were investigated using high-resolution electron microscopy coupled to electron-energy-loss spectroscopy and supported by structural modelling and image simulations. Our results showed that the as-grown ∑=25 GB is composed of two parts: a stable structural region and a variable perturbed core. On the basis of our simulations, it is shown that this boundary can only be formed by a multiplicity of configurations which are energetically close to each other but differently configured along the boundary plane. When sulphurized, drastic changes in the structure of the GB were observed. Energy-filtered electron microscopy imaging revealed a sulphur enrichment at the perturbed part of the boundary. Although sulphur segregation at the boundary is detected, no information can at the present stage be extracted on segregation sites and bonding configurations because of the complexity of the boundary structure. To simplify this aspect, a simpler GB, that is germanium ∑=51, was studied. The structure of such a GB is a well-known configuration, that is a Lomer dislocation, which is basically a fivefold ring adjacent to a sevenfold ring. After sulphur treatment, high-resolution electron microscopy imaging also shows significant contrast modifications apparently concentrated on the dislocation core. Chemical imaging indicates again the presence of sulphur enrichment along the boundary plane strongly sustaining that eauilibrium sulphur segregation in the Ge(S) system oceurs into the GB and therefore confirms our previous results on the ∑= 25 GB. One can therefore argue that it is the presence of those odd-membered rings at the boundary, which should possess a specific crystallographic and electronic nature, coupled to the electronic properties of sulphur, that are responsible for the preferential segregation into the boundary. read less USED (high confidence) D. Wales, “A Microscopic Basis for the Global Appearance of Energy Landscapes,” Science. 2001. link Times cited: 200 Abstract: It is shown that the appearance of a multidimensional potent… read moreAbstract: It is shown that the appearance of a multidimensional potential energy surface, or potential energy landscape, can be related to the form of the interatomic or intermolecular potential. Catastrophe theory enables us to describe how the geometry of the surface changes with parameters in the potential, and provides universal scaling relations that explain, for example, the asymmetric reaction profiles observed for systems bound by long-range forces. The principal result is an unexpected connection between barrier heights, path lengths, and vibrational frequencies, with applications to a wide variety of problems in chemical physics, ranging from Hammond's postulate in organic chemistry, to the relaxation dynamics of complex systems such as glasses and biomolecules. read less USED (high confidence) A. Gannepalli and S. Mallapragada, “Molecular dynamics studies of plastic deformation during silicon nanoindentation,” Nanotechnology. 2001. link Times cited: 44 Abstract: Molecular dynamics studies are performed to investigate the … read moreAbstract: Molecular dynamics studies are performed to investigate the evolution of the deformed region during nanoindentation of silicon. A new approach based on a local strain diagnostic to identify and characterize the plastic rearrangements occurring during indentation is presented. During indentation, the response of the substrate changes from elastic to plastic to relieve the accumulated stress. The plastic rearrangements involve the displacement of atoms from the lattice sites to interstitial sites. The formation of interstitials results in the transformation of the deformed region to a denser amorphous phase. During retraction of the tip, the deformed region undergoes an incomplete elastic recovery signifying the plastic nature of rearrangements. read less USED (high confidence) C. Herrero, “Quantum atomistic simulations of silicon and germanium,” Journal of Materials Research. 2001. link Times cited: 4 Abstract: Quantum atomistic simulations of crystalline silicon and ger… read moreAbstract: Quantum atomistic simulations of crystalline silicon and germanium have been carried out by the path-integral Monte Carlo method. The interatomic interactions were modeled by Stillinger–Weber-type potentials, with parameters adequate to quantum simulations. Quantum zero-point motion together with anharmonicity of the interatomic potential led to a lattice expansion of 7 × 10^−3 Å for both Si and Ge. Results for the equation-of-state (volume versus pressure) and for the thermal expansion coefficient agreed well with experimental results for both materials at T > 100 K and for hydrostatic pressures up to 100 kbar. read less USED (high confidence) T. Aoki, S. Chiba, J. Matsuo, I. Yamada, and J. Biersack, “Molecular dynamics and Monte-Carlo simulation of sputtering and mixing by ion irradiation,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2001. link Times cited: 21 USED (high confidence) D. Drakova, “Theoretical modelling of scanning tunnelling microscopy, scanning tunnelling spectroscopy and atomic force microscopy,” Reports on Progress in Physics. 2001. link Times cited: 77 Abstract: The capability of the atomic force microscope (AFM) and the … read moreAbstract: The capability of the atomic force microscope (AFM) and the scanning tunnelling microscope (STM) to image surfaces with atomic resolution is still amazing us. Theory has been for a long time and in certain respects remains to the present day in debt to experiment. The aim of this review is to describe the development of theoretical models of the AFM, which serves both as an imaging tool and as a tool for manipulating atoms and molecules at surfaces. Models based on classical and quantum mechanical treatment of tip-sample interaction in the AFM are reviewed with emphasis on the explanations of atomic resolution that they provide. The attempts to understand atomic resolution in the STM on metal surfaces started with the local charge-density concept; however, even exact theories based on three-dimensional scattering theory, using different models for the tip and the sample, cannot provide an understanding of the large corrugation amplitudes of the tip height in the constant-current scanning mode in STM on densely packed metal surfaces. A recently developed dynamic theory of STM, regarding the tunnelling as an excited-state property of the interacting tip-plus-sample system, provides an insight into the physical background of atomic resolution in these cases. Other issues in the theory of STM and scanning tunnelling spectroscopy (STS) addressed relate to the equivalence of the current-density formulation of STM theory and the generalized Ehrenfest theorem, tunnelling via surface states and resonances, the mirror theorem of STS, image reversal in STM, many-particle effects in STM. With the prospect of converting the AFM and STM into tools for surface technology on the nanoscopic scale, theory will be challenged to suggest models going beyond the single-particle approaches and the adiabatic approximation. read less USED (high confidence) K. Edagawa, H. Koizumi, Y. Kamimura, and T. Suzuki, “Temperature dependence of the flow stress of III–V compounds,” Philosophical Magazine A. 2000. link Times cited: 19 Abstract: An interpretation for the temperature dependence of the plas… read moreAbstract: An interpretation for the temperature dependence of the plastic flow stress of III–V compounds is presented, invoking only non-dissociated screw dislocations. With the aid of the Stillinger-Weber potential for the interatomic interaction, the Peierls potential of a non-dissociated screw dislocation is deduced in twodimensional space normal to the dislocation line. A saddle-point configuration and the formation energy of a kink pair are calculated in three-dimensional space. The relation obtained between the flow stress T c and temperature T under a constant strain rate describes the experimental T c−T relation of III–V compound well: a strong T dependence at highT c and low T, a stronger T dependence at low Tc and high T, and a plateau-like T c at intermediate T. The hump in the T c−T relation is interpreted as a transition between different paths of the non-dissociated screw dislocation: a planar path and a zigzag path in the (111) plane. read less USED (high confidence) H.-C. Huang and G. Gilmer, “Atomistic simulation of texture competition during thin film deposition,” Journal of Computer-Aided Materials Design. 2000. link Times cited: 18 USED (high confidence) H. Lu and J. Y. Feng, “Molecular-dynamics simulation of Ge film growth by cluster deposition,” Modelling and Simulation in Materials Science and Engineering. 2000. link Times cited: 6 Abstract: Ge thin-film growth from cluster beams has been investigated… read moreAbstract: Ge thin-film growth from cluster beams has been investigated with molecular-dynamics simulations utilizing the Stillinger-Weber two- and three-body interaction potentials. The spreading of Ge-atom clusters and the structure of grown films have been studied as a function of incident cluster velocity. Higher surface diffusion and spreading of the deposited clusters were achieved with a moderate cluster velocity. The epitaxial Ge (111) growth was obtained under this cluster velocity. read less USED (high confidence) A. Abdurixit, A. Baratoff, and E. Meyer, “Molecular dynamics simulations of dynamic force microscopy: applications to the Si(111)-7×7 surface,” Applied Surface Science. 2000. link Times cited: 38 USED (high confidence) S. Brochard, P. Beauchamp, and J. Grilhé, “Dislocation nucleation from surface steps: Atomistic simulation in aluminium,” Philosophical Magazine A. 2000. link Times cited: 44 Abstract: The possible role of surface steps in the nucleation of disl… read moreAbstract: The possible role of surface steps in the nucleation of dislocations from a free surface has been studied by means of a static atomistic simulation using a many-body potential for aluminium. The fcc crystal with a {100} free surface containing a monatomic step lying along a (110) dense direction is submitted to an increasing uniaxial stress along a direction belonging to the {100} plane. For a sufficiently high applied stress, well below the theoretical strength. dislocations are nucleated at the step and glide in the {111} planes emerging at the step. The effect of a stress orientation is examined. The type of dislocation formed. that is Shockley partials of 90° and 30° character or perfect dislocations, is rationalized by considering the resolved shear stress in the {111} planes. The plane where glide will occur is favoured well before nucleation; a shear of increasing amplitude and extension is progressively localized on this plane. The role of the stress field due to the step, in the formation of the localized shear, is discussed. read less USED (high confidence) J. Kang, E. Kang, M. Son, and H. Hwang, “Ultra-low-energy ion-implant simulation using computational-efficient molecular dynamics schemes and the local damage accumulation model,” Journal of Vacuum Science & Technology B. 2000. link Times cited: 2 Abstract: We have investigated effects of atomic dynamics for ultra-lo… read moreAbstract: We have investigated effects of atomic dynamics for ultra-low-energy As and B ion implants using a highly efficient molecular dynamics scheme. We simulated ion implantation by molecular dynamics simulation using the recoil ion approximation method and the local damage accumulation model proposed in the article. The Local damage accumulation probability function consists of deposited energy in a unit cell, implant dose rate, target material, projectile atom, and the history of the recoil event in a cell. The results of simulations agree with the experimental results. The MDRANGE results considering no damage were different from the tail region. Using the local damage accumulation model and the recoil ion approximation method, we simulated dopant two-dimensional profiles and two-dimensional damage profiles. read less USED (high confidence) P. B. Allen, J. Feldman, J. Fabian, and F. Wooten, “Diffusons, locons and propagons: Character of atomie yibrations in amorphous Si,” Philosophical Magazine Part B. 1999. link Times cited: 352 Abstract: Numerical studies of amorphous Si show that the lowest 4% of… read moreAbstract: Numerical studies of amorphous Si show that the lowest 4% of vibrational modes are piane wave like (‘propagons’) and the highest 3% of modes are localized (‘locons’). The rest are neither piane wave like nor localized. We cali them ‘diffusons’. Since diffusons are by far the most numerous, we try to characterize them by calculating such properties as the wave-vector and polarization (which do not seem to be useful), ‘phase auotient’ (a measure of the change of vibrational phase between first-neighbour atoms), spadal polarization memory and diffusivity. Localized states are characterized by finding decay lengths, inverse participation ratios and coordination numbers of the participating atoms. read less USED (high confidence) A. Buldum, S. Ciraci, and C. Y. Fong, “Quantum heat transfer through an atomic wire,” Journal of Physics: Condensed Matter. 1999. link Times cited: 18 Abstract: We studied the phononic heat transfer through an atomic diel… read moreAbstract: We studied the phononic heat transfer through an atomic dielectric wire with both infinite and finite lengths by using a model Hamiltonian approach. At low temperature under ballistic transport, the thermal conductance contributed by each phonon branch of a uniform and harmonic chain cannot exceed the well known value which depends linearly on temperature but is material independent. We predict that this ballistic thermal conductance will exhibit stepwise behaviour as a function of temperature. By performing numerical calculations on more realistic systems, where small atomic chains are placed between two reservoirs, we also found resonant modes, which should also lead to stepwise behaviour in the thermal conductance. read less USED (high confidence) D. Wolff and W. Rudd, “Tabulated potentials in molecular dynamics simulations,” Computer Physics Communications. 1999. link Times cited: 36 USED (high confidence) J. Finder, D. Richards, and J. B. Adams, “A molecular dynamics study of defect production due to low-energy collisions,” Modelling and Simulation in Materials Science and Engineering. 1999. link Times cited: 3 Abstract: Molecular dynamics (MD) simulations of collision cascades we… read moreAbstract: Molecular dynamics (MD) simulations of collision cascades were studied in order to understand the effect of energy, temperature and direction of the primary knock-on atom (PKA) on the defect production in single crystal silicon for low-energy collision events. MD simulations were performed with ion energies ranging from 100 eV to 1 keV where the PKA was directed along the three major crystallographic directions at 0, 300 and 600 K. Collision cascades resulting from PKA energies above 100 eV appeared to undergo a solid- to liquid-like transformation at the height of the cascade event. Upon cooling, the liquid-like regions collapse resulting in the formation of numerous isolated defects and clusters of defects. We found that bulk and near-surface collision events followed the modified Kinchin-Pease model for defect production in silicon for the energies studied. Minimal temperature dependence was found for collision events that occurred in the bulk of the silicon crystal within the first 10 ps of the simulation. read less USED (high confidence) M. Doyama, “Creation and motion of dislocations and fracture in metal and silicon crystals,” Bulletin of Materials Science. 1999. link Times cited: 0 USED (high confidence) J. Q. Xie, J. Feng, and H. Lu, “Molecular-dynamics simulation of low-temperature growth of silicon films by cluster deposition,” Modelling and Simulation in Materials Science and Engineering. 1999. link Times cited: 8 Abstract: Silicon thin-film growth from cluster beams at a substrate t… read moreAbstract: Silicon thin-film growth from cluster beams at a substrate temperature of 300 K has been investigated with molecular-dynamics simulations utilizing the Stillinger-Weber two- and three-body interaction potential. The spreading of Si-atom clusters and the structure of grown films have been studied as a function of the incident cluster velocity. Our simulation results show that the films grown at a low substrate temperature of 300 K are amorphous and the substrates suffer heavier damage with an increase in the cluster velocity. As compared with our previous results on Si thin-film growth at a substrate temperature of 1000 K, we found that substrate temperature and cluster velocity had a significant impact in determining the structure of the grown films and the cluster spreading on the substrate. read less USED (high confidence) P. Keblinski, D. Wolf, S. Phillpot, and H. Gleiter, “Role of bonding and coordination in the atomic structure and energy of diamond and silicon grain boundaries,” Journal of Materials Research. 1998. link Times cited: 59 Abstract: The high-temperature equilibrated atomic structures and ener… read moreAbstract: The high-temperature equilibrated atomic structures and energies of large-unit-cell grain boundaries (GB’s) in diamond and silicon are determined by means of Monte-Carlo simulations using Tersoff’s potentials for the two materials. Silicon provides a relatively simple basis for understanding GB structural disorder in a purely sp ^3 bonded material against which the greater bond stiffness in diamond combined with its ability to change hybridization in a defected environment from sp ^3 to sp ^2 can be elucidated. We find that due to the purely sp ^3-type bonding in Si, even in highly disordered, high-energy GB’s at least 80% of the atoms are fourfold coordinated in a rather dense confined amorphous structure. By contrast, in diamond even relatively small bond distortions exact a considerable price in energy that favors a change to sp ^2-type local bonding; these competing effects translate into considerably more ordered diamond GB’s; however, at the price of as many as 80% of the atoms being only threefold coordinated. Structural disorder in the Si GB’s is therefore partially replaced by coordination disorder in the diamond GB’s. In spite of these large fractions of three-coordinated GB carbon atoms, however, the three-coordinated atoms are rather poorly connected amongst themselves, thus likely preventing any type of graphite-like electrical conduction through the GB’s. read less USED (high confidence) S. Bickham and J. Feldman, “Molecular dynamics simulations of vibrational lifetimes in amorphous silicon,” Philosophical Magazine Part B. 1998. link Times cited: 3 Abstract: Recent theoretical and time resolved Raman studies disagree … read moreAbstract: Recent theoretical and time resolved Raman studies disagree on the lifetime of high energy vibrational modes in amorphous silicon. The latter suggests that the lifetime increases with increasing frequency and is of the order of 10 ns for the highest frequency modes, while the former predicts a picosecond timescale that follows the two-phonon density of states. Here we present the results of molecular dynamics simulations which are complementary to the perturbative calculations. At different temperatures, kinetic energy is put into selected modes of vibration in 216 and 4096 atom systems with periodic boundary conditions and the Stillinger—Weber potential. The lifetime of medium and high frequency modes is found to be of the order of 1 ops at 5, 10 and 30 K, in qualitative agreement with the perturbative calculations. read less USED (high confidence) K. Nordlund, R. Averback, and T. D. Rubia, “Effect of atomic bonding on defect production in collision cascades,” MRS Proceedings. 1997. link Times cited: 0 Abstract: We study the mechanisms of damage production during ion irra… read moreAbstract: We study the mechanisms of damage production during ion irradiation using molecular dynamics simulations of 400 eV 10 keV collision cascades in four different mater ials. The materials Al, Si, Cu and Ge are contrasted to each other with respect to the mass, melting temperature and crystal structure. The results show that the crystal struc ture clearly has the strongest effect on the nature of the damage produced, and elucidate how the open crystal structure affects the nature of defects produced in silicon. read less USED (high confidence) K. Kilian and J. B. Adams, “First-principles simulations of a-Si:H surfaces,” Modelling and Simulation in Materials Science and Engineering. 1997. link Times cited: 2 Abstract: We have constructed atomistic models of a-Si:H surfaces whic… read moreAbstract: We have constructed atomistic models of a-Si:H surfaces which differ in their bulk H concentration. The models are constructed by cleaving bulk a-Si:H structures and passivating the new surfaces with H. We analyse the geometric and electronic structure of each surface and compare them. These models will be useful for future studies of chemical reactions on the surface. read less USED (high confidence) R. Ramírez, “Efficient calculation of free-energy barriers in quantum activated processes. A path-integral centroid approach,” Journal of Chemical Physics. 1997. link Times cited: 7 Abstract: The key quantity in the study of rates of activated processe… read moreAbstract: The key quantity in the study of rates of activated processes by the quantum transition-state theory based on the Feynman path-integral formulation is a free-energy barrier associated to a reaction coordinate. The free-energy barrier represents the reversible work done against the quantum potential of mean force acting on thermal paths whose centroid (center of mass) is held fixed, along a reaction coordinate defined by the centroid. A reversible thermodynamic cycle leads to a simple method to calculate this barrier by thermodynamic integration. The capability of the method is demonstrated in three models: a flux of protons impinging on a symmetric Eckart barrier; a particle in a double-well potential; and a point defect in a silicon lattice. Analysis of the temperature dependence of the free-energy barrier shows a crossover from a high-temperature regime, where the potential energy increment gives a good approximation to the barrier, to a low-temperature one, where the barrier is close to the difference ... read less USED (high confidence) D. Belashchenko, “Computer simulation of the structure and properties of non-crystalline oxides,” Russian Chemical Reviews. 1997. link Times cited: 61 Abstract: The results of the studies of the structure and properties o… read moreAbstract: The results of the studies of the structure and properties of non-crystalline (liquid and amorphous) oxide systems obtained using computer simulation methods are summarised. The models of simple oxides, homologous series of non-crystalline oxides and of binary and multi-component oxide systems are considered. The results of the simulation of the ion transfer are discussed. The ionic theory of oxides allows one to predict adequately the structural and thermodynamic properties of oxide systems except for the phosphate oxides and some other systems. The bibliography includes 222 references. read less USED (high confidence) K. Nordlund and R. Averback, “Atomic displacement processes in irradiated amorphous and crystalline silicon,” Applied Physics Letters. 1997. link Times cited: 20 Abstract: Ion beam mixing was investigated in crystalline and amorphou… read moreAbstract: Ion beam mixing was investigated in crystalline and amorphous Si using molecular dynamics simulations. The magnitude of mixing was found to be larger in amorphous Si by a factor of about 2. The difference is attributed to local relaxation mechanisms occurring during the cooling down phase of the cascade. Comparison of mixing between Si and Al shows that short range structural order also has a significant influence on mixing. read less USED (high confidence) P. Keblinski, S. Phillpot, D. Wolf, and H. Gleiter, “Comparison of the structure of grain boundaries in silicon and diamond by molecular-dynamics simulations,” MRS Proceedings. 1997. link Times cited: 0 Abstract: Molecular-dynamics simulations were used to synthesize nanoc… read moreAbstract: Molecular-dynamics simulations were used to synthesize nanocrystalline silicon with a grain size of up to 75 {angstrom} by crystallization of randomly misoriented crystalline seeds from the melt. The structures of the highly-constrained interfaces in the nanocrystal were found to be essentially indistinguishable from those of high-energy bicrystalline grain boundaries (GBs) and similar to the structure of amorphous silicon. Despite disorder, these GBs exhibit predominantly four-coordinated (sp{sup 3}-like) atoms and therefore have very few dangling bonds. By contrast, the majority of the atoms in high-energy bicrystalline GBs in diamond are three-coordinated (sp{sup 2}-like). Despite the large fraction of three-coordinated GB carbon atoms, they are rather poorly connected amongst themselves, thus likely preventing any type of graphite-like electrical conduction through the GBs. read less USED (high confidence) P. Bedrossian, M. Caturla, and T. D. Rubia, “Damage evolution and surface defect segregation in low-energy ion-implanted silicon,” Applied Physics Letters. 1997. link Times cited: 30 Abstract: We have combined computer simulations and atomic-resolution … read moreAbstract: We have combined computer simulations and atomic-resolution tunneling microscopy to investigate the kinetics of defect migration during annealing of ion implanted Si(111)-7×7. Using atomically-clean and flat surfaces as sinks for bulk point defects introduced by the irradiation, we observe distinct, temperature-dependent surface arrival rates for vacancies and interstitials, and we demonstrate that the distinct kinetics of each type of bulk point defect govern their surface segregation kinetics. A combination of simulation tools provides a detailed description of the processes that underlie the observed temperature-dependence of defect migration. read less USED (high confidence) R. Ramírez, C. Herrero, E. Artacho, F. Madrid, and U. Madrid, “Low-energy quantum dynamics of atoms at defects. Interstitial oxygen in silicon,” Journal of Physics: Condensed Matter. 1996. link Times cited: 10 Abstract: The problem of the low-energy highly anharmonic quantum dyna… read moreAbstract: The problem of the low-energy highly anharmonic quantum dynamics of isolated impurities in solids is addressed by using path-integral Monte Carlo simulations. Interstitial oxygen in silicon is studied as a prototypical example showing such a behaviour. The assignment of a `geometry' to the defect is discussed. Depending on the potential (or on the impurity mass), there is a `classical' regime, where the maximum probability density for the oxygen nucleus is at the potential minimum. There is another regime, associated with highly anharmonic potentials, where this is not the case. The two regimes are separated by a sharp transition. Also, the decoupling of the many-nuclei problem into a one-body Hamiltonian to describe the low-energy dynamics is studied. The adiabatic potential obtained from the relaxation of all of the other degrees of freedom at each value of the coordinate associated with the low-energy motion gives the best approximation to the full many-nuclei problem. read less USED (high confidence) L. Marqués, M. Caturla, H. Huang, and T. D. Rubia, “Molecular dynamics studies of the ion beam induced crystallization in silicon,” MRS Proceedings. 1995. link Times cited: 11 Abstract: We have studied the ion bombardment induced amorphous-to-cry… read moreAbstract: We have studied the ion bombardment induced amorphous-to-crystal transition in silicon using molecular dynamics techniques. The growth of small crystal seeds embedded in the amorphous phase has been monitored for several temperatures in order to get information on the effect of the thermal temperature increase introduced by the incoming ion. The role of ion-induced defects on the growth has been also studied. read less USED (high confidence) F. Ladouceur, A. Selmani, C. Tannous, and G. Spronken, “Molecular dynamics calculations of infrared absorption spectra in the canonical ensemble: H on Si(100),” Journal of Physics: Condensed Matter. 1989. link Times cited: 5 Abstract: The infrared absorption spectrum of a hydrogenated Si(100)2*… read moreAbstract: The infrared absorption spectrum of a hydrogenated Si(100)2*1 surface is calculated with a constant-temperature molecular dynamics technique (Nose dynamics). The equations of motion embody radial and angular forces between Si atoms, encompassing previous calculations based on force constants. A novel pair potential determined by ab initio quantum chemistry techniques is used for the interactions between H and Si atoms. The spectra obtained, free of any adjustable parameters, compare well with experiment and with previous numerical works model a shift of 200 cm-1 towards low frequencies. This was noticed previously by Tully and co-workers (1985). The origin of the shift is investigated in detail. read less USED (high confidence) S. Bergmann, “Derivation, asymptotic analysis and numerical solution of atomistically consistent phase-field models.” 2019. link Times cited: 0 Abstract: In this thesis a systematic derivation and analysis of phase… read moreAbstract: In this thesis a systematic derivation and analysis of phase-field models with parameters based on molecular-dynamical simulations is developed. Applications of our models describe the anisotropic growth of solid-liquid interfaces during crystallization from a melt. We focus here on silicon, while other materials with different anisotropies and material parameters are also possible. We combine molecular dynamic simulations with phase-field modelling to yield quantitatively accurate models that are amenable to large scale simulations. We show how to determine the model parameters consistently with atomistic and experimental results. For silicon, where experiments on grain growth exhibit {111} and {100} facets [103], we show how to obtain the interfacial energy to a given shape and thus obtain an appropriate anisotropic surface function. The comparison to experimental equilibrium shapes and Wulff shapes allows for finding accurate ratios between the surface energies for different crystallographic orientations, but not directly their magnitude. We find the latter by using classical nucleation theory in combination with molecular dynamical simulations of the critical nucleation radius. From that we gain the interface energy for three distinct crystallographic orientations. For realistic simulation of 3D surfaces a four-fold anisotropic function of sixth order is required to provide the necessary three degrees of freedom for the interface energy. Further experiments on silicon grain growth show that the growth velocity has a Vogel-Fulcher type temperature dependence [89]. In addition, this velocity depends on the crystallographic orientation [13]. The incorporation of an anisotropic and temperature dependent interface velocity into a phase-field model then leads to an anisotropic and temperature-dependent mobility. In order to make quantitative predictions that are at the scale of experimental results one has to tackle the constraints on the computational efficiency of the phasefield approach. By using matched asymptotic expansions we derive free boundary problems for our systems that yield correction terms on the mobility and allow for a higher-order validity in the interface thickness. In our case, the double-well potential is non-symmetric and hence dictates highly complex solvability conditions. The complications in the asymptotic analysis arise in particular from the temperature dependence of the anisotropic mobility, which is necessary in order to reproduce a Vogel-Fulcher type interface velocity. In addition, this velocity is anisotropic, which has to be taken into account within the asymptotics. read less USED (high confidence) R. Aguirre, J. J. Chavez, X. W. Zhou, S. Almeida, and D. Zubia, “Molecular dynamics simulations of ZnTe/Cu back contacts for CdTe solar cells,” 2017 IEEE 44th Photovoltaic Specialist Conference (PVSC). 2017. link Times cited: 0 Abstract: Molecular dynamics (MD) simulations have been applied to stu… read moreAbstract: Molecular dynamics (MD) simulations have been applied to study the growth of ZnTe/Cu/CdTe layers on CdTe substrates. Our studies show that Cu forms pure clusters and ejects Cd atoms within the CdTe layer out towards the film's surface. Elemental concentration plots indicate that the amount of Cu added to the growth plays an important role on the intermixing between ZnTe and CdTe layers and the doping of CdTe. These results provide useful insight to the development of effective and reliable back contacts used in CdTe solar cells. read less USED (high confidence) M. Verdier, D. Lacroix, and K. Termentzidis, “Effect of the amorphization around spherical nano-pores on the thermal conductivity of nano-porous Silicon,” Journal of Physics: Conference Series. 2017. link Times cited: 3 Abstract: The thermal conductivity of nano-porous Silicon with amorpho… read moreAbstract: The thermal conductivity of nano-porous Silicon with amorphous shells around the pores is computed by Molecular Dynamics simulations. For the latter property, a systematic investigation of the porosity and the thickness of the amorphous shells has been performed. Sub-amorphous thermal conductivity is reached for systems with large porosity and amorphous shell, while a non-negligible fraction of crystalline Silicon phase is still present. The thermal conductivity of all studied systems can be controlled by a key parameter which is the ratio of crystalline/amorphous or crystalline/void interface to the volume of material. read less USED (high confidence) A. Jay et al., “Simulation of Single Particle Displacement Damage in Silicon–Part II: Generation and Long-Time Relaxation of Damage Structure,” IEEE Transactions on Nuclear Science. 2017. link Times cited: 44 Abstract: A statistical study of displacement cascades induced by sili… read moreAbstract: A statistical study of displacement cascades induced by silicon Primary Knock-on Atoms (PKA) in bulk silicon is performed by running a large number of molecular dynamics (MD) simulations. The choice of the PKA species and energy varying from 1 to 100 keV comes from a previous particle-matter simulation [1]. The electronic stopping power missing in standard MD simulations is here taken into account using the Two Temperature Model (TTM). This prevents from overestimating the number of created defects. The damaged atomic structures obtained after one nanosecond of MD simulation are not representative of what is observed in image sensors for example after several minutes. For this reason, the kinetic Activation Relaxation Technique (k-ART) is used in a second step, allowing to access longer simulation times of up to second. The obtained damaged structures can then be compared with experimental observations. Analyses reveal two possible links between the simulated structures and the measurements in solid-state image sensors. First, the cluster size distribution exhibits a shape similar to the measured exponential distribution of Dark Current (DC). Second, the temporal evolution of metastable atomic configurations resembles experimental DC-Random-Telegraph-Signals. read less USED (high confidence) P. A. Pluchino, X. Chen, M. Garcia, L. Xiong, D. McDowell, and Y. Chen, “Dislocation migration across coherent phase interfaces in SiGe superlattices,” Computational Materials Science. 2016. link Times cited: 15 USED (high confidence) H. Yabuhara and A. Miyamoto, “Prediction of low-energy boron doping profile for ultrashallow junction formation by hybrid molecular dynamics method,” Japanese Journal of Applied Physics. 2015. link Times cited: 0 Abstract: Our original hybrid method combining tight-binding quantum c… read moreAbstract: Our original hybrid method combining tight-binding quantum chemical and classical molecular dynamics was first applied to the low-energy doping process of boron into a silicon substrate, which has a depth of more than 10 nm that is needed to evaluate an ultrashallow junction position. Tight-binding quantum chemical molecular dynamics calculation was used for an injected boron atom and surrounding silicon atoms within a sphere with a radius of 0.5 nm centered at the boron atom. This method is advantageous in treating the many-body collision effect and electron–electron interaction, which are more important in low-energy doping, compared with the Monte Carlo method with binary collision approximation. A comparison with a plasma doping experiment was also carried out. The junction positions were 6.2 nm for boron doping at an initial kinetic energy of 200 eV in the simulation results and 6.4 nm for 200 eV in the experimental results. Good agreement between simulation and experimental results indicates that our hybrid molecular dynamics method is applicable to doping profile prediction in a silicon structure with a depth of more than 10 nm that is needed to evaluate ultrashallow junction formation. read less USED (high confidence) H. Bracht et al., “Thermal conductivity of isotopically controlled silicon nanostructures,” New Journal of Physics. 2014. link Times cited: 23 Abstract: Nanostructured semiconductors open the opportunity to indepe… read moreAbstract: Nanostructured semiconductors open the opportunity to independently tailor electric and thermal conductivity by manipulation of the phonon transport. Nanostructuring of materials is a highly promising strategy for engineering thermoelectric devices with improved efficiency. The concept of reducing the thermal conductivity without degrading the electrical conductivity is most ideally realized by controlled isotope doping. This work reports on experimental and theoretical investigations on the thermal conductivity of isotopically modulated silicon nanostructures. State-of-the-art pump-and-probe experiments are conducted to determine the thermal conductivity of the different nanostructures of isotopically enriched silicon layers epitaxially grown on natural silicon substrates. Concomitant molecular dynamics calculations are performed to study the impact of the silicon isotope mass, isotope interfaces, and of the isotope layer ordering and thickness on the thermal conductivity. Engineering the isotope distribution is a striking concept to reduce the thermal conductivity of silicon without affecting its electronic properties. This approach, using isotopically engineered silicon, might pave the way for future commercial thermoelectric devices. read less USED (high confidence) Y. Qiu, Q. Tan, W. Si, and Y. Chen, “Ion specificity in NaCl solution confined in silicon nanochannels,” Science China Technological Sciences. 2014. link Times cited: 9 USED (high confidence) Y. Wen et al., “Reducing the thermal conductivity of silicon by nanostructure patterning,” Applied Physics A. 2013. link Times cited: 5 USED (high confidence) J. Zhang, C. Wang, R. Chowdhury, and S. Adhikari, “Size- and temperature-dependent piezoelectric properties of gallium nitride nanowires,” Scripta Materialia. 2013. link Times cited: 33 USED (high confidence) X. Zhang, Y. Zhao, and G. Lu, “RECENT DEVELOPMENT IN QUANTUM MECHANICS/MOLECULAR MECHANICS MODELING FOR MATERIALS,” International Journal for Multiscale Computational Engineering. 2011. link Times cited: 13 Abstract: We have introduced two quantum mechanics/molecular mechanics… read moreAbstract: We have introduced two quantum mechanics/molecular mechanics approaches for materials modeling. One is based on quantum mechanical coupling and the other on mechanical coupling. The formalism of both approaches is described in detail. The validations of the methods are demonstrated in terms of atomic and electronic structure. Finally, the applications of the methods are surveyed, including applications in vacancy clusters, dislocations, nanoindentations, and fractures. read less USED (high confidence) P. Sengupta, S. Steiger, S. Lee, H. Ryu, and G. Klimeck, “Multiscale Modeling of Quantum Dot Heterostructures.” 2011. link Times cited: 4 Abstract: A multiscale approach was adopted for the calculation of con… read moreAbstract: A multiscale approach was adopted for the calculation of confined states in self-assembled semiconductor quantum dots (QDs). While results close to experimental data have been obtained with a combination of atomistic strain and tight-binding (TB) electronic structure description for the confined quantum states in the QD, the TB calculation requires substantial computational resources. To alleviate this problem an integrated approach was adopted to compute the energy states from a continuum 8-band k.p Hamiltonian under the influence of an atomistic strain field. Such multiscale simulations yield a roughly six-fold faster simulation. Atomic-resolution strain is added to the k.p Hamiltonian through interpolation onto a coarser continuum grid. Sufficient numerical accuracy is obtained by the multiscale approach. Optical transition wavelengths are within 7% of the corresponding TB results with a proper splitting of p-type sub-bands. The systematically lower emission wavelengths in k.p are attributable to an underestimation of the coupling between the conduction and valence bands. read less USED (high confidence) E. Landry and A. McGaughey, “Thermal Resistance of Silicon/Germanium Interfaces From Lattice Dynamics Calculations.” 2009. link Times cited: 0 Abstract: Phonon scattering at the interface between two materials res… read moreAbstract: Phonon scattering at the interface between two materials results in a thermal resistance, R [1]. An ability to accurately predict the thermal resistance of semiconductor interfaces is important in devices where phonon interface scattering is a significant contributor to the overall thermal resistance (e.g., computer chips with high component density). This ability will also lead to improvements in the design of semiconductor superlattices with low thermal conductivity, desirable in thermoelectric energy conversion applications [2].© 2009 ASME read less USED (high confidence) E. Landry and A. McGaughey, “Designing Si/Si1−xGex Superlattices With Tailored Thermal Transport Properties.” 2008. link Times cited: 0 Abstract: Si/Si1−x Gex superlattices are promising candidates for ther… read moreAbstract: Si/Si1−x Gex superlattices are promising candidates for thermoelectric energy conversion applications [1, 2], as the phonon transport through them can be inhibited while maintaining desirable electrical transport properties. No comprehensive experimental study has been performed to map the thermal conductivity design space accessible by Si/Ge nanocomposites. By using atomistic modeling tools, interesting areas of the design space can be identified and then further explored experimentally.Copyright © 2008 by ASME read less USED (high confidence) A. Galashev, V. Polukhin, I. A. Izmodenov, and O. Rakhmanova, “Simulation of noncrystalline silicon nanoparticles: A computer experiment,” Glass Physics and Chemistry. 2006. link Times cited: 15 USED (high confidence) T. Aoki and J. Matsuo, “Molecular dynamics simulations of surface modification and damage formation by gas cluster ion impacts,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2006. link Times cited: 26 USED (high confidence) D. Landau et al., “Monte Carlo Simulations of Compressible Ising Models: Do We Understand Them?,” Lecture Notes in Physics. 2006. link Times cited: 2 USED (high confidence) T. Hawa and M. Zachariah, “Molecular Dynamics Simulation of Nanoparticle Chain Aggregate Sintering.” 2006. link Times cited: 0 Abstract: Sintering of silicon nanoparticle chain aggregates are inves… read moreAbstract: Sintering of silicon nanoparticle chain aggregates are investigated using molecular dynamics (MD) simulations at 1500 K, which is about melting temperature at the size range we tested. The straight chain aggregates consist of upto 40 particles and the primary particles of 2.5 to 5 nm sizes are considered. The sintering time increases with increase the total volume of the chain aggregate or with increase the exposed initial surface area of the chain. A mathematical model was developed to describe the dynamics of sintering of chain aggregates. The model was able to predict the sintering time with excellent agreement with the results obtained from MD simulations. We also studied the chain aggregate that has a secondary branch coming out from the edge of the primary branch (L-shape) and from the middle of the primary branch (T-shape). In general, sintering time changes as much as 30% of that of a straight chain which contains the same volume of particles. read less USED (high confidence) T. Aoki and J. Matsuo, “Molecular dynamics simulations of sequential cluster ion impacts,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2005. link Times cited: 20 USED (high confidence) A. Galashev, “Growth of a Si nanocrystal in an oxygen atmosphere. Computer simulation,” Crystallography Reports. 2002. link Times cited: 2 USED (high confidence) M. Kratzer, W. Steinhögl, A. Kersch, T. Sachse, and V. Hoeink, “Multi-Scale Simulations of Silicon Etching by Halides: Effects of Surface Reaction Rates.,” MRS Proceedings. 2001. link Times cited: 2 USED (high confidence) A. Belov**, K. Scheerschmidt, and U. Gösele, “Extended Point Defect Structures at Intersections of Screw Dislocations in Si: A Molecular Dynamics Study,” Physica Status Solidi (a). 1999. link Times cited: 12 Abstract: Molecular dynamics computer simulations have been employed w… read moreAbstract: Molecular dynamics computer simulations have been employed with the Tersoff interatomic potential to examine the atomic structure of (a/2) 〈110〉 screw dislocations forming regular two-dimensional arrays in silicon. The main attention is focused on the atomic configurations of dislocation intersections. The dislocations are assumed to be undissociated, following HREM observations on the low-angle (001) twist boundaries produced by silicon wafer bonding in ultrahigh vacuum. It is shown that cores of the dislocation intersections are formed by closed characteristic groups of atoms (extended point defects). The symmetry of these defects strongly depends on the fact whether the screw dislocation arrays generate a twist or a shear boundary. read less USED (high confidence) P. Keblinski, D. Wolf, and H. Gleiter, “Molecular-Dynamics Simulation of Grain-Boundary Diffusion Creep,” Interface Science. 1998. link Times cited: 88 USED (high confidence) A. Belov**, D. Conarad, K. Scheerschmidt, and U. Gösele, “Atomistic study of the (001), 90° twist boundary in silicon,” Philosophical Magazine. 1998. link Times cited: 14 Abstract: A new type of a structural unit (the 42m dreidl) is proposed… read moreAbstract: A new type of a structural unit (the 42m dreidl) is proposed on the basis of molecular dynamics simulations for the core model of the (001), 90 e twist grain boundary in silicon. The structural unit resembles a polyhedron in which some edges, not corresponding to bonds between atoms, are absent. The dreidl has the 42m (D2d) point-group symmetry and consists of 14 atoms which form eight ® vemembered rings maintaining tetrahedral bonding in the boundary core. Molecular dynamics simulations with the empirical TersoA potential were performed to evaluate the energy of the (001), 90 e twist boundary at T = 0K. The eA ect of both rigid-body translations parallel to the grain boundary plane and alternative reconstructions involving conventional structural units was investigated. Despite the high degree of dimerization the twist boundary was found to have a low energy compared with structural models of twist grain boundaries in silicon previously studied. read less USED (high confidence) M. Caturla and T. D. Rubia, “Dose rate effects during damage accumulation in silicon,” MRS Proceedings. 1996. link Times cited: 2 Abstract: We combine molecular dynamics and Monte Carlo simulations to… read moreAbstract: We combine molecular dynamics and Monte Carlo simulations to study damage accumulation and dose rate effects during irradiation of Silicon. We obtain the initial stage of the damage produced by heavy and light ions using classical molecular dynamics simulations. While heavy ions like As or Pt induce amorphization by single ion impact, light ions like B only produce point defects or small clusters of defects. The amorphous pockets generated by heavy ions are stable below room temperature and recrystallize at temperatures below the threshold for recrystallization of a planar amorphous-crystalline interface. The damage accumulation during light ion irradiation is simulated using a Monte Carlo model for defect diffusion. In this approach, we study the damage in the lattice as a function of dose and dose rate. A strong reduction in the total number of defects left in the lattice is observed for lower dose rates. read less USED (high confidence) M. Caturla, T. D. Rubia, and G. Gilmer, “Point defect production, geometry and stability in silicon: A molecular dynamics simulation study,” MRS Proceedings. 1993. link Times cited: 13 Abstract: We present results of molecular dynamics computer simulation… read moreAbstract: We present results of molecular dynamics computer simulation studies of the threshold energy for point defect production in silicon. We employ computational cells with 8000 atoms at ambient temperature of 10 K that interact via the Stillinger-Weber potential. Our simulations address the orientation dependence of the defect production threshold as well as the structure and stability of the resulting vacancy-interstitial pairs. Near the directions, a vacancy tetrahedral-interstitial pair is produced for 25 eV recoils. However, at 30 eV recoil energy, the resulting interstitial is found to be the split dumbbell configuration. This Frenkel pair configuration is lower in energy than the former by 1.2 eV. Moreover, upon warming of the sample from 10 K the tetrahedral interstitial converts to a split before finally recombining with the vacancy. Along directions, a vacancy- split interstitial configuration is found at the threshold energy of 22 eV. Near directions, a wide variety of closed replacement chains are found to occur for recoil energies up to 45 eV. At 45 eV, the low energy vacancy- split configuration is found. At 300 K, the results are similar. We provide details on the atomic structure and relaxations near these defects as well as on their mobilities. read less USED (low confidence) Y. Li, J. Deng, X. Yang, and N. Peng, “Study of subsurface damage during nano-grinding of B3-GaN using molecular dynamics simulations,” Materials Science in Semiconductor Processing. 2024. link Times cited: 0 USED (low confidence) A. Hirano, H. Sakakima, A. Hatano, and S. Izumi, “Charge-transfer interatomic potential to reproduce 30° partial dislocation movements for 4H-SiC in the surface vicinity and its application to BPD-TED conversion,” Computational Materials Science. 2024. link Times cited: 0 USED (low confidence) T. T. Dung and M. Dung, “Evolution of Structure and Dynamic of Simulated CdTe Model According to the Melting Process,” Materials Science Forum. 2023. link Times cited: 0 Abstract: CdTe model containing 9955 atoms was built and simulated by … read moreAbstract: CdTe model containing 9955 atoms was built and simulated by the method of molecular dynamics (MD) with the Stillinger–Weber (SW) potential. The model was obtained by heating from 300K to 3000K at a rate of 1013 K/s. The structural properties of the model are investigated through the total energy per atom, the partial radial distribution functions (PRDFs), the coordination number distributions and the bond-angle distributions. Calculation results have shown that the model has a melting point of about 1370K and changes from tetrahedral to octahedral structure when the temperature of CdTe model is above the melting point. These results are consistent with the reported experimental and simulation results. In addition, the mobility of Cd and Te atoms is also researched through the mean squared displacement (MSD) and the diffusion coefficients of Cd and Te atoms. read less USED (low confidence) M. Grigoryeva et al., “Modeling of Short-Pulse Laser Interactions with Monolithic and Porous Silicon Targets with an Atomistic–Continuum Approach,” Nanomaterials. 2023. link Times cited: 0 Abstract: The acquisition of reliable knowledge about the mechanism of… read moreAbstract: The acquisition of reliable knowledge about the mechanism of short laser pulse interactions with semiconductor materials is an important step for high-tech technologies towards the development of new electronic devices, the functionalization of material surfaces with predesigned optical properties, and the manufacturing of nanorobots (such as nanoparticles) for bio-medical applications. The laser-induced nanostructuring of semiconductors, however, is a complex phenomenon with several interplaying processes occurring on a wide spatial and temporal scale. In this work, we apply the atomistic–continuum approach for modeling the interaction of an fs-laser pulse with a semiconductor target, using monolithic crystalline silicon (c-Si) and porous silicon (Si). This model addresses the kinetics of non-equilibrium laser-induced phase transitions with atomic resolution via molecular dynamics, whereas the effect of the laser-generated free carriers (electron–hole pairs) is accounted for via the dynamics of their density and temperature. The combined model was applied to study the microscopic mechanism of phase transitions during the laser-induced melting and ablation of monolithic crystalline (c-Si) and porous Si targets in a vacuum. The melting thresholds for the monolithic and porous targets were found to be 0.32 J/cm2 and 0.29 J/cm2, respectively. The limited heat conduction mechanism and the absence of internal stress accumulation were found to be involved in the processes responsible for the lowering of the melting threshold in the porous target. The results of this modeling were validated by comparing the melting thresholds obtained in the simulations to the experimental values. A difference in the mechanisms of ablation of the c-Si and porous Si targets was considered. Based on the simulation results, a prediction regarding the mechanism of the laser-assisted production of Si nanoparticles with the desired properties is drawn. read less USED (low confidence) C. Liu, W. Yip, S. To, B. Chen, and J. Xu, “Numerical Investigation on the Effects of Grain Size and Grinding Depth on Nano-Grinding of Cadmium Telluride Using Molecular Dynamics Simulation,” Nanomaterials. 2023. link Times cited: 0 Abstract: Cadmium telluride (CdTe) is known as an important semiconduc… read moreAbstract: Cadmium telluride (CdTe) is known as an important semiconductor material with favorable physical properties. However, as a soft-brittle material, the fabrication of high-quality surfaces on CdTe is quite challenging. To improve the fundamental understanding of the nanoscale deformation mechanisms of CdTe, in this paper, MD simulation was performed to explore the nano-grinding process of CdTe with consideration of the effects of grain size and grinding depth. The simulation results indicate that during nano-grinding, the dominant grinding mechanism could switch from elastic deformation to ploughing, and then cutting as the grinding depth increases. It was observed that the critical relative grain sharpness (RGS) for the transition from ploughing to cutting is greatly influenced by the grain size. Furthermore, as the grinding depth increases, the dominant subsurface damage mechanism could switch from surface friction into slip motion along the <110> directions. Meanwhile, as the grain size increases, less friction-induced damage is generated in the subsurface workpiece, and more dislocations are formed near the machined groove. Moreover, regardless of the grain size, it was observed that the generation of dislocation is more apparent as the dominant grinding mechanism becomes ploughing and cutting. read less USED (low confidence) E. Rosky, W. Cantrell, T. Li, I. Nakamura, and R. Shaw, “Molecular simulations reveal that heterogeneous ice nucleation occurs at higher temperatures in water under capillary tension,” Atmospheric Chemistry and Physics. 2023. link Times cited: 0 Abstract: Abstract. Heterogeneous ice nucleation is thought to be the … read moreAbstract: Abstract. Heterogeneous ice nucleation is thought to be the primary pathway for the formation of ice in mixed-phase clouds, with the number of active ice-nucleating particles (INPs) increasing rapidly with decreasing temperature. Here, molecular-dynamics simulations of heterogeneous ice nucleation demonstrate that the ice nucleation rate is also sensitive to pressure and that negative pressure within supercooled water shifts freezing temperatures to higher temperatures. Negative pressure, or tension, occurs naturally in water capillary bridges and pores and can also result from water agitation. Capillary bridge simulations presented in this study confirm that negative Laplace pressure within the water increases heterogeneous-freezing temperatures. The increase in freezing temperatures with negative pressure is approximately linear within the atmospherically relevant range of 1 to −1000 atm. An equation describing the slope depends on the latent heat of freezing and the molar volume difference between liquid water and ice. Results indicate that negative pressures of −500 atm, which correspond to nanometer-scale water surface curvatures, lead to a roughly 4 K increase in heterogeneous-freezing temperatures. In mixed-phase clouds, this would result in an increase of approximately 1 order of magnitude in active INP concentrations. The findings presented here indicate that any process leading to negative pressure in supercooled water may play a role in ice formation, consistent with experimental evidence of enhanced ice nucleation due to surface geometry or mechanical agitation of water droplets. This points towards the potential for dynamic processes such as contact nucleation and droplet collision or breakup to increase ice nucleation rates through pressure perturbations.
read less USED (low confidence) P. Zhao et al., “Investigation on nano-grinding process of GaN using molecular dynamics simulation: Nano-grinding parameters effect,” Journal of Manufacturing Processes. 2023. link Times cited: 2 USED (low confidence) W. Guo, Q.-X. Bai, Y. Dou, T. Wang, and H. Wang, “Effect of stainless-steel substrate grain boundaries on surface graphene morphology and nano-friction behavior,” Applied Surface Science. 2023. link Times cited: 0 USED (low confidence) T. Bierschenk et al., “Formation and self-organisation of nano-porosity in swift heavy ion irradiated amorphous Ge,” Acta Materialia. 2023. link Times cited: 0 USED (low confidence) L. Martín‐Encinar, L. Marqués, M. Aboy, P. López, I. Santos, and L. Pelaz, “Molecular Dynamics Study of Stress Relaxation During Ge Deposition on Si(100) 2\times 1 Substrates,” 2023 14th Spanish Conference on Electron Devices (CDE). 2023. link Times cited: 0 Abstract: We studied epitaxial growth of Ge films on Si(001) $2\times … read moreAbstract: We studied epitaxial growth of Ge films on Si(001) $2\times 1$ at different temperatures using classical molecular dynamics simulations. Ge-Si intermixing contributes to strain accommodation mostly in the original Si substrate surface and first grown Ge layer. Stress accumulation is further released by the generation of dislocations whose amount and type depend on temperature. At high temperatures, a larger amount and more variety of dislocations are formed, thus affecting the surface morphology and consequently the size of 3D islands. read less USED (low confidence) W. Guo, Q.-X. Bai, Y. Dou, H. Wang, and S. Chen, “Investigation of the effect of stainless-steel grain size on the continuity of graphene frictional behavior using molecular dynamics (MD) simulation,” Computational Materials Science. 2023. link Times cited: 0 USED (low confidence) H. An, J. Wang, and F. Fang, “Material removal on silicon towards atomic and close-to-atomic scale by infrared femtosecond laser,” Materials Science in Semiconductor Processing. 2023. link Times cited: 2 USED (low confidence) T. Shu, N. Hu, F. Liu, and G. Cheng, “Nanoparticles induced intragranular and dislocation substructures in powder bed fusion for strengthening of high-entropy-alloy,” Materials Science and Engineering: A. 2023. link Times cited: 2 USED (low confidence) F. Dai and L. Zhang, “Simulating changes of packing structures, locally loading states and mechanical behaviors for Si lattices with double vacancies at elevated temperatures,” Materials Science in Semiconductor Processing. 2023. link Times cited: 1 USED (low confidence) C. Liu, S. To, X. Sheng, and J. Xu, “Molecular dynamics simulation on crystal defects of single-crystal silicon during elliptical vibration cutting,” International Journal of Mechanical Sciences. 2022. link Times cited: 9 USED (low confidence) X. Chang, Y.-L. Ji, M. Jia, and H. Li, “Molecular dynamics simulations for mechanical properties of the monolayer PtS2 with line defect,” Computational Materials Science. 2022. link Times cited: 1 USED (low confidence) N. G. Korobeishchikov, P. Stishenko, I. Nikolaev, and V. Yakovlev, “Silica sputtering by noble gas projectiles: elucidating the effect of cluster species with molecular dynamic simulation,” Plasma Chemistry and Plasma Processing. 2022. link Times cited: 1 USED (low confidence) B. He, T. Vo, and P. Newell, “Investigation of fracture in porous materials: a phase-field fracture study informed by ReaxFF,” Engineering with Computers. 2022. link Times cited: 4 USED (low confidence) W. Wan, C. Tang, and W. Zou, “Exploring Silicon [001] Small Angle Symmetric Tilt Grain Boundaries: Structures, Energies and Stress fields,” Applied Surface Science. 2022. link Times cited: 4 USED (low confidence) W. Guo, Q.-X. Bai, Y. Dou, S. Chen, and H. Wang, “Molecular dynamics simulation of frictional strengthening behavior of graphene on stainless steel substrate,” Carbon. 2022. link Times cited: 6 USED (low confidence) Y. Chen, Z. Guan, J. Liu, W. Yang, and H. Wang, “Anomalous layer-dependent lubrication on graphene-covered-substrate:Competition between adhesion and plasticity,” Applied Surface Science. 2022. link Times cited: 5 USED (low confidence) V. A. Fabiyi, T. Richmond, B. Helenbrook, and E. Paek, “Molecular Dynamics Determination of Two-dimensional Nucleation Kinetic Coefficient for Modeling the Faceted Growth of Si (111) from an Undercooled Melt,” Journal of Crystal Growth. 2022. link Times cited: 3 USED (low confidence) Y. Deng, Y. Chen, H. Liu, and X. Yan, “The Effects of the Temperature and Termination(-O) on the Friction and Adhesion Properties of MXenes Using Molecular Dynamics Simulation,” Nanomaterials. 2022. link Times cited: 3 Abstract: Two-dimensional transition metal carbides and nitrides (MXen… read moreAbstract: Two-dimensional transition metal carbides and nitrides (MXenes) are widely applied in the fields of electrochemistry, energy storage, electromagnetism, etc., due to their extremely excellent properties, including mechanical performance, thermal stability, photothermal conversion and abundant surface properties. Usually, the surfaces of the MXenes are terminated by –OH, –F, –O or other functional groups and these functional groups of MXenes are related surface properties and reported to affect the mechanical properties of MXenes. Thus, understanding the effects of surface terminal groups on the properties of MXenes is crucial for device fabrication as well as composite synthesis using MXenes. In this paper, using molecular dynamics (MD) simulation, we study the adhesion and friction properties of Ti2C and Ti2CO2, including the indentation strength, adhesion energy and dynamics of friction. Our indentation fracture simulation reveals that there are many unbroken bonds and large residual stresses due to the oxidation of oxygen atoms on the surface of Ti2CO2. By contrast, the cracks of Ti2C keep clean at all temperatures. In addition, we calculate the elastic constants of Ti2C and Ti2CO2 by the fitting force–displacement curves with elastic plate theory and demonstrate that the elastic module of Ti2CO2 is higher. Although the temperature had a significant effect on the indentation fracture process, it hardly influences maximum adhesion. The adhesion energies of Ti2C and Ti2CO2 were calculated to be 0.3 J/m2 and 0.5 J/m2 according to Maugis–Dugdale theory. In the friction simulation, the stick-slip atomic scale phenomenon is clearly observed. The friction force and roughness (Ra) of Ti2C and Ti2CO2 at different temperatures are analyzed. Our study provides a comprehensive insight into the mechanical behavior of nanoindentation and the surface properties of oxygen functionalized MXenes, and the results are beneficial for the further design of nanodevices and composites. read less USED (low confidence) S. Zhao, X. Li, D. Wang, and P. Wu, “Study on surface defects of monocrystalline silicon caused by argon ion beam with different energies,” Other Conferences. 2022. link Times cited: 0 Abstract: In order to study the lattice damage caused by low-energy ar… read moreAbstract: In order to study the lattice damage caused by low-energy argon ions on the single crystal silicon substrate and the influence of incident energy on the substrate damage during the ion beam polishing process, the molecular dynamics (MD) was used to simulate the incidence of a single argon ion on the single crystal silicon substrate. Compare the lattice defects produced by the bombardment of single crystal silicon by ions of different incident energy. Ion beams with different incident energy were used to polish the surface of single crystal silicon, and the surface roughness after polishing was compared. Experimental and simulation results show that ion bombardment will cause lattice damage to the surface of the substrate. As the energy increases, the range of lattice damage will expand and the resulting lattice defects will be more dispersed. The use of low-energy (200~600eV) ion beams can further reduce the surface roughness of the substrate on the basis of reducing lattice damage read less USED (low confidence) V. Kuryliuk, S. Semchuk, K. Dubyk, and R. Chornyi, “Structural features and thermal stability of hollow-core Si nanowires: A molecular dynamics study,” Nano-Structures & Nano-Objects. 2022. link Times cited: 3 USED (low confidence) A. Mahata, T. Mukhopadhyay, and M. A. Zaeem, “Modified embedded-atom method interatomic potentials for Al-Cu, Al-Fe and Al-Ni binary alloys: From room temperature to melting point,” Computational Materials Science. 2022. link Times cited: 27 USED (low confidence) V. Kushch, “Atomistic vs. continuum models of nanoporous elastic solid: Stress fields, size-dependent effective stiffness and surface constants,” Mechanics of Materials. 2022. link Times cited: 4 USED (low confidence) Z.-fang Zhou, J. Cui, Q. Hou, and K. Zhang, “Role of mass redistribution on nanoripple formation and propagation: A molecular dynamics simulation study,” Applied Surface Science. 2022. link Times cited: 2 USED (low confidence) H. Zhan, X. Tan, X. Zhang, G. Xie, and D. Guo, “Layer-dependent fracture strength of few-layer WS2 induced by interlayer sliding: a molecular dynamics study,” Journal of Physics D: Applied Physics. 2021. link Times cited: 1 Abstract: Understanding the relationship between interlayer interactio… read moreAbstract: Understanding the relationship between interlayer interactions and the mechanical properties and behaviors of two-dimensional layered materials is critical in the development of related nanodevices. Nevertheless, it is still challenging due to difficulties in experiments. In this work, nanoindentation simulations on few-layer WS2 were conducted by varying the tip radius, suspended membrane radius, and membrane size using a molecular dynamics simulation. Consistent with our previous experimental results, few-layer WS2 exhibited a layer-dependent reduction in fracture strength owing to the uneven stress distribution among individual layers induced by interlayer sliding under out-of-plane deformation. Furthermore, apparent curve hysteresis was observed due to interlayer sliding in the supported region when a large tip radius and membrane radius were employed. However, instead of the supported part, the interlayer sliding within the suspended part resulted in reduced fracture strength with the increase of layer number. These findings not only provide an in-depth comprehension of the influence of interlayer sliding on fracture strength of few-layer WS2, but also suggest that the role of interlayer interactions should be seriously considered during nanodevice design. read less USED (low confidence) X. Hao, J. Wang, and P. He, “Formation Mechanism of a Silicon-on-Nothing Structure Using the Level-Set Approach and Molecular Dynamics,” Materials Today Communications. 2021. link Times cited: 1 USED (low confidence) H. Dai, W. Wu, and Y. Hu, “Lubricating effect of graphene during ultra-precision mechanical polishing by atomic scale simulation,” Proceedings of the Institution of Mechanical Engineers, Part B: Journal of Engineering Manufacture. 2021. link Times cited: 1 Abstract: As a new two-dimensional material with unique friction and w… read moreAbstract: As a new two-dimensional material with unique friction and wear properties, graphene often serves as a solid lubricant. In order to better understand the lubrication effect of graphene in the process of three-body polishing of single crystal silicon with diamond abrasive, a molecular dynamics model of this process was established in this study. Further, the changes of coordination number, friction coefficient, temperature, potential energy, stress, and surface/subsurface damage in the process of three-body polishing were analyzed in detail. The results showed that graphene lubrication could enhance the heat dissipation and reduce the number of defect atoms, friction coefficient, potential energy, stress, and chips. Therefore, less subsurface damage and material resistance were observed in the workpiece with graphene lubrication during machining. In general, graphene can be used as a high-quality solid lubricant in the three-body polishing of single crystal silicon using diamond abrasive because of its excellent lubricating effect. read less USED (low confidence) H. An, J. Wang, and F. Fang, “Material removal at atomic and close-to-atomic scale by high-energy photon: a case study using atomistic-continuum method,” Advances in Manufacturing. 2021. link Times cited: 6 USED (low confidence) J. Chen and X. Zhang, “Thermal resistance and thermal rectification of silicon device with triangular pores: A molecular dynamics study,” Physics Letters A. 2021. link Times cited: 1 USED (low confidence) Y. Zhang, P. Cao, B. Deng, L. Huang, and Y. Shi, “Strain rate-dependent tensile response of glassy silicon nanowires studied by accelerated atomistic simulations,” Journal of Applied Physics. 2021. link Times cited: 5 Abstract: Mechanical properties of glassy nanowires have been intensiv… read moreAbstract: Mechanical properties of glassy nanowires have been intensively investigated recently by both nanomechanical experiments and atomic-level simulations. Unfortunately, there exists a huge gap in the strain rate of the nanomechanical tests between experiments and simulations, which makes it difficult to compare results even for the same material system. Using accelerated atomistic simulations based on a self-learning metabasin escape algorithm, here, we report the tensile mechanical properties of amorphous Stillinger–Weber silicon nanowires with different intrinsic ductility under strain rates ranging from 1010 to 10−1 s−1. It is found that both brittle and ductile glassy silicon nanowires display weakened strength with a decreasing strain rate, in agreement with the cooperative shear model. Moreover, as the strain rate decreases, the amount of plasticity remains unchanged for the brittle nanowires, yet it decreases for the ductile ones. Such deteriorated plasticity in ductile glassy nanowires is caused by enhanced strain localization at low strain rates. Lastly, we show that via the distance matrix of nonaffine displacement, a more hierarchical potential energy landscape is responsible for the higher strain localization propensity in ductile silicon glassy nanowires. read less USED (low confidence) W. Ding, M. Wang, X. Dai, J. Zhang, G. Xin, and X. Wang, “Dewetting transition of water on nanostructured and wettability patterned surfaces: A molecular dynamics study,” Journal of Molecular Liquids. 2021. link Times cited: 9 USED (low confidence) X. Chang, Y.-yuan Ji, and H. Li, “Mechanical properties of PtS2 monolayer with rectangular defects: A molecular dynamics study,” Computational Materials Science. 2021. link Times cited: 1 USED (low confidence) M. Barhoumi, N. Sfina, M. Said, and S. Znaidia, “Elastic and mechanical properties of aluminium and silicon carbide using density functional theory and beyond,” Solid State Communications. 2021. link Times cited: 3 USED (low confidence) Y. Zhang, L. Huang, and Y. Shi, “Molecular dynamics study on the viscosity of glass‐forming systems near and below the glass transition temperature,” Journal of the American Ceramic Society. 2021. link Times cited: 6 USED (low confidence) S. Fujii and A. Seko, “Structure and lattice thermal conductivity of grain boundaries in silicon by using machine learning potential and molecular dynamics,” Computational Materials Science. 2021. link Times cited: 8 USED (low confidence) H. Xiao, Y.-fan Dai, J. Duan, Y. Tian, and J. Li, “Material removal and surface evolution of single crystal silicon during ion beam polishing,” Applied Surface Science. 2021. link Times cited: 19 USED (low confidence) J. Dora, C. Saraswat, A. Gour, S. Ghosh, N. Yedla, and T. Kundu, “The role of density reduction in lithiated amorphous silicon: Molecular dynamics and ab-initio studies,” Materials Today: Proceedings. 2021. link Times cited: 0 USED (low confidence) G. Ru, W. Qi, Y. Wei, K. Tang, and T. Xue, “Superlubricity in bilayer isomeric tellurene and graphene/tellurene van der Waals heterostructures,” Tribology International. 2021. link Times cited: 13 USED (low confidence) H. Chen, V. Levitas, L. Xiong, and X. Zhang, “Stationary dislocation motion at stresses significantly below the Peierls stress: Example of shuffle screw and 60∘ dislocations in silicon,” Acta Materialia. 2021. link Times cited: 11 USED (low confidence) J. Guo, J. Chen, Y. Lin, Z. Liu, and Y. Wang, “Effects of surface texturing on nanotribological properties and subsurface damage of monocrystalline GaN subjected to scratching investigated using molecular dynamics simulation,” Applied Surface Science. 2021. link Times cited: 31 USED (low confidence) K. Mohammadi, A. A. Madadi, Z. Bajalan, and H. N. Pishkenari, “Analysis of mechanical and thermal properties of carbon and silicon nanomaterials using a coarse-grained molecular dynamics method,” International Journal of Mechanical Sciences. 2020. link Times cited: 8 USED (low confidence) V. On, “To study the structure and thermodynamic properties of silicene materials when melting quickly by molecular dynamics simulation,” Journal of Physics: Conference Series. 2020. link Times cited: 0 Abstract: This paper presents the results of the study of melting sili… read moreAbstract: This paper presents the results of the study of melting silicene by MD simulation with a sample of 6400 atoms. Silicene melting from 300K to 3500K with a rate of 1013K / s. Investigation of energy dependence on temperature shows a jump in the average total energy of molten Silicene at the temperature T = 2500K. The radial distribution function G(r), ring distribution, coordination number distribution, angle distribution, and distance distribution also studied, all show that the phase transition temperature of Silicene is about 2500K. At 3500K, the silicene structure is almost destroyed, but long-term bonds still account for a higher proportion than short-length bonds. The structure is almost homogeneous, symmetrical. read less USED (low confidence) V. Samsonov, A. Kartoshkin, I. Talyzin, S. Vasilyev, and I. Kaplunov, “On phase diagrams for Au-Si nanosystems: thermodynamic and atomistic simulations,” Journal of Physics: Conference Series. 2020. link Times cited: 0 Abstract: Phase diagrams for Au-Si nanosystems were calculated by usin… read moreAbstract: Phase diagrams for Au-Si nanosystems were calculated by using thermodynamic simulation (NANOCALPHAD methodology) and molecular dynamics (MD). Thermodynamic simulations have been carried out for two Au-Si nanosystems: (i) a solid (crystalline) Si or Au nanoparticle (NP) contacting with an Au-Si nanodroplet of the same radius; (ii) a cylindrical Si nanowire (nanowhisker) with an Au-Si nanodroplet on its butt. We have found that the eutectic temperature of the first system decreases in comparison with the bulk eutectic temperature, and the position of the eutectic point slightly shifts to a lower value of the molar fraction of Si that agree with MD results obtained on another system, i.e. on spherical Au-Si NPs. Contrary to the first system, the eutectic temperature of the second one, i.e. of the system “Si nanowhisker -- Au-Si nanodroplet” increases in comparison with the bulk phase diagram. An explanation of such a result is proposed and discussed. read less USED (low confidence) J. Luo, C. Zhou, Y. Cheng, and L. Liu, “Assessing the EDIP potential for atomic simulation of carbon diffusion, segregation and solubility in silicon melt,” Journal of Crystal Growth. 2020. link Times cited: 2 USED (low confidence) N. Orekhov, G. Ostroumova, and V. Stegailov, “High temperature pure carbon nanoparticle formation: Validation of AIREBO and ReaxFF reactive molecular dynamics,” Carbon. 2020. link Times cited: 40 USED (low confidence) A. O. Tipeev, E. D. Zanotto, and J. Rino, “Crystal Nucleation Kinetics in Supercooled Germanium: MD Simulations Versus Experimental Data.,” The journal of physical chemistry. B. 2020. link Times cited: 16 Abstract: The validity of the Classical Nucleation Theory (CNT), the m… read moreAbstract: The validity of the Classical Nucleation Theory (CNT), the most important tool to describe and predict nucleation kinetics in supercooled liquids, has been at stake for almost a century. Here we carried out comprehensive molecular dynamics simulations of the nucleation kinetics of a fast quenched supercooled germanium using the Stillinger-Weber potential at 6 temperatures, covering a supercooling range of T/Tm=0.70-0.86, where Tm is the equilibrium melting temperature. We used the seeding method to determine the number of particles in the critical crystal nuclei at each supercooling, which yielded n*=150-1300 atoms. The transport coefficient at the liquid/nucleus interface, and the melting point were also obtained from the simulations. Using the parameters resulting directly from the simulations, the CNT embraces the experimental nucleation rates, J(T), with the following fitted (average) values of the nucleus/liquid interfacial free energy: γ=0.244 J/m2 and 0.201 J/m2, for experimental and calculated values of thermodynamic driving force, Δμ(T), respectively, which are close to the value obtained from n*(T). Without using any fit parameter, the calculated nucleation rates for experimental and calculated values of Δμ(T) embrace the experimental J(T) curve. Therefore, this finding favors the validity of the CNT. read less USED (low confidence) D. Chen et al., “Influence of atomic-scale defect on thermal conductivity of single-layer MoS2 sheet,” Journal of Alloys and Compounds. 2020. link Times cited: 21 USED (low confidence) W. Xu and W. K. Kim, “Role of boundary conditions and thermostats in the uniaxial tensile loading of silicon nanowires,” Computational Materials Science. 2020. link Times cited: 1 USED (low confidence) M. Saaoud, K. Sadki, L. B. Drissi, and F. Djeffal, “Mechanical response of η-layered borophene: impact of strain, temperature, vacancies and intercalation,” The European Physical Journal Applied Physics. 2020. link Times cited: 3 Abstract: The mechanical behavior of few-layered borophene (η-LB), at … read moreAbstract: The mechanical behavior of few-layered borophene (η-LB), at different temperatures ranging from 10 to 800 K in conjunction with a variant strain-rate, is studied by employing molecular dynamics simulations based on the Stillinger-Weber potential. The uniaxial tensile deformations along the zigzag- and armchair-direction of the hexagonal lattice are considered for η-LB, with η = 1, 2, 3, 4. We find an extremely anisotropic mechanical response. Parameters such as Young’s modulus and fracture strength are higher along the armchair-traction than the zigzag one due to the corrugated structure along the zigzag-axis. The fracture resistances of η-LB are strongly sensitive to temperature, while their dependence on the strain-rate is relatively low. The influence of nitrogen intercalation as well as vacancy defects on elastic behavior is also determined and discussed. The results are significantly affected by the defect’s type, concentration, and location. Our findings provide useful insights for the design of LB for many applications requiring a practical large magnitude strain engineering. read less USED (low confidence) J. Zhang, “Electrocaloric effects in monolayer germanium sulfide: A study by molecular dynamics simulations and thermodynamic analyses,” Journal of Applied Physics. 2020. link Times cited: 4 Abstract: In this paper, molecular dynamics (MD) simulations and therm… read moreAbstract: In this paper, molecular dynamics (MD) simulations and thermodynamics analyses are performed to investigate the electrocaloric (EC) effect in monolayer germanium sulfide (GeS). Our MD simulations show a large EC effect in the armchair direction of monolayer GeS at room temperature, since monolayer GeS only has polarization in the armchair direction due to its anisotropic structure. Moreover, an enhancement in the EC effect is observed in monolayer GeS by increasing the ambient temperature. A thermodynamic model is proposed to explain this impact of temperature on the EC effect, which originates from the thermally enhanced thermal expansion property of monolayer GeS. Moreover, the thermodynamic model incorporated with the material parameters extracted from MD simulations is able to predict the EC coefficient. The predicted value is found to be identical to the value obtained from MD simulations, which further proves the EC effect observed in monolayer GeS. The observation of the EC effect in monolayer GeS ... read less USED (low confidence) N. H. Giang, V. V. Hoang, and T. T. Hanh, “Melting of two-dimensional perfect crystalline and polycrystalline germanene,” Physica E-low-dimensional Systems & Nanostructures. 2020. link Times cited: 10 USED (low confidence) J. Li, Y. S. Li, Z. Wang, and H. Wang, “Molecular dynamics simulations of ionic hydration of Na+ inside the nanochannel,” Journal of Physics: Conference Series. 2020. link Times cited: 0 Abstract: Molecular dynamics simulations were carried out to investiga… read moreAbstract: Molecular dynamics simulations were carried out to investigate the hydration of Na+ ion in the nanochannels. The height of the channels varies from 0.65 nm to 3.0 nm, and the surface charge density varies from 0 to -0.2991 C/m2. The simulation results showed that the channel height and surface charge had special effect on the hydration of Na+ ion, and the peak height of radial distribution functions and coordination number increased as the channel height and surface charge density decreased. In the region of electrical double layer, hydration radius increased with the decreased of the channel height and the surface charge density, but the hydration radius of the Na+ ion of the bulk region was kept at a constant. read less USED (low confidence) J. Li, Y. S. Li, Z. Wang, and H. Wang, “Water distribution confined in the nanochannel: the impact of the thermal motion of silicon atoms,” Journal of Physics: Conference Series. 2020. link Times cited: 0 Abstract: Using molecular dynamics simulations, the impact of the ther… read moreAbstract: Using molecular dynamics simulations, the impact of the thermal motion of atoms in silicon walls on the water distribution confined in nanochannel has been investigated. The results show that thermal motion of silicon atoms has marginal effect on water distribution when the surface was not charged. However, when the surface is charged, the thermal motion of silicon atoms decreases the adsorbed peak of water molecular, and moves the position of the Na+ ion concentration peak far away from the surface. read less USED (low confidence) J. Yan and S. Y. Chen, “Mechanical properties of monolayer antimony carbide: A molecular dynamics simulation,” Materials today communications. 2020. link Times cited: 0 USED (low confidence) R. Khadka, N. Baishnab, G. Opletal, and R. Sakidja, “Study of amorphous boron carbide (a-BxC) materials using Molecular Dynamics (MD) and Hybrid Reverse Monte Carlo (HRMC),” Journal of Non-crystalline Solids. 2020. link Times cited: 5 USED (low confidence) M. Abdollahi, J. Davoodi, and M. Mohammadi, “Influence of point and linear defects on thermal and mechanical properties of germanium nanowire: a molecular dynamics study,” Materials Research Express. 2020. link Times cited: 0 Abstract: In the nanoscale dimensions, semiconductor nanowires such as… read moreAbstract: In the nanoscale dimensions, semiconductor nanowires such as germanium nanowires (GeNWs) are appropriate candidates for using field-effect transistors, Josephson junctions, sensors and so on. However, such uses require detailed knowledge of the physical properties of GeNW. Thus we investigated the thermal conductivity and stress-strain diagram of GeNW with lattice vacancy and linear imperfection. Non-equilibrium molecular dynamics simulation as numerical method was employed in this research. The three body Tersoff potential was employed to describe interaction between germanium atoms in GeNW. Two types of defects, point and linear, were applied to the nanowire. The Nose-Hoover thermostat was employed to control temperature of the system. We then studied thermal conductivity and Young’s modulus in three crystallography directions [100], [110] and [111]. Our MD results showed that in the case of 8% point vacancy, the thermal conductivity decreased greater than 70% and Yong’s modulus decreased about 25% for three crystallography directions. read less USED (low confidence) T. Vo, B. Reeder, A. Damone, and P. Newell, “Effect of Domain Size, Boundary, and Loading Conditions on Mechanical Properties of Amorphous Silica: A Reactive Molecular Dynamics Study,” Nanomaterials. 2019. link Times cited: 11 Abstract: Mechanical properties are very important when choosing a mat… read moreAbstract: Mechanical properties are very important when choosing a material for a specific application. They help to determine the range of usefulness of a material, establish the service life, and classify and identify materials. The size effect on mechanical properties has been well established numerically and experimentally. However, the role of the size effect combined with boundary and loading conditions on mechanical properties remains unknown. In this paper, by using molecular dynamics (MD) simulations with the state-of-the-art ReaxFF force field, we study mechanical properties of amorphous silica (e.g., Young’s modulus, Poisson’s ratio) as a function of domain size, full-/semi-periodic boundary condition, and tensile/compressive loading. We found that the domain-size effect on Young’s modulus and Poisson’s ratio is much more significant in semi-periodic domains compared to full-periodic domains. The results, for the first time, revealed the bimodular and anisotropic nature of amorphous silica at the atomic level. We also defined a “safe zone” regarding the domain size, where the bulk properties of amorphous silica can be reproducible, while the computational cost and accuracy are in balance. read less USED (low confidence) J. Miao, Y. Zhou, Q. Zhang, J.-yang Jiang, and W. Duan, “Wrinkling process in a single silicene sheet caused by in-plane shear,” Engineering Structures. 2019. link Times cited: 2 USED (low confidence) P. P. Jadhav, T. Dongale, and R. Vhatkar, “Effect of temperature on thermal conductivity of silicon germanium square nanowire using nonequilibrium molecular dynamics simulation,” PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON ADVANCED MATERIALS: ICAM 2019. 2019. link Times cited: 0 Abstract: Silicon germanium nanowire has varieties of applications in … read moreAbstract: Silicon germanium nanowire has varieties of applications in nanoelectronics and optoelectronics due to technological advances. Nowadays, Computational Material Science is evolving because computer simulation is a tool to get insight about the properties of materials at atomic or molecular level which is used to predict and/or verify experiments. This is considered as a bridge between theory and experiment. In this paper, silicon germanium square nanowire having simulation length of 97.74 A° is simulated by Nonequilibrium molecular dynamics simulation. Empirical interatomic potential used is Stillinger Weber potential. For canonical ensemble, effect of temperatures on thermal conductivity of silicon germanium square nanowire is studied.Silicon germanium nanowire has varieties of applications in nanoelectronics and optoelectronics due to technological advances. Nowadays, Computational Material Science is evolving because computer simulation is a tool to get insight about the properties of materials at atomic or molecular level which is used to predict and/or verify experiments. This is considered as a bridge between theory and experiment. In this paper, silicon germanium square nanowire having simulation length of 97.74 A° is simulated by Nonequilibrium molecular dynamics simulation. Empirical interatomic potential used is Stillinger Weber potential. For canonical ensemble, effect of temperatures on thermal conductivity of silicon germanium square nanowire is studied. read less USED (low confidence) W. Xu and W. K. Kim, “Molecular dynamics simulation of the uniaxial tensile test of silicon nanowires using the MEAM potential,” Mechanics of Materials. 2019. link Times cited: 24 USED (low confidence) Z. J. Choong, D. Huo, P. Degenaar, and A. O’Neill, “Edge chipping minimisation strategy for milling of monocrystalline silicon: A molecular dynamics study,” Applied Surface Science. 2019. link Times cited: 8 USED (low confidence) H. Chen, V. Levitas, and L. Xiong, “Amorphization induced by 60° shuffle dislocation pileup against different grain boundaries in silicon bicrystal under shear,” Acta Materialia. 2019. link Times cited: 37 USED (low confidence) E. Guerrero and D. A. Strubbe, “Computational generation of voids in
a
-Si and
a
-Si:H by cavitation at low density,” Physical Review Materials. 2019. link Times cited: 3 Abstract: Use of amorphous silicon ($a$-Si) and hydrogenated amorphous… read moreAbstract: Use of amorphous silicon ($a$-Si) and hydrogenated amorphous silicon ($a$-Si:H) in photovoltaics has been limited by light-induced degradation (the Staebler-Wronski effect) and low hole mobilities, and voids have been implicated in both problems. Accurately modeling the void microstructure is critical to theoretically understanding the cause of these issues. Previous methods of modeling voids have involved removing atoms according to an {\it a priori} idea of void structure and/or using computationally expensive molecular dynamics. We propose a new fast and unbiased approach based on the established and efficient Wooten-Winer-Weaire (WWW) Monte Carlo method, by using a range of fixed densities to generate equilibrium structures of $a$-Si and $a$-Si:H that maintain 4-coordination. We find a smooth evolution in bond lengths, bond angles, and bond angle deviations $\Delta \theta$ as the density is changed around the equilibrium value of $4.9\times10^{22}\ $atoms/cm$^3$. However, a significant change occurs at densities below $4.3\times10^{22}\ $atoms/cm$^3$, where voids begin to form to relieve tensile stress, akin to a cavitation process in liquids. We find both small voids (radius $\sim$3 \AA) and larger ones (up to 7 \AA), which compare well with available experimental data. The voids have an influence on atomic structure up to 4 \AA beyond the void surface and are associated with decreasing structural order, measured by $\Delta\theta$. We also observe an increasing medium-range dihedral order with increasing density. Our method allows fast generation of statistical ensembles, resembles a physical process during experimental deposition, and provides a set of void structures for further studies of their effects on degradation, hole mobility, two-level systems, thermal transport, and elastic properties. read less USED (low confidence) A. Sycheva, E. Voronina, T. Rakhimova, and A. Rakhimov, “Influence of porosity and pore size on sputtering of nanoporous structures by low-energy Ar ions: Molecular dynamics study,” Applied Surface Science. 2019. link Times cited: 13 USED (low confidence) Y. Li, W. Li, X. Chen, A. Diaz, D. McDowell, and Y. Chen, “Phonon spectrum and phonon focusing in coarse-grained atomistic simulations,” Computational Materials Science. 2019. link Times cited: 8 USED (low confidence) S. Li, J. Chen, and P. Ruterana, “The [10-10] Edge Dislocation in the Wurtzite Structure: A High-Resolution Transmission Electron Microscopy Investigation of [0001] Tilt Grain Boundaries in GaN and ZnO,” Acta Materialia. 2019. link Times cited: 1 USED (low confidence) H. Dai, J. Chen, and G. Liu, “A numerical study on subsurface quality and material removal during ultrasonic vibration assisted cutting of monocrystalline silicon by molecular dynamics simulation,” Materials Research Express. 2019. link Times cited: 30 Abstract: Molecular dynamics (MD) simulation is used to study the subs… read moreAbstract: Molecular dynamics (MD) simulation is used to study the subsurface quality and material removal of single crystal silicon with a diamond tool during ultrasonic elliptical vibration assisted cutting (UEVAC), 1D ultrasonic vibration assisted cutting (1D UVAC) and traditional cutting (TC) process. In the simulations, a long-range analytical bond order potential is used to describe the interaction inside the silicon specimen, providing a more accurate depiction of the atomic scale mechanisms of ductile plasticity, brittle fracture, and structural changes in silicon. The results show that UEVAC and 1D UVAC in cutting brittle material silicon causes a much smaller cutting force, much lower von Mises stress at the subsurface, larger material remove rate, lower compressive normal stress σ x x and σ y y , and smaller shear stress τ x y . In addition, the hydrostatic stress of subsurface for TC and 1D UVAC is much higher than that for UEVAC, which results in fewer Si-II and bct5-Si formed from the original Si-I in UEVAC. Moreover, the number of other atoms for UEVAC is overall smaller than those of using TC and 1D UVAC, which confirms that UEVAC produces a better subsurface. And atomic flow field analysis shows that the UEVAC tends to cut silicon in a more ductile mode. Besides, the temperature in front of tool edge and below the tool flank face of TC is much higher. This means that 1D UVAC and UEVAC have a positive effect on the tool life. However, the temperature in subsurface zone is overall larger, which reveals that 1D UVAC and UEVAC have a negative effect on the subsurface temperature. read less USED (low confidence) P. Grammatikopoulos, “Atomistic modeling of the nucleation and growth of pure and hybrid nanoparticles by cluster beam deposition,” Current Opinion in Chemical Engineering. 2019. link Times cited: 15 USED (low confidence) X. Wang and D. Jing, “Determination of thermal conductivity of interfacial layer in nanofluids by equilibrium molecular dynamics simulation,” International Journal of Heat and Mass Transfer. 2019. link Times cited: 43 USED (low confidence) P. Goj and P. Stoch, “Molecular dynamics simulations of P2O5-Fe2O3-FeO-Na2O glasses,” Journal of Non-Crystalline Solids. 2018. link Times cited: 19 USED (low confidence) G. Custer, H. Xu, S. Matysiak, and P. Das, “How Hydrophobic Hydration Destabilizes Surfactant Micelles at Low Temperature: A Coarse-Grained Simulation Study.,” Langmuir : the ACS journal of surfaces and colloids. 2018. link Times cited: 6 Abstract: Micelles are self-assembled aggregates of amphiphilic surfac… read moreAbstract: Micelles are self-assembled aggregates of amphiphilic surfactant molecules that are important in a variety of applications, including drug delivery, detergency, and catalysis. It is known that the micellization process is driven by the same physiochemical forces that drive protein folding, aggregation, and biological membrane self-assembly. Nevertheless, the molecular details of how micelle stability changes in water at low temperature are not fully clear. We develop and use a coarse-grained model to investigate how the interplay between nonionic surfactants and the surrounding water at the nanoscale affects the stability of micelles at high and low temperatures. Simulations of preformed C12E5 micelles in explicit water at a range of temperatures reveal the existence of two distinct surfactant conformations within the micelle, a bent structure and an extended structure, the latter being more prevalent at low temperature. Favorable interactions of the surfactant with more ordered solvation water stabilizes the extended configuration, allowing nanoscale wetting of the dry, hydrophobic core of the micelle, leading to the micelle breaking. Taken together, our coarse-grained simulations unravel how energetic and structural changes of the surfactant and the surrounding water destabilize micelles at low temperature, which is a direct consequence of the weakened hydrophobicity. Our approach thus provides an effective mean for extracting the molecular-level changes during hydrophobicity-driven destabilization of molecular self-assembly, which is important in a wide range of fields, including biology, polymer science, and nanotechnology. read less USED (low confidence) A. U. H. Meem, O. Chowdhury, and A. Morshed, “Effect of vacancy defects on thermal conductivity of silicon nanowire: A molecular dynamics study.” 2018. link Times cited: 0 Abstract: Reducing the thermal conductivity of silicon nanowires (SiNW… read moreAbstract: Reducing the thermal conductivity of silicon nanowires (SiNWs) can enhance the thermoelectric figure of merit. Applying non-equilibrium molecular dynamics (NEMD) simulation, it has been demonstrated that the thermal conductivity of SiNWs is approximately two orders of magnitude lower than bulk silicon crystal and that it can be reduced remarkably by including vacancy defects. It has been found that “surface vacancy defect” reduces thermal conductance much more than “center vacancy defect”. The thermal conductivity reaches the minimum, which is about 17% of that of pristine SiNW, when 2% surface vacancy defect is introduced in the nanowire. In order to reveal the origin of this drastic reduction of thermal conductivity, the vibrational density of states (VDOS) analysis is performed and it has been found that due to the high surface to volume ratio, the various boundary inelastic scatterings of phonon reduce thermal conductivity significantly. Also, larger mass difference due to voids induces smaller thermal conductivity values. These results indicate that the inclusion of vacancy defects offers an available way for improving the thermoelectric performance of silicon nanowires.Reducing the thermal conductivity of silicon nanowires (SiNWs) can enhance the thermoelectric figure of merit. Applying non-equilibrium molecular dynamics (NEMD) simulation, it has been demonstrated that the thermal conductivity of SiNWs is approximately two orders of magnitude lower than bulk silicon crystal and that it can be reduced remarkably by including vacancy defects. It has been found that “surface vacancy defect” reduces thermal conductance much more than “center vacancy defect”. The thermal conductivity reaches the minimum, which is about 17% of that of pristine SiNW, when 2% surface vacancy defect is introduced in the nanowire. In order to reveal the origin of this drastic reduction of thermal conductivity, the vibrational density of states (VDOS) analysis is performed and it has been found that due to the high surface to volume ratio, the various boundary inelastic scatterings of phonon reduce thermal conductivity significantly. Also, larger mass difference due to voids induces smaller therma... read less USED (low confidence) M. A. Lively, S. X. Bennett, and J. Allain, “Molecular dynamics studies of ion beam implantation and patterning of silicon: Effect of noble gas cluster formation,” Physical Review B. 2018. link Times cited: 7 USED (low confidence) J. Li, H. Wang, and Y. Li, “Impact of the thermal motion of silicon atoms on the viscosity of nanoconfined aqueous NaCl solution,” Modern Physics Letters B. 2018. link Times cited: 0 Abstract: The properties of nanoconfined fluid are critical for the de… read moreAbstract: The properties of nanoconfined fluid are critical for the design and precise control of nanofluidic devices. To understand the fundamental details of the viscosity of nanoconfined aqueous NaCl solution, we investigated the impact of the thermal motion of silicon atoms on the viscosity of nanoconfined aqueous NaCl solution using molecular dynamic simulations. The results show that thermal motion of silicon atoms can decrease the viscosity of NaCl solution, and this impact is significant when the shear rate is small. read less USED (low confidence) Z. Zhang and H. Urbassek, “Dislocation-based strengthening mechanisms in metal-matrix nanocomposites: a molecular dynamics study of the influence of reinforcement shape in the Al-Si system,” Computational Materials Science. 2018. link Times cited: 20 USED (low confidence) L. Wang and K. Cai, “Brittle-to-ductile transition in fracture of few-layered black phosphorus ribbons under uniaxial stretching,” Computational Materials Science. 2018. link Times cited: 3 USED (low confidence) Y. Hong, N. Zhang, and M. A. Zaeem, “Metastable phase transformation and deformation twinning induced hardening-stiffening mechanism in compression of silicon nanoparticles,” Acta Materialia. 2018. link Times cited: 20 USED (low confidence) S. Starikov, N. Lopanitsyna, D. Smirnova, and S. Makarov, “Atomistic simulation of Si-Au melt crystallization with novel interatomic potential,” Computational Materials Science. 2018. link Times cited: 20 USED (low confidence) W. Zhou, K. Gong, J. Wan, L. Quan, Y. Chu, and Y. Cao, “Molecular dynamics simulation study on ablation of silicon by water-jet-guided laser,” Proceedings of the Institution of Mechanical Engineers, Part E: Journal of Process Mechanical Engineering. 2017. link Times cited: 5 Abstract: Stillinger–Weber potential and Z-layer energy model were ado… read moreAbstract: Stillinger–Weber potential and Z-layer energy model were adopted in molecular dynamics simulation to study the ablation of silicon by water-jet-guided femtosecond laser, and comparison was made by ablating silicon with or without water-jet cooling in our simulations. Simulation results indicated that with water-jet cooling, the thermal-affected zone could be reduced in area, and the peak of density could disappear more quickly. It was therefore concluded that water-jet-guided laser could be used to considerably improve the ablation quality of silicon. read less USED (low confidence) T. Gao et al., “Structural properties and defects of GaN crystals grown at ultra-high pressures: A molecular dynamics simulation,” Superlattices and Microstructures. 2017. link Times cited: 4 USED (low confidence) M. Ren, L. Deng, and J. Du, “Bulk, surface structures and properties of sodium borosilicate and boroaluminosilicate nuclear waste glasses from molecular dynamics simulations,” Journal of Non-crystalline Solids. 2017. link Times cited: 34 USED (low confidence) T. Gao et al., “Properties of polycrystals and nanotwinned structures in silicon during rapid cooling process,” Materials Research Express. 2017. link Times cited: 0 Abstract: The evolution characteristics of polycrystals and nano-twinn… read moreAbstract: The evolution characteristics of polycrystals and nano-twinned structures during the rapid solidification of silicon under cooling rate of 1010 K s−1 are investigated based on molecular dynamics simulation. The microstructural properties of silicon were analyzed by several structural characterization methods. The distorted tetrahedral units with 5 nearest-neighbor atoms play different roles in three stages of the quenching process. As transitional structures, they play a significant part in liquid to liquid and liquid to crystal transition, and break the translational symmetry of the crystalline structures. The tetrahedral units can aggregate to form polycrystals with high stability in this system. When the temperature was decreased at a cooling rate of 1010 K s−1, Coherent twin boundaries, having excellent structural stability and configurational continuity, were easily formed between zinc-blende and wurtzite structures. read less USED (low confidence) A. Kubo, S. Nagao, and Y. Umeno, “Molecular dynamics study of deformation and fracture in SiC with angular dependent potential model,” Computational Materials Science. 2017. link Times cited: 7 USED (low confidence) P. Zhang, R. Zhu, M. Jiang, Y. Song, D. Zhang, and Y. Cui, “Size effect caused significant reduction of thermal conductivity of GaAs/AlAs distributed Bragg reflector used in semiconductor disk laser,” Optics and Laser Technology. 2017. link Times cited: 4 USED (low confidence) Q. Xiang et al., “Deformation mechanisms and twin boundary effects in cadmium telluride under nanoindentation,” Ceramics International. 2017. link Times cited: 4 USED (low confidence) G. Liang et al., “The tensile effect on crack formation in single crystal silicon irradiated by intense pulsed ion beam,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2017. link Times cited: 4 USED (low confidence) P. Cumpson, M. Jaskiewicz, and W. K. Kim, “Argon cluster‐ion sputter yield: Molecular dynamics simulations on silicon and equation for estimating total sputter yield,” Surface and Interface Analysis. 2017. link Times cited: 2 Abstract: Argon Gas Cluster‐Ion Beam sources have become widely‐used o… read moreAbstract: Argon Gas Cluster‐Ion Beam sources have become widely‐used on X‐ray photoelectron spectroscopy (XPS) and secondary ion mass spectrometry (SIMS) instruments in recent years, but there is little reference data on sputter yields in the literature as yet. Total sputter yield reference data is needed in order to calibrate the depth scale, of XPS or SIMS depth profiles. We previously published a semi‐empirical ‘Threshold’ equation for estimating cluster total sputter yield from the energy‐per‐atom of the cluster and the effective monatomic sputter threshold of the material. This has been shown to agree extremely well with sputter yield measurements on a range or organic and inorganic materials for clusters of around a thousand atoms. Here we use the molecular dynamics (MD) approach to explore a wider range of energy and cluster size than is easy to do experimentally to high precision. We performed MD simulations using the ‘Large‐scale Atomic/Molecular Massively Parallel Simulator’ (LAMMPS) parallel MD code on high‐performance computer (HPC) systems. We performed 1150 simulations of individual collisions with a silicon (100) surface as an archetypal inorganic substrate, for cluster sizes between 30 and 3000 argon atoms and energies in the range 5 to 40 eV per atom. This corresponds to the most important regime for experimental cluster depth‐profiling in SIMS and XPS. Our MD results show a dependence on cluster size as well as energy‐per‐atom. Using the exponent previously suggested by Paruch et al., we modified the Threshold model equation published previously to take this into account. The modified Threshold equation fits all our MD results extremely well, building on its success in fitting experimental sputter yield measurements. read less USED (low confidence) H. Xiang, H. Li, T. Fu, C. Huang, and X. Peng, “Formation of prismatic loops in AlN and GaN under nanoindentation,” Acta Materialia. 2017. link Times cited: 85 USED (low confidence) S. Khanniche, D. Mathieu, F. Pereira, and L. Hairault, “Atomistic models of hydroxylated, ethoxylated and methylated silica surfaces and nitrogen adsorption isotherms: A molecular dynamics approach,” Microporous and Mesoporous Materials. 2017. link Times cited: 9 USED (low confidence) Y. Makoudi et al., “Supramolecular self-assembly on the B-Si(111)-(√3x√3) R30° surface: From single molecules to multicomponent networks,” Surface Science Reports. 2017. link Times cited: 21 USED (low confidence) P. Manimunda et al., “Nanoscale deformation and friction characteristics of atomically thin WSe2 and heterostructure using nanoscratch and Raman spectroscopy,” 2D Materials. 2017. link Times cited: 21 Abstract: 2D transition metals di-selenides are attracting a lot of at… read moreAbstract: 2D transition metals di-selenides are attracting a lot of attention due to their interesting optical, chemical and electronics properties. Here, the deformation characteristics of monolayer, multi- layer WSe2 and its heterostructure with MoSe2 were investigated using a new technique that combines nanoscratch and Raman spectroscopy. The 2D monolayer WSe2 showed anisotropy in deformation. Effect of number of WSe2 layers on friction characteristics were explored in detail. Experimental observations were further supported by MD simulations. Raman spectra recorded from the scratched regions showed strain induced degeneracy splitting. Further nano-scale scratch tests were extended to MoSe2–WSe2 lateral heterostructures. Effect of deformation on lateral hetero junctions were further analysed using PL and Raman spectroscopy. This new technique is completely general and can be applied to study other 2D materials. read less USED (low confidence) V. T. T. Ha, V. Hùng, P. Hanh, V. T. Nguyen, and H. Hieu, “Structural and thermomechanical properties of the zinc-blende AlX (X = P, As, Sb) compounds,” International Journal of Modern Physics B. 2017. link Times cited: 1 Abstract: The structural and thermomechanical properties of zinc-blend… read moreAbstract: The structural and thermomechanical properties of zinc-blende aluminum class of III–V compounds have been studied based on the statistical moment method (SMM) in quantum statistical mechanics. Within the SMM scheme, we derived the analytical expressions of the nearest-neighbor distance, thermal expansion coefficient, atomic mean-square displacement and elastic moduli (Young’s modulus, bulk modulus and shear modulus). Numerical calculations have been performed for zinc-blende AlX (X = As, P, Sb) at ambient conditions up to the temperature of 1000 K. Our results are in good and reasonable agreements with earlier measurements and can provide useful references for future experimental and theoretical works. This research presents a systematic approach to investigate the thermodynamic and mechanical properties of materials. read less USED (low confidence) M. Faruq, A. Villesuzanne, M. Guo, and G. Shao, “Structure, Melting and Transport Properties of Binary Liquid Pd-Si Metal Alloys: Molecular Dynamics Simulations.” 2017. link Times cited: 4 Abstract: Quantum Sutton-Chen (Q-SC) potentials for molecular dynamic … read moreAbstract: Quantum Sutton-Chen (Q-SC) potentials for molecular dynamic (MD) simulation were derived for the Pd-Si system, which were then used to obtain an atomistic description of melting and transport properties for palladium metal, metallic silicon and their alloys. Melting and structural properties were investigated by analysing the radial distribution function, enthalpy, density, and diffusion coefficient as a function of temperature. The agreement between the MD/Q-SC results and experimental values for the estimated melting points and structural properties was excellent for both pure elements: Pd and metallic Si, while melting of alloys was shown to be complicated by chemical association between the interacting constituents, which led to difficulty in the dissociation of long-range order and thus significant overshoot in calculated melting points owing to high heating rate for achievable MD execution. read less USED (low confidence) V. T. T. Ha, V. Hùng, P. Hanh, N. V. Tuyen, T. T. Hai, and H. Hieu, “Investigation of thermodynamic and mechanical properties of AlyIn1−yP alloys by statistical moment method,” Physica B-condensed Matter. 2017. link Times cited: 8 USED (low confidence) X. Wang, Y. Hong, P. Chan, and J. Zhang, “Phonon thermal transport in silicene-germanene superlattice: a molecular dynamics study,” Nanotechnology. 2017. link Times cited: 34 Abstract: Two-dimensional (2D) hybrid materials have drawn enormous at… read moreAbstract: Two-dimensional (2D) hybrid materials have drawn enormous attention in thermoelectric applications. In this work, we apply a molecular dynamics (MD) simulation to investigate the phonon thermal transport in silicene-germanene superlattice. A non-monotonic thermal conductivity of silicene-germanene superlattice with period length is revealed, which is due to the coherent–incoherent phonon conversion and phonon confinement mechanisms. We also calculate the thermal conductivity of a Si-Ge random mixing monolayer, showing a U-shaped trend. Because of the phonon mode localizations at Ge concentration of <20% and >80%, thermal conductivity varies dramatically at low doping regions. By changing the total length (Ltotal), the infinite-length thermal conductivities of pure silicene, pure germanene, silicene-germanene superlattice, and Si-Ge random mixing monolayer are extracted as 16.08, 15.95, 5.60 and 4.47 W/m-K, respectively. The thermal boundary conductance (TBC) of the silicene-germanene is also evaluated, showing a small thermal rectification. At Ltotal = 274.7 nm, the TBC of silicene to germanene is 620.49 MW/m2-K, while that of germanene to silicene is 528.76 MW/m2-K. read less USED (low confidence) R. Aguirre, J. J. Chavez, X. W. Zhou, and D. Zubia, “Crystal Growth Phenomena in Polycrystalline (Cu)ZnTe/CdTe/CdS Via Molecular Dynamics.” 2017. link Times cited: 0 Abstract: Molecular Dynamics (MD) simulations were applied to study th… read moreAbstract: Molecular Dynamics (MD) simulations were applied to study the crystal growth phenomena in polycrystalline (Cu)ZnTe/CdTe/CdS heterostructures. Our results show that polycrystallinity, polytypism and Cu clustering are accurately predicted. The resulted films are zinc blende structure preferentially. The CdTe/CdS interface exhibits a high degree of disorder compared to the (Cu)ZnTe/CdTe interface. Stoichiometry plays an important role for the formation of Cu clusters and diffusion of Zn and Cu into the CdTe substrate. Dislocation motion is captured and analyzed. read less USED (low confidence) K. Cai, L. Liu, J. Shi, and Q. Qin, “Winding a nanotube from black phosphorus nanoribbon onto a CNT at low temperature: A molecular dynamics study,” Materials & Design. 2017. link Times cited: 28 USED (low confidence) J. Zhang, J. Zhang, Z. Wang, A. Hartmaier, Y. Yan, and T. Sun, “Interaction between phase transformations and dislocations at incipient plasticity of monocrystalline silicon under nanoindentation,” Computational Materials Science. 2017. link Times cited: 37 USED (low confidence) T. Zhang et al., “Ultralow thermal conductivity of silicon nanowire arrays by molecular dynamics simulation,” Materials Research Express. 2017. link Times cited: 1 Abstract: We investigate the thermal conductivities of silicon nanowir… read moreAbstract: We investigate the thermal conductivities of silicon nanowires (SiNWs) and their arrays based on molecular dynamics simulations. It is found that diminishing diameter, roughing surface and doping impurity of SiNWs can reduce their thermal conductivities by two or three orders of magnitude compared with that of bulk silicon crystals due to the strong phonon boundary and phonon impurity scattering. The simulated thermal conductivities of SiNW arrays demonstrate that arraying nanowires can further lower the thermal conductivity owing to the laterally-coupled effect, and the thermal conductivity of arrays decreases notably with the increased nanowire volume fraction, resulting in an ultralow thermal conductivity for the doped SiNW arrays with rough surfaces, which provides theoretical guidance of thermal management for semiconductor nanowire based microelectronic and thermoelectric devices. read less USED (low confidence) J. Bohrer, K. Schroer, L. Brendel, and D. Wolf, “Thermal resistance of twist boundaries in silicon nanowires by nonequilibrium molecular dynamics,” AIP Advances. 2017. link Times cited: 7 Abstract: The thermal boundary resistance (Kapitza resistance) of (001… read moreAbstract: The thermal boundary resistance (Kapitza resistance) of (001) twist boundaries in silicon is investigated by nonequilibrium molecular dynamics simulations. In order to enable continuous adjustment of the mismatch angle, a cylindrical geometry with fixed atomic positions at the boundaries is devised. The influence of the boundary conditions on the Kapitza resistance is removed by means of a finite size analysis. Due to the diamond structure of silicon, twist boundaries with mismatch angles ϕ and 90 ° − ϕ are not equivalent, whereas those with ± ϕ or with 90 ° ± ϕ are. The Kapitza resistance increases with mismatch angle up to 45 ° , where it reaches a plateau around 1.56 ± 0.05 K m 2 / GW . Between 80 ° and the 90 ° Σ 1 grain boundary it drops by about 30%. Surprisingly, lattice coincidence at other angles ( Σ 5 , Σ 13 , Σ 27 , Σ 25 ) has no noticable effect on the Kapitza resistance. However, there is a clear correlation between the Kapitza resistance and the width of a non-crystalline layer at the twist ... read less USED (low confidence) H. Araghi, Z. Zabihi, P. Nayebi, and M. Ehsani, “Growth of CdTe on Si(100) surface by ionized cluster beam technique: Experimental and molecular dynamics simulation,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2016. link Times cited: 2 USED (low confidence) Y. Hong, N. Zhang, and L. Xiong, “Nanoscale plastic deformation mechanisms of single crystalline silicon under compression, tension and indentation.” 2016. link Times cited: 18 Abstract: Mechanical behavior and underlying nanoscale plastic deforma… read moreAbstract: Mechanical behavior and underlying nanoscale plastic deformation mechanisms of single crystalline silicon under compression, tension and indentation are investigated through molecular dynamics in this work. Simulation results show that phase transformation from diamond cubic Si-I to β-Sn is responsible for the plastic deformation behavior of Si both under compression and nanoindentation. A stress plateau is observed when the specimen is compressed uniaxially. Si-I to β-Sn phase transformation has been demonstrated to be responsible for such stress plateau. Periodic boundary condition is found not suitable to study the tensile strength of silicon pillars. A pop-in behavior is observed in the force–displacement curve of nanoindentation. It has been proved that this pop-in region is induced by Si-I to β-Sn phase transformation. Through tracking the atom stress, shear stress rather than normal stress is revealed to dominate the phase transformation process. During nanoindentation, to exclude size effect the substrate should be larger enough than the indenter. read less USED (low confidence) P. Käshammer, N. Borgardt, M. Seibt, and T. Sinno, “Quantitative assessment of molecular dynamics-grown amorphous silicon and germanium films on silicon (111),” Surface Science. 2016. link Times cited: 3 USED (low confidence) C.-ying Wang et al., “Effects of 30° partial dislocation and stacking fault on Na and Mg storage and diffusion in Si anode,” Computational Materials Science. 2016. link Times cited: 5 USED (low confidence) C. Angell and V. Kapko, “Potential tuning in the S–W system. (i) Bringing Tc,2 to ambient pressure, and (ii) colliding Tc,2 with the liquid–vapor spinodal,” Journal of Statistical Mechanics: Theory and Experiment. 2016. link Times cited: 10 Abstract: Following Vasisht et al’s identification of the second criti… read moreAbstract: Following Vasisht et al’s identification of the second critical point (Tc2, Pc2) for liquid silicon in the Stillinger–Weber (S–W) model for silicon, we study the variation of Tc2, Pc2 with tetrahedral repulsion parameter in an extension of the earlier ‘potential tuning’ study of this system. We use the simple isochore crossing approach to identify the location of the second critical point (before any crystallization can occur) as a function of the ‘tuning’ or ‘tetrahedrality’, parameter λ, and identify two phenomena of high interest content. The first is that the second critical point pressure Pc2, becomes less negative as λ decreases from the silicon value (meaning the drive to high tetrahedrality is decreased) and reaches zero pressure at the same value of lambda found to mark the onset of glassforming ability in an earlier study of this tunable system. The second is that, as the Tc,2 approaches the temperature of the liquid–gas spinodal, λ > 22, the behavior of the temperature of maximum density (TMD) switches from the behavior seen in most current water pair potential models (locus of TMDs has a maximum), to the behavior seen in empirical engineering multiparameter equations of state (EoS) (and also by two parameter Speedy isothermal expansion EoS) for water, according to which the locus of TMDs of HDL phase has no maximum, and the EoS for HDL has no second critical point. At λ = 23 the behavior is isomorphic with that of the mW model of water, which is now seen to conform, at least closely, to the ‘critical point free’ scenario for water. read less USED (low confidence) M. Verdier, K. Termentzidis, and D. Lacroix, “Crystalline-amorphous silicon nano-composites: Nano-pores and nano-inclusions impact on the thermal conductivity,” Journal of Applied Physics. 2016. link Times cited: 34 Abstract: The thermal conductivities of nanoporous and nanocompositesi… read moreAbstract: The thermal conductivities of nanoporous and nanocompositesilicon with incorporated amorphous phases have been computed by molecular dynamics simulations. A systematic investigation of the porosity and the width of the amorphous shell contouring a spherical pore has been made. The impact of amorphous phase nanoinclusions in a crystalline matrix has also been studied with the same amorphous fraction as the porosity of nanoporoussilicon to achieve comparison. The key parameter for all configurations with or without the amorphous phase is proved to be the interface (between the crystalline and amorphous phases or crystalline and void) to volume ratio. We obtain the sub-amorphous thermal conductivity for several configurations by combining pores, amorphous shell, and crystalline phase. These configurations are promising candidates for low cost and not toxic thermoelectric devices based on abundant semiconductors. read less USED (low confidence) S. Y. Matsushita, C. Hu, E. Kawamoto, H. Kato, K. Watanabe, and S. Suto, “Surface phonon dispersion on hydrogen-terminated Si(110)-(1 × 1) surfaces studied by first-principles calculations.,” The Journal of chemical physics. 2015. link Times cited: 3 Abstract: We studied the lattice constants, surface-phonon dispersion … read moreAbstract: We studied the lattice constants, surface-phonon dispersion curves, spectral densities, and displacement vectors of the hydrogen-terminated Si(110)-(1 × 1) [H:Si(110)-(1 × 1)] surface using the first-principles calculations within the framework of density functional theory (DFT). The symmetry of the H:Si(110)-(1 × 1) surface belongs to the two-dimensional space group p2mg, which has two highly symmetric and orthogonal directions, ΓX¯ and ΓX(')¯, with the glide planes along the ΓX¯ direction. Because glide symmetry separates the even and odd surface phonon modes, we mapped the even surface modes in the first surface Brillouin zone (SBZ) and the odd surface modes in the second SBZ using the spectral densities and displacement vectors. The surface phonon modes were analyzed with respect to their physical origin, spatial localization properties, polarization, and the charge density of their electronic states. Our calculated surface phonon modes were in good agreement with recent high-resolution electron-energy-loss spectroscopy data in the first and second SBZs of the ΓX¯ direction. In the SBZ of the ΓX(')¯ direction, our calculated surface phonon modes agree well with the data in the energy region below 65 meV but are not satisfactorily compatible with those in the stretching and bending modes. In addition, we discuss the microscopic nature of the surface phonon dispersion of the H:Si(110)-(1 × 1) surface using the phonon eigen modes. read less USED (low confidence) M. G. Shahraki and Z. Zeinali, “Effects of vacancy defects and axial strain on thermal conductivity of silicon nanowires: A reverse nonequilibrium molecular dynamics simulation,” Journal of Physics and Chemistry of Solids. 2015. link Times cited: 20 USED (low confidence) P. Hecquet, “Subcritical damping of SA step energy on Si(001) vicinals by lowering terrace stress,” Surface Science. 2015. link Times cited: 0 USED (low confidence) S. Amokrane, A. Ayadim, and L. Levrel, “Structure of the glass-forming metallic liquids by ab-initio and classical molecular dynamics, a case study: Quenching the Cu60Ti20Zr20 alloy,” Journal of Applied Physics. 2015. link Times cited: 9 Abstract: We consider the question of the amorphization of metallic al… read moreAbstract: We consider the question of the amorphization of metallic alloys by melt quenching, as predicted by molecular dynamics simulations with semi-empirical potentials. The parametrization of the potentials is discussed on the example of the ternary Cu-Ti-Zr transition metals alloy, using the ab-initio simulation as a reference. The pair structure in the amorphous state is computed from a potential of the Stillinger-Weber form. The transferability of the parameters during the quench is investigated using two parametrizations: from solid state data, as usual and from a new parametrization on the liquid structure. When the adjustment is made on the pair structure of the liquid, a satisfactory transferability is found between the pure components and their alloys. The liquid structure predicted in this way agrees well with experiment, in contrast with the one obtained using the adjustment on the solid. The final structure, after quenches down to the amorphous state, determined with the new set of parameters is show... read less USED (low confidence) P. Stoch and A. Stoch, “Structure and properties of Cs containing borosilicate glasses studied by molecular dynamics simulations,” Journal of Non-crystalline Solids. 2015. link Times cited: 23 USED (low confidence) S. Zhang et al., “Polymorphism in glassy silicon: Inherited from liquid-liquid phase transition in supercooled liquid,” Scientific Reports. 2015. link Times cited: 15 USED (low confidence) S. Sh and M. Foroutan, “Study on formation of unstable clathrate-like water molecules at freezing/melting temperatures of water and salty water,” Fluid Phase Equilibria. 2014. link Times cited: 7 USED (low confidence) Z. Zhang et al., “Deformation and crack mechanisms of nanotwinned cadmium telluride under cyclic nanoindentations,” Scripta Materialia. 2014. link Times cited: 6 USED (low confidence) P. Ghosh and M. Ranganathan, “Submonolayer growth study using a solid-on-solid model for 2 × 1 reconstructed surfaces of diamond-like lattices,” Surface Science. 2014. link Times cited: 7 USED (low confidence) S. Zhang and W. Gao, “Molecular Dynamics Simulation on Liquid Nucleation in Ideal Silicon Crystal upon Melting,” Advanced Materials Research. 2014. link Times cited: 3 Abstract: Liquid nucleation in an ideal silicon crystal is studied in … read moreAbstract: Liquid nucleation in an ideal silicon crystal is studied in the framework of Lindemann criteria by using molecular dynamics simulations. Lindemann parameter is traced during the transition. It is found that when Lindemann parameter reaches a critical value δL*=0.328, liquid emerges, and when 9.4% atoms in the crystal exceeds the critical value, a complete melting is achieved. read less USED (low confidence) L. Lupi, N. Kastelowitz, and V. Molinero, “Vapor deposition of water on graphitic surfaces: formation of amorphous ice, bilayer ice, ice I, and liquid water.,” The Journal of chemical physics. 2014. link Times cited: 59 Abstract: Carbonaceous surfaces are a major source of atmospheric part… read moreAbstract: Carbonaceous surfaces are a major source of atmospheric particles and could play an important role in the formation of ice. Here we investigate through molecular simulations the stability, metastability, and molecular pathways of deposition of amorphous ice, bilayer ice, and ice I from water vapor on graphitic and atomless Lennard-Jones surfaces as a function of temperature. We find that bilayer ice is the most stable ice polymorph for small cluster sizes, nevertheless it can grow metastable well above its region of thermodynamic stability. In agreement with experiments, the simulations predict that on increasing temperature the outcome of water deposition is amorphous ice, bilayer ice, ice I, and liquid water. The deposition nucleation of bilayer ice and ice I is preceded by the formation of small liquid clusters, which have two wetting states: bilayer pancake-like (wetting) at small cluster size and droplet-like (non-wetting) at larger cluster size. The wetting state of liquid clusters determines which ice polymorph is nucleated: bilayer ice nucleates from wetting bilayer liquid clusters and ice I from non-wetting liquid clusters. The maximum temperature for nucleation of bilayer ice on flat surfaces, T(B)(max) is given by the maximum temperature for which liquid water clusters reach the equilibrium melting line of bilayer ice as wetting bilayer clusters. Increasing water-surface attraction stabilizes the pancake-like wetting state of liquid clusters leading to larger T(B)(max) for the flat non-hydrogen bonding surfaces of this study. The findings of this study should be of relevance for the understanding of ice formation by deposition mode on carbonaceous atmospheric particles, including soot. read less USED (low confidence) L. Si and X. Wang, “Nano-adhesion influenced by atomic-scale asperities: A molecular dynamics simulation study,” Applied Surface Science. 2014. link Times cited: 17 USED (low confidence) B. Song, A. Nguyen, and V. Molinero, “Can Guest Occupancy in Binary Clathrate Hydrates Be Tuned through Control of the Growth Temperature,” Journal of Physical Chemistry C. 2014. link Times cited: 30 Abstract: Clathrate hydrates are nonstoichiometric compounds comprised… read moreAbstract: Clathrate hydrates are nonstoichiometric compounds comprised of a hydrogen-bonded water network that forms polyhedral cages that can be occupied by small guest molecules. Clathrates are candidate materials for storage and transportation of methane and H2. Promoter molecules, such as THF, reduce the pressure or temperature needed to form clathrates of these gases, resulting in the formation of binary clathrates with the promoter molecule hosted in the large cages of the hydrate. In this work, we study the growth and occupancy of binary clathrates as a function of supercooling of the solution using molecular dynamics simulations with the mW water model and small and large guest molecules of sizes similar to those of H2 and THF, respectively, but that are both highly soluble in water and produce single hydrates with identical melting point. The large guest molecules only fit into the 51264 cages, while the small guest molecules can fit into both types of cages. We find that the large guest act as a kinetic p... read less USED (low confidence) M. Schowalter et al., “Influence of Static Atomic Displacements on Composition Quantification of AlGaN/GaN Heterostructures from HAADF-STEM Images,” Microscopy and Microanalysis. 2014. link Times cited: 10 Abstract: In an earlier publication Rosenauer et al. introduced a meth… read moreAbstract: In an earlier publication Rosenauer et al. introduced a method for determination of composition in AlGaN/GaN heterostructures from high-angle annular dark field (HAADF) images. Static atomic displacements (SADs) were neglected during simulation of reference data because of the similar covalent radii of Al and Ga. However, SADs have been shown (Grillo et al.) to influence the intensity in HAADF images and therefore could be the reason for an observed slight discrepancy between measured and nominal concentrations. In the present study parameters of the Stillinger–Weber potential were varied in order to fit computed elastic constants, lattice parameters and bonding energies to experimental ones. A reference data set of HAADF images was simulated, in which the new parameterization was used to account for SADs. Two reference samples containing AlGaN layers with different Al concentrations were investigated and Al concentrations in the layers determined based on the new data set. We found that these concentrations were in good agreement with nominal concentrations as well as concentrations determined using alternative techniques such as strain state analysis and energy dispersive X-ray spectroscopy. read less USED (low confidence) T. Zientarski and D. Chocyk, “Strain and structure in nano Ag films deposited on Au: Molecular dynamics simulation,” Applied Surface Science. 2014. link Times cited: 9 USED (low confidence) T. Zientarski and D. Chocyk, “Structure and stress in Cu/Au and Fe/Au systems: A molecular dynamics study,” Thin Solid Films. 2014. link Times cited: 12 USED (low confidence) Z. Wang, G. Yin, L. Jing, J. Shi, and Z. Li, “Tensile behavior of single crystalline GaN nanotube bundles: An atomistic-level study,” International Journal of Modern Physics B. 2014. link Times cited: 1 Abstract: The tensile behavior of single crystalline GaN nanotube bund… read moreAbstract: The tensile behavior of single crystalline GaN nanotube bundles was studied using classical molecular dynamics. Stillinger–Weber potential was used to describe the atom–atom interactions. The GaN bundles consisted of several individual GaN nanotubes with {100} side planes. The simulation results show that the nanotube bundles show a brittle to ductile transition (BDT) by changing the temperatures. The fracture of GaN nanotube bundles is ruled by a thermal activated process, higher temperature will lead to the decrease of the critical stress. At high temperatures the individual nanotube in the bundles interact with each other, which induces the increase of the critical stress of bundles. read less USED (low confidence) P. Hecquet, “Interaction energy between dipole lines applied on symmetric (2 × 1) reconstructed Si(001),” Surface Science. 2014. link Times cited: 1 USED (low confidence) J. Delaye, S. Peuget, G. Calas, and L. Galoisy, “Comparative effects of thermal quenching and ballistic collisions in SiO2–B2O3–Na2O glass,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2014. link Times cited: 15 USED (low confidence) N. Nakazaki, Y. Takao, K. Eriguchi, and K. Ono, “Molecular dynamics simulations of silicon chloride ion incidence during Si etching in Cl-based plasmas,” Japanese Journal of Applied Physics. 2014. link Times cited: 17 Abstract: Classical molecular dynamics (MD) simulations have been perf… read moreAbstract: Classical molecular dynamics (MD) simulations have been performed for SiClx+ (x = 0–4) ions incident on Si(100) surfaces, using an improved Stillinger–Weber (SW) potential form, to understand the surface reaction kinetics of etch byproduct ion incidence during Si etching in Cl-based plasmas. The ions were normally incident on surfaces with translational energies in the range of Ei = 20–500 eV, and the surface reaction kinetics of Clx+ (x = 1, 2) ion incidence were also simulated for reference. The etch yields and thresholds presently simulated were in agreement with the experimental results previously reported for the respective ion beam incidences on Si. Numerical results indicated that the etch yields y* per halogen (or per constituent Cl atom of incident ions), thresholds, surface coverages of Cl atoms adsorbed, and thicknesses of chlorinated surface layers are almost the same, when compared at the same translational energy per halogen; moreover, the stoichiometries of product species desorbed, stoichiometries of chlorinated surface layers, and their depth profiles are also similar when compared at the same . Thus, it follows that the etching characteristics for SiClx+ as well as Clx+ incidences on Si are determined primarily or scaled universally by , unless the deposition is significant at low Ei or for SiCl+ and SiCl2+. read less USED (low confidence) Y. Gao, W. Bao, Q. Meng, Y. Jing, and X. Song, “The thermal transport properties of single-crystalline nanowires covered with amorphous shell: A molecular dynamics study,” Journal of Non-crystalline Solids. 2014. link Times cited: 16 USED (low confidence) A. Pham, M. Barisik, and B. H. Kim, “Molecular dynamics simulations of Kapitza length for argon-silicon and water-silicon interfaces,” International Journal of Precision Engineering and Manufacturing. 2014. link Times cited: 0 USED (low confidence) H. Hieu and V. Hùng, “Pressure-dependent EXAFS mean-square relative displacements of germanium and silicon crystals,” High Pressure Research. 2013. link Times cited: 4 Abstract: In this paper, the statistical moment method (SMM) has been … read moreAbstract: In this paper, the statistical moment method (SMM) has been developed to study the pressure dependence of thermodynamic quantities of germanium and silicon crystals. We have derived the analytical expressions of the pressure-dependent parallel mean-square relative displacement (MSRD) or extended X-ray absorption fine structure (EXAFS) Debye–Waller factor, mean-square displacement (MSD) as well as lattice constant and volume change of diamond-type crystals. Numerical calculations performed for these semiconductors up to 11 GPa are found to be in good and reasonable agreement with available experimental data as well as with previous theoretical studies. Our results indicate that the SMM can be efficiently used for determining the relative change of the pressure-dependent MSRDs of germanium and silicon semiconductors. The research also shows the advantage of SMM on studying other thermodynamic properties of materials under high pressures. read less USED (low confidence) P. Hecquet, “Surface stresses on symmetric (2 × 1) reconstructed Si(001) calculated from surface energy variations,” Surface Science. 2013. link Times cited: 3 USED (low confidence) Z. Zhang, X. Zhang, X. Guo, F. Ye, and Y. Huo, “Hardening mechanism of twin boundaries during nanoindentation of soft-brittle CdTe crystals,” Scripta Materialia. 2013. link Times cited: 12 USED (low confidence) Y. Rosandi and H. Urbassek, “Influence of the ion impact azimuth on glancing-incidence keV ion impact on the Si(100) surface,” Surface Science. 2013. link Times cited: 3 USED (low confidence) X. W. Zhou, D. Ward, J. E. Martin, F. Swol, J. Cruz-Campa, and D. Zubia, “Stillinger-Weber potential for the II-VI elements Zn-Cd-Hg-S-Se-Te,” Physical Review B. 2013. link Times cited: 86 Abstract: X. W. Zhou,1,* D. K. Ward,2 J. E. Martin,3 F. B. van Swol,4 … read moreAbstract: X. W. Zhou,1,* D. K. Ward,2 J. E. Martin,3 F. B. van Swol,4 J. L. Cruz-Campa,5 and D. Zubia6 1Mechanics of Materials Department, Sandia National Laboratories, Livermore, California 94550, USA 2Radiation and Nuclear Detection Materials and Analysis Department, Sandia National Laboratories, Livermore, California 94550, USA 3Nanoscale Sciences Department, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA 4Computational Materials and Data Science Department, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA 5MEMS Technologies Department, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA 6Department of Electrical Engineering, University of Texas at El Paso, El Paso, Texas 79968, USA (Received 30 May 2013; published 9 August 2013; corrected 13 November 2013) read less USED (low confidence) J.-W. Jiang, H. S. Park, and T. Rabczuk, “Molecular dynamics simulations of single-layer molybdenum disulphide (MoS2): Stillinger-Weber parametrization, mechanical properties, and thermal conductivity,” Journal of Applied Physics. 2013. link Times cited: 303 Abstract: We present a parameterization of the Stillinger-Weber potent… read moreAbstract: We present a parameterization of the Stillinger-Weber potential to describe the interatomic interactions within single-layer MoS2 (SLMoS2). The potential parameters are fitted to an experimentally obtained phonon spectrum, and the resulting empirical potential provides a good description for the energy gap and the crossover in the phonon spectrum. Using this potential, we perform classical molecular dynamics simulations to study chirality, size, and strain effects on the Young's modulus and the thermal conductivity of SLMoS2. We demonstrate the importance of the free edges on the mechanical and thermal properties of SLMoS2 nanoribbons. Specifically, while edge effects are found to reduce the Young's modulus of SLMoS2 nanoribbons, the free edges also reduce the thermal stability of SLMoS2 nanoribbons, which may induce melting well below the bulk melt temperature. Finally, uniaxial strain is found to efficiently manipulate the thermal conductivity of infinite, periodic SLMoS2. read less USED (low confidence) M. Zhai, T. Yoshioka, J. Yang, J. Lu, D. Yin, and J. Wang, “Preparation and characterization of amorphous carbon (a-C) membranes by molecular dynamics simulation,” Desalination and Water Treatment. 2013. link Times cited: 2 Abstract: Amorphous carbon (a-C) membranes with 1,728 particles were p… read moreAbstract: Amorphous carbon (a-C) membranes with 1,728 particles were prepared from diamond at four different densities (1.8, 2.0, 2.28, and 2.4 g/cm3) using molecular dynamics simulation. Stillinger and Weber potential for carbon was introduced with kinetic energy abided by classical Newton equation. Time mesh was chosen 0.01 or 1 fs. The melt-quenching technology method was adopted with the corresponding cooling rate 5 and 0.05 K/fs, respectively. Different membranes were obtained from higher initial temperature (7,500, 7,000, or 6,500 K at different densities and cooling rates) to room temperature. We compared the radial distribution function, bond angle distribution, and pore size distribution with experimental data. The results agreed well and one membrane at lower density with larger pores was chosen to calculate the gas permeation further. Gas molecules (He, Ne, H2, CO2, N2, CH4, and SF6) permeation through the a-C membrane at low density (1.8 g/cm3) when time mesh equal to 1 fs were calculated at 30... read less USED (low confidence) T. Sipkens et al., “In Situ Particle Size Measurements of Gas-Borne Silicon Nanoparticles by Time-Resolved Laser-Induced Incandescence.” 2013. link Times cited: 0 Abstract: The functionality of silicon nanoparticles is strongly size-… read moreAbstract: The functionality of silicon nanoparticles is strongly size-dependent, so there is a pressing need for laser diagnostics that can characterize aerosolized silicon nanoparticles. The present work is the first attempt to extend time-resolved laser-induced incandescence (TiRe-LII), a combustion diagnostic used for sizing soot, to size silicon nanoparticles. TiRe-LII measurements are made on silicon nanoparticles synthesized in a low-pressure plasma reactor containing argon. Molecular dynamics (MD) is used to predict the accommodation coefficient between silicon nanoparticles and argon and helium, which is needed to interpret the TiRe-LII data. The MD-derived thermal accommodation coefficients will be validated by comparing them to experimentally-derived values found using transmission electron microscopy (TEM) and Brunauer-Emmett-Teller (BET) analysis.Copyright © 2013 by ASME read less USED (low confidence) D. Chocyk and T. Zientarski, “Study of Structure and Strain in Au/Cu Systems Using Molecular Dynamics Simulation: X-Ray Scattering Analysis,” Solid State Phenomena. 2013. link Times cited: 1 Abstract: The aim of this work is to investigate structure and stress … read moreAbstract: The aim of this work is to investigate structure and stress evolution in Au/Cu bilayer systems during deposition. The approach used here is based on an embedded atom method (EAM). interatomic potential database for different metal elements, their alloys and multilayers. We applied the kinematical scattering theory to calculate the X-ray scattering profiles. In this case the X-ray scattering techniques are used for the structural characterization of crystal structures obtained from simulation data. This method was applied to determine the lattice parameters in any directions. The lattice parameters in deposited layers were directly determined by the analysis of X-ray diffraction profiles. Results shows that on the interface of Au/Cu system, the crystalline lattice of Au layer is fitted to crystalline lattice of Cu layer. We found that deformation of the crystal lattice near the interface has a major influence on the stress. read less USED (low confidence) T. Aoki, T. Seki, and J. Matsuo, “Molecular dynamics simulation study of damage formation and sputtering with huge fluorine cluster impact on silicon,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2013. link Times cited: 3 USED (low confidence) R. Jones, J. Duda, X. W. Zhou, C. Kimmer, and P. Hopkins, “Investigation of size and electronic effects on Kapitza conductance with non-equilibrium molecular dynamics,” Applied Physics Letters. 2013. link Times cited: 55 Abstract: In nanosystems, the thermal resistance between materials typ… read moreAbstract: In nanosystems, the thermal resistance between materials typically dominates the overall resistance. While size effects on thermal conductivity are well documented, size effects on thermal boundary conductance have only been speculated. In response, we characterize the relationship between interfacial resistance and material dimension using molecular dynamics. We find that the interfacial resistance increases linearly with inverse system length but is insensitive to cross-sectional area. Also, from the temperature-dependence of interfacial resistance, we conclude that contributions of short-wavelength phonons dominate. Lastly, by coupling the molecular dynamics to a two-temperature model, we show that electron-mediated transport has little effect on thermal resistance. read less USED (low confidence) L. Xiong, Q. Deng, and Y. Chen, “Coarse-Grained Atomistic Simulations of Dislocation and Fracture in Metallic Materials.” 2013. link Times cited: 1 USED (low confidence) K.-H. Lin and A. Strachan, “Thermal transport in SiGe superlattice thin films and nanowires: Effects of specimen and periodic lengths,” Physical Review B. 2013. link Times cited: 47 USED (low confidence) K. Shimamura, J. Okuma, S. Ohmura, and F. Shimojo, “Molecular-Dynamics Study of Void-Formation inside Silicon Wafers in Stealth Dicing,” Journal of Physics: Conference Series. 2012. link Times cited: 11 Abstract: The mechanism of void formation in crystalline silicon after… read moreAbstract: The mechanism of void formation in crystalline silicon after laser irradiation is extensively studied by molecular-dynamics simulations. When the laser-irradiated region is melted due to a rapid temperature increase, small voids are generated in that region because of large density fluctuations. Because tensile stresses are generated in the melting region, the large empty hole is formed upon cooling. When the temperature drops below the melting point, recrystallization occurs around the large void. We find that the void persists even after the recrystallization process is stopped, and that a part of the laser-irradiated region is amorphous even at room temperature. The stress distribution around the void and the amorphous region in crystalline silicon is also discussed. read less USED (low confidence) X. J. Yang, S. Zhan, and Y. Chi, “Molecular Dynamics Simulation of Nanoscale Sliding Friction Process between Sphere and Plane,” Applied Mechanics and Materials. 2012. link Times cited: 2 Abstract: Contact surface of nanoscale sliding friction represent some… read moreAbstract: Contact surface of nanoscale sliding friction represent some new features that are different from the macro scale sliding friction, which need to seek new analysis methods. Molecular dynamics simulation is an effective method to describe microscopic phenomena. Therefore, Molecular dynamics method was used to study mechanical behavior of contact surface of nanoscale sliding friction. A molecular dynamics model of hemisphere sphere sliding on rectangular solid plane was built. State change of the micro contact area and friction force variation in the process of sliding friction were observed and analyzed after solution and simulation. The results show that, at the beginning position of the sliding, with different contact depth, contact action region of hemisphere and plane generated the atoms displacement, re-arranged and close-packed accumulation is also different. The deeper the contact depth is, the greater the atoms close-packed accumulation is, and the greater the contact deformation is. In the process of sliding friction, the contact surface of the basal body has produced lattice destruction, surface upheaval and silicon atoms close-packed accumulation, and then formed furrow scratches. At the same time the silicon atoms of the hemisphere generated atomic migration obviously and adhered on the basal body surface. The top of the hemisphere was torn and peeled, which resulted in wear. The deeper contact depth is, the more loss of the material of the hemisphere is, and wear become heavier. The curve of friction force and sliding displacement in different contact depths shows that the deeper contact depth is, the greater friction force is. The friction force increases quickly at the beginning of the sliding. Then the friction force remains steady relatively at stable sliding phase. In subsequent sliding process, due to hemisphere was worn and the original contact surface changed in size, shape and configuration state, friction force decreases obviously. Besides, in process of sliding friction, due to stick-slip effect, friction force appears obviously fluctuations. Moreover, if the sliding speed is large the changes of sliding speed have less effect on friction force when the nanoscale sphere sliding on the plane at the different speeds. read less USED (low confidence) H. Gong, W. Lu, L. Wang, G. Li, and S. Zhang, “The effect of deposition velocity and cluster size on thin film growth by Cu cluster deposition,” Computational Materials Science. 2012. link Times cited: 23 USED (low confidence) Q. Liu and S. Shen, “On the large-strain plasticity of silicon nanowires: Effects of axial orientation and surface,” International Journal of Plasticity. 2012. link Times cited: 33 USED (low confidence) L. Xiong, D. McDowell, and Y. Chen, “Nucleation and growth of dislocation loops in Cu, Al and Si by a concurrent atomistic-continuum method,” Scripta Materialia. 2012. link Times cited: 46 USED (low confidence) S. Murad and I. Puri, “Molecular simulations of thermal transport across interfaces: solid–vapour and solid–solid,” Molecular Simulation. 2012. link Times cited: 6 Abstract: Using molecular simulations, we have investigated heat trans… read moreAbstract: Using molecular simulations, we have investigated heat transfer across the solid–fluid interface between water and silicon and silica wafers, and solid–solid interfaces in superlattices and thin solid films. The system set-up has allowed us to focus on the resistance associated with both the fluid and solid interfaces. For instance, by maintaining the solid phase at a constant temperature we can focus solely on the fluid-side resistance. Our results show that the thermal or Kapitza resistance at fluid side of the solid–fluid decreases significantly as the surface is made more hydrophilic. This is primarily due to increases in fluid adsorption and absorption at the surface, which enhance the intermolecular collision frequency at the interface. Increasing this frequency also reduces the dependence of thermal transport on variations in the interfacial temperature and pressure. Hence, decreasing the density diminishes the intermolecular collision frequency, which increases the thermal resistance. By maintaining the fluid at a constant temperature we have also examined the interface resistance on the solid side. Our results show that these interfacial resistances can diminish the wall heat flux by an order of magnitude in comparison with a hypothetical system for which the overall fluid–solid contact resistances are negligible. Finally, we consider the solid phase as a superlattice in which case the interfacial resistances produced between different solid layers can significantly lower the heat transfer. Our simulations show significant resistance to thermal transport between thin films of the solid phase which constitute the superlattice, providing insight into how a superinsulator can be designed. read less USED (low confidence) W. Huang, W. Ge, C. Li, C. Hou, X. Wang, and X. He, “Atomic and electronic structures of Si[001] (130) symmetric tilt grain boundaries based on first-principles calculations,” Computational Materials Science. 2012. link Times cited: 12 USED (low confidence) Y. Rosandi and H. Urbassek, “Glancing ion incidence on Si(100): Influence of surface reconstruction on ion subsurface channeling,” Physical Review B. 2012. link Times cited: 9 USED (low confidence) Y. Qiu, Y. Chen, L. Liu, and G. Zhao, “Water and ion distributions in a silicon nanochannel: a molecular dynamics study,” Proceedings of the Institution of Mechanical Engineers, Part N: Journal of Nanoengineering and Nanosystems. 2012. link Times cited: 2 Abstract: By way of molecular dynamics simulation, a physically realis… read moreAbstract: By way of molecular dynamics simulation, a physically realistic nanochannel with consideration of the thermal motion of channel walls is proposed, and the distributions of water and ions in the electrical double layer region on a charged silicon surface are observed. It is found that the distribution profile of Na+ ions has double peaks corresponding to the Stern electrical double layer model. Also, the water distribution profile in the 3.0 nm nanochannel agrees very well with that observed in a previous experiment (Cheng et al. Phys. Rev. Lett. 2001; 87: 156103). In addition, the height of nanochannel has negligible effect on the thicknesses of the water layers, but affects the peak numbers of water density distributions dramatically. read less USED (low confidence) E. Holmstrom, J. Kotakoski, L. Lechner, U. Kaiser, and K. Nordlund, “Atomic-scale effects behind structural instabilities in Si lamellae during ion beam thinning,” AIP Advances. 2012. link Times cited: 9 Abstract: The rise of nanotechnology has created an ever-increasing ne… read moreAbstract: The rise of nanotechnology has created an ever-increasing need to probe structures on the atomic scale, to which transmission electron microscopy has largely been the answer. Currently, the only way to efficiently thin arbitrary bulk samples into thin lamellae in preparation for this technique is to use a focused ion beam (FIB). Unfortunately, the established FIB thinning method is limited to producing samples of thickness above ∼20 nm. Using atomistic simulations alongside experiments, we show that this is due to effects from finite ion beam sharpness at low milling energies combined with atomic-scale effects at high energies which lead to shrinkage of the lamella. Specifically, we show that attaining thickness below 26 nm using a milling energy of 30 keV is fundamentally prevented by atomistic effects at the top edge of the lamella. Our results also explain the success of a recently proposed alternative FIB thinning method, which is free of the limitations of the conventional approach due to the absence... read less USED (low confidence) G. Liu and Y.-P. Yao, “Large Scale Molecular Dynamics Simulation of Femtosecond Laser Ablation of Silicon Using Sensing-VISICOM,” Advanced Materials Research. 2011. link Times cited: 2 Abstract: Silicon is widely used as substrate material for the fabrica… read moreAbstract: Silicon is widely used as substrate material for the fabrication of micro-electro and micromechanical components. Since silicon is very brittle, how to cut it into complex shapes remains a hot topic. Thanks to the small spot diameter, laser cutting is a promising alternative. However, during laser cutting, different kinds of defects can be generated depending on the beam-material interaction phenomena (ablation, melting, etc). Molecular Dynamics simulation is an effective way to study the beam-material interaction phenomena. Lots of work has been done to develop MD models of laser ablation of silicon. However, due to lack of support from high performance parallel simulation platform, the scale of the molecular systems is limited. This paper presents a component-based parallel simulation platform Sensing-VISICOM, for large scale molecular dynamics simulation. To test its runtime performance, a molecular system of femtosecond laser ablation of silicon is designed and implemented under Sensing-VISICOM. The results of the simulation show the platform can scales well to millions of atoms. read less USED (low confidence) J. Guénolé, S. Brochard, and J. Godet, “Unexpected slip mechanism induced by the reduced dimensions in silicon nanostructures: Atomistic study,” Acta Materialia. 2011. link Times cited: 20 USED (low confidence) H. Kim and V. Tomar, “Nanometer to Micron Scale Atomistic Mechanics of Silicon Using Atomistic Simulations at Accelerated Time Steps,” Journal of Nanomechanics and Micromechanics. 2011. link Times cited: 2 Abstract: Atomistic simulations have a unique capability to reveal the… read moreAbstract: Atomistic simulations have a unique capability to reveal the material deformation mechanisms and the corresponding deformation-based constitutive behavior. However, atomistic simulations are limited by the accessible length and time scales. In the present work, an equivalent crystal lattice method is used to analyze atomistic mechanical deformation of nanometer- to micrometer-sized polycrystalline silicon (Si) samples at accelerated time steps. The equivalent crystal lattice method’s validity is verified by the results of classical molecular dynamics (MD) simulations at MD strain rates. The method is then used to predict material behavior at subcontinuum length scales. An extrapolation of the thin film polycrystalline silicon stress-strain relationships to lower strain-rate values indicates that the thin film peak stress values at the experimental strain rates are in agreement with experimental values. Analyses reveal that the peak stress values in the case of polycrystalline Si follow inverse Hall-Petch ... read less USED (low confidence) G. Samolyuk, S. Golubov, Y. Osetsky, and R. Stoller, “Molecular dynamics study of influence of vacancy types defects on thermal conductivity of β-SiC,” Journal of Nuclear Materials. 2011. link Times cited: 30 USED (low confidence) H. Kim and V. Tomar, “Nanometer to micron scale mechanics of [100] silicon nanowires using atomistic simulations at accelerated time steps,” physica status solidi (a). 2011. link Times cited: 10 Abstract: Atomistic simulations have a unique capability to reveal the… read moreAbstract: Atomistic simulations have a unique capability to reveal the material deformation mechanisms and the corresponding deformation‐based constitutive behavior. However, atomistic simulations are limited by the accessible length and time scales. In the present work an equivalent crystal lattice method is used to perform mechanical deformation atomistic simulations of nanometer to micrometer sized silicon (Si) nanowires at accelerated time steps. The equivalent crystal lattice method's validity is verified by comparing the method's results with the results of classical molecular dynamics (MD) simulations at MD strain rates. The simulations predict that when the nanowire cross‐sectional size exceeds 50 nm, the dependence of the nanowire Young's moduli values on the changes in nanowire cross‐sectional size is considerably reduced. Analyses show a transition in nanowire failure mechanism from being ductile to being brittle with increase in the nanowire cross‐sectional size. Examinations of the surface effect reveal that below a critical surface to volume ratio value of 0.05 nm−1, the peak nanowire strength is independent of further reduction in the surface to volume ratio value. This finding places a size limit on the surface effect observed in Si nanowires. read less USED (low confidence) M. Richard et al., “Tracking defect type and strain relaxation in patterned Ge/Si(001) islands by x-ray forbidden reflection analysis,” Physical Review B. 2011. link Times cited: 15 Abstract: Plastic relaxation and formation of defects are crucial issu… read moreAbstract: Plastic relaxation and formation of defects are crucial issues in the epitaxial growth of nanoparticles and thin films. Indeed, defects generate local stress in the crystalline lattice, which affects their surroundings and may lead to undesired effects such as reduced charge-carrier lifetime or nonradiative recombinations. Here, we use a nondestructive method based on x-ray diffuse scattering close to forbidden reflections to identify the defect types with a high sensitivity and quantify their average size and strain field. Combined with transmission electron microscopy, it offers opportunities to track both ensemble average and single defects inside three-dimensional structures. These techniques have been applied to partially embedded and high-Ge-content (x{sub Ge}=0.87{+-}0.06) dots selectively grown in 20-nm-sized pits on Si(001) surfaces through openings in a SiO{sub 2} template. The stress in the 20-nm-wide Ge islands is relaxed not only by interfacial dislocations but also by microtwins and/or stacking faults located at the interface, proving the importance of {l_brace}111{r_brace} planes and twinning in the relaxation process of nanometer-size Ge dots. read less USED (low confidence) J. Lee, K. Na, S.-C. Lee, C. Hwang, and J.-H. Choi, “Effects of magnitude and direction of the biaxial compressive strain on the formation and migration of a vacancy in Ge by using density functional theory,” Journal of Applied Physics. 2011. link Times cited: 2 Abstract: The effects of the magnitude and direction of biaxial compre… read moreAbstract: The effects of the magnitude and direction of biaxial compressive strain on the formation and migration barrier of a neutral vacancy in germanium were studied using density functional theory. Bulk Ge cells with (100) and (111) planes under various in-plane biaxial compressive strains were investigated to model epitaxial Ge on Si1–xGex substrate. Biaxial compressive strain decreases the vacancy formation energy by 68% and 81% for the (100) and (111) supercells, respectively, when Ge is assumed to be epitaxially grown on Si. The biaxial compressive strain hardly affects the migration behavior of a vacancy in the (100) supercell. On the contrary, in the (111) supercell, the migration barrier energy shows anisotropic behavior; the migration along the perpendicular and virtually parallel directions with respect to the strain becomes distinctly more difficult and slightly easier, respectively. The effects of strain on the formation and migration of the vacancy were explained by the atomic relaxation around it a... read less USED (low confidence) M. Timonova and B. Thijsse, “Molecular Dynamics simulations of the formation and crystallization of amorphous Si,” Computational Materials Science. 2011. link Times cited: 6 USED (low confidence) C. Thaulow, D. Sen, and M. Buehler, “Atomistic study of the effect of crack tip ledges on the nucleation of dislocations in silicon single crystals at elevated temperature,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2011. link Times cited: 33 USED (low confidence) S. Ogata, Y. Abe, N. Ohba, and R. Kobayashi, “Stress-induced nano-oxidation of silicon by diamond-tip in moisture environment: A hybrid quantum-classical simulation study,” Journal of Applied Physics. 2010. link Times cited: 14 Abstract: This paper reports a numerical simulation study about the ch… read moreAbstract: This paper reports a numerical simulation study about the chemical reactions of a nanosized water droplet inserted between H-terminated Si(001) surface and a nanosized, H-terminated diamond-tip when the tip is either slid on or pushed to the surface. The hybrid quantum-classical simulation method, in which the quantum region described with the density-functional theory is embedded in the total system of classical atoms, is used to perform the simulation runs in realistic settings. A feature to select the quantum region adaptively during the run is added to trace the time evolution of the contact area of the tip and surface. When the tip pushes the water droplet, while the Si surface interacts weakly with the water molecule, the tip draws a water molecule from the droplet into a unique metastable state in close proximity to the end of the tip. When the tip is further slid on or pushed to the Si surface, the water molecule in the metastable state decomposes due to high stresses concentrated at the contact a... read less USED (low confidence) Z.-H. Hong, S. Hwang, and T. Fang, “Atomic-level stress calculation and surface roughness of film deposition process using molecular dynamics simulation,” Computational Materials Science. 2010. link Times cited: 32 USED (low confidence) H. Tsuda, M. Mori, Y. Takao, K. Eriguchi, and K. Ono, “Atomic-scale cellular model and profile simulation of Si etching: Formation of surface roughness and residue,” Thin Solid Films. 2010. link Times cited: 16 USED (low confidence) H. Lei, J. Chen, and P. Ruterana, “Role of c-screw dislocations on indium segregation in InGaN and InAlN alloys,” Applied Physics Letters. 2010. link Times cited: 37 Abstract: Indium segregation induced by c-screw dislocations in wurtzi… read moreAbstract: Indium segregation induced by c-screw dislocations in wurtzite InGaN and InAlN alloys is investigated with molecular dynamics based on Stillinger–Weber potentials [Stillinger and Weber, Phys. Rev. B 31, 5262 (1985)]. Beginning with the analysis of atomic structures and energetic stability of c-screw dislocations in AlN, GaN, and InN compounds, their interaction with In atoms in GaN and AlN is explored. The results show that In atoms reduce the core energy of c-screw dislocation when they are located at the center of the core region. The distance dependence of the interaction energy indicates that In atoms will tend to gather around the dislocation line and form an In-rich region. These results agree with experimental observations in InGaN and should predict a similar behavior in InAlN. read less USED (low confidence) J. Rouviere, F. Lançon, K. Rousseau, D. Caliste, P. Jouneau, and F. Fournel, “Structure of an incommensurate 90° Si grain boundary resolved with the help of a Cs-corrector for illumination.” 2010. link Times cited: 3 Abstract: The atomic structure of an incommensurate (001)/(110) Si gra… read moreAbstract: The atomic structure of an incommensurate (001)/(110) Si grain boundary (GB) or 90° Si GB has been studied by transmission electron microscopy (TEM) and refined by atomistic simulations (Stillinger-Weber potential). Samples were made by bonding one (001) Si wafer with one (110) Si wafer and carefully orienting the 2 wafers in order that they have a common [10] direction. In the interfacial direction perpendicular to [10], the [110]I direction of grain I is parallel to the [001]II direction of grain II and, as the ratio of these 2 vectors is , it is impossible to find 2 integers n and m such that n[110]I=m[001]II. The structure is incommensurate in this direction. Z-contrast images obtained in an FEI-Titan microscope equipped with a probe Cs-corrector easily resolve the Si dumb-bells in the two grains and allow us to determine the complex atomic structures of the interface. On the other hand, near on-axis high resolution TEM images obtained in a JEOL 4000EX microscope are very efficient to analyse the long range order of the interface. read less USED (low confidence) T. Li, D. Donadio, and G. Galli, “Nucleation of tetrahedral solids: A molecular dynamics study of supercooled liquid silicon.,” The Journal of chemical physics. 2009. link Times cited: 33 Abstract: The early stages of crystallization of tetrahedral systems r… read moreAbstract: The early stages of crystallization of tetrahedral systems remain largely unknown, due to experimental limitations in spatial and temporal resolutions. Computer simulations, when combined with advanced sampling techniques, can provide valuable details about nucleation at the atomistic level. Here we describe a computational approach that combines the forward flux sampling method with molecular dynamics, and we apply it to the study of nucleation in supercooled liquid silicon. We investigated different supercooling temperatures, namely, 0.79, 0.86, and 0.95 of the equilibrium melting point T(m). Our results show the calculated nucleation rates decrease from 5.52+/-1.75x10(28) to 4.77+/-3.26x10(11) m(-3) s(-1) at 0.79 and 0.86 T(m), respectively. A comparison between simulation results and those of classical nucleation theory shows that the free energy of the liquid solid interface gamma(ls) inferred from our computations differ by about 28% from that obtained for bulk liquid solid interfaces. However the computed values of gamma(ls) appear to be rather insensitive to supercooling temperature variations. Our simulations also yield atomistic details of the nucleation process, including the atomic structure of critical nuclei and lifetime distributions of subcritical nuclei. read less USED (low confidence) 陈智辉, 俞重远, 芦鹏飞, and 刘玉敏, “Surface diffusion of Si, Ge and C adatoms on Si (001) substrate studied by the molecular dynamics simulation.” 2009. link Times cited: 5 USED (low confidence) T. Aoki, T. Seki, S. Ninomiya, K. Ichiki, and J. Matsuo, “Study of crater formation and sputtering process with large gas cluster impact by molecular dynamics simulations,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2009. link Times cited: 11 USED (low confidence) C. Li, Q. Meng, and K. Zhong, “ATOMISTIC STUDY OF THE STRENGTH AND ELASTIC CONSTANTS OF PERFECT AND DEFECTED SILICON,” International Journal of Modern Physics B. 2009. link Times cited: 6 Abstract: The effects of vacancies on the strength and elastic constan… read moreAbstract: The effects of vacancies on the strength and elastic constants of silicon, such as Young's modulus and Poisson's ratio are investigated using the molecular dynamics simulations with the Stillinger–Weber potential. The defected crystalline cells contain randomly generated defect distributions in the simulation models. The ideal strength is found to be 33.6 GPa at the strain 0.26. The Young's modulus and Poisson's ratio is 148 GPa and 0.252, respectively. It is found that the strength decreases as the point defect fraction increases, and the variation of the strength versus the point defect fraction coincides with a decaying exponential function. In addition, vacancies are shown to reduce the elastic constants. In general, the elastic constants of silicon vary linearly versus the defect fraction. read less USED (low confidence) Y. Jing, Q. Meng, and Y. Gao, “Molecular dynamics simulation on the buckling behavior of silicon nanowires under uniaxial compression,” Computational Materials Science. 2009. link Times cited: 29 USED (low confidence) M. Hu, P. Keblinski, and P. Schelling, “Kapitza conductance of silicon–amorphous polyethylene interfaces by molecular dynamics simulations,” Physical Review B. 2009. link Times cited: 142 Abstract: We use nonequilibrium molecular dynamics simulation to eluci… read moreAbstract: We use nonequilibrium molecular dynamics simulation to elucidate the interfacial thermal conductance between single-crystal silicon and amorphous polyethylene. In particular, we investigate the role of solid stiffness and the bonding strength across the interface on the interfacial thermal conductance. Simulations of interfacial scattering of individual phonon wave packets indicate that neither diffuse mismatch model nor acoustic mismatch model describes the interfacial scattering process quantitatively. In general, transmission coefficients for longitudinal phonons are significantly higher than those for transverse phonons. We also observe that anharmonic processes can be important for interfacial conductance. read less USED (low confidence) L. J. Lewis and D. Perez, “Laser ablation with short and ultrashort laser pulses: Basic mechanisms from molecular-dynamics simulations,” Applied Surface Science. 2009. link Times cited: 70 USED (low confidence) T. Cao, L.-xia Zhao, X. Feng, Y. Lei, and Y.-hua Luo, “Structural and electronic properties of LuSin (n = 1–12) clusters: A density functional theory investigation,” Journal of Molecular Structure-theochem. 2009. link Times cited: 33 USED (low confidence) Y. Jing, Q. Meng, and W. Zhao, “Molecular dynamics simulations of the tensile and melting behaviours of silicon nanowires,” Physica E-low-dimensional Systems & Nanostructures. 2009. link Times cited: 30 USED (low confidence) D. Danilov, B. Nestler, M. Guerdane, and H. Teichler, “Bridging the gap between molecular dynamics simulations and phase-field modelling: dynamics of a [NixZr1−x]liquid–Zrcrystal solidification front,” Journal of Physics D: Applied Physics. 2009. link Times cited: 12 Abstract: Results are presented from phase-field modelling and molecul… read moreAbstract: Results are presented from phase-field modelling and molecular dynamics simulations concerning the relaxation dynamics in a finite-temperature two-phase crystal–liquid sample subjected to an abrupt temperature drop. Relaxation takes place by propagation of the solidification front under formation of a spatially varying concentration profile in the melt. The molecular dynamics simulations are carried out with an interatomic model appropriate for the NiZr alloy system and provide the thermophysical data required for setting up the phase-field simulations. Regarding the concentration profile and velocity of the solidification front, best agreement between the phase-field model and molecular dynamics simulation is obtained when increasing the apparent diffusion coefficients in the phase-field treatment by a factor of four against their molecular dynamics estimates. read less USED (low confidence) K. Amara, B. Soudini, D. Rached, and A. Boudali, “Molecular dynamics simulations of the structural, elastic and thermodynamic properties of cubic BBi,” Computational Materials Science. 2008. link Times cited: 16 USED (low confidence) H. Amara, J. Roussel, C. Bichara, J. Gaspard, and F. Ducastelle, “Tight-binding potential for atomistic simulations of carbon interacting with transition metals: Application to the Ni-C system,” Physical Review B. 2008. link Times cited: 95 Abstract: We present a tight-binding potential for transition metals, … read moreAbstract: We present a tight-binding potential for transition metals, carbon, and transition-metal carbides, which has been optimized through a systematic fitting procedure. A minimal basis, including the s and p electrons of carbon and the d electrons of the transition metal, is used to obtain a transferable tight-binding model of the carbon-carbon, metal-metal, and metal-carbon interactions applicable to binary systems. The Ni-C system is more specifically discussed. The successful validation of the potential for different atomic configurations indicates a good transferability of the model and makes it a good choice for atomistic simulations sampling a large configuration space. This approach appears to be very efficient to describe interactions in systems containing carbon and transition-metal elements. By way of example, we present results concerning the epitaxial growth of graphene sheets on (111) Ni surfaces, as well as the catalytic nucleation of carbon nanotubes. read less USED (low confidence) D. Buta, M. Asta, and J. Hoyt, “Atomistic simulation study of the structure and dynamics of a faceted crystal-melt interface.,” Physical review. E, Statistical, nonlinear, and soft matter physics. 2008. link Times cited: 49 Abstract: A detailed analysis of the structure and dynamics of the cry… read moreAbstract: A detailed analysis of the structure and dynamics of the crystal-melt interface region in silicon, modeled with the Stillinger-Weber potential, is performed via molecular dynamics simulations. The focus is on the faceted (111) crystal-melt interface, but properties of the rough (100) interface are also determined. We find an intrinsic 10-90 interface width of 0.681+/-0.001 nm for the coarse-grained density profile at the (111) interface and a 0.570+/-0.005 nm width at the (100) interface. Coarse-grained profiles of a suitably defined local order parameter are found to show a smaller width anisotropy between (111) and (100) interfaces while the order profiles exhibit a 0.20-0.25 nm shift in position toward the crystal phase relative to the corresponding density profiles. The structural analysis of the layer of melt adjacent to the (111) facet of the crystal finds ordered clusters with average lifetimes of 16 ps , as determined from autocorrelations of time-dependent layer structure factors, and cluster radii of gyration from 0.2 nm for the smallest cells to as large as 1.5 nm . read less USED (low confidence) G. Bureau, J. Delaye, S. Peuget, and G. Calas, “Molecular dynamics study of structural changes versus deposited energy dose in a sodium borosilicate glass,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2008. link Times cited: 26 USED (low confidence) Y. Shirakawa et al., “Molecular dynamics simulations of structural disordering and forming defects in a milling process for selenium,” Journal of Nanoparticle Research. 2008. link Times cited: 6 USED (low confidence) C. Wang, Y. Jia, X. Wang, X. Li, X. Hu, and S. Wang, “MOLECULAR DYNAMICS SIMULATIONS OF SINGLE Si ADATOM DIFFUSION ON THE Si(001) SURFACE AND ACROSS SINGLE-LAYER Si(001) STEPS,” Modern Physics Letters B. 2008. link Times cited: 1 Abstract: By using the Stillinger–Weber atomic interactional potential… read moreAbstract: By using the Stillinger–Weber atomic interactional potential, we have carried out molecular dynamics simulations of single Si adatom diffusing on the Si(001) surface and single-layer Si(001) steps at temperatures ranging from 1000 K to 1300 K. We have presented one new diffusion pathway of a single Si adatom diffusing on the Si(001) along the direction perpendicular to dimer rows, that can weaken the diffusion anisotropy. We have investigated the process of the single Si adatom diffusing across single-layer Si(001) steps as well and given adatom diffusion pathways of step-flow and transformation of single-layer into double-layer steps. Our results show that the exchange between an adatom and a surface atom plays an important role in the adatom diffusion process above 1000 K. read less USED (low confidence) S. Munejiri, T. Masaki, T. Itami, F. Shimojo, and K. Hoshino, “Static and dynamic structure and the atomic dynamics of liquid Ge from first-principles molecular-dynamics simulations,” Physical Review B. 2008. link Times cited: 8 Abstract: The first-principles molecular-dynamics simulation was perfo… read moreAbstract: The first-principles molecular-dynamics simulation was performed for liquid Ge at $1253\phantom{\rule{0.3em}{0ex}}\mathrm{K}$ by using two kinds of simulation cells: The cubic cell of 64 atoms and the rectangular parallelepiped one of 128 atoms. The rectangular parallelepiped cell of 128 atoms was adopted to obtain the dynamic structure factor of liquid Ge in the small wave number region. The long simulation time was adopted, i.e., $66\phantom{\rule{0.3em}{0ex}}\mathrm{ps}$ for the cubic cell and $75\phantom{\rule{0.3em}{0ex}}\mathrm{ps}$ for the rectangular parallelepiped one. The present first-principles molecular-dynamics simulation reproduces well the experimental static structure factor and radial distribution function. A broad peak around $100\ifmmode^\circ\else\textdegree\fi{}$ in the obtained bond angle distribution function implies the existence of the tetrahedral atomic unit in liquid Ge. The self-diffusion coefficient for the rectangular parallelepiped cell is 20% larger than that of the cubic one. The obtained dynamic structure factor agrees well with the experimental one obtained by the inelastic x-ray scattering experiment [Hosokawa et al., Phys. Rev. B 63, 134205 (2001)], which shows the ``de Gennes narrowing'' of the main peak and the existence of the side peaks. These side peaks represent a longitudinal vibrational motion, which was also supported by the subsidiary peak around $30\phantom{\rule{0.3em}{0ex}}{\mathrm{ps}}^{\ensuremath{-}1}$ in the spectral density of the velocity autocorrelation function. The gradient of the dispersion relation in the present simulation agrees well with the experimental sound velocity. This ``no positive dispersion'' accords well with the inelastic x-ray scattering experiment of Hosokawa et al. The reason for this ``no positive dispersion'' for liquid Ge is discussed in particular concern with its low kinematic viscosity. Though the velocity autocorrelation function itself does not show a cage effect, a microscopic cage effect can be found by the detailed analysis for the trace and environment of the single atomic motion. The atomic movement as a group of 3\char21{}5 atoms seems to be present in liquid Ge in addition to individual atomic motions. The covalent bond seems to be also present at least instantaneously in liquid Ge. read less USED (low confidence) G. Moras, L. Ciacchi, G. Csányi, and A. Vita, “Modelling (100) hydrogen-induced platelets in silicon with a multi-scale molecular dynamics approach,” Physica B-condensed Matter. 2007. link Times cited: 4 USED (low confidence) Z.-H. Hong, S. Hwang, and T. Fang, “Critical conditions of epitaxy, mixing and sputtering growth on Cu(1 0 0) surface using molecular dynamics,” Computational Materials Science. 2007. link Times cited: 17 USED (low confidence) T. Kawahara, Y. Matsui, S. Tagawa, T. Kawai, and H. Matsumura, “Possibility of reverse Monte Carlo modelling for hydrogenated amorphous Si deposited on reactive ion etched Si substrate,” Journal of Physics: Condensed Matter. 2007. link Times cited: 0 Abstract: We examined the x-ray diffraction (XRD) patterns of hydrogen… read moreAbstract: We examined the x-ray diffraction (XRD) patterns of hydrogenated amorphous Si (a-Si:H) and of crystalline Si (c-Si) substrate for high-Q measurements. A structural analysis of thin films on substrates is important for the development of real devices. A transmission geometry with high-energy x-rays was used for this investigation, together with very thin substrates, in an effort to reduce substrate signals. A small area of the substrate was etched using the reactive ion etching (RIE) plasma process to maintain free-standing structures, and a-Si was deposited using catalytic chemical vapour deposition techniques. The x-ray beam was focused on the processed area and a-Si diffraction using a thin Si layer was measured. Unlike a-Si:H films on substrates without etching, we succeeded in detecting amorphous signals from samples deposited on the processed substrate. Application of reverse Monte Carlo (RMC) modelling using these data and subtracting Si substrate peaks was investigated. Direct subtraction and MCGR program (Pusztai and McGreevy 1997 Physica B 234–236 357–8) normalization for the ratio estimation between c-Si and a-Si:H structure factors was employed. MCGR normalization was found to improve subtraction of the c-Si peaks and the first peak at r = 2.3 in the pair distribution function g(r) could be calculated. read less USED (low confidence) D. Buta, M. Asta, and J. Hoyt, “Kinetic coefficient of steps at the Si(111) crystal-melt interface from molecular dynamics simulations.,” The Journal of chemical physics. 2007. link Times cited: 64 Abstract: Nonequilibrium molecular dynamics simulations are applied to… read moreAbstract: Nonequilibrium molecular dynamics simulations are applied to the investigation of step-flow kinetics at crystal-melt interfaces of silicon, modeled with the Stillinger-Weber potential [Phys. Rev. B 31, 5262 (1985)]. Step kinetic coefficients are calculated from crystallization rates of interfaces that are vicinals of the faceted (111) orientation. These vicinal interfaces contain periodic arrays of bilayer steps, and they are observed to crystallize in a step-flow growth mode at undercoolings lower than 40 K. Kinetic coefficients for both [110] and [121] oriented steps are determined for several values of the average step separation, in the range of 7.7-62.4 A. The values of the step kinetic coefficients are shown to be highly isotropic, and are found to increase with increasing step separation until they saturate at step separations larger than approximately 50 A. The largest step kinetic coefficients are found to be in the range of 0.7-0.8 m(sK), values that are more than five times larger than the kinetic coefficient for the rough (100) crystal-melt interface in the same system. The dependence of step mobility on step separation and the relatively large value of the step kinetic coefficient are discussed in terms of available theoretical models for crystal growth kinetics from the melt. read less USED (low confidence) Z. Sun, X.-xi Wang, A. Soh, H. Wu, and Y. Wang, “Bending of nanoscale structures: Inconsistency between atomistic simulation and strain gradient elasticity solution,” Computational Materials Science. 2007. link Times cited: 35 USED (low confidence) W. Chen, H. C. Cheng, and Y. Hsu, “Mechanical Properties of Carbon Nanotubes Using Molecular Dynamics Simulations with the Inlayer van der Waals Interactions,” Cmes-computer Modeling in Engineering & Sciences. 2007. link Times cited: 34 Abstract: The evaluation of the fundamental mechanical properties of s… read moreAbstract: The evaluation of the fundamental mechanical properties of single/multi-walled carbon nanotubes(S/MWCNTs) is of great importance for their industrial applications. The present work is thus devoted to the determination of various mechanical properties of S/MWCNTs using molecular dynamics (MD) simulations. The study first focuses on the exploration of the effect of the weak inlayer van der Waals (vdW) atomistic interactions on the mechanical properties of S/MWCNTs. Secondly, in addition to the zig-zag and armchair types of CNTs, the hybrid type of MWCNTs that comprise a zig-zag outer tube and an inner armchair tube is also analyzed. Thirdly, the investigation is extended to deal with the influence of the axial orientation mismatch between the inner and outer layers of MWCNTs on the associated mechanical properties. Lastly, the behaviors of the interlayer shear force/strength of MWCNTs are discussed in detail. In the MD simulations, the force field between two carbon atoms is modeled with the Tersoff-Brenner (TB) potential while the inlayer/interlayer vdW atomistic interactions are simulated with the Lennard-Jones (L-J) potential. The effectiveness of the MD simulations is demonstrated by comparing the computed results with the theoretical/experimental data available in literature. Some interesting and essential results are pre1 Tsing Hua Chair Professor, Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan 30013, R.O.C., whchen@pme.nthu.edu.tw 2 Professor, Department of Aerospace and Systems Engineering, Feng Chia University, Taichung, Taiwan 40724, R.O.C., hccheng@fcu.edu.tw 3 Graduate Student, Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan 30013, R.O.C. sented. With different dimensions and geometries of CNTs, the inlayer vdW atomistic interactions can have up to about 9% increase of the elastic moduli, 27% decrease of the Poisson’s ratios, 12% growth of the shear moduli, and 13% enhancement of the interlayer shear strength. The mechanical properties of the hybrid MWCNTs are found to be midway between the zig-zag and armchair MWCNTs. It is also detected that the axial orientation mismatch between the inner and outer layers of a double-walled CNT has a trivial impact on the mechanical properties of CNTs. To separate the inner layer of a double-walled CNT from its outer layer, it requires a minimum external force of 0.889nN for the zig-zag type, 0.550 nN for hybrid type and 0.493nN for the armchair type. In summary, the effect of the inlayer vdW atomistic interactions can not be neglected and should receive attention in the MD simulations of the mechanical properties of CNTs. Keyword: Molecular Dynamics Simulation, Carbon Nanotubes, Inlayer van der Waals Force, Mechanical Properties. read less USED (low confidence) C. Becker, J. Hoyt, D. Buta, and M. Asta, “Crystal-melt interface stresses: atomistic simulation calculations for a Lennard-Jones binary alloy, Stillinger-Weber Si, and embedded atom method Ni.,” Physical review. E, Statistical, nonlinear, and soft matter physics. 2007. link Times cited: 19 Abstract: Molecular-dynamics and Monte Carlo simulations have been use… read moreAbstract: Molecular-dynamics and Monte Carlo simulations have been used to compute the crystal-melt interface stress (f) in a model Lennard-Jones (LJ) binary alloy system, as well as for elemental Si and Ni modeled by many-body Stillinger-Weber and embedded-atom-method (EAM) potentials, respectively. For the LJ alloys the interface stress in the (100) orientation was found to be negative and the f vs composition behavior exhibits a slight negative deviation from linearity. For Stillinger-Weber Si, a positive interface stress was found for both (100) and (111) interfaces: f{100}=(380+/-30)mJ/m{2} and f{111}=(300+/-10)mJ/m{2}. The Si (100) and (111) interface stresses are roughly 80 and 65% of the value of the interfacial free energy (gamma) , respectively. In EAM Ni we obtained f{100}=(22+/-74)mJ/m{2}, which is an order of magnitude lower than gamma. A qualitative explanation for the trends in f is discussed. read less USED (low confidence) T. Aoki and J. Matsuo, “Molecular dynamics simulations of surface smoothing and sputtering process with glancing-angle gas cluster ion beams,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2007. link Times cited: 15 USED (low confidence) C.-T. Lin and K. Chiang, “From Atomic-Level Lattice Structure to Estimate the Silicon Mechanical Bulk Behaviour Using the Atomistic-Continuum Mechanics,” Key Engineering Materials. 2007. link Times cited: 3 Abstract: This paper proposes a novel atomistic-continuum mechanics (A… read moreAbstract: This paper proposes a novel atomistic-continuum mechanics (ACM) based on the finite element method (FEM) to investigate the mechanical bulk behavior of atomic-level single crystal silicon under uniaxial tensile loading. The ACM could be reduced efficiently the computational time and maintained the simulation accuracy. A general form of Stillinger-Weber potential function was used for interaction between the silicon atoms in the ACM simulations. Simulation results shows that the Young’s modulus of single crystal silicon were 121.8, 153 and 174.6 GPa along the (100), (110) and (111) crystallographic plane, respectively. These results are in reasonable agreement with the experiment and simulation results reported in the literature. read less USED (low confidence) G. Otto, G. Hobler, L. Palmetshofer, and P. Pongratz, “Amorphous pockets in Si: Comparison of coupled molecular dynamics and TEM image contrast simulations with experimental results,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2007. link Times cited: 3 USED (low confidence) T. Aoki and J. Matsuo, “Molecular dynamics study of surface modification with a glancing angle gas cluster ion beam,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2007. link Times cited: 9 USED (low confidence) M. Timonova, B.-J. Lee, and B. Thijsse, “Sputter erosion of Si(001) using a new silicon MEAM potential and different thermostats,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2007. link Times cited: 32 USED (low confidence) A. Valladares and A. Sutton, “First principles simulations of kink defects on the SP 90° partial dislocation in silicon,” Progress in Materials Science. 2007. link Times cited: 5 USED (low confidence) C. Gomes, M. Madrid, J. Goicochea, and C. Amon, “In-Plane and Out-Of-Plane Thermal Conductivity of Silicon Thin Films Predicted by Molecular Dynamics,” Journal of Heat Transfer-transactions of The Asme. 2006. link Times cited: 76 Abstract: The thermal conductivity of silicon thin films is predicted … read moreAbstract: The thermal conductivity of silicon thin films is predicted in the directions parallel and perpendicular to the film surfaces (in-plane and out-of-plane, respectively) using equilibrium molecular dynamics, the Green-Kubo relation, and the Stillinger-Weber interatomic potential. Three different boundary conditions are considered along the film surfaces: frozen atoms, surface potential, and free boundaries. Film thicknesses range from 2 to 217 nm and temperatures from 300 to 1000 K. The relation between the bulk pho.-non mean free path (A) and the film thickness (d s ) spans from the ballistic regime (A ≥ d s ) at 300 K to the diffusive, bulk-like regime (Λ «d s ) at 1000 K. When the film is thin enough, the in-plane and out-of-plane thermal conductivity differ from each other and decrease with decreasing film thickness, as a consequence of the scattering of phonons with the film boundaries. The in-plane thermal conductivity follows the trend observed experimentally at 300 K. In the ballistic limit, in accordance with the kinetic and phonon radiative transfer theories, the predicted out-of-plane thermal conductivity varies linearly with the film thickness, and is temperature-independent for temperatures near or above the Debye's temperature. read less USED (low confidence) M. Bachlechner et al., “Mechanisms of pit formation at strained crystallineSi(111)∕Si3N4(0001)interfaces: Molecular-dynamics simulations,” Physical Review B. 2006. link Times cited: 8 USED (low confidence) T. Kawamura, Y. Kangawa, and K. Kakimoto, “Investigation of thermal conductivity of nitride mixed crystals and superlattices by molecular dynamics,” Physica Status Solidi (c). 2006. link Times cited: 12 Abstract: The thermal conductivities of AlxGa1–xN and InxGa1–xN mixed … read moreAbstract: The thermal conductivities of AlxGa1–xN and InxGa1–xN mixed crystal and AlN/GaN superlattices were investigated by molecular dynamics simulation. We used Stillinger-Weber potentials, and Green-Kubo's formula was employed to calculate thermal conductivity. The results showed that the value of thermal conductivity of Al0.5Ga0.5N was about 1/20 smaller than that of GaN. It was also found that the thermal conductivity of AlN/GaN superlattices along the c-axis, which is parallel to the growth direction, was much less than that of bulk GaN. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) read less USED (low confidence) J. Evans, P. Thiel, and M. Bartelt, “Morphological evolution during epitaxial thin film growth: Formation of 2D islands and 3D mounds,” Surface Science Reports. 2006. link Times cited: 544 USED (low confidence) P. Krasnochtchekov, R. Averback, and P. Bellon, “Phase separation and dynamic patterning in Cu 1 − x Co x films under ion irradiation,” Physical Review B. 2005. link Times cited: 33 Abstract: Phase separation behavior in thin ${\mathrm{Cu}}_{1\ensurema… read moreAbstract: Phase separation behavior in thin ${\mathrm{Cu}}_{1\ensuremath{-}x}{\mathrm{Co}}_{x}$ films under irradiation ($1.8\phantom{\rule{0.3em}{0ex}}\mathrm{MeV}$ ${\mathrm{Kr}}^{+}$ ions) at different temperatures has been systematically studied for $0.10\ensuremath{\leqslant}x\ensuremath{\leqslant}0.20$. The development of phase separation in irradiated films (estimates of the average size of Co precipitates and concentration of Co in solution) was monitored using magnetic measurements. Analysis of magnetization data in the framework of superparamagnetic theory has shown that at irradiation temperatures $T\ensuremath{\leqslant}330\phantom{\rule{0.2em}{0ex}}\ifmmode^\circ\else\textdegree\fi{}\mathrm{C}$, phase separation in $\mathrm{Cu}\char21{}\mathrm{Co}$ films of all compositions stabilizes at high doses $(\ensuremath{\approx}1\ifmmode\times\else\texttimes\fi{}{10}^{16}\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}2})$, indicating the existence of temperature-dependent dynamic steady states. At temperatures higher than $\ensuremath{\approx}350\phantom{\rule{0.2em}{0ex}}\ifmmode^\circ\else\textdegree\fi{}\mathrm{C}$, indications of thermodynamic-like coarsening are observed. Below $\ensuremath{\approx}300\phantom{\rule{0.3em}{0ex}}\mathrm{K}$ FC/ZFC (field-cooled/zero-field cooled) measurements clearly show the randomizing effect of irradiation. The observed phase separation behavior of $\mathrm{Cu}\char21{}\mathrm{Co}$ system under irradiation agrees qualitatively well with kinetic Monte Carlo simulations performed in this work and with theoretical predictions of phase evolution in irradiated immiscible alloys. read less USED (low confidence) E. Lidorikis, M. Bachlechner, R. Kalia, A. Nakano, and P. Vashishta, “Coupling atomistic and continuum length scales in heteroepitaxial systems: Multiscale molecular-dynamics/finite-element simulations of strain relaxation in Si ∕ Si 3 N 4 nanopixels,” Physical Review B. 2005. link Times cited: 9 Abstract: A hybrid atomistic-continuum simulation approach has been im… read moreAbstract: A hybrid atomistic-continuum simulation approach has been implemented to study strain relaxation in lattice-mismatched Si/ Si3N4 nanopixels on a Si111 substrate. We couple the molecular-dynamics MD and finite-element simulation approaches to provide an atomistic description near the interface and a continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are validated against full multimillion-atom MD simulations. We find that strain relaxation in Si/ Si3N4 nanopixels may occur through the formation of a network of interfacial domain boundaries reminiscent of interfacial misfit dislocations. They result from the nucleation of domains of different interfacial bonding at the free edges and corners of the nanopixel, and subsequent to their creation they propagate inwards. We follow the motion of the domain boundaries and estimate a propagation speed of about 2.5 10 3 m / s. The effects of temperature, nanopixel architecture, and film structure on strain relaxation are also investigated. We find: i elevated temperature increases the interfacial domain nucleation rates; ii a thin compliant Si layer between the film and the substrate plays a beneficial role in partially suppressing strain relaxation; and iii additional control over the interface morphology may be achieved by varying the film structure. read less USED (low confidence) M. Yu et al., “Roughness of amorphous/crystalline interface in pre-amorphization implantation: Molecular dynamic simulation and modeling,” Microelectronic Engineering. 2005. link Times cited: 2 USED (low confidence) H. Noguchi and G. Gompper, “Dynamics of fluid vesicles in shear flow: effect of membrane viscosity and thermal fluctuations.,” Physical review. E, Statistical, nonlinear, and soft matter physics. 2005. link Times cited: 186 Abstract: The dynamical behavior of vesicles is investigated in simple… read moreAbstract: The dynamical behavior of vesicles is investigated in simple shear flow. A simulation technique is presented that combines a three-dimensional particle-based mesoscopic model (multiparticle collision dynamics) for the solvent with a dynamically triangulated surface model for the membrane. In this model, thermal fluctuations of the solvent and of the membrane are consistently taken into account. The membrane viscosity can be varied by changing the bond-flip rate of the dynamically triangulated surface. Vesicles are found to transit from steady tank-treading to unsteady tumbling motion with increasing membrane viscosity. At small reduced volumes, the shear induces a transformation from a discocyte to a prolate shape at low membrane viscosity. On the other hand, at high membrane viscosity, the shear induces a transformation from prolate to discocyte, or tumbling motion accompanied by shape oscillations between these two states. Thermal fluctuations induce intermittent tumbling and smooth out the transitions. This effect can be understood from a simplified stochastic model. read less USED (low confidence) N. Lümmen and T. Kraska, “Molecular dynamics investigations of the coalescence of iron clusters embedded in an inert-gas heat bath,” Physical Review B. 2005. link Times cited: 32 Abstract: A detailed analysis of the coalescence of iron clusters over… read moreAbstract: A detailed analysis of the coalescence of iron clusters over the course of their growth in an inert-gas atmosphere is presented. The investigation is performed by molecular dynamics simulations, using a recent version of the embedded atom method for iron. For several coalescence events extracted from realistic particle-growth simulations, the change of temperature, the atomic structure, and the morphology are analyzed. Here, the change in morphology is investigated by the relative number of atoms in the surface related to the driving force of the coalescence, the surface energy. The duration of the coalescence depends on the state of the colliding clusters, which is related to their temperature. At elevated temperatures an exponential decay of the relaxation of the cluster shape is found in case of liquid clusters. Clusters at lower temperatures exhibit a regular atomic structure. The coalescence includes the restructuring of the clusters, leading to deviations from the exponential decay of the cluster properties. Here, a distinct three-step coalescence process has been identified for structured clusters under nonadiabatic conditions. Each of these steps is related to a different extent of heat exchange with the carrier gas. read less USED (low confidence) T. Hawa and M. Zachariah, “Coalescence kinetics of bare and hydrogen-coated silicon nanoparticles : A molecular dynamics study,” Physical Review B. 2005. link Times cited: 40 Abstract: One of the significant challenges in the use of nanoparticle… read moreAbstract: One of the significant challenges in the use of nanoparticles is the control of primary particle size and extent of agglomeration when grown from the gas phase. In this paper we consider the role of surface passivation of the rate of nanoparticle coalescence. We have studied the coalescence of bare and H-coated silicon nanoparticles of sizes between 2\char21{}6 nm using molecular dynamics simulation at 1000 and 1500 K. We found that coalescence of coated particles consists of two steps, where reaction between particles and relocations of surface atoms near the reacting region, occur in the first step, which comprise an induction period. The second step consists of the nominal coalescence event, which depends on the surface tension and solid-state diffusion in the particle. The hydrogen passivation layer was found to remain on the surface of coalescing pair of the particles during the entire coalescence event. We also develop a mathematical model to describe the dynamics of coalescence of coated particles. The model is able to describe both the initial induction period and the coalescence period, and the role of the extent of surface coverage on the coalescence rate. In general, the entire coalescence time of coated particles is about 3\char21{}5 times that of bare particles, and the exothermicity from coalescence is about half that for the unpassivated particles. read less USED (low confidence) K. Kakimoto, A. Murakawa, and Y. Hashimoto, “An investigation of thermal conductivity of isotope silicon as a function of temperature estimated by molecular dynamics,” Journal of Crystal Growth. 2005. link Times cited: 1 USED (low confidence) S.-P. Huang and W.-C. Wang, “Structural and Dynamic Properties of Amorphous Silicon: Tight-Binding Molecular Dynamics Simulation,” Chinese Physics Letters. 2004. link Times cited: 3 Abstract: The tight-binding molecular dynamics simulation has been per… read moreAbstract: The tight-binding molecular dynamics simulation has been performed to study structural and dynamical properties of amorphous silicon. It is found that the radial distribution function and static structure factor are in good agreement with the experimental measurements. The bond order parameters Ql are sensitive to the structure change at different quenching rates. For the dynamical properties, we have calculated the vibration and electronic density of states. The simulation results show that the transverse acoustic is in good agreement with the experimental data, and the high frequency transverse optical (TO) peak shifts to the right of the experimental TO peak. read less USED (low confidence) S. Izumi, S. Hara, T. Kumagai, and S. Sakai, “A method for calculating surface stress and surface elastic constants by molecular dynamics: application to the surface of crystal and amorphous silicon,” Thin Solid Films. 2004. link Times cited: 65 USED (low confidence) M. Yu et al., “Defects in ion implantation and annealing studied by atomistic model,” Proceedings. 7th International Conference on Solid-State and Integrated Circuits Technology, 2004. 2004. link Times cited: 0 Abstract: Atomistic modeling has been applied in studying and simulati… read moreAbstract: Atomistic modeling has been applied in studying and simulating the advanced junction technologies. We present in this paper the application of molecular dynamics method in simulation of amorphization ion implantation and that of kinetic Monte Carlo method in simulation of annealing. Roughness at amorphous/crystal (a/c) interface is interpreted as transition field and related to the steepness of defects profile. The dissipation of Si extended defects are simulated for both 40kev and 5kev Si implantation. Evolution of extended defects for low energy implantation is well simulated. The simulation indicates that at the initial stage of annealing, the density of extended defects should be larger than that predicted by +1 model. read less USED (low confidence) R. Belkada, T. Igarashi, and S. Ogata, “Effects of H2O on Si fracture: a hybrid quantum-classical simulation,” Computational Materials Science. 2004. link Times cited: 5 USED (low confidence) B. Thijsse, T. Klaver, and E. Haddeman, “Molecular Dynamics simulation of silicon sputtering: sensitivity to the choice of potential,” Applied Surface Science. 2004. link Times cited: 24 USED (low confidence) A. Mattoni, L. Colombo, S. Meloni, A. Federico, and M. Rosati, “Boron ripening in amorphous silicon by large scale molecular dynamics simulations,” Computational Materials Science. 2004. link Times cited: 2 USED (low confidence) T. Kirichenko, S. Banerjee, and G. Hwang, “Mechanisms of monovacancy annihilation and type-A defect creation on Si(0 0 1)–2 × 1,” Surface Science. 2004. link Times cited: 6 USED (low confidence) H. Shi et al., “Atomic simulation of ion implantation into HfO/sub 2/: LEACS vs. TSUPREM4,” The Fourth International Workshop on Junction Technology, 2004. IWJT ’04. 2004. link Times cited: 1 Abstract: Traditional Monte Carlo ion implantation simulator TSUPREM4 … read moreAbstract: Traditional Monte Carlo ion implantation simulator TSUPREM4 is used to investigate ion implantation into HfO/sub 2/, but cannot get satisfactory results. In this paper, an atomic simulator named LEACS is developed using molecular dynamics method. By virtue of considering the basic physical interactions more precisely and with only one fitting parameter r/sub s//sup 0/ named one electron radius used in the atomic simulator, it is found that LEACS rather than TSUPREM4 has a better precision in simulating ion implantations into HfO/sub 2/. B, As and P implantations into HfO/sub 2/ material in the energy range of ReV to 40 keV are simulated using LEACS. Very high accuracy is achieved in our simulation, which proves that molecular dynamics method is successfully implemented in our atomic simulator and the molecular dynamics method shows greater advantage than Monte Carlo method in TSUPREM4. read less USED (low confidence) P. Ganster, M. Benoit, W. Kob, and J. Delaye, “Structural properties of a calcium aluminosilicate glass from molecular-dynamics simulations: a finite size effects study.,” The Journal of chemical physics. 2004. link Times cited: 101 Abstract: We study a calcium aluminosilicate glass of composition (SiO… read moreAbstract: We study a calcium aluminosilicate glass of composition (SiO(2))(0.67)-(Al(2)O(3))(0.12)-(CaO)(0.21) by means of molecular-dynamics simulations, using a potential made of two-body and three-body interactions. In order to prepare small samples that can subsequently be studied by first principles, the finite size effects on the liquid dynamics and on the glass structural properties are investigated. We find that finite size effects affect the Si-O-Si and Si-O-Al angular distributions, the first peaks of the Si-O, Al-O, and Ca-O pair correlation functions, the Ca coordination, and the oxygen atoms' environment in the smallest system (100 atoms). We give evidence that these finite size effects can be directly attributed to the use of three-body interactions. read less USED (low confidence) J. Xu and J. Feng, “Molecular-dynamics simulation of Si1-xGex epitaxial growth on Si(1 0 0),” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2004. link Times cited: 4 USED (low confidence) J. Delaye and D. Ghaleb, “Molecular dynamics study of the influence of mobile cations on the reconstruction of an irradiated silicate glass,” Journal of Non-crystalline Solids. 2003. link Times cited: 13 USED (low confidence) M. Makeev, W. Yu, and A. Madhukar, “Stress distributions and energetics in the laterally ordered systems of buried pyramidal Ge/Si(001) islands: An atomistic simulation study,” Physical Review B. 2003. link Times cited: 11 Abstract: Stress distributions in laterally ordered arrays of coherent… read moreAbstract: Stress distributions in laterally ordered arrays of coherent Ge islands of shallow pyramidal shape buried in a Si(001) matrix are studied via large-scale atomistic simulations, using Stillinger-Weber Ge/Si systems as a vehicle. The existence of tensile hydrostatic stress regions is observed on the spacer surface, above the buried islands. Our previously reported finding [M. A. Makeev and A. Madhukar, Phys. Rev. Lett. 86, 5542 (2001)] that the hydrostatic stress at the spacer layer surface above the island apex is nearly inversely proportional to the spacer layer thickness is validated by a comparison with experimental data. The lateral variations of the hydrostatic stress on the spacer layer surface show "bell-shape" profiles, with the effective size of the tensile regions above the island apex varying as a power law with the spacer layer thickness, with the power exponent being greater than 1. Studies of the energetics of twofold stacks of island systems show that the elastic interaction energy between the islands is minimized for the vertically aligned geometry. The spacer layer thickness dependence of the hydrostatic and biaxial stress field distributions in the interior of the Si(001) matrix are presented as these define the behavior of the electron and hole three-dimensional confinement potentials that determine the electronic properties of the pyramidal island quantum dots. read less USED (low confidence) G. Otto, G. Hobler, and K. Gärtner, “Defect characterization of low-energy recoil events in silicon using classical molecular dynamics simulation,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2003. link Times cited: 17 USED (low confidence) E. Haddeman and B. Thijsse, “Transient sputtering of silicon by argon studied by molecular dynamics simulations,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2003. link Times cited: 21 USED (low confidence) M. Makeev and A. Madhukar, “Stress and strain fields from an array of spherical inclusions in semi-infinite elastic media: Ge nanoinclusions in Si,” Physical Review B. 2003. link Times cited: 13 Abstract: Atomically resolved stress and strain fields from arrays of … read moreAbstract: Atomically resolved stress and strain fields from arrays of laterally ordered spherical Ge nanoinclusions in a semi-infinite Si(001) matrix are studied via atomistic simulations. We find that the hydrostatic stress and strain on the Si(001) matrix surface, induced by the inclusion buried at depth d, are tensile and follow the inverse cubic dependence for both small and intermediate d. The magnitudes of the stress and strain fields from inclusions of different volumes are found to be nearly proportional to the volume of the inclusion for large radii of inclusions, while for small radii the volume dependence overestimates the effect. Furthermore, we find that the magnitude of the stress and strain fields on the matrix surface is nearly proportional to the lattice mismatch between the inclusion and host material. The obtained simulation results are compared with the predictions of continuum-elasticity-based models and an overall good agreement is found. read less USED (low confidence) L. Pizzagalli, P. Beauchamp, and J. Rabier, “Undissociated screw dislocations in silicon: Calculations of core structure and energy,” Philosophical Magazine. 2003. link Times cited: 47 Abstract: The stability of the perfect screw dislocation in silicon ha… read moreAbstract: The stability of the perfect screw dislocation in silicon has been investigated using both classical potentials and first-principles calculations. Although a recent study by Koizumi et al. stated that the stable screw dislocation was located in both the 'shuffle' and the 'glide' sets of {111} planes, it is shown that this result depends on the classical potential used, and that the most stable configuration belongs to the 'shuffle' set only, in the centre of one (amp;1tilde;01) hexagon. We also investigated the stability of an sp2 hybridization in the core of the dislocation, obtained for one metastable configuration in the 'glide' set. The core structures are characterized in several ways, with a description of the three-dimensional structure, differential displacement maps and derivatives of the disregistry. read less USED (low confidence) M. Makeev and A. Madhukar, “Large-scale atomistic simulations of atomic displacements, stresses, and strains in nanoscale mesas: Effect of mesa edges, corners, and interfaces,” Applied Physics Letters. 2002. link Times cited: 8 Abstract: Large-scale atomistic simulations are performed to study the… read moreAbstract: Large-scale atomistic simulations are performed to study the atomic displacements, stresses, and strains in the Stillinger–Weber model of nanoscale Si(001) bare and Ge overlayer covered mesas. Considerable inhomogeneity in the atomic displacement fields in the vicinity of the mesa edges, corners, and at the lattice-mismatched Ge/Si interface is observed, maximum displacements being as large as 0.6 A even for an uncovered mesa. For Ge overlayer covered mesas, relaxation in the mesa interior and deep into the substrate is observed. The relationship between the off-diagonal components of the stress and strain tensors is found to become non-linear in the vicinity of the mesa edges for both bare and covered mesas. read less USED (low confidence) Y. Kadiri, N. Jakse, J. Wax, and J. Bretonnet, “Structure factor and atomic dynamics of stable and supercooled liquid silicon by molecular dynamics,” Journal of Non-crystalline Solids. 2002. link Times cited: 4 USED (low confidence) J. Chen, A. Hairie, E. Paumier, and G. Nouet, “Energy of the Two Variants 11A and 11B in Silicon and Germanium by the Semi-Empirical Tight-Binding Method,” Physica Status Solidi B-basic Solid State Physics. 2002. link Times cited: 2 Abstract: A semi-empirical tight-binding model was used to study the t… read moreAbstract: A semi-empirical tight-binding model was used to study the total energy of Σ = 11 tilt grain boundaries in silicon and germanium. At low temperature the structures A in silicon and B in germanium were found to be more stable in agreement with the experimental results. read less USED (low confidence) S. Chitra and K. Ramachandran, “MONTE CARLO SIMULATION USING JOHNSON POTENTIAL ON Gd Mg ALLOY FOR DEBYE WALLER FACTOR AND DEBYE TEMPERATURE,” International Journal of Modern Physics C. 2002. link Times cited: 2 Abstract: Monte Carlo simulation (MCS) on the thermal properties in Gd… read moreAbstract: Monte Carlo simulation (MCS) on the thermal properties in Gd–Mg alloy becomes essential as there are only limited experiments available. A realistic Johnson potential is used to workout the specific heats for various temperatures and hence the Debye temperature. The results from the present simulation technique are very well compared with our shell model calculation. The need of better X-ray measurements for Debye–Waller factor and Debye temperature other than the measurements of Subadhra and Sirdeshmukh, is discussed in detail. read less USED (low confidence) J. Nord, K. Nordlund, and J. Keinonen, “Molecular dynamics simulation of ion-beam-amorphization of Si, Ge and GaAs,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2002. link Times cited: 24 USED (low confidence) J. Xu and J. Feng, “Study of Ge epitaxial growth on Si substrates by cluster beam deposition,” Journal of Crystal Growth. 2002. link Times cited: 6 USED (low confidence) A. Knizhnik, A. Bagaturyants, I. Belov, B. Potapkin, and A. Korkin, “An integrated kinetic Monte Carlo molecular dynamics approach for film growth modeling and simulation: ZrO2 deposition on Si(100) surface,” Computational Materials Science. 2002. link Times cited: 19 USED (low confidence) K. Scheerschmidt, D. Conrad, and A. Belov, “Atomic processes at bonded Si-interfaces studied by molecular dynamics: tayloring densities and bandgaps?,” Computational Materials Science. 2002. link Times cited: 4 USED (low confidence) J. Cai and J.-S. Wang, “ADSORPTION AND DIFFUSION OF Si ON THE Si(001): AN EMPIRICAL POTENTIAL CALCULATION,” International Journal of Modern Physics B. 2002. link Times cited: 1 Abstract: A recently developed potential function for covalent materia… read moreAbstract: A recently developed potential function for covalent materials (Phys. Stat. Sol.B212, 9 (1999)) is used to simulate the surface adsorption, and diffusion of Si adtom and ad-dimer on the Si(001) surface. We calculate the formation energies and diffusion activation energies of several possible binding sites. The predicted stable and metastable configurations and diffusion paths of Si ad-atom and Si ad-dimer on Si(001)-(2×1) surface are in agreement with that from the first principle calculations or experiments. read less USED (low confidence) M. Liang, X. P. Xie, and S. Li, “COMPUTER SIMULATION OF EPITAXIAL GROWTH OF SILICON ON Si (001) SURFACE,” International Journal of Modern Physics B. 2002. link Times cited: 2 Abstract: Epitaxial growth of silicon on Si (001) surface has been stu… read moreAbstract: Epitaxial growth of silicon on Si (001) surface has been studied with interatomic potential based molecular dynamics simulation method. Three silicon interatomic potentials developed separately by Stillinger-Weber, Tersoff, and Bazant-Kaxiras were used. Energetic beam of 8 eV, substrate temperature of 500K and deposition rate of 1.15 ps/atom were used as the deposition conditions. Morphologies of the growth were obtained and densities in the growth direction analyzed. Epitaxial growth under the deposition conditions imposed was found possible only using the Stillinger-Weber potential. Disordered growths of differing degree were obtained using the Bazant-Kaxiras and Tersoff potentials. The disordered growth may be attributed to the existence of an epitaxial transition temperature higher than 500K that these potentials might have. read less USED (low confidence) M. Rouhani, H. Kassem, J. D. Torre, G. Landa, A. Rocher, and D. Estève, “Role of the substrate imperfections on the island nucleation and defect formation: case of GaSb/GaAs(001),” Materials Science and Engineering B-advanced Functional Solid-state Materials. 2002. link Times cited: 5 USED (low confidence) X. Su, R. Kalia, A. Nakano, P. Vashishta, and A. Madhukar, “Critical lateral size for stress domain formation in InAs/GaAs square nanomesas: A multimillion-atom molecular dynamics study,” Applied Physics Letters. 2001. link Times cited: 17 Abstract: Lateral size effects on the stress distribution and morpholo… read moreAbstract: Lateral size effects on the stress distribution and morphology of InAs/GaAs square nanomesas are investigated using molecular dynamics (MD) method. Two mesas with the same vertical size but different lateral sizes are simulated. For the smaller mesa, a single stress domain is observed in the InAs overlayer, whereas two stress domains are found in the larger mesa. This indicates the existence of a critical lateral size for stress domain formation in accordance with recent experimental findings. The InAs overlayer in the larger mesa is laterally constrained to the GaAs bulk lattice constant but vertically relaxed to the InAs bulk lattice constant. read less USED (low confidence) K. Kholmurodov, I. Puzynin, W. Smith, K. Yasuoka, and T. Ebisuzaki, “MD simulation of cluster–surface impacts for metallic phases: soft landing, droplet spreading and implantation,” Computer Physics Communications. 2001. link Times cited: 11 USED (low confidence) A. Mazzone, “FRAGMENTATION, COALESCENCE AND DEPOSITION OF SILICON CLUSTERS STUDIED BY MOLECULAR DYNAMICS,” International Journal of Modern Physics C. 2001. link Times cited: 0 Abstract: Cluster deposition is a technique recently developed for the… read moreAbstract: Cluster deposition is a technique recently developed for the production of films of a nanometric thickness. The technique consists on driving a beam of clusters onto a substrate with an energy sufficient to obtain their fragmentation and the adhesion of the fragments to the substrate. Therefore the main mechanisms involved by this technique are (i) cluster fragmentation, (ii) cluster–substrate adhesion and (iii) coalescence of the deposited fragments.The focus of this study is on these three mechanisms. To illustrate their peculiar features, three structures have been selected. Two of these structures, that is a cluster and a cluster dimer, are free standing. The third one represents a cluster deposited onto a substrate. The temperature response of the two free standing structures illustrates the effects of the cluster geometry and shape on the response to an external energy input. The comparison of these responses with the behavior occurring during deposition illustrates the main properties of cluster–substrate interactions. read less USED (low confidence) A. Mazzone, “Ar and B low-energy implants into a vicinal silicon surface: A molecular dynamics study,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2001. link Times cited: 3 USED (low confidence) D. Wolf, “High-temperature structure and properties of grain boundaries: long-range vs. short-range structural effects,” Current Opinion in Solid State & Materials Science. 2001. link Times cited: 26 USED (low confidence) D. H. Kim, D. H. Kim, and K. Lee, “Molecular dynamics simulation of energetic ion bombardment onto a-Si3N4 surfaces,” Journal of Crystal Growth. 2001. link Times cited: 3 USED (low confidence) K. Gärtner and B. Weber, “Simulation of ion beam induced crystallization and amorphization in (0 0 1) silicon,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2001. link Times cited: 17 USED (low confidence) X. Su, R. Kalia, A. Nakano, P. Vashishta, and A. Madhukar, “Million-atom molecular dynamics simulation of flat InAs overlayers with self-limiting thickness on GaAs square nanomesas,” Applied Physics Letters. 2001. link Times cited: 12 Abstract: Large-scale molecular dynamics simulations are performed to … read moreAbstract: Large-scale molecular dynamics simulations are performed to investigate the mechanical stresses in InAs/GaAs nanomesas with {101}-type sidewalls. The in-plane lattice constant of InAs layers parallel to the InAs/GaAs(001) interface starts to exceed the InAs bulk value at the twelfth monolayer (ML) and the hydrostatic stresses in InAs layers become tensile above ∼12 ML. As a result, it is not favorable to have InAs overlayers thicker than 12 ML. This may explain the experimental findings of the growth of flat InAs overlayers with self-limiting thickness of ∼11 ML on GaAs nanomesas. read less USED (low confidence) B. Weber and K. Gärtner, “The role of point defects in ion beam induced crystallization of silicon investigated by molecular dynamics simulations,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2001. link Times cited: 2 USED (low confidence) Y. Kikuchi, H. Sugii, and K. Shintani, “Strain profiles in pyramidal quantum dots by means of atomistic simulation,” Journal of Applied Physics. 2001. link Times cited: 72 Abstract: The minimum energy configurations of the atomic structure of… read moreAbstract: The minimum energy configurations of the atomic structure of a Ge island on a Si(001) substrate are calculated by using the conjugate gradient minimization of the potential energy of the system. The island is assumed to be covered or uncovered by a Si layer and assumed to be of pyramidal shape with the sidewalls of {110} or {105} facets; the base length of the island ranges from 5.43 to 10.9 nm. Two empirical potentials, the Keating and Stillinger–Weber potentials, are used. At the interfaces between the regions occupied by the atoms of different species, the potential parameters for such bondings are properly adopted. The strain profiles along the three selected paths within the structure and along the cap surface are calculated. While the profiles of the normal strain component exx obtained by the two potentials are in good agreement with each other except within the substrate and at the edges of the island in the uncovered structures, the two profiles of the normal strain component ezz show a considera... read less USED (low confidence) Mazzone, “Ion-beam thinning. An atomistic view by molecular dynamics simulations,” Ultramicroscopy. 2000. link Times cited: 4 USED (low confidence) H. Lu, J. Q. Xie, and J. Feng, “Simulation study on Si and Ge film growth by cluster deposition,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2000. link Times cited: 10 USED (low confidence) T. Watanabe and I. Ohdomari, “Modeling of a SiO2/Si(001) structure including step and terrace configurations,” Applied Surface Science. 2000. link Times cited: 12 USED (low confidence) M. Kanoun, W. Sekkal, H. Aourag, and G. Merad, “Molecular-dynamics study of the structural, elastic and thermodynamic properties of cadmium telluride,” Physics Letters A. 2000. link Times cited: 50 USED (low confidence) K. Nishihira, S. Munetoh, and T. Motooka, “Uniaxial strain observed in solid/liquid interface during crystal growth from melted Si: A molecular dynamics study,” Journal of Crystal Growth. 2000. link Times cited: 1 USED (low confidence) H. Zhang and Z. Xia, “Molecular dynamics simulation of cluster beam Al deposition on Si (100) substrate,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2000. link Times cited: 8 USED (low confidence) M. Bachlechner et al., “Structural correlations at Si/Si3N4 interface and atomic stresses in Si/Si3N4 nanopixel-10 million-atom molecular dynamics simulation on parallel computers,” Journal of The European Ceramic Society. 1999. link Times cited: 7 USED (low confidence) A. Kubota and D. J. Economou, “A molecular dynamics simulation of ultrathin oxide films on silicon: Growth by thermal O atoms and sputtering by 100 eV Ar/sup +/ ions,” IEEE Transactions on Plasma Science. 1999. link Times cited: 8 Abstract: Molecular dynamics was applied to study the growth and sputt… read moreAbstract: Molecular dynamics was applied to study the growth and sputtering of ultrathin oxide films on [100] Si surfaces. A multibody potential which stabilized the Si/SiO/sub 2/ interface was used for this purpose. Oxide growth by exposure to O atoms was found to follow Langmuir-type kinetics with unity initial sticking coefficient of O and saturation coverage of around four monolayers, in agreement with experimental data. Sputtering of an ultrathin oxide film on silicon by 100 eV Ar/sup +/ ions was simulated to study ion-assisted surface cleaning. Ion irradiation was found to promote restructuring of the surface into oxide islands, as observed experimentally. Island formation was accompanied with an increase in surface roughness. The evolution of the surface state with ion dose was predicted quantitatively. read less USED (low confidence) M. Hane, T. Ikezawa, and A. Furukawa, “Molecular dynamics calculation studies of interstitial-Si diffusion and arsenic ion implantation damage,” 1999 International Conference on Simulation of Semiconductor Processes and Devices. SISPAD’99 (IEEE Cat. No.99TH8387). 1999. link Times cited: 2 Abstract: Silicon self-interstitial atom diffusion and implantation in… read moreAbstract: Silicon self-interstitial atom diffusion and implantation induced damage were studied by using molecular dynamics methods. The diffusion coefficient of interstitial silicon was calculated using a molecular dynamics method based on the Stillinger-Weber potential. A comparison was made between the calculation method based on the Einstein relationship and the method based on a hopping analysis. For interstitial silicon diffusion, atomic site exchanges to the lattice atoms occur, and thus the total displacement-based calculation underestimates the ideal value of the diffusivity of the interstitial silicon. Through a study of molecular dynamics calculation for the arsenic ion implantation process, it was found that the damage self-recovering process depends on the extent of damage. That is, damage caused by a single large impact easily recovers itself. In contrast, the damage leaves significant defects when two large impacts in succession cause an overlapped damage region. read less USED (low confidence) C. Wang, B. Pan, J. Xiang, and K. Ho, “Adatom vacancies on the Si(111)-(7 × 7) surface,” Surface Science. 1999. link Times cited: 5 USED (low confidence) D. Hanson, J. Kress, and A. Voter, “Reactive ion etching of Si by Cl and Cl2 ions: Molecular dynamics simulations with comparisons to experiment,” Journal of Vacuum Science and Technology. 1999. link Times cited: 18 Abstract: We present results of molecular dynamics simulations of reac… read moreAbstract: We present results of molecular dynamics simulations of reactive ion etching (RIE) of a reconstructed Si(100)(2×1) surface. The existing Stillinger–Weber interatomic potential for Si/Cl of Feil et al. has been modified by correcting the Si–Si bond strength for a SiCln moiety bound to a Si surface and the Si–Cl bond strength in SiClm molecules. This potential has been used to study RIE of Si by Cl and Cl2 ions. The calculated properties such as the Si yield, product stoichiometry, stoichiometry of the chlorosilyl surface, and Cl content of the chlorosilyl layer are in reasonable agreement with experiment. The dissociative chemisorption probability of Cl2 on Si(100)(2×1) as a function of energy has been simulated and the results are in reasonable agreement with experiment. read less USED (low confidence) M. Doyama, T. Nozaki, and Y. Kogure, “Cutting, compression and shear of silicon small single crystals,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1999. link Times cited: 1 USED (low confidence) B. Weber, D. Stock, and K. Gärtner, “MD simulations of ion beam induced epitaxial crystallization at a-Si/c-Si interfaces: interface structure and elementary processes of crystallization,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1999. link Times cited: 15 USED (low confidence) J. D. Torre, M. Rouhani, G. Landa, A. Rocher, R. Malek, and D. Estève, “Dislocation half loop formation in GaSb/(001)GaAs islands and steps role: a Monte Carlo simulation,” Thin Solid Films. 1998. link Times cited: 1 USED (low confidence) M. Ishimaru, S. Munetoh, T. Motooka, K. Moriguchi, and A. Shintani, “Behavior of impurity atoms during crystal growth from melted silicon: carbon atoms,” Journal of Crystal Growth. 1998. link Times cited: 3 USED (low confidence) H. Li, X. Zongning, Z. Hao, F. Jiayou, and L. Yunwen, “Deposition of an energetic Al cluster on Si(111) substrate: a molecular dynamics simulation,” Modelling and Simulation in Materials Science and Engineering. 1998. link Times cited: 4 Abstract: A molecular dynamics simulation on the deposition of an ener… read moreAbstract: A molecular dynamics simulation on the deposition of an energetic Al cluster on Si(111) substrate was studied. We employed the Stillinger-Weber three-body potential to simulate the Si substrate and the Born-Mayer-Higgins potential to compute the interactions between cluster and substrate. For one impacting Al cluster, the migration distance of the cluster atoms and the deposition morphology were investigated under different substrate temperatures, impacting cluster energies and cluster sizes. It can be found that diffusion distance increases with the increasing substrate temperature, cluster energy and cluster size; moreover the deposition morphologies also change under similar conditions. read less USED (low confidence) J. Oh and C. Grein, “Epitaxial growth simulations of CdTe(1 1 1)B on Si(0 0 1),” Journal of Crystal Growth. 1998. link Times cited: 15 USED (low confidence) S. W. Levine, J. R. Engstrom, and P. Clancy, “A kinetic Monte Carlo study of the growth of Si on Si(100) at varying angles of incident deposition,” Surface Science. 1998. link Times cited: 52 USED (low confidence) P. Vermaut, A. Béré, P. Ruterana, G. Nouet, A. Hairie, and E. Paumier, “The volume expansion of the 112̄0 planar defect in 2H–GaN/6H–SiC (0001)Si grown by MBE,” Thin Solid Films. 1998. link Times cited: 1 USED (low confidence) P. Kelires, “Simulations of Carbon Containing Semiconductor Alloys:. Bonding, Strain Compensation, and Surface Structure,” International Journal of Modern Physics C. 1998. link Times cited: 19 Abstract: This paper reviews recent Monte Carlo simulations within the… read moreAbstract: This paper reviews recent Monte Carlo simulations within the empirical potential approach, which give insights into fundamental aspects of the bulk and surface structure of group-IV semiconductor alloys containing carbon. We focus on the binary Si1-xCx and ternary Si1-x-yGexCy alloys strained on silicon substrates. The statistical treatment of these highly strained alloys is made possible by using the semigrand canonical ensemble. We describe here improvements in the algorithm which considerably speed up the method. We show that the identity switches, which are the basic ingredients in this statistical ensemble, must be accompanied by appropriate relaxations of nearest neighbors in order to reach "quasiequilibrium" in metastable systems with large size mismatch between the constituent atoms. This effectively lowers the high formation energies and large barriers for diffusion which make molecular dynamics methods impractical for this problem. The most important findings of our studies are: (a) The prediction of a repulsive Ge–C interaction and of a preferential C–C interaction in the lattice. (b) The prediction for significant deviations of the structural parameters and of the elastic constants from linearly interpolated values (Vegard's law). As a result, for a given amount of carbon, strain compensation is shown to be more drastic than previously thought. (c) Investigation of the surface problem shows that the competition between the reconstruction strain field and the preferential arrangement of carbon atoms leads to new complicated structural patterns. read less USED (low confidence) S. Takeda, “Structure analysis of defects in nanometer space inside a crystal: Creation and agglomeration of point defects in Si and Ge revealed by high‐resolution electron microscopy,” Microscopy Research and Technique. 1998. link Times cited: 17 Abstract: Recent structural studies of point‐defect‐agglomerates in Si… read moreAbstract: Recent structural studies of point‐defect‐agglomerates in Si and Ge by high‐resolution transmission electron microscopy (HRTEM) are compiled along with some new results. After examining the wave nature of incident electrons on defect formation during HRTEM observation and the correlated recombination of point defects under electron irradiation, we show that HRTEM is the unique means to analyze the atomic structure of small agglomerates of point defects, nanometer in size, inside a crystal. Emphasis is placed on the extension of studies made possible only by the elaborate and crucial structure determination by HRTEM: the mechanism of agglomeration at the atomic level, the extraction of novel unit structures of point defects, and the electronic structure of the agglomerate. Some examples on the subjects are demonstrated in cases of the {113} and {001} defects. The effect of specimen surfaces on structure determination is also discussed. Finally, a development of TEM technique with in‐situ optical spectroscopy is described, which is utilized to pursue interaction of point defects under electron irradiation and thus may reinforce HRTEM experiments. Microsc. Res. Tech. 40:313–335, 1998. © 1998 Wiley‐Liss, Inc. read less USED (low confidence) A. Natori, R. Nishiyama, and H. Yasunaga, “Stability of ordered missing-dimer structures and the ordering dynamics on Si(001),” Surface Science. 1998. link Times cited: 15 USED (low confidence) T. Iijima and O. Sugino, “Molecular dynamics study of adatom diffusion on Si(100) surface — importance of the exchange mechanism,” Surface Science. 1997. link Times cited: 3 USED (low confidence) D. Hanson, A. Voter, and J. Kress, “MOLECULAR DYNAMICS SIMULATION OF REACTIVE ION ETCHING OF SI BY ENERGETIC CL IONS,” Journal of Applied Physics. 1997. link Times cited: 70 Abstract: We report results from molecular dynamics simulations of the… read moreAbstract: We report results from molecular dynamics simulations of the etching of a Si surface by energetic Cl atoms (15 eV⩽E⩽200 eV). We find that the energy dependence of the Si yield (number of Si atoms desorbed per incident Cl ion) is in reasonable agreement with recent experiments and with previous simulations performed up to 50 eV. We also investigate the variation of the Si yield with the impact angle of incidence, the stoichiometry of the desorbed material, and the effect of a thermal background Cl flux to the surface in the presence of an ion flux at 50 eV. Surface roughening due to etching was observed and the calculated rms roughness is in reasonable agreement with experiments. read less USED (low confidence) H. Hensel and H. Urbassek, “Disordering and annealing of a Si surface under low-energy Si bombardment,” Radiation Effects and Defects in Solids. 1997. link Times cited: 4 Abstract: We simulated the bombardment of Si(100)(2 × 1) by Si atoms u… read moreAbstract: We simulated the bombardment of Si(100)(2 × 1) by Si atoms using molecular dynamics. The kinetic energies of the projectiles were 100 and 50 eV. To model the Si–Si-interactions the empirical potential of Stillinger and Weber with the two body part of the potential splined to the universal potential was used. A geometric criterion based on the Lindemann radius was defined to study damage in the Si target. We observed clusters of disordered Si atoms in the target induced by the bombardment. Large clusters of about 50 atoms are formed in the beginning of the bombardment; they shrink and decay into smaller clusters until and equilibrium cluster size of about 10 atoms is reached. Upon annealing at elevated temperature the disordered zones dissolve into point defects. read less USED (low confidence) A. Dyson and P. V. Smith, “A molecular dynamics study of the chemisorption of C2H2 and CH3 on the SI(001)-(2 × 1) surface,” Surface Science. 1997. link Times cited: 32 USED (low confidence) C. Chou, D. Cockayne, J. Zou, P. Kringhøj, and C. Jagadish, “111 and (311) rod-like defects in silicon ion implanted silicon,” 1996 Conference on Optoelectronic and Microelectronic Materials and Devices. Proceedings. 1996. link Times cited: 0 Abstract: Rodlike defects in Si ion implanted Si have been studied by … read moreAbstract: Rodlike defects in Si ion implanted Si have been studied by transmission electron microscopy and molecular dynamics calculations. Three aspects of these defects are presented here: (1) The defects with {111} habit planes have been identified and the interstitial nature of these defects has been confirmed by matching of the experimental and the calculated images based on the model established by atomistic calculations. (2) The defects with {311} habit planes have complicated high resolution electron microscopy images. This is explained by the coexistence of the Tan model and the Takeda model along an interstitial chain. A bond reconstruction is involved to transform the Tan model into the Takeda model. The energy barrier for this reconstruction is about 1.5 eV. (3) The early stage of the formation of a <011> interstitial chain has been studied by molecular dynamics calculations, when two interstitial atoms form a dimer an interstitial chain with a unit length of the Tan model or the Takeda model is formed, leaving two dangling bonds at two ends promoting other interstitial atoms to stick on to the dimer along the <011> direction. read less USED (low confidence) L. Marqués, M. Caturla, T. D. Rubia, and G. Gilmer, “Ion beam induced recrystallization of amorphous silicon: A molecular dynamics study,” Journal of Applied Physics. 1996. link Times cited: 43 Abstract: We use molecular dynamics techniques to study the ion beam i… read moreAbstract: We use molecular dynamics techniques to study the ion beam induced enhancement in the growth rate of microcrystals embedded in an amorphous silicon matrix. The influence of the ion beam on the amorphous‐to‐crystal transformation was separated into thermal annealing effects and defect production effects. Thermal effects were simulated by heating the sample above the amorphous melting point, and damage induced effects by introducing several low energy recoils in the amorphous matrix directed at the crystalline grain. In both cases, the growth rate of the microcrystals is enhanced several orders of magnitude with respect to the pure thermal process, in agreement with experimental results. The dynamics of the crystallization process and the defect structures generated during the growth were analyzed and will be discussed. read less USED (low confidence) A. Natori, T. Suzuki, and H. Yasunaga, “Atomic structures and atomic dynamics on ‘1 × 1’ Si(111) at high temperatures,” Surface Science. 1996. link Times cited: 11 USED (low confidence) B. Weber, E. Wendler, K. Gärtner, D. Stock, and W. Wesch, “Investigation of weakly damaged 〈110〉, 〈111〉 and 〈100〉 silicon by means of temperature dependent dechanneling measurements,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1996. link Times cited: 8 USED (low confidence) A. Galijatovic et al., “Molecular Dynamics Simulations of Reactions of Hyperthermal Fluorine Atoms with Fluorosilyl Adsorbates on the Si100-(2 × 1) Surface,” The Journal of Physical Chemistry. 1996. link Times cited: 12 Abstract: Molecular dynamics simulations of the reactions between gase… read moreAbstract: Molecular dynamics simulations of the reactions between gaseous fluorine atoms and (SiFx)n adsorbates on the Si{100}-(2 × 1) surface are performed using the SW potential with the WWC reparameteriza... read less USED (low confidence) J. Rubio, L. Marqués, L. Pelaz, M. Jaraíz, and J. Barbolla, “Molecular dynamics study of the fluence dependence of Si sputtering by 1 keV Ar+ ions,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1996. link Times cited: 9 USED (low confidence) S. Uhlmann and T. Frauenheim, “Structure formation in low-energy methyl radical collisions onto diamond (100): an MD study,” Diamond and Related Materials. 1996. link Times cited: 5 USED (low confidence) T. Muranaka and Y. Hiwatari, “Study on the β Peak of χ″ for a Two-Dimensional Supercooled Fluid State Via Molecular Dynamics Simulation,” Molecular Simulation. 1996. link Times cited: 5 Abstract: We have computed the generalized susceptibility (imaginary p… read moreAbstract: We have computed the generalized susceptibility (imaginary part of χ) of two-dimensional supercooled fluid states through molecular dynamics simulations with different system sizes. It is found that when the temperature of the system is higher than Tc (critical temperature) there is no significant difference between the large (10,000-particle) and small (100-particle) systems in the χ obtained, but for much lower temperatures the spectra of the χ″ obtained reveal a remarkable system-size dependent behavior such as the β peak becomes much broader for the large system. This phenomenon is physically understood in terms of the strongly correlated motion of atoms extending over a wide range of space of the system. We will discuss in this work about the relaxations on two-dimensional supercooled fluids and their microscopic origins as well as their system-size dependence. read less USED (low confidence) M. Kitabatake and J. Greene, “Molecular dynamics and quasidynamic simulations of low-energy particle bombardment effects during vapour-phase crystal growth: 10–50 eV Si and In atoms incident on (2 × 1)-terminated Si(001),” Thin Solid Films. 1996. link Times cited: 24 USED (low confidence) T. Motooka, “Atomistic simulations of amorphization processes in ion-implanted Si : roles of defects during amorphization, relaxation, and crystallization,” Thin Solid Films. 1996. link Times cited: 9 USED (low confidence) J. Wang, D. A. Drabold, and A. Rockett, “Binding and diffusion of a Si adatom around type B steps on Si(001) c(4 × 2),” Surface Science. 1995. link Times cited: 9 USED (low confidence) M. Caturla, T. D. Rubia, and G. Gilmer, “Disordering and defect production in silicon by keV ion irradiation studied by molecular dynamics,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1995. link Times cited: 56 USED (low confidence) M. E. Barone and D. Graves, “Molecular‐dynamics simulations of direct reactive ion etching of silicon by fluorine and chlorine,” Journal of Applied Physics. 1995. link Times cited: 105 Abstract: We report results from molecular‐dynamics simulations of F+ … read moreAbstract: We report results from molecular‐dynamics simulations of F+ and Cl+ impact of silicon surfaces, at normal incidence and over a range of energies (10, 25, and 50 eV). The halogen content of the silicon layer increases with halogen fluence, and the simulations are continued until an apparent, quasisteady state in halogen coverage has occurred. Although in some cases the quantitative results differ, F+ and Cl+ are qualitatively similar in steady‐state halogen coverage, depth of penetration, etch mechanisms, and etch yield dependence on ion energy. In both cases, a mixed halogenated silicon layer forms, with a substantial degree of surface roughness (∼1–2 nm for 25 or 50 eV ions). At 10 eV for both F+ and Cl+, the apparent steady‐state coverage is about 2 equivalent monolayers and the depth of F+ (Cl+) penetration is about 15 A. For 25 and 50 eV ions, the corresponding coverage (approximately independent of ion energy and type) is about 3 monolayers. The corresponding depth of penetration is about 35 A. The s... read less USED (low confidence) J. E. Angelo and M. Mills, “Investigations of the misfit dislocation structure at a CdTe(001)/ga As(001) interface using Stillinger-Weber potentials and high-resolution transmission electron microscopy,” Philosophical Magazine. 1995. link Times cited: 15 Abstract: In this paper, Stillinger-Weber potentials which accurately … read moreAbstract: In this paper, Stillinger-Weber potentials which accurately describe the elastic constants of CdTe and GaAs are developed. These potentials are applied to investigate the misfit dislocation structure at a CdTe(001)/GaAs(001) interface. Based on these calculated structures, simulated high-resolution transmission electron microscopy images are compared with experimentally observed images. It will be shown that, although the exact energetics of the interface are not provided by these potentials, dislocation stand-off is more strongly influenced by the Poisson expansion or contraction of the individual materials. Further, the best agreement between the experimentally observed and simulated images is obtained when the dislocations occur at the interface with no stand-off being exhibited. The calculated structures indicate that the misfit dislocation structure exhibited along the [110] direction is different from that along the [110] direction if the initial monolayer of material, in this case believed... read less USED (low confidence) D. Stock, G. Gilmer, M. Jaraíz, and T. D. Rubia, “Point defect accumulation in silicon irradiated by energetic particles: A molecular dynamics simulation,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1995. link Times cited: 14 USED (low confidence) M. Ichimuraa and J. Narayan, “Atomistic study of dislocation nucleation in Ge/(001)Si heterostructuses,” Philosophical Magazine. 1995. link Times cited: 39 Abstract: Nucleation of misfit dislocations in Ge/(001)Si heterostruct… read moreAbstract: Nucleation of misfit dislocations in Ge/(001)Si heterostructures is investigated theoretically by an atomistic model based on the Stillinger-Weber potential (Stillinger and Weber 1985, Phys. Rev. B, 31, 5262). Both 60° and 90° dislocations are considered, and the energy is calculated as a function of distance of dislocations from the free surface in a thin-film heterostructure. The critical thicknesses of the dislocation nucleation obtained from the atomistic simulation are larger than the previously reported results of the continuum analysis, and we attribute this difference mainly to core energy of dislocations. The activation bamer for dislocation nucleation from the surface is estimated from the variation of energy with distance of a dislocation from the surface. The calculated activation energy is much larger than the thermal energy at normal growth temperatures. We also discuss the interaction between two 60° dislocations and the formation of a 90° dislocation at the interface by a dislocat... read less USED (low confidence) V. Konoplev, A. Gras-marti, E. P. Andribet, Pérez-Martı́n A., and Jiménez-Rodrı́guez J. J., “Effect of temperature on the bulk atomic relocation in low-energy collision cascades in silicon: a molecular dynamics study,” Radiation Effects and Defects in Solids. 1995. link Times cited: 4 Abstract: The production of damage in a Si lattice by internally start… read moreAbstract: The production of damage in a Si lattice by internally starting 100 eV self-recoils has been studied using a MD simulation. Different initial lattice temperatures below the Debye temperature for Si have been considered. The number of stable atomic displacements and the amount of atomic mixing increase with the initial target temperature. The increase with temperature of atomic mixing is nonlinear -appreciable changes take place between 300 and 500 K, while the difference between the amount of mixing corresponding to 0 and 300 K is negligibly small. The size of the cascade zone in which stable atomic displacements occur doubles itself for temperature changes between 0 and 300 K, with a value for 500 K lying in between. This nonmonotonic variation with the initial target temperature of the size of the cascade zone may have its origin in the correlation between the initial direction of motion of the starting recoil and the directions of thermal velocities of the neighbouring atoms around this recoil. read less USED (low confidence) P. Nachtigall and K. Jordan, “Barriers for hydrogen atom diffusion on the Si(100)‐2×1 surface,” Journal of Chemical Physics. 1995. link Times cited: 29 Abstract: Density functional theory is used in conjunction with cluste… read moreAbstract: Density functional theory is used in conjunction with cluster models to calculate activation energies for diffusion of H atoms on the Si(100)‐2×1 surface. The activation energy for diffusion along the surface dimer rows is calculated to be 52 kcal/mol, and that for diffusion perpendicular to the dimer rows is even higher, leading us to conclude that H‐atom diffusion on the Si(100)‐2×1 surface probably does not play an important role in the H2 desorption process. The activation energies obtained in the present study are appreciably higher than those obtained from prior calculations using density functional theory. A major factor causing these differences is our use of the Becke3‐LYP functional rather than the Becke–Perdew functional, used previously. read less USED (low confidence) Q. Yu and P. Clancy, “Molecular dynamics simulation of crystal growth in Si1−xGexSi (100) heterostructures,” Journal of Crystal Growth. 1995. link Times cited: 26 USED (low confidence) K. Chen et al., “Triangular step instability and 2D/3D transition during the growth of strained Ge films on Si(100),” MRS Proceedings. 1995. link Times cited: 1 Abstract: We show that an activation energy barrier exists to the form… read moreAbstract: We show that an activation energy barrier exists to the formation of wavy step edges due to stress-driven 2D instability. The barrier height and the barrier width depend sensitively on the surface stress anisotropy and step free energy. The large misfit strain of Ge films significantly reduces the barrier by lowering the S{sub B} step energy, inducing S{sub A} steps to undergo a triangular instability even during low temperature growth of Ge on Si(100). The step instability results in a novel arrangement of stress domains, and the interaction between the domains causes a spatial variation of surface strain with a surprisingly large influence on the energy barrier for island nucleation. Calculations indicate a dramatic enhancement in the nucleation of 3D islands at the apex regions of triangular steps, in good agreement with our experimental measurements. read less USED (low confidence) M. Caturla, T. D. Rubia, and G. Gilmer, “Recrystallization of a planar amorphous‐crystalline interface in silicon by low energy recoils: A molecular dynamics study,” Journal of Applied Physics. 1995. link Times cited: 48 Abstract: We discuss the motion of an amorphous‐crystalline interface … read moreAbstract: We discuss the motion of an amorphous‐crystalline interface in silicon induced by low energy recoils. We employ molecular dynamics simulation with the Stillinger–Weber interatomic potential for silicon. The temperature of the substrate in these simulations was 250 K. Our results show that when 15 or 20 eV recoils are initiated from the amorphous side of the interface, the crystal regrows by solid‐phase epitaxy. On the other hand, no interface motion was detected for 15 eV recoils launched from the crystalline side, and damage accumulation resulted when the recoil energy was set to 20 eV. The efficiency of recrystallization for this process is 0.67, for both 20 and 15 eV recoils. That is, approximately two silicon atoms transform from the amorphous to the crystalline phase per every three incident recoils. The calculated threshold energy required to produce a stable defect in silicon was found to be substantially lower in an amorphous matrix than in a crystalline lattice. read less USED (low confidence) K. Nordlund, “Molecular dynamics simulation of ion ranges in the 1–100 keV energy range,” Computational Materials Science. 1995. link Times cited: 382 USED (low confidence) A. Dyson and P. V. Smith, “Empirical molecular dynamics calculations for the (001) and (111) 2×1 reconstructed surfaces of diamond,” Surface Science. 1994. link Times cited: 12 USED (low confidence) A. Spinelli and L. Colombo, “Growth and structural characterization of thin Ge films by molecular dynamic simulation,” Materials Science and Engineering B-advanced Functional Solid-state Materials. 1994. link Times cited: 0 USED (low confidence) Q. Yu and P. Clancy, “Molecular dynamics simulation of the surface reconstruction and strain relief in Si1-xGex/Si(100) heterostructures,” Modelling and Simulation in Materials Science and Engineering. 1994. link Times cited: 5 Abstract: The structure of a variety of Si1-xGex/Si heterostructures, … read moreAbstract: The structure of a variety of Si1-xGex/Si heterostructures, as well as bulk Si(100) and Ge(100) modelled by the Stillinger-Weber potential, have been simulated by molecular dynamics to investigate the surface reconstruction and strain relief in the SiGe thin films. It was found that the strain in SiGe/Si(100) thin films was relaxed by the segregation of Ge to the surface. Rebonding of sub-surface atoms into dimers in the presence of a vacancy or cluster of vacancies above them was observed in the ensuing surface reconstruction. For SiGe/Si, the amount of 'rebonded missing dimers' in the surface increased with increasing Ge composition. However, for Ge/Si(100), a V-shaped defect was observed in the Ge thin film. For bulk Si, several rebonded missing dimers were found at the surface, while for bulk Ge(100) the surface showed a typical 2*1 reconstruction. All these findings corroborate recent related experimental studies and theoretical predictions. read less USED (low confidence) J. Keinonen, A. Kuronen, K. Nordlund, R. Nieminen, and A. Seitsonen, “First-principles simulation of collision cascades in Si to test pair-potentials for Si-Si interaction at 10 eV–5 keV,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1994. link Times cited: 22 USED (low confidence) Z. El-bayyari and S. Erkoç, “Bulk and surface properties of aluminum: a molecular-dynamics simulation,” Materials Chemistry and Physics. 1994. link Times cited: 4 USED (low confidence) V. Zinovyev, L. Aleksandrov, A. Dvurechenskii, K. Heinig, and D. Stock, “Modelling of layer-by-layer sputtering of Si(111) surfaces under irradiation with low-energy ions,” Thin Solid Films. 1994. link Times cited: 14 USED (low confidence) H. Spjut and D. Faux, “Computer simulation of strain-induced diffusion enhancement of Si adatoms on the Si(001) surface,” Surface Science. 1994. link Times cited: 27 USED (low confidence) A. Horsfield and P. Clancy, “A tight-binding molecular dynamics simulation of the melting and solidification of silicon,” Modelling and Simulation in Materials Science and Engineering. 1994. link Times cited: 9 Abstract: The melting of solid silicon and the cooling of liquid silic… read moreAbstract: The melting of solid silicon and the cooling of liquid silicon are investigated using molecular dynamics. Both the Stillinger-Weber (SW) potential and the tight-binding bond model are used to calculate the forces. The electrical properties are investigated using an empirical pseudopotential method with a plane wave basis. The temperature at which the solid becomes unstable and passes to the liquid phase is found to be about 2300 K. The dependence of this temperature on cell size is investigated. On cooling, there are changes in some of the properties of the liquid: the energy per particle decreases, the diffusion constant decreases, and the low-frequency electrical conductivity decreases slightly as the temperature decreases. Between 1180 K and 980 K the liquid undergoes a transition to a glassy phase. There are large changes in the pair correlation function, the SW three-body energy distribution, the diffusion constant, the density of electron single-particle states and the electrical conductivity. All of these changes are consistent with increased tetrahedral bonding. read less USED (low confidence) J. Zhengming, Y. Genqing, C. Zhaonian, L. Xianghuai, and Z. Shichang, “The two-dimensional pair correlation function for the Si(001) surface: computer simulation results,” Journal of Physics: Condensed Matter. 1994. link Times cited: 4 Abstract: A two-dimensional pair correlation function (TPCF) has been … read moreAbstract: A two-dimensional pair correlation function (TPCF) has been introduced into the study of the surface structure of materials. A molecular dynamics simulation was then performed to obtain the TPCFs for the Si(001) surface and deeper layers. The atoms interact via a potential developed by Stillinger and Weber, which includes both two-body and three-body contributions. The analysis of TPCFS shows that the atoms in deeper layers of Si(001) do not derive from their original (001) atomic plane lattice sites, but just thermally vibrate in the vicinity of their equilibrium sites, and the nearer to the surface layer the atoms are, the more violent the vibration is. The analysis also indicates that a rearrangement of atoms has occurred in the Si(001) surface and, while the majority of these atoms form bonds, a minority still exists as non-bonding atoms. read less USED (low confidence) C. Toh, S. Seow, and C. K. Ong, “Kink assisted growth of single height steps on the Si(001)-2 × 1 surface,” Surface Science. 1993. link Times cited: 4 USED (low confidence) Z. Zhang and H. Metiu, “The self-organization of Si atoms adsorbed on a Si(100) surface: an atomic level kinetic model,” Surface Science. 1993. link Times cited: 9 USED (low confidence) M. Kitabatake and J. Greene, “Molecular dynamics and quasidynamics simulations of low‐energy particle bombardment effects during vapor‐phase crystal growth: Production and annihilation of defects due to 50 eV Si incident on (2×1)‐terminated Si(001),” Journal of Applied Physics. 1993. link Times cited: 35 Abstract: Molecular dynamics and quasidynamics simulations, utilizing … read moreAbstract: Molecular dynamics and quasidynamics simulations, utilizing the Tersoff many‐body potential, were used to investigate projectile incorporation and defect production as well as lattice relaxation, diffusion, and annihilation of defects resulting from 50 eV Si irradiation of (2×1)‐terminated Si(001). A unity trapping probability, in sites distributed between the epitaxial overlayer and the fourth lattice layer (l=4), was obtained for Si projectiles irradiating an array of high‐ and low‐symmetry points in the primitive surface unit cell. Exchange epitaxy events were observed in which a lattice atom came to rest at an epitaxial (1×1) bridge site while the projectile stopped in a substitutional lattice site. In addition, several collision sequences resulted in the opening of additional dimers, up to four per irradiation event, thus providing (1×1) sites for migrating adatoms during ion‐assisted crystal growth. The primary residual lattice defects produced were split and hexagonal interstitials, although tetrag... read less USED (low confidence) E. Beam, “Computer simulation of the surface topology of (001) silicon resulting from the termination of 12〈110〉 edge dislocations with Burgers vectors parallel to the surface,” Materials Science and Engineering B-advanced Functional Solid-state Materials. 1993. link Times cited: 0 USED (low confidence) M. Crowley, D. Srivastava, and B. Garrison, “Molecular dynamics investigation of the MBE growth of Si on Si?110?,” Surface Science. 1993. link Times cited: 10 USED (low confidence) W. Choi, C. Kim, and H. Kang, “Interactions of low energy (10–600 eV) noble gas ions with a graphite surface: surface penetration, trapping and self-sputtering behaviors,” Surface Science. 1993. link Times cited: 51 USED (low confidence) Feil, Zandvliet, Tsai, Dow, and Tsong, “Random and ordered defects on ion-bombarded Si(100)-(2 x 1) surfaces.,” Physical review letters. 1992. link Times cited: 71 Abstract: Scanning tunneling microscopy STM images of Si(100)-(2×1) su… read moreAbstract: Scanning tunneling microscopy STM images of Si(100)-(2×1) surfaces bombarded by low-dose 3-keV Ar+ ions showed random defects which ordered into line defects perpendicular to the dimer rows upon annealing at elevated temperatures. Molecular-dynamics simulations were performed to explain the shapes and sizes of the observed random defects and also to examine the stability of ordered defects. Our simulations showed good agreement with STM observations. read less USED (low confidence) S. Ethier and L. J. Lewis, “Epitaxial growth of Si_1−xGe_x on Si(100)2 × 1: A molecular-dynamics study,” Journal of Materials Research. 1992. link Times cited: 21 Abstract: We use molecular-dynamics simulations to study the growth of… read moreAbstract: We use molecular-dynamics simulations to study the growth of pure Si, Si_0.5Ge_0.5, and pure Ge on the 2 × 1 reconstructed surface of Si(100) in a way appropriate to the fabrication of thin films by the method of molecular-beam epitaxy (MBE), namely sequential deposition of energetic atoms. The atoms interact with one another via effective potentials of the Stillinger–Weber form, with parameters adjusted such as to describe all possible types of triplet interactions. Motivated by numerous experimental studies of MBE-grown films, we investigate in particular the structure of the deposits as a function of substrate temperature. We find in all three cases that at low substrate temperatures, poorly ordered structures form, while at high substrate temperatures, epitaxial growth takes place. The presence of Ge limits the number of crystalline overlayers that form, even though it appears to favor a more-ordered structure in the initial stages of growth. For pure Ge epitaxy, in particular, only the first three layers are crystalline, after which growth appears to proceed by the formation of islands, reminiscent of the Stranski–Krastanow growth scheme, and in qualitative agreement with recent experimental and theoretical work. In all samples, annealing improves the quality of the films—at least when grown at sufficiently high substrate temperatures. The interdiffusion of the species at the substrate-deposit interface is also examined. read less USED (low confidence) D. Athanasopoulos and S. Garofalini, “Effect of adsorption on the surface structure of sodium alumino-silicate glasses: a molecular dynamics simulation,” Surface Science. 1992. link Times cited: 8 USED (low confidence) P. Weakliem and E. Carter, “Constant temperature molecular dynamics simulations of Si(100) and Ge(100): Equilibrium structure and short‐time behavior,” Journal of Chemical Physics. 1992. link Times cited: 37 Abstract: The structures of the (100) surfaces of silicon and germaniu… read moreAbstract: The structures of the (100) surfaces of silicon and germanium generally have been interpreted in a static manner in the past. We present molecular dynamics (MD) simulations that show these surfaces to consist of a mixture of rapidly interconverting buckled and unbuckled dimers. Over a time average, the surface is found to have long p(2×1) rows of symmetric, unbuckled dimers, as seen in recent scanning tunneling microscopy images of silicon. However, higher order unit cells are observed in He scattering and low energy electron diffraction experiments at low temperatures. We present a dynamical interpretation of the structure to explain both sets of observations. The simulations have been performed on different size slabs at both constant energy and constant temperature utilizing a new method for effective removal of heat from an exothermic system while retaining the correct dynamics. Several different interaction potentials were analyzed in an attempt to find the most realistic one for simulations of these surfaces. The effect of surface defects and annealing were also investigated. The surface phonon densities of states were calculated and for Si(100) are in good agreement with experiments and other theoretical treatments. Such simulations and structural analyses are reported for the first time for Ge(100). read less USED (low confidence) Z. Zhang, Y. Lu, and H. Metiu, “Effects of kink-kink interactions on the thermal roughening of Si( 100) surfaces with single layer steps,” Surface Science. 1991. link Times cited: 2 USED (low confidence) D. Srivastava and B. Garrison, “The dynamics of surface rearrangements in Si adatom diffusion on the Si100(2 × 1) surface,” Journal of Chemical Physics. 1991. link Times cited: 33 Abstract: The Si adatom adsorption and diffusion on the fully relaxed … read moreAbstract: The Si adatom adsorption and diffusion on the fully relaxed Si{100}(2×1) surface is studied by a combination of molecular dynamics simulations with Tersoff’s potential for the Si interactions, a simplified transition state theory of Voter and lattice gas simulations. Six local minima for adsorption are found on the surface and the activation energies between each are determined. The Arrhenius behavior for the macroscopic diffusion is found to be D=5.67×10−3 exp(−0.75 eV/kT) cm2/s. In addition, it is found that the adatom diffusion is strongly anisotropic in nature and the direction of easy diffusion is perpendicular to the dimers (i.e., parallel to the dimer rows) of the original surface. The minimum energy path for the diffusion is found to be activated by the local unreconstruction (dimer opening) of the otherwise fully reconstructed surface. read less USED (low confidence) A. D. V. D. Gon, D. Frenkel, J. Frenken, R. J. Smith, and P. Stoltze, “Calculation of ion scattering yields from simulated crystal surfaces: theory and application to melting and non-melting Al surfaces,” Surface Science. 1991. link Times cited: 21 USED (low confidence) J. Holender and G. J. Morgan, “Generation of a large structure (105 atoms) of amorphous Si using molecular dynamics,” Journal of Physics: Condensed Matter. 1991. link Times cited: 29 Abstract: A method for generating amorphous tetrahedral structures hav… read moreAbstract: A method for generating amorphous tetrahedral structures having 13824 and 110592 atoms is presented. The authors took the Wooten, Winer and Weaire amorphous model (1985) of 216 atoms and put together a number of these blocks. This larger structure was annealed using molecular dynamics and then cooled. Comparison with experiment was carried out using the structure factors calculated directly. Very good agreement has been attained. The generated structures contrary to the original www model, contain coordination defects. read less USED (low confidence) Z. Zhang, Y. Lu, and H. Metiu, “Pathways for dimer string growth during Si deposition on Si(100)−2 × 1☆,” Surface Science. 1991. link Times cited: 19 USED (low confidence) B. Pailthorpe, “Molecular‐dynamics simulations of atomic processes at the low‐temperature diamond (111) surface,” Journal of Applied Physics. 1991. link Times cited: 42 Abstract: The deposition of low‐energy carbon atoms onto a low‐tempera… read moreAbstract: The deposition of low‐energy carbon atoms onto a low‐temperature diamond (111) surface is studied by molecular‐dynamics computer simulations. A Stillinger–Weber potential [F. H. Stillinger and T. A. Weber, Phys. Rev. B 31, 5262 (1985)], with a reparametrization derived from quantum‐mechanical energy calculations for small tetrahedral carbon clusters, is used to model the interatomic interactions. The penetration of 1–100‐eV neutral carbon atoms into the diamond (111) surface at 100 K and the resultant surface atom rearrangements and induced film stress are studied. For intermediate energies (20–60 eV) the incident atom penetrates beneath the exposed (111) surface and significantly increases the lateral compressive stress in the diamond film. The emerging picture is that diamond films grow from below the exposed surface in a region of locally high stress and tetrahedral coordination. read less USED (low confidence) Z. Zhang, Y. Lu, and H. Metiu, “Adsorption and diffusion sites of a Si atom on a reconstructed Si(100)-(2 × 1) surface☆,” Surface Science. 1991. link Times cited: 25 USED (low confidence) J. Narayan and A. Nandedkar, “Atomic structure and energy of grain boundaries in silicon, germanium and diamond,” Philosophical Magazine Part B. 1991. link Times cited: 36 Abstract: We have used Stillinger-Weber and Tersoffpotentials to calcu… read moreAbstract: We have used Stillinger-Weber and Tersoffpotentials to calculate and simulate the atomic structures of ⟨011⟩ tilt boundaries with Σ = 1+2n2 (n = 1,2,3,4) in silicon, germanium and diamond lying in (111), (122), (133) and (144) planes with corresponding angles of 70.53°, 38.94°, 26.53° and 20.05° respectively. Both Stillinger-Weber and Tersoff potentials gave consistent values of grain boundary energies for silicon. The energies for diamond were considerably higher (about a factor of 6–7) than the corresponding values for silicon and germanium. The calculated values of the grain boundary period are in good agreement with coincidence site lattice periods. The boundaries with tilt angles θ< 20.05° can be represented by arrays of (a/2)⟨110⟩{001} dislocations with no dangling bonds. High-resolution electron microscopy results on the atomie structures of Σ=3, fivefold twins, and Σ = 9 are discussed. The high energy Σ = 9 boundary (second order twin) has been shown to split into two Iow energy Σ = 3 (fi... read less USED (low confidence) J. Narayan, “Dislocations, twins, and grain boundaries in CVD diamond thin films: Atomic structure and properties,” Journal of Materials Research. 1990. link Times cited: 69 Abstract: We have used transmission electron microscopy techniques to … read moreAbstract: We have used transmission electron microscopy techniques to study the nature of dislocations, stacking faults, twins, and grain boundaries in CVD (chemical-vapor-deposition) diamond thin films. Perfect a /2(110) and partial a /6(112) and a /3(111) type dislocations are observed; the partial dislocations are also associated with twins and stacking faults. The most common defect in diamond thin films, particularly in (110) textured films, is Σ = 3 grain boundary or the primary twin. These twins in (110) textured films can lead to formation of fivefold microcrystallites. We have also investigated the splitting of Σ = 9 grain boundary (second order twin) into two Σ = 3 boundaries or primary twins via reaction Σ9 = 2Σ3. A rapid thermal annealing treatment has been shown to result in annealing of Σ = 3 boundaries and produce “defect-free” regions in thin films. A mechanism of annealing (removal) of Σ = 3 boundaries is discussed. Atomic structure and energetics of dislocations, twins, and grain boundaries are calculated using Tersoff potentials. The calculated atomic structure for Σ = 3 boundary is compared with high-resolution TEM images and a good agreement is obtained. These boundaries consist of periodic units of 5–7 rings which are similar to the core structure of 90° a /2<110>{001} dislocations. The energy of the 5–7 rings in the grain boundaries is considerably lower, due to overlapping and strain cancellation effects, than that associated with single dislocations. The 5–7 ring energy and consequently the boundary energy increases as the overlapping effects decrease. An interesting analogy between the diamond and silicon results is drawn. read less USED (low confidence) C. Engler, “Adsorption of H2O (Molecular and Dissociative) on Si(100) and Si(111) Surfaces Considered by an Empirical Pair Potential Method,” Physica Status Solidi B-basic Solid State Physics. 1990. link Times cited: 7 Abstract: The adsorption of H2O on Si(100) and Si(111) surfaces is exa… read moreAbstract: The adsorption of H2O on Si(100) and Si(111) surfaces is examined by an empirical method, which connects pair potential considerations with the BEBO-concept. For both surfaces, only small energetic differences between molecular SiH2O and dissociative SiH and SiOH species are obtained, which lie within the margin of error of the method. For the dissociation process of adsorbed H2O-molecules on Si(100)−(2 × 1), the course of the total energy along a possible reaction path is discussed. read less USED (low confidence) A. Nandedkar and J. Narayan, “Atomic structure of dislocations in silicon, germanium and diamond,” Philosophical Magazine. 1990. link Times cited: 61 Abstract: Atomic structures of perfect (90° and 60°) and partial (90°)… read moreAbstract: Atomic structures of perfect (90° and 60°) and partial (90°) dislocations including total and core energies have been calculated using four different interatomic potentials in silicon, germanium and diamond. The core energies of dislocations do not scale with the magnitudes of Burgers vectors associated with them. However, the energies of dislocations in the elastic region are found to be directly proportional to the square of the Burgers vector, as predicted by the theory of elasticity. The Stillinger-Weber (SW) and TersofT(T) potentials are more suitable for calculating the core structures with large distortions including the dangling bonds such as found in 60° dislocations. In the absence of dangling bonds, the core energies are highest for Keating (K) potentials, followed by T, SW and Baraff-Kane-Schluter (B) potentials (Si). The core energies calculated using B potentials are considerably lower as a result of much lower values for the bond-bending parameter. As an example, the core energies ... read less USED (low confidence) R. Smith, D. E. Harrison, and B. Garrison, “Simulation of keV particle bombardment of covalent materials: An investigation of the yield dependence on incidence angle,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1990. link Times cited: 18 USED (low confidence) S. Ghaisas, “Study of the kinetics of Ga on strained GaAs(001) surface using atomic potentials,” Surface Science. 1989. link Times cited: 14 USED (low confidence) A. Nandedkar and J. Narayan, “Atomic structure of 60° and 90° dislocations in Ge/Si systems and critical phenomena,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 1989. link Times cited: 14 USED (low confidence) D. Wolf, “Structure-energy correlation for grain boundaries in F.C.C. metals—I. Boundaries on the (111) and (100) planes,” Acta Metallurgica. 1989. link Times cited: 168 USED (low confidence) D. Wolf, “Correlation between the energy and structure of grain boundaries in b.c.c. metals I. Symmetrical boundaries on the (110) and (100) planes,” Philosophical Magazine Part B. 1989. link Times cited: 77 Abstract: The zero-temperature energies and equilibrium volume expansi… read moreAbstract: The zero-temperature energies and equilibrium volume expansions of point-defect-free grain boundaries (GBs) on the two densest planes of b.c.c. metals have been determined using a Finnis—Sinclair potential for Mo and Johnson's potential for α-Fe. The energies and volume expansions of the (100) boundaries are found to be about two to three times larger than those of the (110) boundaries. A close correlation between large volume expansion and high GB energy is observed. Since both potentials yield qualitatively very similar results it is concluded that the short-range repulsion between atoms is the dominating contribution to the energy in the GB region and therefore, electronic many-body effects arising from a local volume dependence of the interatomic interactions are relatively unimportant. read less USED (low confidence) Stansfield, Broomfield, and Clary, “Classical-trajectory calculations on Ar+ sputtering of a Si(001) surface using an ab initio potential.,” Physical review. B, Condensed matter. 1989. link Times cited: 37 Abstract: We describe classical-trajectory calculations of sputtering … read moreAbstract: We describe classical-trajectory calculations of sputtering yields for Ar/sup +/-ion collisions with a Si(001) surface. The Ar/sup +/-Si and short-ranged Si-Si interaction potentials were calculated using the ab initio Hartree-Fock and configuration-interaction methods. The low-energy potential describing the silicon solid is the two- and three-body form due to Stillinger and Weber. We compare the calculated sputtering yields with experiment. The potential-energy surface strongly influences the calculated sputtering yields, and it is found that the most reasonable agreement is obtained from our potentials using the (2 x 1) Si(001) reconstructed surface rather than the bulk-terminated surface. Analysis of the kinetic energy and angular distributions of the sputtered silicon atoms and of cluster yields has provided a mechanism of ejection. read less USED (low confidence) S. Phillpot, J. Lutsko, and D. Wolf, “Nucleation and kinetics of thermodynamic melting: A molecular dynamics study of grain-boundary induced melting in silicon,” Solid State Communications. 1989. link Times cited: 7 USED (low confidence) J. Lampinen, R. Nieminen, and K. Kaski, “Molecular dynamics simulation of epitaxial growth of the Si(001) surface,” Surface Science. 1988. link Times cited: 16 USED (low confidence) J. Berger, A. Selmani, C. Tannous, and G. Spronken, “Langevin dynamics simulation of infrared absorption spectra: H on Si(100),” Surface Science. 1988. link Times cited: 2 USED (low confidence) D. Wolf and S. Phillpot, “Role of the densest lattice planes in the stability of crystalline interfaces: A computer simulation study☆,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 1988. link Times cited: 48 USED (low confidence) H. Balamane, T. Halicioǧlu, and W. Tiller, “Computer simulation of ledge formation and ledge interaction for the silicon (111) free surface,” Journal of Crystal Growth. 1987. link Times cited: 4 USED (low confidence) J. Hafner, T. Egami, S. Aur, and B. Giessen, “The structure of calcium-aluminium glasses: X-ray diffraction and computer simulation studies,” Journal of Physics F: Metal Physics. 1987. link Times cited: 11 Abstract: The authors present an investigation of the atomic structure… read moreAbstract: The authors present an investigation of the atomic structure of the metallic glass Ca60Al40 by energy-dispersive X-ray diffraction and computer simulation studies based on pseudopotential-derived interatomic forces. The characteristic features of the structure of Ca60Al40 are the large contraction of the Ca-Ca nearest-neighbour distances compared with pure Ca metal and a rather broad and asymmetric nearest-neighbour peak in the pair correlation function. The theoretical model explains the contraction of the Ca-Ca distances but not the large asymmetry of the peaks. They tentatively attribute the asymmetry to a modification of the dielectric screening function arising from the short electronic mean free path in this high-resistivity alloy. The theoretical model also points to a well defined topological short-range order and a negligible chemical short-range order. read less USED (low confidence) J. C. Phillips, “Structure and properties of ionized and neutral condensed clusters of Si, Ge, Sn, and Pb,” Journal of Chemical Physics. 1987. link Times cited: 23 Abstract: The relative abundances of medium‐size clusters X(+,−,0)n of… read moreAbstract: The relative abundances of medium‐size clusters X(+,−,0)n of X=Si, Ge, Sn, or Pb, with 7≤n≤30, as prepared in various ways after vapor‐phase condensation, are determined by enthalpic, entropic, and dynamic factors. Valence electronic structure determines chemical trends in (magic number) peaks in these relative abundances. Theoretical models of the valence structure explain these trends in detail. New cylindrical structures are identified at n=15, 18, and 21 for X(−)n with X=Si and Ge. General trends in ionization potentials and electron affinities are discussed. read less USED (low confidence) J. Broughton and F. F. Abraham, “Rapid cooling of silicon (111)-melt interfaces by molecular dynamics,” Journal of Crystal Growth. 1986. link Times cited: 14 USED (low confidence) S. Nosé and F. Yonezawa, “Isothermal–isobaric computer simulations of melting and crystallization of a Lennard‐Jones system,” Journal of Chemical Physics. 1986. link Times cited: 171 Abstract: By means of constant‐temperature, constant‐pressure molecula… read moreAbstract: By means of constant‐temperature, constant‐pressure molecular dynamics techniques, we simulate the melting and crystallization processes of a model system composed of 864 Lennard‐Jones (LJ) particles under periodic boundary conditions. On heating an fcc crystal of LJ particles, it is ascertained that melting takes place. On the other hand, a LJ liquid, when quenched slowly, crystallizes into a stacking of layers with stacking faults where each layer forms a close‐packed structure with occasional point defects. The atomic configuration is not always nucleated into a completely ordered structure. A large hysteresis in the volume‐temperature curve is observed. The volume contraction at the transition is characterized by two different growth rates, relatively slow at the first stage and relatively fast at the final stage. The critical cooling rate which separates the crystal‐forming cooling rates and the glass‐forming cooling rates is between 4×1010 and 4×1011 K/s for argon. On taking advantage of computer si... read less USED (low confidence) Y. Wang, S. Zhang, H. Xia, Y. Wu, and H. Huang, “Unveiling the effect of crystal orientation on gallium nitride cutting through MD simulation,” International Journal of Mechanical Sciences. 2023. link Times cited: 2 USED (low confidence) M.-W. Tan et al., “Cascade mechanism and mechanical property of the dislocation loop formation in GaN twin crystal-induced crystallization,” Materials Science in Semiconductor Processing. 2022. link Times cited: 5 USED (low confidence) T. Gao et al., “Microstructure evolution of Si nanoparticles during the melting process: Insights from molecular dynamics simulation,” Materials Science in Semiconductor Processing. 2022. link Times cited: 0 USED (low confidence) Y. Wang and J. Guo, “Effect of abrasive size on nano abrasive machining for wurtzite GaN single crystal via molecular dynamics study,” Materials Science in Semiconductor Processing. 2021. link Times cited: 9 USED (low confidence) O. Kushnerov, V. Bashev, and S. Ryabtsev, “Deposition and Growth of the AlCoCuFeNi High-Entropy Alloy Thin Film: Molecular Dynamics Simulation,” Springer Proceedings in Physics. 2021. link Times cited: 0 USED (low confidence) T. Mahadevan and J. Du, “Atomic and micro‐structure features of nanoporous aluminosilicate glasses from reactive molecular dynamics simulations,” Journal of the American Ceramic Society. 2020. link Times cited: 12 USED (low confidence) K. Termentzidis and D. Lacroix, “Tuning thermal transport in nanowires: molecular dynamics and Monte Carlo simulations.” 2020. link Times cited: 0 USED (low confidence) M. J. Echeverría, S. Suresh, and A. Dongare, “Damage initiation and evolution in Al-Si layered microstructures under shock loading conditions at atomic scales.” 2020. link Times cited: 0 USED (low confidence) A. Utkin, V. M. Fomin, and E. Golovneva, “Parallel molecular dynamics for silicon and silicon carbide: MPI, CUDA and CUDA-MPI implementation.” 2020. link Times cited: 2 USED (low confidence) H. Dai, F. Zhang, and Y. Zhou, “Numerical study of three-body diamond abrasive polishing single crystal Si under graphene lubrication by molecular dynamics simulation,” Computational Materials Science. 2020. link Times cited: 21 USED (low confidence) H. Dai, S. Li, and G. Chen, “Comparison of subsurface damages on mono-crystalline silicon between traditional nanoscale machining and laser-assisted nanoscale machining via molecular dynamics simulation,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2018. link Times cited: 46 USED (low confidence) M. Khalkhali and F. Khoeini, “Impact of torsion and disorder on the thermal conductivity of Si nanowires: A nonequilibrium molecular dynamics study,” Journal of Physics and Chemistry of Solids. 2018. link Times cited: 16 USED (low confidence) J. C. Noyola-Pineda and A. Valladares, “The effect of porosity on the vibrational and low temperature equilibrium thermodynamic properties of amorphous silicon via computer simulation,” Journal of Non-crystalline Solids. 2017. link Times cited: 2 USED (low confidence) P. Saidi and J. Hoyt, “Atomistic simulation of the step mobility at the Al–Si(1 1 1) crystal–melt interface using molecular dynamics,” Computational Materials Science. 2016. link Times cited: 8 USED (low confidence) L. Sang, “Affect of the graphene layers on the melting temperature of silicon by molecular dynamics simulations,” Computational Materials Science. 2016. link Times cited: 8 USED (low confidence) P. Lin et al., “Tensile response of bi-crystalline Si nanofilms with twist and tilt grain boundaries,” Computational Materials Science. 2015. link Times cited: 5 USED (low confidence) S. N. Divi and A. Chatterjee, “Study of Silicon Thin Film Growth at High Deposition Rates Using Parallel Replica Molecular Dynamics Simulations,” Energy Procedia. 2014. link Times cited: 5 USED (low confidence) T. Zushi, K. Shimura, M. Tomita, K. Ohmori, K. Yamada, and T. Watanabe, “Phonon dispersion in (100) Si nanowire covered with SiO2 film calculated by molecular dynamics simulation,” ECS Journal of Solid State Science and Technology. 2014. link Times cited: 6 USED (low confidence) G. Samolyuk, S. Golubov, Y. Osetsky, and R. Stoller, “Impact of Vacancy-Type Defects on Thermal Conductivity of β-SiC: Molecular Dynamics Versus an Analytical Approach.” 2013. link Times cited: 0 USED (low confidence) H. Kassem, “(113) FACETS of Si-Ge/Si ISLANDS; ATOMIC SCALE SIMULATION,” Physics Procedia. 2011. link Times cited: 0 USED (low confidence) E. Holmström, A. Krasheninnikov, and K. Nordlund, “Quantum and Classical Molecular Dynamics Studies of the Threshold Displacement Energy in Si Bulk and Nanowires,” MRS Proceedings. 2009. link Times cited: 6 USED (low confidence) E. Landry, T. Matsuura, and A. McGaughey, “Predicting the Thermal Boundary Resistance of Isolated and Closely-Spaced Si/Si1−XGeX Interfaces With Molecular Dynamics Simulations.” 2008. link Times cited: 1 Abstract: Phonon scattering at an interface between two materials resu… read moreAbstract: Phonon scattering at an interface between two materials results in a thermal boundary resistance R, given by [1] R = ΔTq, (1) where ΔT and q are the temperature drop and heat flux across the interface. Predicting the thermal boundary resistance of semiconductor/semiconductor interfaces is important in devices where phonon interface scattering is a significant contributor to the overall thermal resistance (e.g., computer chips with high component density). Such predictions will also lead to improvements in the design of nanocomposite materials (e.g., superlattices) with low thermal conductivity, desirable in thermoelectric energy conversion applications [2].Copyright © 2008 by ASME read less USED (low confidence) H. Swygenhoven and P. Derlet, “Chapter 81 – Atomistic Simulations of Dislocations in FCC Metallic Nanocrystalline Materials.” 2008. link Times cited: 27 USED (low confidence) Z. Wang, X. Zu, L. Yang, F. Gao, and W. J. Weber, “Molecular dynamics simulation on the buckling behavior of GaN nanowires under uniaxial compression,” Physica E-low-dimensional Systems & Nanostructures. 2008. link Times cited: 25 USED (low confidence) C.-T. Lin, C. Chou, and K. Chiang, “Validation of Mechanical Properties of Single Crystal Silicon by Atomic-Level Numerical Model.” 2007. link Times cited: 0 USED (low confidence) N. Skoulidis and H. Polatoglou, “Stress distribution, strains and energetics of Si-capped Ge quantum dots: an atomistic simulation study.” 2005. link Times cited: 1 Abstract: We study Si-capped Ge quantum dots which are very interestin… read moreAbstract: We study Si-capped Ge quantum dots which are very interesting as these nanostructures emit/absorb light in the near infrared and visible. Their preparation proceeds by the deposition of Ge on Si, which forms small islands. By successive deposition of Si and Ge, a periodic structure is formed in three dimensions, of Si-capped Ge (QDs). Experimentally has been found that these QDs have different shapes and sizes, which are strongly depended on their preparation conditions and method. For our study we created atomistic models representing nanostructures consisting from a few hundreds to tenths of thousands atoms of Si where a portion of them replaced with Ge atoms. The replaced atoms were selected in order the Ge atoms to form small islands shaped in pyramids or domes and with different sizes. This nanostructure was repeated periodically in three dimensions, forming finally a periodic QD structure. For these structures we used the Stillinger-Weber interatomic potential models to relax them to the minimum total energy. Then we studied the strains distribution and energetics and their dependence on the substrate composition and the alignment of the QD along the growth direction. It is found that the distribution of the strains differ compared to an equivalent alloy, with the Ge atoms having a broader one, there is a buffer layer composition for which that nanostructure has the lowest energy and the distribution of strains are proportionally divided in the Ge and Si atoms, and that the alignment along the growth axis with the lowest energy corresponds to each QD on top of the next one. read less USED (low confidence) S. Hao, Y. Min, H. Ru, W. Yangyuan, S. Kunihiro, and O. Hideki, “Molecular Dynamics Simulation of Ion Implantation into HfO2 and HfO2/Si Multi-Layer Structure,” Chinese Physics Letters. 2005. link Times cited: 1 Abstract: We simulate the B, As and P implantations into HfO2 from 3 k… read moreAbstract: We simulate the B, As and P implantations into HfO2 from 3 keV to 40 keV by a simulator LEACS developed based on molecular dynamics method and by the traditional Monte Carlo simulator TSUPREM4 respectively. The LEACS results accurately fit with the SIMS (secondary ion mass spectroscopy) data, while the TSUPREM4 results deviate from the SIMS data obviously except B implantation. Based on the verification of the simulator, influence of the oxide thickness on the retained range profiles in the Si layer has been quantitatively investigated in the case of HfO2/Si and SiO2/Si structures. The range profiles in the Si layer through HfO2 shift to the surface obviously for about 0.68 times of the oxide layer thickness on the average in comparison to those through SiO2. It can be predicted that this effect will have a significant impact on MOSFET (metallic oxide semiconductor field effect transistor) device performance in the integrated circuit process of the next decade if HfO2 is used to replace SiO2 as the gate dielectric. read less USED (low confidence) G. Hadjisavvas, P. Sonnet, and P. Kelires, “Carbon-Induced Ge Dots On Si(100): Interplay of Strain and Chemical Effects.” 2005. link Times cited: 0 USED (low confidence) M. Mckay, J. Drucker, and J. Shumway, “Real-time coarsening dynamics of Ge/Si(100) nanostructures using elevated temperature scanning tunneling microscopy,” MRS Proceedings. 2004. link Times cited: 0 USED (low confidence) C. Massobrio, M. Celino, Y. Pouillon, and I. Billas, “7. From the Cluster to the Liquid: Ab-Initio Calculations on Realistic Systems Based on First-Principles Molecular Dynamics.” 2004. link Times cited: 0 USED (low confidence) R. Belkada, S. Ogata, F. Shimojo, A. Nakano, P. Vashishta, and R. Kalia, “Mechanisms of stress corrosion cracking in Si: A hybrid quantum-mechanical/molecular-dynamics simulation,” MRS Proceedings. 2002. link Times cited: 1 USED (low confidence) A. Noreyan, I. Marinescu, and J. Amar, “Molecular Dynamic Simulation of Nanoindentation of Silicon Carbide by Diamond Tip.” 2002. link Times cited: 1 USED (low confidence) A. Mazzone, “Motions of Si(100) Steps at Low Temperature. A Study by Molecular Dynamics,” MRS Proceedings. 2002. link Times cited: 0 Abstract: An isothermal Molecular Dynamics simulation method has been … read moreAbstract: An isothermal Molecular Dynamics simulation method has been applied to the study of motions of steps on Si(100). The steps have a monolayer height and their temperature is below the roughening transition (i.e. T ≤ 1000K). The calculations predict spontaneous motions even in this low temperature range and describe the functional dependence of the displacements of step-edge atoms on the step geometry, size and temperature and on the nature of the interatomic forces. Owing to the use of the Fourier analysis, these results can be applied to structures of realistic size by a proper scaling of the wavevectors. read less USED (low confidence) A. Satta, L. Colombo, and F. Cleri, “A molecular dynamics investigation on grain disappearance at a triple junction in polycrystalline silicon,” MRS Proceedings. 2001. link Times cited: 0 USED (low confidence) J. Que, M. Radny, P. V. Smith, and A. Dyson, “Application of the extended Brenner potential to the Si(111)7 × 7:H system I : cluster calculations,” Surface Science. 2000. link Times cited: 13 USED (low confidence) M. Bachlechner et al., “Multi-Million Atom Molecular-Dynamics Simulations of Stresses in Si(111)/Si3N4 Nanopixels,” MRS Proceedings. 1999. link Times cited: 0 USED (low confidence) L. J. Lewis and N. Mousseau, “Structural and Electronic Properties of a-Gaas: A Tight-Binding–Molecular-Dynamics–Art Simulation,” MRS Proceedings. 1997. link Times cited: 1 USED (low confidence) C. Roland, Q. Zhang, P. Bogusławski, J. Bernholc, and G. Gilmer, “Simulations of SI(100) Growth: Step Flow and Low Temperature Growth,” MRS Proceedings. 1995. link Times cited: 1 USED (low confidence) M. Kohyama, R. Yamamoto, and Y. Watanabe, “Energies and Atomic Structures of Grain Boundaries in Silicon: Comparison Between Tilt and Twist Boundaries,” MRS Proceedings. 1994. link Times cited: 2 Abstract: The energies and atomic structures of tilt and twist boundar… read moreAbstract: The energies and atomic structures of tilt and twist boundaries in Si have been examined by using the tight-binding electronic theory, and the reason why twist boundaries are seldom found in polycrystalline Si has been investigated. About the frequently observed {122} Σ=9 and {255} Σ=27 tilt boundaries, the configurations without any coordination defects consistent with the electron microscopy observations have relatively small interfacial energies with small bond distortions. About the Σ=7, Σ=3 and Σ = 5 twist boundaries, the configurations contain larger bond distortions or more coordination defects, and much larger interfacial energies than those of the tilt boundaries. The twist boundaries have very complex structures as compared with the other twist boundaries, which can be explained by the morphology of the ideal surfaces. The stability of the tilt boundaries in Si can be explained by the viewpoint of the stable structural units consisting of atomic rings. read less USED (low confidence) P. Weakliem and E. Carter, “Surface chemical reactions studied via ab initio‐derived molecular dynamics simulations: Fluorine etching of Si(100),” Journal of Chemical Physics. 1993. link Times cited: 54 Abstract: Previous isothermal dynamics simulations of the interaction … read moreAbstract: Previous isothermal dynamics simulations of the interaction of F with Si(100) failed to predict any reaction beyond saturation of the surface dangling bonds. We show that this lack of reactivity was due to the overly repulsive nature of the empirical potential employed. We used the method of simulated annealing to fit a new analytic interaction potential to data from ab initio configuration interaction calculations. This potential was then utilized in isothermal molecular dynamics simulations to explore the mechanism by which fluorine begins to etch silicon. Calculated adsorption and reaction probabilities, as a function of both fluorine coverage and structure, reveal that the buildup of the fluorosilyl layer occurs via several competing reactions and that it does not follow a well defined reaction sequence. This competition creates disorder in the adsorbed fluorosilyl layer, which is shown to be an important precursor to continued reaction. Idealized ordered surface structures are shown to be unstable re... read less USED (low confidence) K. Heinig, D. Stock, H. Boettger, V. Zinovyev, A. Dvurechenskii, and L. Aleksandrov, “Formation of Double-Height Si(001) Steps by Sputtering with Xe Ions - A Computer Simulation,” MRS Proceedings. 1993. link Times cited: 5 USED (low confidence) T. Inamura, N. Takezawa, and N. Taniguchi, “Atomic-scale cutting in a computer using crystal models of copper and diamond,” CIRP Annals. 1992. link Times cited: 92 USED (low confidence) Q. Yu and P. Clancy, “Surface Reconstruction and Strain Relief in Si 1− x - Ge x Films on Si(100),” MRS Proceedings. 1992. link Times cited: 2 USED (low confidence) Y. Khait, A. Silverman, R. Weil, and J. Adler, “Large picosecond energy fluctuations of single atoms in a-Si revealed by molecular dynamics,” Journal of Non-crystalline Solids. 1991. link Times cited: 0 USED (low confidence) P. Fedders, “Defects, tight binding, and ab initio molecular dynamics simulations on a-Si,” Journal of Non-crystalline Solids. 1991. link Times cited: 0 USED (low confidence) C. Roland and G. Gilmer, “Growth Properties of the Si(100) Steps: A Molecular Dynamics Study,” MRS Proceedings. 1991. link Times cited: 0 Abstract: We have mapped out the energy surfaces seen by a single sili… read moreAbstract: We have mapped out the energy surfaces seen by a single silicon adatom over the Si(100) surface and Si(100) steps, using Molecular Dynamics methods. This identifies the most likely binding sites as well as the activation energies for diffusion over the terraces and steps. We find that only the 5e step with no rebonded atoms is a good sink for adatoms - the S A , rebonded S b and D b steps are weak sinks. Because of a higher density of binding sites and lower activation energies for surface diffusion along die step edge, we expect mat growth at the S b and D b steps take place much more readily man at the S A step. read less USED (low confidence) S. Ethier and L. J. Lewis, “Molecular-Dynamics Study of the Growth of Si1- xGe x on Si(100)2×1,” MRS Proceedings. 1990. link Times cited: 0 USED (low confidence) B. Pailthorpe and P. Mahon, “Molecular dynamics simulations of thin film diamond,” Thin Solid Films. 1990. link Times cited: 8 USED (low confidence) S. Phillpot, J. Lutsko, D. Wolf, and S. Yip, “Grain-Boundary and Free-Surface Induced Thermodynamic Melting: A Molecular Dynamics Study in Silicon.” 1989. link Times cited: 1 USED (low confidence) J. Chelikowsky, “The Atomistic Structure of Silicon Clusters and Crystals: From the Finite to the Infinite.” 1989. link Times cited: 0 USED (low confidence) V. Vítek, D. Srolovitz, and W. Morgan, “MOLECULAR DYNAMICS SIMULATION OF THE PHYSICS OF THIN FILM GROWTH ON SILICON: EFFECTS OF THE PROPERTIES OF INTERATOMIC POTENTIAL MODELS.” 1989. link Times cited: 0 USED (low confidence) J. Lampinen, R. Nieminen, and K. Kaski, “Molecular dynamics simulation of the structure and melting transition of the Si(001) surface,” Surface Science. 1988. link Times cited: 18 NOT USED (low confidence) A. Hirano, H. Sakakima, A. Hatano, and S. Izumi, “Long-range Tersoff potential for silicon to reproduce 30° partial dislocation migration,” Computational Materials Science. 2024. link Times cited: 0 NOT USED (low confidence) J. Zhang, H. Zhang, and G. Zhang, “Nanophononic metamaterials induced proximity effect in heat flux regulation,” Frontiers of Physics. 2023. link Times cited: 0 NOT USED (low confidence) T. Nie et al., “The behavior of surface nanobubbles on different substrates in electrochemistry,” Journal of Molecular Liquids. 2023. link Times cited: 0 NOT USED (low confidence) P. Desmarchelier, V. M. Giordano, J. Raty, and K. Termentzidis, “a-C/GeTe superlattices: Effect of interfacial impedance adaptation modeling on the thermal properties,” Journal of Applied Physics. 2023. link Times cited: 0 Abstract: Recently, nanostructuration has been proposed to improve the… read moreAbstract: Recently, nanostructuration has been proposed to improve the performance of phase change memories. This is the case of superlattices composed of amorphous carbon and crystalline germanium telluride, which we have investigated by molecular dynamics. For this, a modified Stillinger–Weber potential is adapted to reproduce their stiffness contrast/impedance ratio. In order to study the effect of the interface interaction, two sets of parameters are used to model the interfaces with different interactions between the two materials using the properties of the softer material or the average properties between the two creating an adaptation of impedance across the layers. The effects of interface roughness and carbon diffusion at grain boundaries are studied. Using equilibrium molecular dynamics as well as the propagation of wave-packets, we show first that without impedance adaptation, the anisotropy is high, and the roughness has a marked impact on the properties. However, the introduction of impedance adaptation destroys those effects on the thermal conductivity. Finally, we show that the periodic texturing of the interface increases the transmission of in-plane transverse phonons. read less NOT USED (low confidence) Y. Wang, S. Patel, and C. Ortner, “A Theoretical Case Study of the Generalisation of Machine-learned Potentials,” ArXiv. 2023. link Times cited: 0 Abstract: Machine-learned interatomic potentials (MLIPs) are typically… read moreAbstract: Machine-learned interatomic potentials (MLIPs) are typically trained on datasets that encompass a restricted subset of possible input structures, which presents a potential challenge for their generalization to a broader range of systems outside the training set. Nevertheless, MLIPs have demonstrated impressive accuracy in predicting forces and energies in simulations involving intricate and complex structures. In this paper we aim to take steps towards rigorously explaining the excellent observed generalisation properties of MLIPs. Specifically, we offer a comprehensive theoretical and numerical investigation of the generalization of MLIPs in the context of dislocation simulations. We quantify precisely how the accuracy of such simulations is directly determined by a few key factors: the size of the training structures, the choice of training observations (e.g., energies, forces, virials), and the level of accuracy achieved in the fitting process. Notably, our study reveals the crucial role of fitting virials in ensuring the consistency of MLIPs for dislocation simulations. Our series of careful numerical experiments encompassing screw, edge, and mixed dislocations, supports existing best practices in the MLIPs literature but also provides new insights into the design of data sets and loss functions. read less NOT USED (low confidence) В. И. Мажукин et al., “Модификация кинетической модели Вильсона-Френкеля и атомистическое моделирование скорости плавления/кристаллизации металлов,” Математическое моделирование. 2023. link Times cited: 0 Abstract: В рамках кинетико-атомистического подхода предложен новый по… read moreAbstract: В рамках кинетико-атомистического подхода предложен новый подход к построению температурной зависимости стационарной скорости распространения межфазной границы «твeрдое тело-жидкость» в металлах (алюминий, медь и железо) с различной кристаллографической ориентацией. Рассматриваемый температурный диапазон включает область предельно допустимых значений перегрева/переохлаждения для каждого из металлов. Выполнена существенная модификация известной кинетической модели с диффузионным ограничением Вильсона-Френкеля, которая использовалась для построения функции отклика. Проведено атомистическое моделирование процессов плавления/кристаллизации алюминия, меди и железа в рассматриваемом температурном диапазоне с использованием трех потенциалов взаимодействия семейства потенциалов «погруженного атома». Из сопоставления результатов моделирования с данными модифицированной кинетической модели построена функция отклика скорости интерфейса в области предельно допустимых значений перегрева/переохлаждения в металлах с использованием критерия наименьших квадратов. Использование в расчeтах модифицированной кинетической модели Вильсона-Френкеля существенно увеличивает точность функции отклика в рассматриваемом температурном диапазоне. Полученная температурная зависимость скорости движения межфазной границы является диффузионно-ограниченной и описывается одним и тем же уравнением для каждого металла в рассматриваемом температурном диапазоне. read less NOT USED (low confidence) H. Yang, Y. Shen, L. Li, Y. Pan, and P. Yang, “Surface modification to induce efficient heat transfer at graphene/silicon heterointerface,” Applied Thermal Engineering. 2023. link Times cited: 0 NOT USED (low confidence) V. K. Sinha, A. K. Metya, and C. K. Das, “Estimation of Solid-Liquid Coexistence Curve for Coarse-grained Water Models through Reliable Free Energy Method,” Fluid Phase Equilibria. 2023. link Times cited: 0 NOT USED (low confidence) J. Zhang, X. Shang, B. B. He, and B. Zhang, “Towards understanding the crack suppression mechanism in brittle materials with high grinding speed at different temperatures,” International Journal of Machine Tools and Manufacture. 2023. link Times cited: 0 NOT USED (low confidence) J. A. Vita and D. Trinkle, “Spline-based neural network interatomic potentials: blending classical and machine learning models,” ArXiv. 2023. link Times cited: 0 Abstract: While machine learning (ML) interatomic potentials (IPs) are… read moreAbstract: While machine learning (ML) interatomic potentials (IPs) are able to achieve accuracies nearing the level of noise inherent in the first-principles data to which they are trained, it remains to be shown if their increased complexities are strictly necessary for constructing high-quality IPs. In this work, we introduce a new MLIP framework which blends the simplicity of spline-based MEAM (s-MEAM) potentials with the flexibility of a neural network (NN) architecture. The proposed framework, which we call the spline-based neural network potential (s-NNP), is a simplified version of the traditional NNP that can be used to describe complex datasets in a computationally efficient manner. We demonstrate how this framework can be used to probe the boundary between classical and ML IPs, highlighting the benefits of key architectural changes. Furthermore, we show that using spline filters for encoding atomic environments results in a readily interpreted embedding layer which can be coupled with modifications to the NN to incorporate expected physical behaviors and improve overall interpretability. Finally, we test the flexibility of the spline filters, observing that they can be shared across multiple chemical systems in order to provide a convenient reference point from which to begin performing cross-system analyses. read less NOT USED (low confidence) Y. Peng et al., “OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining,” The Journal of Physical Chemistry. B. 2023. link Times cited: 5 Abstract: The “bottom-up” approach to coarse-graining, for building ac… read moreAbstract: The “bottom-up” approach to coarse-graining, for building accurate and efficient computational models to simulate large-scale and complex phenomena and processes, is an important approach in computational chemistry, biophysics, and materials science. As one example, the Multiscale Coarse-Graining (MS-CG) approach to developing CG models can be rigorously derived using statistical mechanics applied to fine-grained, i.e., all-atom simulation data for a given system. Under a number of circumstances, a systematic procedure, such as MS-CG modeling, is particularly valuable. Here, we present the development of the OpenMSCG software, a modularized open-source software that provides a collection of successful and widely applied bottom-up CG methods, including Boltzmann Inversion (BI), Force-Matching (FM), Ultra-Coarse-Graining (UCG), Relative Entropy Minimization (REM), Essential Dynamics Coarse-Graining (EDCG), and Heterogeneous Elastic Network Modeling (HeteroENM). OpenMSCG is a high-performance and comprehensive toolset that can be used to derive CG models from large-scale fine-grained simulation data in file formats from common molecular dynamics (MD) software packages, such as GROMACS, LAMMPS, and NAMD. OpenMSCG is modularized in the Python programming framework, which allows users to create and customize modeling “recipes” for reproducible results, thus greatly improving the reliability, reproducibility, and sharing of bottom-up CG models and their applications. read less NOT USED (low confidence) T. Li, H. Xu, and F. Shang, “A refined numerical simulation approach to assess the neutron irradiation effect on the mechanical behavior of wurtzite GaN,” Computational Materials Science. 2023. link Times cited: 0 NOT USED (low confidence) A. Saha and A. K. Das, “Multiscale simulation of nanodrop over surfaces with varying hydrophilicity,” Comput. Phys. Commun. 2023. link Times cited: 0 NOT USED (low confidence) I. A. Kutlubulatova et al., “Molecular Dynamics Modeling of Pulsed Laser Fragmentation of Solid and Porous Si Nanoparticles in Liquid Media,” International Journal of Molecular Sciences. 2023. link Times cited: 0 Abstract: The production of non-toxic and homogeneous colloidal soluti… read moreAbstract: The production of non-toxic and homogeneous colloidal solutions of nanoparticles (NPs) for biomedical applications is of extreme importance nowadays. Among the various methods for generation of NPs, pulsed laser ablation in liquids (PLAL) has proven itself as a powerful and efficient tool in biomedical fields, allowing chemically pure silicon nanoparticles to be obtained. For example, laser-synthesized silicon nanoparticles (Si NPs) are widely used as contrast agents for bio visualization, as effective sensitizers of radiofrequency hyperthermia for cancer theranostics, in photodynamic therapy, as carriers of therapeutic radionuclides in nuclear nanomedicine, etc. Due to a number of complex and interrelated processes involved in the laser ablation phenomenon, however, the final characteristics of the resulting particles are difficult to control, and the obtained colloidal solutions frequently have broad and multimodal size distribution. Therefore, the subsequent fragmentation of the obtained NPs in the colloidal solutions due to pulsed laser irradiation can be utilized. The resulting NPs’ characteristics, however, depend on the parameters of laser irradiation as well as on the irradiated material and surrounding media properties. Thus, reliable knowledge of the mechanism of NP fragmentation is necessary for generation of a colloidal solution with NPs of predesigned properties. To investigate the mechanism of a laser-assisted NP fragmentation process, in this work, we perform a large-scale molecular dynamics (MD) modeling of FS laser interaction with colloidal solution of Si NPs. The obtained NPs are then characterized by their shape and morphological properties. The corresponding conclusion about the relative input of the properties of different laser-induced processes and materials to the mechanism of NP generation is drawn. read less NOT USED (low confidence) R. Atta-Fynn, S. J. Rathi, H. Arya, and P. Biswas, “Ab initio study of the structure and properties of amorphous silicon hydride from accelerated molecular dynamics simulations,” Journal of Non-Crystalline Solids. 2023. link Times cited: 1 NOT USED (low confidence) Z. Liu et al., “Nonmonotonic dependence of adhesion between liquid aluminum and silicon surface on the temperature of the surface,” Physica Scripta. 2023. link Times cited: 0 Abstract: In this paper, the effect of temperature on the adhesion pro… read moreAbstract: In this paper, the effect of temperature on the adhesion properties between liquid aluminum (Al) and solid silicon (Si) in the presence and absence of vacancy defects is elucidated. Firstly, the perfect defect-free and vacancy defect models consist of crystalline Al probe and Si substrate are established by classical molecular dynamics simulation method. Then, the melting and adhesion process of probe Al are simulated, and the adhesion performance and microscopic permeation evolution of liquid Al/solid Si are analyzed. The results show that the adhesion force changes nonmonotonically with increasing substrate temperature T without vacancy defects. Specifically, when the substrate temperature varies at relatively low values smaller than the melting point of Al, that is, 100 K < T < 933 K, the thermal excitation provides more energy to the substrate Si atoms, which intensifies the aggregation of the substrate atoms, makes the interfacial atoms more dense and the number of atoms permeating into the substrate decreases, resulting in a decrease in adhesion force. On the contrary, when 933 K < T < 1500 K, due to the thermal effect, higher temperatures intensify the thermal vibration of the substrate atoms, resulting in violent collisions between the interfacial atoms, and the space for free movement increases, thus making the distance between the atoms larger. And the number of Al atoms permeating into the substrate Si increases, leading to an increase in interfacial adhesion. Furthermore, the adhesion force shows an upward trend with the elevated temperature in the presence of vacancy defects at low temperatures, this is attributed to the fact that more atoms are broken away from the equilibrium lattice structure, and the number of permeating atoms increases by increasing temperature. In particular, the interfacial adhesion is the largest when the vacancy defects of the substrate are the most serious. read less NOT USED (low confidence) K. W. Kayang and A. N. Volkov, “Turning nanopowder into nanomaterial: Effect of continuous SiC coating on mechanical properties of Si nanoparticle arrays,” Materialia. 2023. link Times cited: 0 NOT USED (low confidence) K. Matsunoshita et al., “Optimization of force-field potential parameters using conditional variational autoencoder,” Science and Technology of Advanced Materials: Methods. 2023. link Times cited: 0 Abstract: ABSTRACT Owing to their high-speed, force-field (FF) calcula… read moreAbstract: ABSTRACT Owing to their high-speed, force-field (FF) calculations for inorganic solid-state materials using the parametric potential have been widely employed as an effective tool for high-throughput calculations such as exhaustive property evaluation of material databases and/or calculations for models containing tens of thousands of atoms or more, including amorphous and grain boundary models. However, the accuracy of such calculations strongly depends on the choice of the FF parameters. Today, compounds containing three or more elements are targeted in the research and development of functional materials, in which case the number of parameters often exceeds 10 dimensions. This significantly increases the search space, making it difficult to determine the parameters rationally. To resolve this issue, we previously reported an FF parameter determination approach based on meta-heuristics (APL Materials, 8, 081111 (2020)). In this study, we further investigated a methodology to efficiently determine the FF parameters using a conditional variational autoencoder (CVAE), a type of deep learning method, which can reduce the dimension of the input parameters and distribute them in a probabilistic manner in the latent space. As a demonstration, we applied the method to the optimization of 11 FF parameters for an argyrodite-type Li7PS6 material, which has attracted considerable attention as a solid electrolyte for all-solid-state batteries. The results confirmed that the proposed approach can generate valid FFs that are highly consistent with the results of first-principles calculations, even when using a limited set of meta-heuristics-generated FF parameters. Graphical Abstract IMPACT STATEMENT Towards the development of functional materials, we applied our previously reported force-field (FF) parameter determination approach based on meta-heuristics to develop a methodology to efficiently determine the FF parameters using a conditional variational autoencoder (CVAE). As part of a demonstration, we selected argyrodite-type Li7PS6 material and applied the proposed method to its FF optimization. We believe that our study makes a significant contribution to the literature because it can serve as a basis for FF optimization of advanced materials. read less NOT USED (low confidence) D. Fijan and M. Wilson, “Thermodynamic anomalies, polyamorphism and all that,” Philosophical transactions. Series A, Mathematical, physical, and engineering sciences. 2023. link Times cited: 1 Abstract: The appearance and evolution of thermodynamics anomalies, an… read moreAbstract: The appearance and evolution of thermodynamics anomalies, and related properties, are studied for two classes of system, modelling those dominated by covalent and ionic interactions, respectively. Such anomalies are most familiar in the density but are also present in other thermodynamics variables such as the compressibility and heat capacity. By systematically varying key model parameters the emergence and evolution of these anomalies can be tracked across the phase space. The interaction of the anomalies can often be rationalized by thermodynamics ‘rules’. The emergence of these anomalies may also be correlated with the appearance of polyamorphism, the existence of multiple amorphous states which differ in density and entropy. This article is part of the theme issue ‘Exploring the length scales, timescales and chemistry of challenging materials (Part 1)’. read less NOT USED (low confidence) J. Lees et al., “Nanoscale Si fishbone structures for manipulating heat transport using phononic resonators for thermoelectric applications,” Physica Scripta. 2023. link Times cited: 0 Abstract: Thermoelectric materials have the potential to convert waste… read moreAbstract: Thermoelectric materials have the potential to convert waste heat into electricity, but their thermoelectric efficiency must be improved before they are effective and economically viable. One promising route to improving thermoelectric efficiency in thin-film thermoelectric materials is to reduce the material’s thermal conductivity through nanopatterning the surface. In this work nanoscale phononic resonators are introduced to the surface, and their potential to reduce thermal conductivity is explored via coupled experimental and theoretical techniques. Atomistic modelling is used to predict the dependence of the thermal conductivity on different design parameters and used to guide the design and fabrication of silicon fishbone nanostructures. The nanostructure design incorporates a variation on design parameters such as barb length, width and spacing along the shaft length to enable correlation with changes in thermal conductivity. The thermal characteristics of the nanostructures are investigated experimentally using the spatial resolution of scanning thermal microscopy to correlate changes in thermal conductivity with the changes in the structure parameters. The method developed uses a microheater to establish a temperature gradient along the structure which will be affected by any local variations in thermal conductivity. The impact on the thermal gradient and consequently on the tip temperature is modelled using finite element computer simulations. Experimental changes as small as 7.5% are shown to be detectable in this way. Despite the experimental technique being shown to be able to detect thermal changes far smaller than those predicted by the modelling, no modifications of the thermal conductivity are detected. It is concluded that in order to realise the effects of phononic resonators to reduce thermal conductivity, that much smaller structures with a greater ratio of resonator to shaft will be needed. read less NOT USED (low confidence) Y. Huang, Y. Zhou, J. Li, and F. Zhu, “Understanding the role of surface mechanical properties in SiC surface machining,” Materials Science in Semiconductor Processing. 2023. link Times cited: 0 NOT USED (low confidence) Y. D. Fomin, E. N. Tsiok, S. A. Bobkov, and V. Ryzhov, “Molecular Simulation of Water Structure in Narrow Slitlike Pores,” Colloid Journal. 2023. link Times cited: 0 NOT USED (low confidence) A. Tanguy, “Vibrations and Heat Transfer in Glasses: The Role Played by Disorder,” Comptes Rendus. Physique. 2023. link Times cited: 1 Abstract: Amorphous materials are also distinguished from crystals by … read moreAbstract: Amorphous materials are also distinguished from crystals by their thermal properties. The structural disorder seems to be responsible both for a significant increase in heat capacity compared to crystals of the same composition, but also for a significant decrease in thermal conductivity. The temperature dependence of thermal conductivity, unusual for common interpretations of solid-state physics, gave rise to a lot of debates. We review in this article different interpretations of thermal conductivity in amorphous materials. We show finally that the temperature dependence of thermal conductivity in dielectric materials can be understood by relating it to the disorder-dependent harmonic vibrational eigenmodes. read less NOT USED (low confidence) U. Nwankwo, Y.-D. Wang, C. Lam, and N. Onofrio, “Charge equilibration model with shielded long-range Coulomb for reactive molecular dynamics simulations.,” The Journal of chemical physics. 2023. link Times cited: 1 Abstract: Atomic description of electrochemical systems requires react… read moreAbstract: Atomic description of electrochemical systems requires reactive interaction potential to explicitly describe the chemistry between atoms and molecules and the evolving charge distribution and polarization effects. Calculating Coulomb electrostatic interactions and polarization effects requires a better estimate of the partial charge distribution in molecular systems. However, models such as reactive force fields and charge equilibration (QEq) include Coulomb interactions up to a short-distance cutoff for better computational speeds. Ignoring long-distance electrostatic interaction affects the ability to describe electrochemistry in large systems. We studied the long-range Coulomb effects among charged particles and extended the QEq method to include long-range effects. By this extension, we anticipate a proper account of Coulomb interactions in reactive molecular dynamics simulations. We validate the approach by computing charges on a series of metal-organic frameworks and some simple systems. Results are compared to regular QEq and quantum mechanics calculations. The study shows slightly overestimated charge values in the regular QEq approach. Moreover, our method was combined with Ewald summation to compute forces and evaluate the long-range effects of simple capacitor configurations. There were noticeable differences between the calculated charges with/without long-range Coulomb interactions. The difference, which may have originated from the long-range influence on the capacitor ions, makes the Ewald method a better descriptor of Coulomb electrostatics for charged electrodes. The approach explored in this study enabled the atomic description of electrochemical systems with realistic electrolyte thickness while accounting for the electrostatic effects of charged electrodes throughout the dielectric layer in devices like batteries and emerging solid-state memory. read less NOT USED (low confidence) P. Lafourcade et al., “Robust crystal structure identification at extreme conditions using a density-independent spectral descriptor and supervised learning,” Computational Materials Science. 2023. link Times cited: 0 NOT USED (low confidence) A. Allera, A. Goryaeva, P. Lafourcade, J. Maillet, and M. Marinica, “Neighbors Map: An efficient atomic descriptor for structural analysis,” Computational Materials Science. 2023. link Times cited: 1 NOT USED (low confidence) Q. Mao, M. Feng, X. Jiang, Y. Ren, K. Luo, and A. V. van Duin, “Classical and reactive molecular dynamics: Principles and applications in combustion and energy systems,” Progress in Energy and Combustion Science. 2023. link Times cited: 10 NOT USED (low confidence) J. Trieschmann, L. Vialetto, and T. Gergs, “Machine learning for advancing low-temperature plasma modeling and simulation,” ArXiv. 2023. link Times cited: 0 Abstract: Machine learning has had an enormous impact in many scientif… read moreAbstract: Machine learning has had an enormous impact in many scientific disciplines. Also in the field of low-temperature plasma modeling and simulation it has attracted significant interest within the past years. Whereas its application should be carefully assessed in general, many aspects of plasma modeling and simulation have benefited substantially from recent developments within the field of machine learning and data-driven modeling. In this survey, we approach two main objectives: (a) We review the state-of-the-art focusing on approaches to low-temperature plasma modeling and simulation. By dividing our survey into plasma physics, plasma chemistry, plasma-surface interactions, and plasma process control, we aim to extensively discuss relevant examples from literature. (b) We provide a perspective of potential advances to plasma science and technology. We specifically elaborate on advances possibly enabled by adaptation from other scientific disciplines. We argue that not only the known unknowns, but also unknown unknowns may be discovered due to the inherent propensity of data-driven methods to spotlight hidden patterns in data. read less NOT USED (low confidence) L. N. Ngoc, H. Nguyen, V. V. Hoang, and T. N. T. Thuy, “Compression-induced hexa-to-tetra phase transition of confined germanene.,” Journal of molecular graphics & modelling. 2023. link Times cited: 0 NOT USED (low confidence) X. Li et al., “Theoretical basis and performance research on advanced non-contacting ion beam manufacturing process for optical materials,” Journal of Physics: Conference Series. 2023. link Times cited: 0 Abstract: Ultra-smooth surface is very important for the performance o… read moreAbstract: Ultra-smooth surface is very important for the performance of high energy optical system in the defence field. Low quality optical elements will cause energy loss and affect the performance of the optical system. Ultra-precision manufacturing technology of optical components is the key technology to obtain high quality optical components. As an advanced ultra-precision and no-contact surface processing technology, Ion Beam Manufacturing (IBM) was studied. Based on the analysis of the relationship between the ion beam current density distribution parameters obtained by faraday scan and the removal function, more effective removal function calculation method was found, the removal function model for IBF fused silica was established. The Molecular Dynamics(MD)simulation to study interaction between incident ion and optical substrate. Ion particle motion behaviour were obtained under different incident energies. The effect of incidence angle on surface roughness were carried out, lower surface roughness by smaller angle incident, ultra-precision surface of optical components were obtained by IBF experiments. read less NOT USED (low confidence) S. S. P. Chowdhury, A. Samudrala, and S. Mogurampelly, “Modeling interlayer interactions and phonon thermal transport in silicene bilayers,” Physical Review B. 2023. link Times cited: 0 Abstract: We develop an accurate interlayer pairwise potential derived… read moreAbstract: We develop an accurate interlayer pairwise potential derived from the \textit{ab-initio} calculations and investigate the thermal transport of silicene bilayers within the framework of equilibrium molecular dynamics simulations. The electronic properties are found to be sensitive to the temperature with the opening of the band gap in the $\Gamma$$\rightarrow$M direction. The calculated phonon thermal conductivity of bilayer silicene is surprisingly higher than that of monolayer silicene, contrary to the trends reported for other classes of 2D materials like graphene and hBN bilayers. This counterintuitive behavior of the bilayer silicene is attributed to the interlayer interaction effects and inherent buckling, which lead to a higher group velocity in the LA$_1$/LA$_2$ phonon modes. The thermal conductivity of both the mono- and bilayer silicene decreases with temperature as $\kappa\sim T^{-0.9}$ because of the strong correlations between the characteristic timescales of heat current autocorrelation function and temperature ($\tau\sim T^{-0.75}$). The mechanisms underlying phonon thermal transport in silicene bilayers are further established by analyzing the temperature induced changes in acoustic group velocity. read less NOT USED (low confidence) X. Ling, Y. Zhang, and F. Xu, “Dynamic characteristics of rectangular single-layered black phosphorus-based mass sensor,” Physica Scripta. 2023. link Times cited: 0 Abstract: Recently, anisotropic black phosphorus (BP) has been reporte… read moreAbstract: Recently, anisotropic black phosphorus (BP) has been reported to have significant physical and mechanical properties, and BP-based mass sensors have the latent applications in detecting the mass of nanoparticles attached on BP. In this paper, an orthotropic plate model (OPM) attached concentrated mass and molecular dynamics (MD) simulations are adopted to investigate the dynamic characteristics of rectangular single-layered BP-based (RSLBP-based) mass sensors. The influences of mass, position of the attachment and RSLBP size on the fundamental frequency of RSLBP-based mass sensor are discussed. The results show that when attachment mass increases, or the position of attachment moves from the edge to the middle of RSLBP, the fundamental frequency of the RSLBP-based mass sensor decreases. The fundamental frequency of RSLBP-based mass sensors decreases more significantly with increasing the attachment mass when the size of RSLBP is very small. The results calculated by OPM attached concentrated mass are agreed well with the results calculated by MD simulations, which indicates that the OPM attached concentrated mass can forecast the dynamic characteristics of RSLBP-based mass sensors significantly. read less NOT USED (low confidence) Y. Xie, K. Shibata, and T. Mizoguchi, “A defect formation mechanism induced by structural reconstruction of a well-known silicon grain boundary.,” Acta Materialia. 2023. link Times cited: 1 NOT USED (low confidence) D. Wang, T. Zhao, and Y. Yu, “In/Ga-Doped Si as Anodes for Si–Air Batteries with Restrained Self-Corrosion and Surface Passivation: A First-Principles Study,” Molecules. 2023. link Times cited: 1 Abstract: Silicon–air batteries (SABs) are attracting considerable att… read moreAbstract: Silicon–air batteries (SABs) are attracting considerable attention owing to their high theoretical energy density and superior security. In this study, In and Ga were doped into Si electrodes to optimize the capability of Si-air batteries. Varieties of Si-In/SiO2 and Si-Ga/SiO2 atomic interfaces were built, and their properties were analyzed using density functional theory (DFT). The adsorption energies of the SiO2 passivation layer on In- and Ga-doped silicon electrodes were higher than those on pure Si electrodes. Mulliken population analysis revealed a change in the average number of charge transfers of oxygen atoms at the interface. Furthermore, the local device density of states (LDDOS) of the modified electrodes showed high strength in the interfacial region. Additionally, In and Ga as dopants introduced new energy levels in the Si/SiO2 interface according to the projected local density of states (PLDOS), thus reducing the band gap of the SiO2. Moreover, the I-V curves revealed that doping In and Ga into Si electrodes enhanced the current flow of interface devices. These findings provide a mechanistic explanation for improving the practical efficiency of silicon–air batteries through anode doping and provide insight into the design of Si-based anodes in air batteries. read less NOT USED (low confidence) M. Lauricella, S. Meloni, and G. Ciccotti, “Effect of coarse graining in water models for the study of kinetics and mechanisms of clathrate hydrates nucleation and growth.,” The Journal of chemical physics. 2023. link Times cited: 1 Abstract: Clathrate hydrates are crystalline inclusion compounds where… read moreAbstract: Clathrate hydrates are crystalline inclusion compounds wherein a water framework encages small guest atoms/molecules within its cavities. Among the others, methane clathrates are the largest fossil fuel resource still available. They can also be used to safely transport gases and can also form spontaneously under suitable conditions plugging pipelines. Understanding the crystallization mechanism is very important, and given the impossibility of experimentally identifying the atomistic path, simulations played an important role in this field. Given the large computational cost of these simulations, in addition to all-atom force fields, scientists considered coarse-grained water models. Here, we have investigated the effect of coarse-graining, as implemented in the water model mW, on the crystallization characteristics of methane clathrate in comparison with the all-atom TIP4P force field. Our analyses revealed that although the characteristics directly depending on the energetics of the water models are well reproduced, dynamical properties are off by the orders of magnitude. Being crystallization a non-equilibrium process, the altered kinetics of the process results in different characteristics of crystalline nuclei. Both TIP4P and mW water models produce methane clathrate nuclei with some amount of the less stable (in the given thermodynamic conditions) structure II phase and an excess of pentagonal dodecahedral cages over the tetrakaidecahedral ones regarding the ideal ratio in structure I. However, the dependence of this excess on the methane concentration in solution is higher with the former water model, whereas with the latter, the methane concentration in solution dependence is reduced and within the statistical error. read less NOT USED (low confidence) L. Rovigatti and F. Sciortino, “Entropy-driven phase behavior of associative polymer networks,” SciPost Physics. 2023. link Times cited: 0 Abstract: Polymer chains decorated with a fraction of monomers capable… read moreAbstract: Polymer chains decorated with a fraction of monomers capable of forming reversible bonds form transient polymer networks that are important in soft and biological systems. If chains are flexible and the attractive monomers are all of the same species, the network formation occurs continuously as density increases. By contrast, it has been recently shown [Phys. Rev. Lett. 129, 047801 (2022)] that, if the attractive monomers are of two different and alternating types, the entropic gain of swapping intra-molecular bonds for inter-molecular connections induces a first order phase transition in the fully-bonded (i.e. low-temperature or, equivalently, large monomer-monomer attraction strength) limit and the network forms abruptly on increasing density. Here we use simulations to show that this phenomenon is robust with respect to thermal fluctuations, disorder and change in the polymer architecture, demonstrating its generality and likely relevance for the wide class of materials that can be modelled as associative (transient) polymer networks. read less NOT USED (low confidence) S. R. Maalouf and S. Vel, “Nonlinear elastic behavior of 2D materials using molecular statics and comparisons with first principles calculations,” Physica E: Low-dimensional Systems and Nanostructures. 2023. link Times cited: 2 NOT USED (low confidence) K. Zhao, Y. Wang, and P. Cao, “Fracture universality in amorphous nanowires,” Journal of the Mechanics and Physics of Solids. 2023. link Times cited: 3 NOT USED (low confidence) S. Paul, D. Schwen, M. Short, and K. Momeni, “A Modified Embedded-Atom Method Potential for a Quaternary Fe-Cr-Si-Mo Solid Solution Alloy,” Materials. 2023. link Times cited: 0 Abstract: Ferritic-martensitic steels, such as T91, are candidate mate… read moreAbstract: Ferritic-martensitic steels, such as T91, are candidate materials for high-temperature applications, including superheaters, heat exchangers, and advanced nuclear reactors. Considering these alloys’ wide applications, an atomistic understanding of the underlying mechanisms responsible for their excellent mechano-chemical properties is crucial. Here, we developed a modified embedded-atom method (MEAM) potential for the Fe-Cr-Si-Mo quaternary alloy system—i.e., four major elements of T91—using a multi-objective optimization approach to fit thermomechanical properties reported using density functional theory (DFT) calculations and experimental measurements. Elastic constants calculated using the proposed potential for binary interactions agreed well with ab initio calculations. Furthermore, the computed thermal expansion and self-diffusion coefficients employing this potential are in good agreement with other studies. This potential will offer insightful atomistic knowledge to design alloys for use in harsh environments. read less NOT USED (low confidence) Z. Wang et al., “Investigation on the Dynamic Behaviors of Single Surface CO Nanobubbles during CO2 Electroreduction in Ionic Liquids,” Chemical Engineering Science. 2023. link Times cited: 1 NOT USED (low confidence) D. Khan, S. Heinen, and O. A. von Lilienfeld, “Kernel based quantum machine learning at record rate: Many-body distribution functionals as compact representations.,” The Journal of chemical physics. 2023. link Times cited: 2 Abstract: The feature vector mapping used to represent chemical system… read moreAbstract: The feature vector mapping used to represent chemical systems is a key factor governing the superior data efficiency of kernel based quantum machine learning (QML) models applicable throughout chemical compound space. Unfortunately, the most accurate representations require a high dimensional feature mapping, thereby imposing a considerable computational burden on model training and use. We introduce compact yet accurate, linear scaling QML representations based on atomic Gaussian many-body distribution functionals (MBDF) and their derivatives. Weighted density functions of MBDF values are used as global representations that are constant in size, i.e., invariant with respect to the number of atoms. We report predictive performance and training data efficiency that is competitive with state-of-the-art for two diverse datasets of organic molecules, QM9 and QMugs. Generalization capability has been investigated for atomization energies, highest occupied molecular orbital-lowest unoccupied molecular orbital eigenvalues and gap, internal energies at 0 K, zero point vibrational energies, dipole moment norm, static isotropic polarizability, and heat capacity as encoded in QM9. MBDF based QM9 performance lowers the optimal Pareto front spanned between sampling and training cost to compute node minutes, effectively sampling chemical compound space with chemical accuracy at a sampling rate of ∼48 molecules per core second. read less NOT USED (low confidence) N. T. Long, T. Q. Tuan, D. N. A. Thuy, Q. D. Ho, and H. A. Huy, “Molecular dynamics study of the finite-size effect in 2D nanoribbon silicene,” Molecular Simulation. 2023. link Times cited: 1 Abstract: ABSTRACT
We present the molecular dynamics (MD) simulation … read moreAbstract: ABSTRACT
We present the molecular dynamics (MD) simulation of the finite-size effect in 2D silicene nanoribbons (SiNRs). Five silicene nanoribbon structures were modelled with the same length and buckling, but different width sizes. All models were melted from the perfect honeycomb silicene structure and then cooled from the disordered liquid state. Structural properties such as ring sizes, radial distribution function, coordination numbers, and interatomic distances have been carefully analysed. All models’ critical melting and cooling temperature were determined via total energy per atom. We found that 2D SiNRs transition temperature is lower than the pristine silicene. Particularly, the SiNRs present a noticeable finite-size effect on nanoribbons, resulting in a domain-type structure of 4, 5, and 6-fold rings. read less NOT USED (low confidence) M. Maździarz, “Transferability of interatomic potentials for silicene,” Beilstein Journal of Nanotechnology. 2023. link Times cited: 1 Abstract: The ability of various interatomic potentials to reproduce t… read moreAbstract: The ability of various interatomic potentials to reproduce the properties of silicene, that is, 2D single-layer silicon, polymorphs was examined. Structural and mechanical properties of flat, low-buckled, trigonal dumbbell, honeycomb dumbbell, and large honeycomb dumbbell silicene phases, were obtained using density functional theory and molecular statics calculations with Tersoff, MEAM, Stillinger–Weber, EDIP, ReaxFF, COMB, and machine-learning-based interatomic potentials. A quantitative systematic comparison and a discussion of the results obtained are reported. read less NOT USED (low confidence) J. Wang, Y. Yan, C. Li, and Y. Geng, “Material removal mechanism and subsurface characteristics of silicon 3D nanomilling,” International Journal of Mechanical Sciences. 2023. link Times cited: 16 NOT USED (low confidence) R. Guo, G. Li, J. Tang, Y. Wang, and X. Song, “Small-data-based Machine Learning Interatomic Potentials for Graphene Grain Boundaries Enabled by Structural Unit Model,” Carbon Trends. 2023. link Times cited: 2 NOT USED (low confidence) N. Mitra and K. Ramesh, “Physics of molecular deformation mechanism in 6H-SiC,” Modelling and Simulation in Materials Science and Engineering. 2023. link Times cited: 2 Abstract: Even though there have been several studies in literature of… read moreAbstract: Even though there have been several studies in literature of 6H SiC, a proper physics based understanding of the molecular deformation mechanisms of the material under different loading conditions is still lacking. Experimentally, the brittle nature of the material leads to difficulties associated with in-situ determination of molecular deformation mechanisms of the material under an applied load; whereas, the complex material structure along with the bonding environment prevents proper computational identification of different types of inelasticity mechanisms within the material. Molecular dynamics study (on successful verification of the interatomic potential with experimental results) of pristine single crystals of 6H SiC have been used to probe the physics of molecular deformation mechanisms of the material along with its inherent orientational anisotropy. The study elucidates the experimentally observed mechanisms of defect nucleation and evolution through a detailed analysis of radial distribution functions, x-ray diffraction as well as phonon vibrational studies of the single crystal. Studies have been presented at room temperature, initial high temperature and different types of confinement effects of the material (including hydrostatic and different biaxial loading cases). The confinement resulted in an increase in stress and stiffness whereas increase in initial temperature resulted in a decrease compared to uniaxial stress loading conditions at room temperature. read less NOT USED (low confidence) A. Aditya et al., “Wrinkles, Ridges, Miura-Ori, and Moiré Patterns in MoSe2 Using Neural Networks,” The Journal of Physical Chemistry Letters. 2023. link Times cited: 1 Abstract: Effects of lateral compression on out-of-plane deformation o… read moreAbstract: Effects of lateral compression on out-of-plane deformation of two-dimensional MoSe2 layers are investigated. A MoSe2 monolayer develops periodic wrinkles under uniaxial compression and Miura-Ori patterns under biaxial compression. When a flat MoSe2 monolayer is placed on top of a wrinkled MoSe2 layer, the van der Waals (vdW) interaction transforms wrinkles into ridges and generates mixed 2H and 1T phases and chain-like defects. Under a biaxial strain, the vdW interaction induces regions of Miura-Ori patterns in bilayers. Strained systems analyzed using a convolutional neural network show that the compressed system consists of semiconducting 2H and metallic 1T phases. The energetics, mechanical response, defect structure, and dynamics are analyzed as bilayers undergo wrinkle–ridge transformations under uniaxial compression and moiré transformations under biaxial compression. Our results indicate that in-plane compression can induce self-assembly of out-of-plane metasurfaces with controllable semiconducting and metallic phases and moiré patterns with unique optoelectronic properties. read less NOT USED (low confidence) V. Klippenstein and N. V. D. van der Vegt, “Bottom-Up Informed and Iteratively Optimized Coarse-Grained Non-Markovian Water Models with Accurate Dynamics,” Journal of Chemical Theory and Computation. 2023. link Times cited: 3 Abstract: Molecular dynamics (MD) simulations based on coarse-grained … read moreAbstract: Molecular dynamics (MD) simulations based on coarse-grained (CG) particle models of molecular liquids generally predict accelerated dynamics and misrepresent the time scales for molecular vibrations and diffusive motions. The parametrization of Generalized Langevin Equation (GLE) thermostats based on the microscopic dynamics of the fine-grained model provides a promising route to address this issue, in conjunction with the conservative interactions of the CG model obtained with standard coarse graining methods, such as iterative Boltzmann inversion, force matching, or relative entropy minimization. We report the application of a recently introduced bottom-up dynamic coarse graining method, based on the Mori–Zwanzig formalism, which provides accurate estimates of isotropic GLE memory kernels for several CG models of liquid water. We demonstrate that, with an additional iterative optimization of the memory kernels (IOMK) for the CG water models based on a practical iterative optimization technique, the velocity autocorrelation function of liquid water can be represented very accurately within a few iterations. By considering the distinct Van Hove function, we demonstrate that, with the presented methods, an accurate representation of structural relaxation can be achieved. We consider several distinct CG potentials to study how the choice of the CG potential affects the performance of bottom-up informed and iteratively optimized models. read less NOT USED (low confidence) W. Liu, X. Huang, and Y. Yue, “Tuning thermal transport across monolayer MoS2/Si heterostructure via substrate nanogrooving,” International Journal of Heat and Mass Transfer. 2023. link Times cited: 6 NOT USED (low confidence) H. Niu et al., “A machine-learning interatomic potential to understand primary radiation damage of silicon,” Computational Materials Science. 2023. link Times cited: 3 NOT USED (low confidence) V. Bihani, S. Manchanda, S. Sastry, S. Ranu, and N. Krishnan, “StriderNET: A Graph Reinforcement Learning Approach to Optimize Atomic Structures on Rough Energy Landscapes,” ArXiv. 2023. link Times cited: 1 Abstract: Optimization of atomic structures presents a challenging pro… read moreAbstract: Optimization of atomic structures presents a challenging problem, due to their highly rough and non-convex energy landscape, with wide applications in the fields of drug design, materials discovery, and mechanics. Here, we present a graph reinforcement learning approach, StriderNET, that learns a policy to displace the atoms towards low energy configurations. We evaluate the performance of StriderNET on three complex atomic systems, namely, binary Lennard-Jones particles, calcium silicate hydrates gel, and disordered silicon. We show that StriderNET outperforms all classical optimization algorithms and enables the discovery of a lower energy minimum. In addition, StriderNET exhibits a higher rate of reaching minima with energies, as confirmed by the average over multiple realizations. Finally, we show that StriderNET exhibits inductivity to unseen system sizes that are an order of magnitude different from the training system. read less NOT USED (low confidence) Y. Goswami and S. Sastry, “Kinetic reconstruction of free energies as a function of multiple order parameters.,” The Journal of chemical physics. 2023. link Times cited: 0 Abstract: A vast array of phenomena, ranging from chemical reactions t… read moreAbstract: A vast array of phenomena, ranging from chemical reactions to phase transformations, are analyzed in terms of a free energy surface defined with respect to a single or multiple order parameters. Enhanced sampling methods are typically used, especially in the presence of large free energy barriers, to estimate free energies using biasing protocols and sampling of transition paths. Kinetic reconstructions of free energy barriers of intermediate height have been performed, with respect to a single order parameter, employing the steady state properties of unconstrained simulation trajectories when barrier crossing is achievable with reasonable computational effort. Considering such cases, we describe a method to estimate free energy surfaces with respect to multiple order parameters from a steady state ensemble of trajectories. The approach applies to cases where the transition rates between pairs of order parameter values considered is not affected by the presence of an absorbing boundary, whereas the macroscopic fluxes and sampling probabilities are. We demonstrate the applicability of our prescription on different test cases of random walkers executing Brownian motion in order parameter space with an underlying (free) energy landscape and discuss strategies to improve numerical estimates of the fluxes and sampling. We next use this approach to reconstruct the free energy surface for supercooled liquid silicon with respect to the degree of crystallinity and density, from unconstrained molecular dynamics simulations, and obtain results quantitatively consistent with earlier results from umbrella sampling. read less NOT USED (low confidence) Q.-X. Bai, W. Guo, Y. Dou, X. He, S. Liu, and Y.-bo Guo, “Cryogenic friction behavior and thermolubricity effect of graphene film on copper substrate,” Industrial Lubrication and Tribology. 2023. link Times cited: 1 Abstract:
Purpose
The purpose of this paper is to reveal the mechanis… read moreAbstract:
Purpose
The purpose of this paper is to reveal the mechanism of graphene low-temperature friction and provide a theoretical basis for the application of graphene.
Design/methodology/approach
A probe etching model of graphene on the copper substrate was established to obtain the friction pattern of graphene with different layers in the temperature interval from 100 to 300 K. The friction mechanism was also explained from a microscopic perspective based on thermal lubrication theory. Low-temperature friction experiments of graphene were carried out by atomic force microscopy to further verify the graphene low-temperature friction law.
Findings
Graphene nanofriction experiments were conducted at 230–300 K. Based on this, more detailed simulation studies were performed. It is found that the combined effect of thermolubricity and thermal fluctuations affects the variation of friction. For monolayer graphene, thermolubricity is the main influence, and friction decreases with increasing temperature. For multilayer graphene, thermal fluctuations gradually become the main influencing factor as the temperature rises, and the overall friction becomes larger with increasing temperature.
Originality/value
Graphene with excellent mechanical properties provides a new way to reduce the frictional wear of metallic materials in low-temperature environments. The friction laws and mechanisms of graphene in low-temperature environments are of great significance for the expansion of graphene application environments.
read less NOT USED (low confidence) P. Henadeera, N. Samaraweera, C. Ranasinghe, and A. Wijewardane, “Surface and Constriction Engineering of Nanoparticle Based Structures Towards Ultra-Low Thermal Conductivity as Prospective Thermoelectric Materials,” Nanoscale and Microscale Thermophysical Engineering. 2023. link Times cited: 1 Abstract: ABSTRACT The superior thermal insulating properties of nanos… read moreAbstract: ABSTRACT The superior thermal insulating properties of nanostructured semiconductor materials over their bulk counterparts, make them promising candidates for Thermo-Electric (TE) applications. In this study, the superior thermal insulating properties of a new class of one-dimensional nanostructures made by sintering linearly placed nanoparticles, called Nano Particle Chains (NPC) are analyzed for a variety of surface and constriction modifications. The NPC structure which has been shown to be capable of achieving a one-order reduction in thermal conductivity over comparably sized nanowires is revealed to house a new phonon suppression mechanism in addition to commonly discussed phonon boundary scattering and quantum confinement effects. In the current work, this quantum confinement based thermal conductivity reduction mechanism is revealed to be a variation in the phonon Density of States (DoS) along the longitudinal/transport direction of the structure due to the presence of the nanoscale constrictions. Subsequently, the phonons are forced to change the distribution of modes while traveling across the structure, thus resulting in lower thermal conductivity. Additionally, the effects of common phonon suppression techniques such as superlattice, shell alloy, and surface atom removal, used in semiconductor nanostructures are also evaluated on NPC configurations to fully determine the phonon transport characteristics within different classes of the material. read less NOT USED (low confidence) T. Graham et al., “Disordered interfaces of alkaline aluminate salt hydrates provide glimpses of Al3+ coordination changes.,” Journal of colloid and interface science. 2023. link Times cited: 0 NOT USED (low confidence) H. Lei, J. Chen, and P. Ruterana, “Comparative studies of interatomic potentials for modeling point defects in wurtzite GaN,” AIP Advances. 2023. link Times cited: 0 Abstract: In this paper, a new version of the Stillinger–Weber (SW) po… read moreAbstract: In this paper, a new version of the Stillinger–Weber (SW) potential for wurtzite GaN is presented, by which we systematically explore the structural and thermodynamical properties of native point defects and their complexes. In parallel, the semi-empirical Modified Embedded-Atom Method (MEAM) potential is selected for comparison. The SW and MEAM potentials are assessed by the reproduction of the fundamental properties of wurtzite GaN and by the ability to describe the inversion domain boundaries and the wurtzite–rocksalt phase transition. Then the structural search of native point defects and their complexes in GaN is implemented using both SW and MEAM potentials with the benchmark of Density Functional Theory (DFT) calculations. Besides vacancies and antisites, four N and five Ga interstitials are confirmed by refining the DFT calculations, among which two N split interstitials [Formula: see text] and [Formula: see text], and two Ga split interstitials, [Formula: see text] and [Formula: see text], are observed for the first time. The SW potential correctly predicts the octahedral occupation GaOct to be the most stable Ga interstitial, while the MEAM potential predicts the ground state of the [Formula: see text] split interstitial [Formula: see text] as the most stable N interstitial. However, neither of the two potentials could simultaneously generate the most stable configurations of N and Ga interstitials. The investigations of point defect complexes reveal that N octahedral Frenkel [FrenkelOct(N)] and paired antisite (NGaGaN) defects are unstable and get converted into [Formula: see text] configurations with different separations between VN and [Formula: see text] point defects based on the DFT calculations. The formation energies calculated by the DFT and SW potential demonstrate that Schottky, Ga octahedral Frenkel [FrenkelOct(Ga)], and [Formula: see text] point defect complexes are energetically feasible and that they should not dissociate into two isolated point defects. In contrast, the MEAM potential predicts the dissociation to be exothermic for Schottky and [Formula: see text]. Overall, the structural features concerned with N–N or Ga–Ga bonds relaxed by the SW potential are more consistent with DFT calculations than the MEAM counterpart. read less NOT USED (low confidence) T. Yamashita, H. Kino, K. Tsuda, T. Miyake, and T. Oguchi, “Hybrid algorithm of Bayesian optimization and evolutionary algorithm in crystal structure prediction,” Science and Technology of Advanced Materials: Methods. 2022. link Times cited: 2 Abstract: ABSTRACT We propose a highly efficient searching algorithm i… read moreAbstract: ABSTRACT We propose a highly efficient searching algorithm in crystal structure prediction. The searching algorithm is a hybrid of the evolutionary algorithm and Bayesian optimization. The evolutionary algorithm is widely used in crystal structure prediction, and the Bayesian optimization is one of the selection-type algorithms we have developed. We have performed simulations of crystal structure prediction to compare the success rates of the random search, evolutionary algorithm, Bayesian optimization, and hybrid algorithm for up to ternary systems such as Si, Y2Co17, Al2O3, and CuGaS2, using the CrySPY code. These results demonstrate that the evolutionary algorithm can generate structures more efficiently than random structure generation, and the Bayesian optimization can efficiently select potential candidates from a large number of structures. Moreover, the hybrid algorithm, which has the advantages of both, is proved to be the most efficient searching algorithm among them. GRAPHICAL ABSTRACT read less NOT USED (low confidence) S. Ciarella et al., “Finding defects in glasses through machine learning,” Nature Communications. 2022. link Times cited: 4 NOT USED (low confidence) D. Liu, J. Zhu, F. Zhou, G. Zhang, and D. Yang, “Molecular dynamics study of tensile properties of graphene/GaN heterostructures,” Journal of Physics: Conference Series. 2022. link Times cited: 0 Abstract: Graphene/GaN nanocomposites have been widely used in high-po… read moreAbstract: Graphene/GaN nanocomposites have been widely used in high-power and high-frequency optoelectronic devices. At present, the thermal transport characteristics of graphene/gallium nitride heterostructures have been investigated by many scholars, but their mechanical properties have not been systematically studied. In this paper, the effects of graphene layer number, temperature and interfacial structure on the mechanical properties of graphene/GaN heterostructures were investigated by molecular dynamics method. The mechanical properties of materials were analyzed by failure stress, failure strain and Young’s modulus. The simulation results show that the heterogeneous structure is very sensitive to temperature. When the temperature is set at 2000K, the Young’s modulus of the heterostructure decreases by 25.11% compared with that at 300K, which indicates that the increase of temperature will reduce the mechanical properties of graphene composites, However, when the number of graphene layers increases, the mechanical properties of the heterostructures also improved. With the number of graphene layers is set from 1 layer to 5 layers, the performance of the heterostructure is improved, and its Young’s modulus increases by 48.46%. In addition, the effect of interface structure on the young’s modulus of the heterostructure structure is not obvious, but it will affect the maximum failure stress and maximum failure strain of the material. The mechanical properties of graphene in cross section contact with gallium atom are better than those of nitrogen atom. It is beneficial to improve the reliability of microelectronic devices to control and design heterogeneous structures based on the research results. read less NOT USED (low confidence) K. W. Kayang and A. Volkov, “Effect of the shell thickness on the mechanical properties of arrays composed of hybrid core-shell Si/SiC nanoparticles with overlapped shells,” Ceramics International. 2022. link Times cited: 1 NOT USED (low confidence) O. Kushnerov, “Computer simulation of AlCoCuFeNi high-entropy alloy thin film deposition and crystallization,” Journal of Physics and Electronics. 2022. link Times cited: 0 Abstract: The processes of deposition and crystallization of high-entr… read moreAbstract: The processes of deposition and crystallization of high-entropy AlCoCuFeNi alloy thin film on a substrate of silicon (100) are studied by classical molecular dynamics simulation. Total simulation time reaches 50 ns. The embedded atom model is used to describe the interaction among Al–Co–Cu–Ni–Fe. Interaction between the atoms of Al, Co, Cu, Fe, Ni, and the Si substrate is described using the Lennard–Jones potential, and the interaction between the silicon atoms was modeled using the Stillinger–Weber potential. It is found that at the first stage of deposition small clusters are formed and the process of crystallization starts after ~ 5 ns of simulation, at the characteristic sizes of clusters of about 2 nm. At the end of the simulation, after the 50 ns of modeling, the simulated film contains a face-centered cubic phase, a body-centered cubic phase, a hexagonal close-packed phase, and an amorphous phase. An analysis of the radial distribution of atoms makes it possible to determine the distances between the nearest neighbors and estimate the lattice parameters of these phases. read less NOT USED (low confidence) J. D. Morrow, J. L. A. Gardner, and V. L. Deringer, “How to validate machine-learned interatomic potentials.,” The Journal of chemical physics. 2022. link Times cited: 12 Abstract: Machine learning (ML) approaches enable large-scale atomisti… read moreAbstract: Machine learning (ML) approaches enable large-scale atomistic simulations with near-quantum-mechanical accuracy. With the growing availability of these methods, there arises a need for careful validation, particularly for physically agnostic models-that is, for potentials that extract the nature of atomic interactions from reference data. Here, we review the basic principles behind ML potentials and their validation for atomic-scale material modeling. We discuss the best practice in defining error metrics based on numerical performance, as well as physically guided validation. We give specific recommendations that we hope will be useful for the wider community, including those researchers who intend to use ML potentials for materials "off the shelf." read less NOT USED (low confidence) A. S. Grossek, A. Niggas, R. Wilhelm, F. Aumayr, and C. Lemell, “Model for Nanopore Formation in Two-Dimensional Materials by Impact of Highly Charged Ions,” Nano Letters. 2022. link Times cited: 5 Abstract: We present a first qualitative description of the atomic dyn… read moreAbstract: We present a first qualitative description of the atomic dynamics in two-dimensional (2D) materials induced by the impact of slow, highly charged ions. We employ a classical molecular dynamics simulation for the motion of the target atoms combined with a Monte Carlo model for the diffusive charge transport within the layer. Depending on the velocity of charge transfer (hopping time or hole mobility) and the number of extracted electrons which, in turn, depends on the charge state of the impinging ions, we find regions of stability of the 2D structure as well as parameter combinations for which nanopore formation due to Coulomb repulsion is predicted. read less NOT USED (low confidence) X. Chen, D. S. Kim, and J. Lebeau, “A comparison of molecular dynamics potentials used to account for thermal diffuse scattering in multislice simulations.,” Ultramicroscopy. 2022. link Times cited: 1 NOT USED (low confidence) F. Schmid, “Understanding and Modeling Polymers: The Challenge of Multiple Scales,” ACS Polymers Au. 2022. link Times cited: 16 Abstract: Polymer materials have the characteristic feature that they … read moreAbstract: Polymer materials have the characteristic feature that they are multiscale systems by definition. Already the description of a single molecules involves a multitude of different scales, and coopera-tive processes in polymer assemblies are governed by the interplay of these scales. Polymers have been among the first materials for which systematic multiscale techniques were developed, yet they continue to present extraordinary challenges for modellers. In this perspective, we review popular models that are used to describe polymers on different scales and discuss scale bridging strategies such as static and dynamic coarse-graining methods and multiresolution approaches. We close with a list of hard problems which still need to be solved in order to gain a comprehensive quantitative understanding of polymer systems on all scales. read less NOT USED (low confidence) C. Fridlund, R. Toijala, O. Flinck, J. Laakso, K. Nordlund, and F. Djurabekova, “Adaptive moving environment for efficient molecular dynamics simulations of high-fluence ion irradiation,” Computational Materials Science. 2022. link Times cited: 1 NOT USED (low confidence) A. Hernandez and T. Mueller, “Generalizability of Functional Forms for Interatomic Potential Models Discovered by Symbolic Regression,” ArXiv. 2022. link Times cited: 0 Abstract: In recent years there has been great progress in the use of … read moreAbstract: In recent years there has been great progress in the use of machine learning algorithms to develop interatomic potential models. Machine-learned potential models are typically orders of magnitude faster than density functional theory but also orders of magnitude slower than physics-derived models such as the embedded atom method. In our previous work, we used symbolic regression to develop fast, accurate and transferrable interatomic potential models for copper with novel functional forms that resemble those of the embedded atom method. To determine the extent to which the success of these forms was specific to copper, here we explore the generalizability of these models to other face-centered cubic transition metals and analyze their out-of-sample performance on several material properties. We found that these forms work particularly well on elements that are chemically similar to copper. When compared to optimized Sutton-Chen models, which have similar complexity, the functional forms discovered using symbolic regression perform better across all elements considered except gold where they have a similar performance. They perform similarly to a moderately more complex embedded atom form on properties on which they were trained, and they are more accurate on average on other properties. We attribute this improved generalized accuracy to the relative simplicity of the models discovered using symbolic regression. The genetic programming models are found to outperform other models from the literature about 50% of the time in a variety of property predictions, with about 1/10th the model complexity on average. We discuss the implications of these results to the broader application of symbolic regression to the development of new potentials and highlight how models discovered for one element can be used to seed new searches for different elements. read less NOT USED (low confidence) L. Yang, Q. Zhang, G. Hu, and N. Yang, “Deformation insensitive thermal conductance of the designed Si metamaterial,” Applied Physics Letters. 2022. link Times cited: 0 Abstract: The thermal management has been widely focused due to its br… read moreAbstract: The thermal management has been widely focused due to its broad applications. Generally, the deformation can largely tune the thermal transport. The main challenge of flexible electronics/materials is to maintain thermal conductance under large deformation. This work investigates the thermal conductance of a nano-designed Si metamaterial constructed with curved nanobeams by molecular dynamics simulation. Interestingly, it shows that the thermal conductance of the nano-designed Si metamaterial is insensitive under a large deformation (strain ∼ −41%). The new feature comes from the designed curved nanobeams, which exhibit a quasi-zero stiffness. Further calculations show that, when under large deformation, the average stress in nanobeam is ultra-small (<151 MPa), and its phonon density of states are little changed. This work provides valuable insight on the multifunction, such as both stable thermal and mechanical properties, of nano-designed metamaterials. read less NOT USED (low confidence) M. Qamar, M. Mrovec, Y. Lysogorskiy, A. Bochkarev, and R. Drautz, “Atomic Cluster Expansion for Quantum-Accurate Large-Scale Simulations of Carbon.,” Journal of chemical theory and computation. 2022. link Times cited: 17 Abstract: We present an atomic cluster expansion (ACE) for carbon that… read moreAbstract: We present an atomic cluster expansion (ACE) for carbon that improves over available classical and machine learning potentials. The ACE is parametrized from an exhaustive set of important carbon structures over extended volume and energy ranges, computed using density functional theory (DFT). Rigorous validation reveals that ACE accurately predicts a broad range of properties of both crystalline and amorphous carbon phases while being several orders of magnitude more computationally efficient than available machine learning models. We demonstrate the predictive power of ACE on three distinct applications: brittle crack propagation in diamond, the evolution of amorphous carbon structures at different densities and quench rates, and the nucleation and growth of fullerene clusters under high-pressure and high-temperature conditions. read less NOT USED (low confidence) F. Sammüller, D. de las Heras, and M. Schmidt, “Inhomogeneous steady shear dynamics of a three-body colloidal gel former.,” The Journal of chemical physics. 2022. link Times cited: 3 Abstract: We investigate the stationary flow of a colloidal gel under … read moreAbstract: We investigate the stationary flow of a colloidal gel under an inhomogeneous external shear force using adaptive Brownian dynamics simulations. The interparticle forces are derived from the Stillinger-Weber potential, where the three-body term is tuned to enable network formation and gelation in equilibrium. When subjected to the shear force field, the system develops remarkable modulations in the one-body density profile. Depending on the shear magnitude, particles accumulate either in quiescent regions or in the vicinity of maximum net flow, and we deduce this strong non-equilibrium response to be characteristic of the gel state. Studying the components of the internal force parallel and perpendicular to the flow direction reveals that the emerging flow and structure of the stationary state are driven by significant viscous and structural superadiabatic forces. Thereby, the magnitude and nature of the observed non-equilibrium phenomena differ from the corresponding behavior of simple fluids. We demonstrate that a simple power functional theory reproduces accurately the viscous force profile, giving a rationale of the complex dynamical behavior of the system. read less NOT USED (low confidence) J. Witek et al., “M-Chem: a modular software package for molecular simulation that spans scientific domains,” Molecular Physics. 2022. link Times cited: 0 Abstract: ABSTRACT We present a new software package called M-Chem tha… read moreAbstract: ABSTRACT We present a new software package called M-Chem that is designed from scratch in C++ and parallelised on shared-memory multi-core architectures to facilitate efficient molecular simulations. Currently, M-Chem is a fast molecular dynamics (MD) engine that supports the evaluation of energies and forces from two-body to many-body all-atom potentials, reactive force fields, coarse-grained models, combined quantum mechanics molecular mechanics (QM/MM) models, and external force drivers from machine learning, augmented by algorithms that are focused on gains in computational simulation times. M-Chem also includes a range of standard simulation capabilities including thermostats, barostats, multi-timestepping, and periodic cells, as well as newer methods such as fast extended Lagrangians and high quality electrostatic potential generation. At present M-Chem is a developer friendly environment in which we encourage new software contributors from diverse fields to build their algorithms, models, and methods in our modular framework. The long-term objective of M-Chem is to create an interdisciplinary platform for computational methods with applications ranging from biomolecular simulations, reactive chemistry, to materials research. GRAPHICAL ABSTRACT read less NOT USED (low confidence) I. Shepelev, I. D. Kolesnikov, E. Korznikova, and S. Dmitriev, “Compressive solitary waves in black phosphorene,” Physica E: Low-dimensional Systems and Nanostructures. 2022. link Times cited: 2 NOT USED (low confidence) T. Ma and Y. Wang, “Ex-situ modification of lattice thermal transport through coherent and incoherent heat baths,” Materials Today Physics. 2022. link Times cited: 1 NOT USED (low confidence) R. Ma, S. Xiao, Y.-S. Chang, Y. Fu, J. He, and Z. Zhang, “An interfacial gas-enrichment strategy for mitigating hydrate adhesion and blockage,” Chemical Engineering Journal. 2022. link Times cited: 6 NOT USED (low confidence) S. Fernbach, E. Kraker, E. Zojer, and N. Bedoya-Martínez, “Reliable force field potential for modelling thermal transport in AlN,” 2022 28th International Workshop on Thermal Investigations of ICs and Systems (THERMINIC). 2022. link Times cited: 1 Abstract: A Stillinger-Weber type force field potential (FFP) is param… read moreAbstract: A Stillinger-Weber type force field potential (FFP) is parametrized to describe the thermal transport-related properties of AIN. The FFP was fitted to ab-initio data for structural and vibrational properties, such as the lattice and elastic constants as well as the phonon band structure and mode-Grüneisen parameters. For all fitted quantities the resulting FFP yields results in good agreement with the ab-initio data. Moreover, it provides a better description of the bulk thermal conductivity of AIN compared to other FFPs reported in the literature. read less NOT USED (low confidence) B. McBennett et al., “Universal Behavior of Highly Confined Heat Flow in Semiconductor Nanosystems: From Nanomeshes to Metalattices.,” Nano letters. 2022. link Times cited: 4 Abstract: Nanostructuring on length scales corresponding to phonon mea… read moreAbstract: Nanostructuring on length scales corresponding to phonon mean free paths provides control over heat flow in semiconductors and makes it possible to engineer their thermal properties. However, the influence of boundaries limits the validity of bulk models, while first-principles calculations are too computationally expensive to model real devices. Here we use extreme ultraviolet beams to study phonon transport dynamics in a 3D nanostructured silicon metalattice with deep nanoscale feature size and observe dramatically reduced thermal conductivity relative to bulk. To explain this behavior, we develop a predictive theory wherein thermal conduction separates into a geometric permeability component and an intrinsic viscous contribution, arising from a new and universal effect of nanoscale confinement on phonon flow. Using experiments and atomistic simulations, we show that our theory applies to a general set of highly confined silicon nanosystems, from metalattices, nanomeshes, porous nanowires, to nanowire networks, of great interest for next-generation energy-efficient devices. read less NOT USED (low confidence) M. A. Caro, “Machine learning based modeling of disordered elemental semiconductors: understanding the atomic structure of a-Si and a-C,” Semiconductor Science and Technology. 2022. link Times cited: 1 Abstract: Disordered elemental semiconductors, most notably a-C and a-… read moreAbstract: Disordered elemental semiconductors, most notably a-C and a-Si, are ubiquitous in a myriad of different applications. These exploit their unique mechanical and electronic properties. In the past couple of decades, density functional theory (DFT) and other quantum mechanics-based computational simulation techniques have been successful at delivering a detailed understanding of the atomic and electronic structure of crystalline semiconductors. Unfortunately, the complex structure of disordered semiconductors sets the time and length scales required for DFT simulation of these materials out of reach. In recent years, machine learning (ML) approaches to atomistic modeling have been developed that provide an accurate approximation of the DFT potential energy surface for a small fraction of the computational time. These ML approaches have now reached maturity and are starting to deliver the first conclusive insights into some of the missing details surrounding the intricate atomic structure of disordered semiconductors. In this Topical Review we give a brief introduction to ML atomistic modeling and its application to amorphous semiconductors. We then take a look at how ML simulations have been used to improve our current understanding of the atomic structure of a-C and a-Si. read less NOT USED (low confidence) C. Ortner and Y. Wang, “A framework for a generalisation analysis of machine-learned interatomic potentials,” ArXiv. 2022. link Times cited: 1 Abstract: Machine-learned interatomic potentials (MLIPs) and force fie… read moreAbstract: Machine-learned interatomic potentials (MLIPs) and force fields (i.e. interaction laws for atoms and molecules) are typically trained on limited data-sets that cover only a very small section of the full space of possible input structures. MLIPs are nevertheless capable of making accurate predictions of forces and energies in simulations involving (seemingly) much more complex structures. In this article we propose a framework within which this kind of generalisation can be rigorously understood. As a prototypical example, we apply the framework to the case of simulating point defects in a crystalline solid. Here, we demonstrate how the accuracy of the simulation depends explicitly on the size of the training structures, on the kind of observations (e.g., energies, forces, force constants, virials) to which the model has been fitted, and on the fit accuracy. The new theoretical insights we gain partially justify current best practices in the MLIP literature and in addition suggest a new approach to the collection of training data and the design of loss functions. read less NOT USED (low confidence) J. Jin, A. Pak, A. E. P. Durumeric, T. D. Loose, and G. Voth, “Bottom-up Coarse-Graining: Principles and Perspectives,” Journal of Chemical Theory and Computation. 2022. link Times cited: 58 Abstract: Large-scale computational molecular models provide scientist… read moreAbstract: Large-scale computational molecular models provide scientists a means to investigate the effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship between variations on the molecular scale and macroscopic observable properties facilitates an understanding of the molecular interactions driving the properties of real world materials and complex systems (e.g., those found in biology, chemistry, and materials science). As a result, discovering an explicit, systematic connection between microscopic nature and emergent mesoscopic behavior is a fundamental goal for this type of investigation. The molecular forces critical to driving the behavior of complex heterogeneous systems are often unclear. More problematically, simulations of representative model systems are often prohibitively expensive from both spatial and temporal perspectives, impeding straightforward investigations over possible hypotheses characterizing molecular behavior. While the reduction in resolution of a study, such as moving from an atomistic simulation to that of the resolution of large coarse-grained (CG) groups of atoms, can partially ameliorate the cost of individual simulations, the relationship between the proposed microscopic details and this intermediate resolution is nontrivial and presents new obstacles to study. Small portions of these complex systems can be realistically simulated. Alone, these smaller simulations likely do not provide insight into collectively emergent behavior. However, by proposing that the driving forces in both smaller and larger systems (containing many related copies of the smaller system) have an explicit connection, systematic bottom-up CG techniques can be used to transfer CG hypotheses discovered using a smaller scale system to a larger system of primary interest. The proposed connection between different CG systems is prescribed by (i) the CG representation (mapping) and (ii) the functional form and parameters used to represent the CG energetics, which approximate potentials of mean force (PMFs). As a result, the design of CG methods that facilitate a variety of physically relevant representations, approximations, and force fields is critical to moving the frontier of systematic CG forward. Crucially, the proposed connection between the system used for parametrization and the system of interest is orthogonal to the optimization used to approximate the potential of mean force present in all systematic CG methods. The empirical efficacy of machine learning techniques on a variety of tasks provides strong motivation to consider these approaches for approximating the PMF and analyzing these approximations. read less NOT USED (low confidence) S. Yousefi-Nasab, J. Karimi-Sabet, and J. Safdari, “Investigation of the effect of wall material on the exchange of information between fluid and surface using the hybrid atomistic-continuum method,” Computational Particle Mechanics. 2022. link Times cited: 0 NOT USED (low confidence) X. Nie, J.-ping Xue, L. Zhao, S. Deng, and H. Xiong, “Tunning Lattice Thermal Conductivity of Bilayer and Trilayer Molybdenum Disulfide Thermoelectric Materials Through Twist Angles,” SSRN Electronic Journal. 2022. link Times cited: 7 NOT USED (low confidence) H. Rai et al., “Spatial Variation in Nanoscale Wear Behavior of Chemical Vapor Deposited Monolayer WS2,” Applied Surface Science. 2022. link Times cited: 2 NOT USED (low confidence) A. Akkerman, J. Barak, and M. Murat, “NIEL Calculations for III–V Compound Semiconductors Under Electron or Proton Irradiation,” IEEE Transactions on Nuclear Science. 2022. link Times cited: 0 Abstract: The nonionizing energy loss (NIEL) concept, introduced more … read moreAbstract: The nonionizing energy loss (NIEL) concept, introduced more than 40 years ago, is still used to characterize the damage generated by different particles and $\gamma $ -rays. Its continuing relevance is due to the experimentally established scaling in the creation rate of defects by radiation of different types. NIEL calculations are quite simple, based on classical physics. We thus name them classical NIEL, NIEL c. Their calculation depends on an $a$ priori known $E_{d}$ -displacement threshold energy in monoatomic materials. For the compound semiconductor materials studied here, Ga $X$ and In $X$ , where $X$ are the cations N, P, As, Sb, the experimental $E_{d}$ values vary over a wide range and only approximate values for NIEL c can be calculated. Thanks to some recent studies carried out using the molecular dynamic (MD) method, the NIEL values were estimated using atomic scale calculations. Consequently, we can now compare NIEL c with more precise data. These data also include the “dynamic” behavior of the NIEL, which is related to the annealing of the damage (like Frenkel pair recombination) and the generation of extended crystalline defects. The NIEL calculated using the MD method is referred to in the literature as NIEL eff. A detailed comparison between NIEL c and NIEL eff as a function of electron and proton energies is made here. It shows that the difference between the two quantities is not large and cannot influence the dependence of NIEL on temperature and different radiation types. Both yield similar results in calculating the effect of displacement damage. As an additional use of NIEL c, we analyze its application to estimate the relative tolerance of the different members of the Ga $X$ and In $X$ families to radiation defects as a function of particle energies. read less NOT USED (low confidence) H. Moslemzadeh and S. Mohammadi, “An atomistic entropy based finite element multiscale method for modeling amorphous materials,” International Journal of Solids and Structures. 2022. link Times cited: 0 NOT USED (low confidence) C. Hou et al., “Atomistic simulation of low-dimensional nanostructures toward extreme-scale supercomputing,” CCF Transactions on High Performance Computing. 2022. link Times cited: 0 NOT USED (low confidence) B. Yao, Z. R. Liu, and R. F. Zhang, “EAPOTc: An integrated empirical interatomic potential optimization platform for compound solids,” Computational Materials Science. 2022. link Times cited: 1 NOT USED (low confidence) S. Sharma et al., “Machine Learning Methods for Multiscale Physics and Urban Engineering Problems,” Entropy. 2022. link Times cited: 0 Abstract: We present an overview of four challenging research areas in… read moreAbstract: We present an overview of four challenging research areas in multiscale physics and engineering as well as four data science topics that may be developed for addressing these challenges. We focus on multiscale spatiotemporal problems in light of the importance of understanding the accompanying scientific processes and engineering ideas, where “multiscale” refers to concurrent, non-trivial and coupled models over scales separated by orders of magnitude in either space, time, energy, momenta, or any other relevant parameter. Specifically, we consider problems where the data may be obtained at various resolutions; analyzing such data and constructing coupled models led to open research questions in various applications of data science. Numeric studies are reported for one of the data science techniques discussed here for illustration, namely, on approximate Bayesian computations. read less NOT USED (low confidence) C. Xu et al., “Anisotropic mechanical responses and plastic deformation mechanisms of cadmium telluride under indentations,” Applied Physics A. 2022. link Times cited: 2 NOT USED (low confidence) R. Badal, M. Friedrich, and J. Seutter, “Existence of quasi-static crack evolution for atomistic systems,” Forces in Mechanics. 2022. link Times cited: 0 NOT USED (low confidence) L. Rovigatti and F. Sciortino, “Designing Enhanced Entropy Binding in Single-Chain Nanoparticles.,” Physical review letters. 2022. link Times cited: 3 Abstract: Single-chain nanoparticles (SCNPs) are a new class of bio- a… read moreAbstract: Single-chain nanoparticles (SCNPs) are a new class of bio- and soft-matter polymeric objects in which a fraction of the monomers are able to form equivalently intra- or interpolymer bonds. Here we numerically show that a fully entropic gas-liquid phase separation can take place in SCNP systems. Control over the discontinuous (first-order) change-from a phase of independent diluted (fully-bonded) polymers to a phase in which polymers entropically bind to each other to form a (fully-bonded) polymer network-can be achieved by a judicious design of the patterns of reactive monomers along the polymer chain. Such a sensitivity arises from a delicate balance between the distinct entropic contributions controlling the binding. read less NOT USED (low confidence) J. Garcia‐Suarez, T. Brink, and J. Molinari, “Breakdown of Reye’s theory in nanoscale wear,” Journal of the Mechanics and Physics of Solids. 2022. link Times cited: 3 NOT USED (low confidence) R. Abram, D. Chrobak, J. Byggmästar, K. Nordlund, and R. Nowak, “Comprehensive structural changes in nanoscale-deformed silicon modelled with an integrated atomic potential,” Materialia. 2022. link Times cited: 2 NOT USED (low confidence) M. Müser, “Improved cutoff functions for short-range potentials and the Wolf summation,” Molecular Simulation. 2022. link Times cited: 2 Abstract: ABSTRACT A class of radial, polynomial cutoff functions for … read moreAbstract: ABSTRACT A class of radial, polynomial cutoff functions for short-ranged pair potentials or related expressions is proposed. Their derivatives up to order n and n + 1 vanish at the outer cutoff and an inner radius , respectively. Moreover, and . It is shown that the used order n can qualitatively affect results: stress and bulk moduli of ideal crystals are unavoidably discontinuous with density for n = 0 and n = 1, respectively. Systematic errors on energies and computing times decrease by 20–50% for Lennard-Jones with n = 2 or n = 3 compared to standard cutting procedures. Another cutoff function turns out beneficial to compute Coulomb interactions using the Wolf summation, which is shown to not properly converge when local charge neutrality is obeyed only in a stochastic sense. However, for all investigated homogeneous systems with thermal noise (ionic crystals and liquids), the modified Wolf summation, despite being infinitely differentiable at , converges similarly quickly as the original summation. Finally, it is discussed how to reduce the computational burden of numerically exact Monte Carlo simulations using the Wolf summation even when it does not properly converge. read less NOT USED (low confidence) D. Chrobak, A. Majtyka-Piłat, G. Ziółkowski, and A. Chrobak, “Interatomic Potential for InP,” Materials. 2022. link Times cited: 0 Abstract: Classical modeling of structural phenomena occurring in InP … read moreAbstract: Classical modeling of structural phenomena occurring in InP crystal, for example plastic deformation caused by contact force, requires an interatomic interaction potential that correctly describes not only the elastic properties of indium phosphide but also the pressure-induced reversible phase transition B3↔B1. In this article, a new parametrization of the analytical bond-order potential has been developed for InP. The potential reproduces fundamental physical properties (lattice parameters, cohesive energy, stiffness coefficients) of the B3 and B1 phases in good agreement with first-principles calculations. The proposed interaction model describes the reversibility of the pressure-induced B3↔B1 phase transition as well as the formation of native point defects in the B3 phase. read less NOT USED (low confidence) S. Sassi et al., “Energy loss in low energy nuclear recoils in dark matter detector materials,” Physical Review D. 2022. link Times cited: 5 Abstract: Recent progress in phonon-mediated detectors with eV-scale n… read moreAbstract: Recent progress in phonon-mediated detectors with eV-scale nuclear recoil energy sensitivity requires an understanding of the effect of the crystalline defects on the energy spectrum expected from dark matter or neutrino coherent scattering. We have performed molecular dynamics simulations to determine the amount of energy stored in the lattice defects as a function of the recoil direction and energy. This energy can not be observed in the phonon measurement, thus affecting the observed energy spectrum compared to the underlying true recoil energy spectrum. We describe this effect for multiple commonly used detector materials and demonstrate how the predicted energy spectrum from dark matter scattering is modified. read less NOT USED (low confidence) J. Luo, C. Zhou, Q. Li, and L. Liu, “Thermodynamic Formation Properties of Point Defects in Germanium Crystal,” Materials. 2022. link Times cited: 0 Abstract: Point defects are crucial in determining the quality of germ… read moreAbstract: Point defects are crucial in determining the quality of germanium crystals. A quantitative understanding of the thermodynamic formation properties of the point defects is necessary for the subsequent control of the defect formation during crystal growth. Here, molecular dynamics simulations were employed to investigate the formation energies, total formation free energies and formation entropies of the point defects in a germanium crystal. As far as we know, this is the first time that the total formation free energies of point defects in a germanium crystal have been reported in the literature. We found that the formation energies increased slightly with temperature. The formation free energies decreased significantly with an increase in temperature due to the increase in entropy. The estimated total formation free energies at the melting temperature are ~1.3 eV for self-interstitial and ~0.75 eV for vacancy, corresponding to a formation entropy of ~15 kB for both types of point defects. read less NOT USED (low confidence) Y. Goswami and S. Sastry, “Liquid–liquid phase transition in deeply supercooled Stillinger–Weber silicon,” PNAS Nexus. 2022. link Times cited: 2 Abstract: The existence of a phase transition between two distinct liq… read moreAbstract: The existence of a phase transition between two distinct liquid phases in single-component network-forming liquids (e.g. water, silica, silicon) has elicited considerable scientific interest. The challenge, both for experiments and simulations, is that the liquid–liquid phase transition (LLPT) occurs under deeply supercooled conditions, where crystallization occurs very rapidly. Thus, early evidence from numerical equation of state studies was challenged with the argument that slow spontaneous crystallization had been misinterpreted as evidence of a second liquid state. Rigorous free-energy calculations have subsequently confirmed the existence of a LLPT in some models of water, and exciting new experimental evidence has since supported these computational results. Similar results have so far not been found for silicon. Here, we present results from free-energy calculations performed for silicon modeled with the classical, empirical Stillinger-Weber–potential. Through a careful study employing state-of-the-art constrained simulation protocols and numerous checks for thermodynamic consistency, we find that there are two distinct metastable liquid states and a phase transition. Our results resolve a long-standing debate concerning the existence of a liquid–liquid transition in supercooled liquid silicon and address key questions regarding the nature of the phase transition and the associated critical point. read less NOT USED (low confidence) M. Bauer, M. Probert, and C. Panosetti, “Systematic Comparison of Genetic Algorithm and Basin Hopping Approaches to the Global Optimization of Si(111) Surface Reconstructions,” The Journal of Physical Chemistry. a. 2022. link Times cited: 3 Abstract: We present a systematic study of two widely used material st… read moreAbstract: We present a systematic study of two widely used material structure prediction methods, the Genetic Algorithm and Basin Hopping approaches to global optimization, in a search for the 3 × 3, 5 × 5, and 7 × 7 reconstructions of the Si(111) surface. The Si(111) 7 × 7 reconstruction is the largest and most complex surface reconstruction known, and finding it is a very exacting test for global optimization methods. In this paper, we introduce a modification to previous Genetic Algorithm work on structure search for periodic systems, to allow the efficient search for surface reconstructions, and present a rigorous study of the effect of the different parameters of the algorithm. We also perform a detailed comparison with the recently improved Basin Hopping algorithm using Delocalized Internal Coordinates. Both algorithms succeeded in either resolving the 3 × 3, 5 × 5, and 7 × 7 DAS surface reconstructions or getting “sufficiently close”, i.e., identifying structures that only differ for the positions of a few atoms as well as thermally accessible structures within kBT/unit area of the global minimum, with T = 300 K. Overall, the Genetic Algorithm is more robust with respect to parameter choice and in success rate, while the Basin Hopping method occasionally exhibits some advantages in speed of convergence. In line with previous studies, the results confirm that robustness, success, and speed of convergence of either approach are strongly influenced by how much the trial moves tend to preserve favorable bonding patterns once these appear. read less NOT USED (low confidence) H. Liu et al., “Challenges and opportunities in atomistic simulations of glasses: a review,” Comptes Rendus. Géoscience. 2022. link Times cited: 8 Abstract: . Atomistic modeling and simulations have been pivotal in ou… read moreAbstract: . Atomistic modeling and simulations have been pivotal in our understanding of the glassy state. Indeed, atomistic modeling o ff ers direct access to the structure and dynamics of atoms in glasses—which is typically hidden from conventional experiments. Simulations also o ff er a more economical, faster alternative to systematic experiments to decode composition-property relationships and accelerate the discovery of new glasses with desirable properties and functionalities. However, the atomistic modeling of glasses remains plagued by a series of challenges, e read less NOT USED (low confidence) J. Bian and L. Nicola, “Lubrication of rough copper with few-layer graphene,” Tribology International. 2022. link Times cited: 3 NOT USED (low confidence) Z. Liu, B. Lin, X. Liang, A. Du, and X. Ma, “Fracture of single crystal silicon caused by nonlinear evolution of surface acoustic waves,” Engineering Fracture Mechanics. 2022. link Times cited: 3 NOT USED (low confidence) A. Mirzoev, B. Gelchinski, and A. A. Rempel, “Neural Network Prediction of Interatomic Interaction in Multielement Substances and High-Entropy Alloys: A Review,” Doklady Physical Chemistry. 2022. link Times cited: 2 NOT USED (low confidence) I. Shepelev, I. D. Kolesnikov, E. Korznikova, and S. Dmitriev, “Compressive soliton in phosphorene at finite temperature,” Saratov Fall Meeting. 2022. link Times cited: 0 Abstract: Crowdion as one of types of an interstitial mobile defect pr… read moreAbstract: Crowdion as one of types of an interstitial mobile defect propagating in close-packed crystallographic directions can play an important role in relaxation processes occurring in bcc lattices of tungsten in nonequilibrium conditions. The crowdions is an effectively transport of mass and energy in the metal. Tungsten is considered one of the best options as a plasma-oriented material which can be exposed to ion irradiation in nuclear reactors. Recently dynamics of crowdions has been extensively studied for different types of lattices and dimensions. However, the point of energy exchange between crowdions has not been considered earlier. The paper presents an analysis of energy exchange in a complex of crowdions located in neighboring closely packed atomic row. Obtained results reveal that closely located crowdions can intensively transfer energy from one to another thus affecting the dynamics and scenario of defect structure evolution in the crystal. It is known that irradiation of tungsten can lead to microstructural changes, such as bubbles, pores and another types of defects. Moreover, the metal constantly at these conditions are heated up to extremely high temperature. Apparently, the crowdions play an important role in the formation of different defects inside the tungsten. And aim of this work is a numerically analysis of features of the crowdion in this highly heated metal bcc lattice. read less NOT USED (low confidence) P. Lou, H.-Q. Pan, and Y. Wu, “Solid-liquid coexistence simulation of silicon melting point and reverse fitting correction potential function,” Other Conferences. 2022. link Times cited: 0 Abstract: In molecular dynamics simulation, the phase transition is a … read moreAbstract: In molecular dynamics simulation, the phase transition is a rather complex process, and the melting point of materials simulated often deviates greatly from the experimental reported ones. Therefore, this article simulates the phase transition temperature of silicon and tries to reduce the influence of the large error from the simulation results. We use the StillingerWeber (SW) potential to simulate the solid-liquid coexistence method and the direct heating method are used respectively to compare and simulate the melting process of silicon. The influence of atomic number on the solid-liquid coexistence simulation process of melting point is discussed, and the influence of time step and potential function directly on the melting process is further discussed. Finally, we tried to modify the SW potential function to get better results. The selected computer algorithm has been further discussed in the section "Inverse fitting Analysis". read less NOT USED (low confidence) Y. Liu, W. Wan, Q. Li, Z. Xiong, C. Tang, and L. Zhou, “Revisiting the Rate-Dependent Mechanical Response of Typical Silicon Structures via Molecular Dynamics,” Nanomaterials. 2022. link Times cited: 1 Abstract: Strain rate is a critical parameter in the mechanical applic… read moreAbstract: Strain rate is a critical parameter in the mechanical application of nano-devices. A comparative atomistic study on both perfect monocrystalline silicon crystal and silicon nanowire was performed to investigate how the strain rate affects the mechanical response of these silicon structures. Using a rate response model, the strain rate sensitivity and the critical strain rate of two structures were given. The rate-dependent dislocation activities in the fracture process were also discussed, from which the dislocation nucleation and motion were found to play an important role in the low strain rate deformations. Finally, through the comparison of five equivalent stresses, the von Mises stress was verified as a robust yield criterion of the two silicon structures under the strain rate effects. read less NOT USED (low confidence) T. Grieb et al., “Angle-dependence of ADF-STEM intensities for chemical analysis of InGaN/GaN.,” Ultramicroscopy. 2022. link Times cited: 3 NOT USED (low confidence) Y. D. Fomin and A. Teslyuk, “The structure of a core-softened system in a narrow slit pore,” Physics and Chemistry of Liquids. 2022. link Times cited: 2 Abstract: ABSTRACT We have investigated the behaviour of a core-soften… read moreAbstract: ABSTRACT We have investigated the behaviour of a core-softened system in a narrow slit pore (the width of the pore is equal to three diameters of a particle). In the previous studies, it was shown that strongly confined systems formed crystalline phases which consisted of several triangular or square layers. These phases can also be considered as cuts of FCC or HCP structures. We have shown that the behaviour of a core-softened system is more complex. We have also observed a quasicrystalline phase. Moreover, the phase with two triangular layers appears at lower densities than the phase with two square layers, which is in contrast to the behaviour of the systems studied before. These results demonstrate that the phase behaviour of strongly confined systems can be even more complex than it has been supposed before. read less NOT USED (low confidence) L. J. Lewis, “Fifty years of amorphous silicon models : the end of the story?,” Journal of Non-Crystalline Solids. 2022. link Times cited: 8 NOT USED (low confidence) T. Tamadate and C. J. Hogan, “Silicon nanocluster anion-argon cation recombination via hybrid continuum-molecular dynamics calculations,” Journal of Aerosol Science. 2022. link Times cited: 1 NOT USED (low confidence) Y. Dong et al., “Tuning the interfacial friction force and thermal conductance by altering phonon properties at contact interface,” Nanotechnology. 2022. link Times cited: 9 Abstract: Controlling friction force and thermal conductance at solid/… read moreAbstract: Controlling friction force and thermal conductance at solid/solid interface is of great importance but remains a significant challenge. In this work, we propose a method to control the matching degree of phonon spectra at the interface through modifying the atomic mass of contact materials, thereby regulating the interfacial friction force and thermal conductance. Results of Debye theory and molecular dynamics simulations show that the cutoff frequency of phonon spectrum decreases with increasing atomic mass. Thus, two contact surfaces with equal atomic mass have same vibrational characteristics, so that more phonons could pass through the interface. In these regards, the coupling strength of phonon modes on contact surfaces makes it possible to gain insight into the nonmonotonic variation of interfacial friction force and thermal conductance. Our investigations suggest that the overlap of phonon modes increases energy scattering channels and therefore phonon transmission at the interface, and finally, an enhanced energy dissipation in friction and heat transfer ability at interface. read less NOT USED (low confidence) X. Wei, C.-M. Wu, and Y. Li, “Molecular and theoretical identification of adsorption phase transition behaviors via thermo-kinetics analysis,” Journal of Molecular Liquids. 2022. link Times cited: 0 NOT USED (low confidence) O. Trushin, “Competing mechanisms of strain relaxation in Ge/Si(001) heteroepitaxy,” International Conference on Micro- and Nano-Electronics. 2022. link Times cited: 0 Abstract: Atomistic simulation with semiempirical Stillinger-Weber pot… read moreAbstract: Atomistic simulation with semiempirical Stillinger-Weber potential has been used to study the energetics of strain relaxation in Ge/Si(001) heteroepitaxial system. Several alternative scenarios for misfit strain relief through dislocation nucleation have been investigated. Minimal energy path for each transition trajectory has been found using combination of modified DRAG and Nudged Elastic Band methods. Our results showed that standard 90° Lomer dislocation is the most favorable (global minimum) defect for this heteroepitaxial system. Alternative more complex defects containing two shifted 60° dislocations are indeed also local minima for this system, however corresponding to higher energy states. Their appearance in experiments might be the result of growth kinetics. read less NOT USED (low confidence) S. Abdullah, X. W. Zhou, R. Aguirre, and D. Zubia, “A computational approach to analyze grain structures of semiconductor compound films: Case study of CdTe/CdS multilayers,” MRS Advances. 2022. link Times cited: 0 Abstract: Grain structures impact the performance of semiconductor dev… read moreAbstract: Grain structures impact the performance of semiconductor devices. Molecular dynamics has been successfully applied to simulate the growth of semiconductor compounds, reproducing the experimentally observed complex zincblende and wurtzite grains. However, methodologies to characterize the simulated grain structures are still not mature, especially for semiconductors. This limits the usefulness of simulations in material optimization. In this work, the grain tracking algorithm originally developed by Panzarino et al. has been utilized to analyze the CdTe/CdS films obtained from molecular dynamics simulations. This work demonstrates that the parameters obtained from the polyhedral template matching algorithm in OVITO can be used to calculate the orientation of each grain. This provides a variety of useful information such as grain domains, grain orientations, plane indices, and sample texture. Moreover, dynamic analysis of microstructure evolution can be performed to understand grain growth mechanisms and kinetics. There are other useful features that are not included in the current tool such as identification and tracking of point defects (especially vacancies at grain boundaries). Nonetheless, the current approach is useful and our CdTe/CdS results provide input for further computational studies to relate grain structures to physical, chemical, mechanical, and electronic properties. read less NOT USED (low confidence) M.-Q. Le, “Fracture and strength of single-atom-thick hexagonal materials,” Computational Materials Science. 2022. link Times cited: 1 NOT USED (low confidence) C. Hou et al., “Atomistic Simulation toward Real-scale Microprocessor Circuits,” Chemical Physics Letters. 2022. link Times cited: 1 NOT USED (low confidence) K. Li, Y. Cheng, M. Dou, W. Zeng, S. Volz, and S. Xiong, “Tuning the Anisotropic Thermal Transport in 110-Silicon Membranes with Surface Resonances,” Nanomaterials. 2021. link Times cited: 1 Abstract: Understanding the thermal transport in nanostructures has im… read moreAbstract: Understanding the thermal transport in nanostructures has important applications in fields such as thermoelectric energy conversion, novel computing and heat dissipation. Using non-homogeneous equilibrium molecular dynamic simulations, we studied the thermal transport in pristine and resonant Si membranes bounded with {110} facets. The break of symmetry by surfaces led to the anisotropic thermal transport with the thermal conductivity along the [110]-direction to be 1.78 times larger than that along the [100]-direction in the pristine structure. In the pristine membranes, the mean free path of phonons along both the [100]- and [110]-directions could reach up to ∼100 µm. Such modes with ultra-long MFP could be effectively hindered by surface resonant pillars. As a result, the thermal conductivity was significantly reduced in resonant structures, with 87.0% and 80.8% reductions along the [110]- and [100]-directions, respectively. The thermal transport anisotropy was also reduced, with the ratio κ110/κ100 decreasing to 1.23. For both the pristine and resonant membranes, the thermal transport was mainly conducted by the in-plane modes. The current work could provide further insights in understanding the thermal transport in thin membranes and resonant structures. read less NOT USED (low confidence) Y. Kurniawan et al., “Bayesian, frequentist, and information geometric approaches to parametric uncertainty quantification of classical empirical interatomic potentials.,” The Journal of chemical physics. 2021. link Times cited: 6 Abstract: In this paper, we consider the problem of quantifying parame… read moreAbstract: In this paper, we consider the problem of quantifying parametric uncertainty in classical empirical interatomic potentials (IPs) using both Bayesian (Markov Chain Monte Carlo) and frequentist (profile likelihood) methods. We interface these tools with the Open Knowledgebase of Interatomic Models and study three models based on the Lennard-Jones, Morse, and Stillinger-Weber potentials. We confirm that IPs are typically sloppy, i.e., insensitive to coordinated changes in some parameter combinations. Because the inverse problem in such models is ill-conditioned, parameters are unidentifiable. This presents challenges for traditional statistical methods, as we demonstrate and interpret within both Bayesian and frequentist frameworks. We use information geometry to illuminate the underlying cause of this phenomenon and show that IPs have global properties similar to those of sloppy models from fields, such as systems biology, power systems, and critical phenomena. IPs correspond to bounded manifolds with a hierarchy of widths, leading to low effective dimensionality in the model. We show how information geometry can motivate new, natural parameterizations that improve the stability and interpretation of uncertainty quantification analysis and further suggest simplified, less-sloppy models. read less NOT USED (low confidence) J. A. Vita and D. Trinkle, “Exploring the necessary complexity of interatomic potentials,” Computational Materials Science. 2021. link Times cited: 8 NOT USED (low confidence) J. Wang, S. Wu, H. Xie, and L. Xiong, “Theoretical study on thermal properties of molybdenum disulfide/silicon heterostructures,” Computational Materials Science. 2021. link Times cited: 0 NOT USED (low confidence) S. Wyant, A. Rohskopf, and A. Henry, “Machine learned interatomic potentials for modeling interfacial heat transport in Ge/GaAs,” Computational Materials Science. 2021. link Times cited: 4 NOT USED (low confidence) Y.-S. Chang, S. Xiao, R. Ma, X. Wang, Z. Zhang, and J. He, “Displacement dynamics of trapped oil in rough channels driven by nanofluids,” Fuel. 2021. link Times cited: 11 NOT USED (low confidence) D. Dhabal, A. Bertolazzo, and V. Molinero, “Coarse-Grained Model for the Hydrothermal Synthesis of Zeolites,” The Journal of Physical Chemistry C. 2021. link Times cited: 8 NOT USED (low confidence) F. Yang, “Cycling-induced structural damage/degradation of electrode materials–microscopic viewpoint,” Nanotechnology. 2021. link Times cited: 12 Abstract: Most analyses of the mechanical deformation of electrode mat… read moreAbstract: Most analyses of the mechanical deformation of electrode materials of lithium-ion battery in the framework of continuum mechanics suggest the occurring of structural damage/degradation during the de-lithiation phase and cannot explain the lithiation-induced damage/degradation in electrode materials, as observed experimentally. In this work, we present first-principle analysis of the interaction between two adjacent silicon atoms from the Stillinger–Weber two-body potential and obtain the critical separation between the two silicon atoms for the rupture of Si–Si bonds. Simple calculation of the engineering-tensile strain for the formation of Li–Si intermetallic compounds from the lithiation of silicon reveals that cracking and cavitation in lithiated silicon can occur due to the formation of Li–Si intermetallic compounds. Assuming the proportionality between the net mass flux across the tip surface of a slit crack and the migration rate of the crack tip, we develop analytical formulas for the growth and healing of the slit crack controlled by lithiation and de-lithiation, respectively. It is the combinational effects of the state of charge, the radius of curvature of the crack tip and local electromotive force that determine the cycling-induced growth and healing of surface cracks in lithiated silicon. read less NOT USED (low confidence) A. Madadi and A. Khoei, “A coarse-grained – Atomistic multi-scale method to study the mechanical behavior of heterogeneous FCC nano-materials,” Computational Materials Science. 2021. link Times cited: 7 NOT USED (low confidence) A. O. Tipeev, J. Rino, and E. D. Zanotto, “Unveiling relaxation and crystal nucleation interplay in supercooled germanium liquid,” Acta Materialia. 2021. link Times cited: 5 NOT USED (low confidence) S. B. O., A.-S. Smith, and P. Steinmann, “Phonon-based thermal configurational forces: Definitions and applications in rupture of semiconductors,” Engineering Fracture Mechanics. 2021. link Times cited: 0 NOT USED (low confidence) M. Tan et al., “Simulation study on the diversity and characteristics of twin structures in GaN,” Superlattices and Microstructures. 2021. link Times cited: 3 NOT USED (low confidence) Y. Li, A. Diaz, X. Chen, D. McDowell, and Y. Chen, “Interference, Scattering, and Transmission of Acoustic Phonons in Si Phononic Crystals,” Acta Materialia. 2021. link Times cited: 5 NOT USED (low confidence) S. Y. Y. Chung, M. Tomita, R. Yokogawa, A. Ogura, and T. Watanabe, “Atomic mass dependency of a localized phonon mode in SiGe alloys,” AIP Advances. 2021. link Times cited: 5 NOT USED (low confidence) P. Du and J. Zhou, “Thermal property and lattice thermal conductivity of three-dimensional pentagonal silicon,” Physica B-condensed Matter. 2021. link Times cited: 3 NOT USED (low confidence) S. Sami, R. Islam, and R. P. Joshi, “Atomistic calculations of thermal conductivity in films made from graphene sheets for electron emitter applications,” AIP Advances. 2021. link Times cited: 2 NOT USED (low confidence) J. Deng and L. Stixrude, “Thermal Conductivity of Silicate Liquid Determined by Machine Learning Potentials,” Geophysical Research Letters. 2021. link Times cited: 10 Abstract: Silicate liquids are important agents of thermal evolution, … read moreAbstract: Silicate liquids are important agents of thermal evolution, yet their thermal conductivity is largely unknown. Here, we determine the thermal conductivity of a silicate liquid by combining the Green‐Kubo method with a machine learning potential of ab initio quality over the entire pressure regime of the mantle. We find that the thermal conductivity of MgSiO3 liquid is 1.1 W m−1 K−1 at the 1 bar melting point, and 4.0 W m−1 K−1 at core‐mantle boundary conditions. The thermal conductivity increases with compression, while remaining nearly constant on isochoric heating. The pressure dependence arises from the increasing bulk modulus on compression, and the weak temperature dependence arises from the saturation of the phonon mean free path due to structural disorder. The thermal conductivity of silicate liquids is less than that of ambient mantle, a contrast that may be important for understanding melt generation, and heat flux from the core. read less NOT USED (low confidence) J. Wang, Y. Geng, Z. Li, Y. Yan, X. Luo, and P. Fan, “Study on the Vertical Ultrasonic Vibration-Assisted Nanomachining Process on Single-Crystal Silicon,” Journal of Manufacturing Science and Engineering. 2021. link Times cited: 13 Abstract:
Subsurface damage that is caused by mechanical machining i… read moreAbstract:
Subsurface damage that is caused by mechanical machining is a major impediment to the widespread use of hard–brittle materials. Ultrasonic vibration-assisted macro- or micromachining could facilitate shallow subsurface damage compared with conventional machining. However, the subsurface damage that was induced by ultrasonic vibration-assisted nanomachining on hard–brittle silicon crystal has not yet been thoroughly investigated. In this study, we used a tip-based ultrasonic vibration-assisted nanoscratch approach to machine nanochannels on single-crystal silicon, to investigate the subsurface damage mechanism of the hard–brittle material during ductile machining. The material removal state, morphology, and dimensions of the nanochannel, and the effect of subsurface damage on the scratch outcomes were studied. The materials were expelled in rubbing, plowing, and cutting mode in sequence with an increasing applied normal load, and the silicon was significantly harder than the pristine material after plastic deformation. Transmission electron microscope analysis of the subsurface demonstrated that ultrasonic vibration-assisted nanoscratching led to larger subsurface damage compared with static scratching. The transmission electron microscopy results agreed with the Raman spectroscopy and molecular dynamic simulation. Our findings are important for instructing ultrasonic vibration-assisted machining of hard–brittle materials at the nanoscale level. read less NOT USED (low confidence) B. Yao, Z. Liu, and R. Zhang, “EAPOTs: An integrated empirical interatomic potential optimization platform for single elemental solids,” Computational Materials Science. 2021. link Times cited: 3 NOT USED (low confidence) Q. Liang, Y. He, and T. Hung, “Manipulating thermal conductivity of silicon nanowires through surrounded fins and Ge dopant,” International Journal of Heat and Mass Transfer. 2021. link Times cited: 3 NOT USED (low confidence) A. H. M. Faisal and C. Weinberger, “Modeling twin boundary structures in body centered cubic transition metals,” Computational Materials Science. 2021. link Times cited: 6 NOT USED (low confidence) Y. Li et al., “Atomic-scale probing of heterointerface phonon bridges in nitride semiconductor,” Proceedings of the National Academy of Sciences of the United States of America. 2021. link Times cited: 19 Abstract: Significance As high-power devices approach nanoscale, inter… read moreAbstract: Significance As high-power devices approach nanoscale, interface thermal conductance (ITC) becomes a bottleneck to govern the device performance, which is dominated by the interface phonons. In order to gain insights into engineering ITC, here we measure the local phonons across AlN/Si and AlN/Al interfaces by using atomically resolved vibrational electron energy-loss spectroscopy. We find that the dominant types of interface phonons for ITC are very different in these two systems and demonstrate the ability to correlate the measured interface phonons with ITC at atomic scale. Our study reveals the underlying mechanism of ITC and provides useful insights for thermal management in these practically important semiconductors. Interface phonon modes that are generated by several atomic layers at the heterointerface play a major role in the interface thermal conductance for nanoscale high-power devices such as nitride-based high-electron-mobility transistors and light-emitting diodes. Here we measure the local phonon spectra across AlN/Si and AlN/Al interfaces using atomically resolved vibrational electron energy-loss spectroscopy in a scanning transmission electron microscope. At the AlN/Si interface, we observe various interface phonon modes, of which the extended and localized modes act as bridges to connect the bulk AlN modes and bulk Si modes and are expected to boost the phonon transport, thus substantially contributing to interface thermal conductance. In comparison, no such phonon bridge is observed at the AlN/Al interface, for which partially extended modes dominate the interface thermal conductivity. This work provides valuable insights into understanding the interfacial thermal transport in nitride semiconductors and useful guidance for thermal management via interface engineering. read less NOT USED (low confidence) D. Zhao, J. Li, and L. Zhang, “Atomic Simulation of the Melting and Mechanical Behaviors of Silicon Nanowires,” Crystals. 2021. link Times cited: 3 Abstract: Molecular dynamics simulations using a three-body potential … read moreAbstract: Molecular dynamics simulations using a three-body potential show that the melting and mechanical behaviors of silicon nanowires are strongly dependent on their cross-section area. For the wire with a small cross-section area, rearrangements of surface atoms greatly affect thermal stability in a relatively low temperature regime. For these wires with a relatively large area, while some surface atoms adjust their positions, most of the interior atoms hold their tetrahedra packing patterns. At a high temperature, the accumulation of structural disorder can quickly extend into the entire wire, which resembles the melting of the bulk phase. By applying the uniaxial tensile, these silicon nanowires present the typical mechanical behavior of plastic materials. The atomic local stress in the necking region is apparently larger than that outside of the necking region. As the cross-section area becomes large, both the yield strength and tensile strength increase. With the increasing temperature, the elasticity decreases significantly. read less NOT USED (low confidence) L. Alzate-Vargas, S. M. Blau, E. Spotte-Smith, S. Allu, K. Persson, and J. Fattebert, “Insight into SEI Growth in Li-Ion Batteries using Molecular Dynamics and Accelerated Chemical Reactions,” The Journal of Physical Chemistry C. 2021. link Times cited: 20 Abstract: : The performance of lithium-ion batteries (LIB) using organ… read moreAbstract: : The performance of lithium-ion batteries (LIB) using organic electrolytes strongly depends on the formation of a stable solid electrolyte interphase (SEI) fi lm. Elucidating the dynamic evolution and spatial composition of the SEI can be very useful to study the stability of SEI components and help optimize the formation cycles of LIB. We propose a classical molecular dynamics simulation protocol for predicting the fi rst stages of SEI formation using a reaction method involving the decomposition of EC and LiPF 6 molecules in the electrolyte. We accelerate the formation of SEI components near the anode surface by increasing the probability of reactions, implemented through a geometry matching scheme, followed by a force- fi eld recon fi guration. We observe the formation of gases (C 2 H 4 ), inorganic (Li 2 CO 3 and LiF) and organic (LEDC) components. This protocol shows promise to be able to evaluate the e ff ects of varying electrolyte compositions and additives on SEI layer structure and composition. read less NOT USED (low confidence) T. Oyake et al., “Synergistic phonon scattering in epitaxial silicon multilayers with germanium nanodot inclusions,” Physical Review B. 2021. link Times cited: 0 Abstract: Temperature-dependent thermal conductivity of epitaxial sili… read moreAbstract: Temperature-dependent thermal conductivity of epitaxial silicon (Si)/ultrathin silica multilayers film with epitaxial germanium (Ge) nanodot inclusions is measured over the range of temperature from 50 K to room temperature using time-domain thermoreflectance. The measured thermal conductivity with 5-nm Ge nanodots is much smaller than the reported values for Si/Ge superlattices, bulk SiGe, and nanostructured SiGe in the entire temperature range. The thermal conductivity of the film is analyzed with a kinetic model incorporating multiple phonon scattering processes, where intrinsic three-phonon scattering inside the Si layers is calculated by first principles, boundary scattering at the ultrathin silica layer is calculated by the atomistic Green's function, and scattering by the Ge nanodots is approximated with nanovoids. The analysis reveals that summing the multiple scattering rates by Matthiessen's rule cannot explain the extremely low thermal conductivity. The Monte Carlo ray tracing calculation that incorporates the multiple scattering effect reveals that the synergistic effect of ultrathin silica interfaces and Ge nanodots enhances phonon scattering. This suggests the merit in synergistically designing multiple nanostructures to reduce thermal conductivity, which is beneficial for developing thermoelectric materials. read less NOT USED (low confidence) X. Wei, C.-M. Wu, and Y.-R. Li, “Atomistic investigation on the kinetic behavior of vapour adsorption and cluster evolution using a statistical rate theory approach.,” Physical chemistry chemical physics : PCCP. 2021. link Times cited: 2 Abstract: The kinetic behavior of vapor adsorption on a solid surface … read moreAbstract: The kinetic behavior of vapor adsorption on a solid surface in an isobaric-isothermal system is investigated by means of molecular dynamics simulations combined with theoretical studies through a statistical rate theory approach. The molecular insights into the formation and evolution of clusters in the adsorbate are presented. Results show that the argon vapor is adsorbed on the silicon surface as different types of clusters. In the initial stage of adsorption, the empty adsorption sites on the surface decrease, and the adsorbed single-molecule-cluster grows rapidly and dominates the interface. The increasing rate of the adsorbed cluster and the declining rate of the empty adsorption site are dependent on the pressure ratio. For a large pressure ratio, the single-molecule-clusters are aggregated to incubate large clusters, and the fraction of a single-molecule-cluster is decreased with time. When the adsorption isotherm is determined, the chemical potential of the adsorbed cluster is expressed from the zeta isotherm model. Then the adsorption kinetics are analyzed through the statistical rate theory. The molecular exchange rate and the instantaneous driving force are calculated. The higher pressure ratio induces the larger chemical potential difference and accelerates the net adsorption rate. The adsorption kinetics derived from MD simulations are in close agreement with the theoretical analysis of the statistical rate theory. read less NOT USED (low confidence) S. Abramov, V. Roganov, V. Osipov, and G. Matveev, “Implementation of the LAMMPS package using T-system with an Open Architecture,” Informatics and Automation. 2021. link Times cited: 0 Abstract: Supercomputer applications are usually implemented in the C,… read moreAbstract: Supercomputer applications are usually implemented in the C, C++, and Fortran programming languages using different versions of the Message Passing Interface library. The "T-system" project (OpenTS) studies the issues of automatic dynamic parallelization of programs. In practical terms, the implementation of applications in a mixed (hybrid) style is relevant, when one part of the application is written in the paradigm of automatic dynamic parallelization of programs and does not use any primitives of the MPI library, and the other part of it is written using the Message Passing Interface library. In this case, the library is used, which is a part of the T-system and is called DMPI (Dynamic Message Passing Interface). In this way, it is necessary to evaluate the effectiveness of the MPI implementation available in the T-system. The purpose of this work is to examine the effectiveness of DMPI implementation in the T-system. In a classic MPI application, 0% of the code is implemented using automatic dynamic parallelization of programs and 100% of the code is implemented in the form of a regular Message Passing Interface program. For comparative analysis, at the beginning the code is executed on the standard Message Passing Interface, for which it was originally written, and then it is executed using the DMPI library taken from the developed T-system. Сomparing the effectiveness of the approaches, the performance losses and the prospects for using a hybrid programming style are evaluated. As a result of the conducted experimental studies for different types of computational problems, it was possible to make sure that the efficiency losses are negligible. This allowed to formulate the direction of further work on the T-system and the most promising options for building hybrid applications. Thus, this article presents the results of the comparative tests of LAMMPS application using OpenMPI and using OpenTS DMPI. The test results confirm the effectiveness of the DMPI implementation in the OpenTS parallel programming environment read less NOT USED (low confidence) P. Henadeera, N. Samaraweera, C. Ranasinghe, and A. Wijewardane, “Ultra-low thermal conductivity of nanoparticle chains: A nanoparticle based structure for thermoelectric applications,” Journal of Applied Physics. 2021. link Times cited: 4 Abstract: Nanostructured semiconductors are promising candidates for t… read moreAbstract: Nanostructured semiconductors are promising candidates for thermoelectric materials owing to their superior thermal insulating properties over their bulk counterparts. In this study, a one-dimensional, crystalline nanostructure synthesized by sintering Si nanoparticles, called Nano Particle Chain (NPC) structures, is proposed. The structure is systematically analyzed for its thermal transport properties and compared with the nanowire counterparts. Both classical molecular dynamics and lattice dynamics tools were employed to evaluate lattice thermal conductivity (k) and to perform phonon mode level decomposition. A marked reduction in the phonon relaxation time of the NPC structure was observed indicating possible effects of phonon-boundary/constriction scatterings. This has resulted in a two-order reduction in k in NPC structures over bulk Si. Further, one order reduction of k of NPC structures was attained with respect to a nanowire of the same constriction size, indicating the effectiveness of the mismatch of particle and constriction diameters as an efficient thermal suppression mechanism. With the addition of a second material of different mass, the NPC structures can be further diversified to core/shell configurations. It was also identified that a non-monotonic variation of k exists, with a minimum in core/shell NPC structures. This effect is materialized by using a Ge-like fictitious material to coat the original Si nanoparticles, owing to competing effects of two phonon suppression mechanisms. Moreover, these core/shell NPC structures are compared with previously reported diameter modulated core/shell nanowire structures [E. Blandre et al., Phys. Rev. B, 91, 115404 (2015)] to highlight their capability to enhance the thermoelectric performance over conventional one-dimensional nanostructure configurations. read less NOT USED (low confidence) Q. Xu, H. Wang, J. Wu, and Z. Zhang, “How Does the Step on Graphite Surface Impact Ice Nucleation?,” Crystal Growth & Design. 2021. link Times cited: 3 NOT USED (low confidence) Z. Yang, R. E. Ward, N. Tanibata, H. Takeda, M. Nakayama, and R. Kobayashi, “Exploring the diffusion mechanism of Li ions in different modulated arrangements of La(1-X)/3LixNbO3 with fitted force fields obtained via a metaheuristic algorithm,” Solid State Ionics. 2021. link Times cited: 4 NOT USED (low confidence) M. Fujikane, S. Nagao, D. Chrobak, T. Yokogawa, and R. Nowak, “Room-Temperature Plasticity of a Nanosized GaN Crystal,” Nano Letters. 2021. link Times cited: 5 Abstract: GaN wurtzite crystal is commonly regarded as eminently britt… read moreAbstract: GaN wurtzite crystal is commonly regarded as eminently brittle. However, our research demonstrates that nanodeconfined GaN compressed along the M direction begins to exhibit room-temperature plasticity, yielding a dislocation-free structure despite the occurrence of considerable, irreversible deformation. Our interest in M-oriented, strained GaN nanoobjects was sparked by the results of first-principles bandgap calculations, whereas subsequent nanomechanical tests and ultrahigh-voltage (1250 kV) transmission electron microscopy observations confirmed the authenticity of the phenomenon. Moreover, identical experiments along the C direction produced only a quasi-brittle response. Precisely how this happens is demonstrated by molecular dynamics simulations of the deformation of the C- and M-oriented GaN frustum, which mirror our nanopillar crystals. read less NOT USED (low confidence) E. Minamitani, T. Shiga, M. Kashiwagi, and I. Obayashi, “Topological descriptor of thermal conductivity in amorphous Si.,” The Journal of chemical physics. 2021. link Times cited: 6 Abstract: Quantifying the correlation between the complex structures o… read moreAbstract: Quantifying the correlation between the complex structures of amorphous materials and their physical properties has been a longstanding problem in materials science. In amorphous Si, a representative covalent amorphous solid, the presence of a medium-range order (MRO) has been intensively discussed. However, the specific atomic arrangement corresponding to the MRO and its relationship with physical properties, such as thermal conductivity, remains elusive. We solved this problem by combining topological data analysis, machine learning, and molecular dynamics simulations. Using persistent homology, we constructed a topological descriptor that can predict thermal conductivity. Moreover, from the inverse analysis of the descriptor, we determined the typical ring features correlated with both the thermal conductivity and MRO. The results could provide an avenue for controlling material characteristics through the topology of the nanostructures. read less NOT USED (low confidence) A. Rossetto, V. Camargo, D. Vasileska, and G. Wirth, “3-D non-isothermal particle-based device simulator for p-type MOSFETs,” Journal of Computational Electronics. 2021. link Times cited: 1 NOT USED (low confidence) S. Chung et al., “Dependency of a localized phonon mode intensity on compositional cluster size in SiGe alloys,” AIP Advances. 2021. link Times cited: 2 Abstract: Using molecular dynamics, we found that the localized phonon… read moreAbstract: Using molecular dynamics, we found that the localized phonon-mode spectrum in SiGe alloys, which was recently discovered by an inelastic x-ray scattering experiment, changes according to the size distribution of compositional clusters in alloys. By varying the spatial distributions of Si and Ge, alloy models with differing compositions of Si and Ge clusters were able to be produced. For a range of alloys comprising 20%–80% Ge, a mixture of small and intermediate sized clusters will give the highest intensities of the local mode. The Si–Ge optical mode intensity increases with the local mode intensity, but the Si–Ge bond alone is not sufficient to produce the local mode. Si rich alloys with small Ge clusters produce the highest local mode intensities, suggesting that this mode is caused by small Ge clusters surrounded by Si pairs. read less NOT USED (low confidence) J. Simmons and T. Carrington, “Using collocation and solutions for a sum-of-product potential to compute vibrational energy levels for general potentials,” Chemical Physics Letters. 2021. link Times cited: 2 NOT USED (low confidence) G. Manolis, P. Dineva, T. Rangelov, and D. Sfyris, “Mechanical models and numerical simulations in nanomechanics: A review across the scales,” Engineering Analysis with Boundary Elements. 2021. link Times cited: 17 NOT USED (low confidence) J. Zhang et al., “Unifying fluctuation-dissipation temperatures of slow-evolving nonequilibrium systems from the perspective of inherent structures,” Science Advances. 2021. link Times cited: 4 Abstract: Effective temperatures of slow-evolving nonequilibrium syste… read moreAbstract: Effective temperatures of slow-evolving nonequilibrium systems measure characteristic temperatures of equilibrium systems. For nonequilibrium systems, how to define temperature is one of the key and difficult issues to solve. Although effective temperatures have been proposed and studied to this end, it still remains elusive what they actually are. Here, we focus on the fluctuation-dissipation temperatures and report that such effective temperatures of slow-evolving systems represent characteristic temperatures of their equilibrium counterparts. By calculating the fluctuation-dissipation relation of inherent structures, we obtain a temperature-like quantity TIS. For monocomponent crystal-formers, TIS agrees well with the crystallization temperature Tc, while it matches with the onset temperature Ton for glass-formers. It also agrees with effective temperatures of typical nonequilibrium systems, such as aging glasses, quasi-static shear flows, and quasi-static self-propelled flows. From the unique perspective of inherent structures, our study reveals the nature of effective temperatures and the underlying connections between nonequilibrium and equilibrium systems and confirms the equivalence between Ton and Tc. read less NOT USED (low confidence) W. Xi, H. Feng, D. Liu, L.-X. Chen, Y. Zhang, and Q. Li, “Electrocatalytic generation and tuning of ultra-stable and ultra-dense nanometre bubbles: an in situ molecular dynamics study.,” Nanoscale. 2021. link Times cited: 2 Abstract: Electrocatalytic generation of nanometre gas bubbles (nanobu… read moreAbstract: Electrocatalytic generation of nanometre gas bubbles (nanobubbles) and their tuning are important for many energy and chemical processes. Studies have sought to use indirect or ex situ methods to investigate the dynamics and properties of nanobubbles, which are of fundamental interest. Alternatively, we present a molecular dynamics simulation method, which features in situ and high spatial resolution, to directly address these fundamentals. Particularly, our simulations can quantitatively reproduce the generation of ultra-stable and ultra-dense nanobubbles observed in electrochemical experiments. More importantly, our results demonstrate that the classical nucleation theory is still valid even for the scale down to several nanometres, to predict the dynamics and properties of nanobubbles. This provides general guidelines to design efficient nanocatalysts and nanoelectrodes. In our specific case, nanoelectrodes with wetting angles below 71° can suppress the generation of surface nanobubbles. read less NOT USED (low confidence) J. Wan, C. Tan, Y. Rong, L. Zhang, and H. Cai, “Thermal conductivity of short tungsten disulfide nanotubes: A molecular dynamics study,” Journal of Applied Physics. 2021. link Times cited: 3 Abstract: The effects of length, diameter, temperature, and axial stra… read moreAbstract: The effects of length, diameter, temperature, and axial strain on the thermal conductivity of armchair and zigzag WS 2 nanotubes are systematically investigated by nonequilibrium molecular dynamics simulations. It is found that the thermal conductivity gradually increases with the increase in the length, while it is insensitive to nanotube diameter variation. The thermal conductivity of armchair and zigzag WS 2 nanotubes is remarkably reduced as temperature increases due to the increment of phonon–phonon scattering and reduction of the phonon mean free path. In addition, compressive strain can increase thermal conductivity due to increased contributions from low-frequency phonons, while the opposite is true in the case of tensile strain. The chirality has a slight influence on the thermal transport properties of the WS 2 nanotube. read less NOT USED (low confidence) H. Vázquez and F. Djurabekova, “Ultrafast phase transitions in polyamorphic materials triggered by swift heavy ion impacts,” Physical Review Materials. 2021. link Times cited: 1 NOT USED (low confidence) P. Steinmann, A. Smith, E. Birang, A. McBride, and A. Javili, “Atomistic two-, three- and four-body potentials. Spatial and material settings,” Journal of The Mechanics and Physics of Solids. 2021. link Times cited: 5 NOT USED (low confidence) M. An, D. Chen, W. Ma, S. Hu, and X. Zhang, “Directly visualizing the crossover from incoherent to coherent phonons in two-dimensional periodic MoS2/MoSe2 arrayed heterostructure,” International Journal of Heat and Mass Transfer. 2021. link Times cited: 13 NOT USED (low confidence) G. Pilania, “Machine learning in materials science: From explainable predictions to autonomous design,” Computational Materials Science. 2021. link Times cited: 85 NOT USED (low confidence) Y. Wang et al., “Tension–compression asymmetry in amorphous silicon,” Nature Materials. 2021. link Times cited: 27 NOT USED (low confidence) J. Zhang, “Tunable local and global piezopotential properties of graded InGaN nanowires,” Nano Energy. 2021. link Times cited: 4 NOT USED (low confidence) A. Hua, Z.-H. Li, Z. Zhang, H. Wu, N. Wei, and J. Zhao, “An analogous ellipse equation for describing the coupling relationship of friction and adhesion between a probe tip and graphene,” Mechanics of Materials. 2021. link Times cited: 1 NOT USED (low confidence) F. Molaei, M. S. Moghadam, and S. Nouri, “Investigation of thermal properties of crystalline alpha quartz by employing different interatomic potentials: A molecular dynamic study,” Physics of the Earth and Planetary Interiors. 2021. link Times cited: 4 NOT USED (low confidence) T. P. Sheerin, D. Tanner, and S. Schulz, “Atomistic analysis of piezoelectric potential fluctuations in zinc-blende InGaN/GaN quantum wells: A Stillinger-Weber potential based analysis,” Physical Review B. 2021. link Times cited: 4 Abstract: Title Atomistic analysis of piezoelectric potential fluctuat… read moreAbstract: Title Atomistic analysis of piezoelectric potential fluctuations in zinc-blende InGaN/GaN quantum wells: A Stillinger-Weber potential based analysis Author(s) Sheerin, Thomas P.; Tanner, Daniel S. P.; Schulz, Stefan Publication date 2021-04-19 Original citation Sheerin, T. P., Tanner, D. S. P. and Schulz, S. (2021) 'Atomistic analysis of piezoelectric potential fluctuations in zinc-blende InGaN/GaN quantum wells: A Stillinger-Weber potential based analysis', Physical Review B, 103(16), 165201 (13pp). doi: 10.1103/PhysRevB.103.165201 Type of publication Article (peer-reviewed) Link to publisher's version http://dx.doi.org/10.1103/PhysRevB.103.165201 Access to the full text of the published version may require a subscription. Rights © 2021, American Physical Society. All rights reserved. Item downloaded from http://hdl.handle.net/10468/11250 read less NOT USED (low confidence) D. Bilyk, D. Ferizovi’c, A. Glazyrin, R. Matzke, J. Park, and O. Vlasiuk, “Potential theory with multivariate kernels,” Mathematische Zeitschrift. 2021. link Times cited: 3 NOT USED (low confidence) S. Roy, A. Dutta, and N. Chakraborti, “A novel method of determining interatomic potential for Al and Al-Li alloys and studying strength of Al-Al3Li interphase using evolutionary algorithms,” Computational Materials Science. 2021. link Times cited: 13 NOT USED (low confidence) S.-D. Zhang and J. Zhang, “Fatigue-induced dynamic pull-in instability in electrically actuated microbeam resonators,” International Journal of Mechanical Sciences. 2021. link Times cited: 3 NOT USED (low confidence) J. Bian and L. Nicola, “On the lubrication of rough copper surfaces with graphene,” Tribology International. 2021. link Times cited: 12 NOT USED (low confidence) G. Kapteijns, D. Richard, E. Bouchbinder, T. Schrøder, J. Dyre, and E. Lerner, “Does mesoscopic elasticity control viscous slowing down in glassforming liquids?,” The Journal of chemical physics. 2021. link Times cited: 12 Abstract: The dramatic slowing down of relaxation dynamics of liquids … read moreAbstract: The dramatic slowing down of relaxation dynamics of liquids approaching the glass transition remains a highly debated problem, where the crux of the puzzle resides in the elusive increase in the activation barrier ΔE(T) with decreasing temperature T. A class of theoretical frameworks-known as elastic models-attribute this temperature dependence to the variations of the liquid's macroscopic elasticity, quantified by the high-frequency shear modulus G∞(T). While elastic models find some support in a number of experimental studies, these models do not take into account the spatial structures, length scales, and heterogeneity associated with structural relaxation in supercooled liquids. Here, we propose and test the possibility that viscous slowing down is controlled by a mesoscopic elastic stiffness κ(T), defined as the characteristic stiffness of response fields to local dipole forces in the liquid's underlying inherent structures. First, we show that κ(T)-which is intimately related to the energy and length scales characterizing quasilocalized, nonphononic excitations in glasses-increases more strongly with decreasing T than the macroscopic inherent structure shear modulus G(T) [the glass counterpart of liquids' G∞(T)] in several computer liquids. Second, we show that the simple relation ΔE(T) ∝ κ(T) holds remarkably well for some computer liquids, suggesting a direct connection between the liquid's underlying mesoscopic elasticity and enthalpic energy barriers. On the other hand, we show that for other computer liquids, the above relation fails. Finally, we provide strong evidence that what distinguishes computer liquids in which the ΔE(T) ∝ κ(T) relation holds from those in which it does not is that the latter feature highly fragmented/granular potential energy landscapes, where many sub-basins separated by low activation barriers exist. Under such conditions, it appears that the sub-basins do not properly represent the landscape properties relevant for structural relaxation. read less NOT USED (low confidence) Y. Lysogorskiy et al., “Performant implementation of the atomic cluster expansion (PACE) and application to copper and silicon,” npj Computational Materials. 2021. link Times cited: 84 NOT USED (low confidence) M. Dewapriya and R. E. Miller, “Molecular dynamics study of the penetration resistance of multilayer polymer/ceramic nanocomposites under supersonic projectile impacts,” Extreme Mechanics Letters. 2021. link Times cited: 17 NOT USED (low confidence) H. Li et al., “Imaging local discharge cascades for correlated electrons in WS2/WSe2 moiré superlattices,” Nature Physics. 2021. link Times cited: 42 NOT USED (low confidence) Z.-H. Yang, “Speed-dependent adaptive partitioning in QM/MM MD simulations of displacement damage in solid-state systems.,” Physical chemistry chemical physics : PCCP. 2021. link Times cited: 1 Abstract: Solids undergo displacement damage (DD) when interacting wit… read moreAbstract: Solids undergo displacement damage (DD) when interacting with energetic particles, which may happen during the fabrication of semiconductor devices, in harsh environments and in certain analysis techniques. Simulations of DD generation are usually carried out using classical molecular dynamics (MD), but classical MD does not account for all the effects in DD, as demonstrated by ab initio calculations of model systems in the literature. A complete ab initio simulation of DD generation is impractical due to the large number of atoms involved. In my previous paper [Yang, Phys. Chem. Chem. Phys., 2020, 22, 19307], I developed an adaptive-center (AC) method for the adaptive-partitioning (AP) of quantum mechanics/molecular mechanics (QM/MM) simulations, allowing the active region centers and the QM/MM partition to be determined on-the-fly for energy-conserving AP-QM/MM methods. I demonstrated that the AC-AP-QM/MM is applicable to the simulation of DD generation, so that the active regions can be treated using an ab initio method. The AC method could not be used to identify the fast-moving recoil ions in DD generation as active region centers, however, and the accuracy is negatively affected by the rapid change in the QM/MM partition of the system. In this paper, I extend the AC method and develop a speed-dependent adaptive-center (SDAC) method for accurate AP-QM/MM simulations of DD. The SDAC method is applicable to general problems with speed-dependent active regions, and is compatible with all existing energy-conserving partitioning-by-distance AP-QM/MM methods. The artifact due to the speed-dependent potential energy surface can be made small by choosing suitable criteria. I demonstrate the SDAC method by simulations of DD generation in bulk silicon. read less NOT USED (low confidence) Y. Jin et al., “Physics of surface vibrational resonances: pillared phononic crystals, metamaterials, and metasurfaces,” Reports on Progress in Physics. 2021. link Times cited: 88 Abstract: The introduction of engineered resonance phenomena on surfac… read moreAbstract: The introduction of engineered resonance phenomena on surfaces has opened a new frontier in surface science and technology. Pillared phononic crystals, metamaterials, and metasurfaces are an emerging class of artificial structured media, featuring surfaces that consist of pillars—or branching substructures—standing on a plate or a substrate. A pillared phononic crystal exhibits Bragg band gaps, while a pillared metamaterial may feature both Bragg band gaps and local resonance hybridization band gaps. These two band-gap phenomena, along with other unique wave dispersion characteristics, have been exploited for a variety of applications spanning a range of length scales and covering multiple disciplines in applied physics and engineering, particularly in elastodynamics and acoustics. The intrinsic placement of pillars on a semi-infinite surface—yielding a metasurface—has similarly provided new avenues for the control and manipulation of wave propagation. Classical waves are admitted in pillared media, including Lamb waves in plates and Rayleigh and Love waves along the surfaces of substrates, ranging in frequency from hertz to several gigahertz. With the presence of the pillars, these waves couple with surface resonances richly creating new phenomena and properties in the subwavelength regime and in some applications at higher frequencies as well. At the nanoscale, it was shown that atomic-scale resonances—stemming from nanopillars—alter the fundamental nature of conductive thermal transport by reducing the group velocities and generating mode localizations across the entire spectrum of the constituent material well into the terahertz regime. In this article, we first overview the history and development of pillared materials, then provide a detailed synopsis of a selection of key research topics that involve the utilization of pillars or similar branching substructures in different contexts. Finally, we conclude by providing a short summary and some perspectives on the state of the field and its promise for further future development. read less NOT USED (low confidence) V. L. Deringer et al., “Origins of structural and electronic transitions in disordered silicon,” Nature. 2021. link Times cited: 162 NOT USED (low confidence) S. Midori, D. Hikmawati, and A. Supardi, “Molecular dynamics study of mechanical properties of Zn – xMg alloy for metal biomaterial.” 2020. link Times cited: 0 Abstract: The goal of this research is to know the mechanical properti… read moreAbstract: The goal of this research is to know the mechanical properties of Zn – xMg alloy through the molecular dynamics method with LAMMPS software. The potential used in this computational calculation are Lennard – Jones, Morse hybrid LJ, and Stillinger – Weber hybrid LJ. Structure properties of Zn – xMg before temperature treatment is HCP with space group P63/mmc. Mechanical properties are explained by bulk modulus and elastic constant. Temperature treatment will be done before mechanical properties simulation by doing heating – cooling on the material structure that has been made before. The study of bulk modulus with a value of that appropriate to experiment is 67,492 GPa with error percentage 5,17349% that simulated by Lennard – Jones potential. Elastic constants with a value of that appropriate for C11 dan C12 is 26,198 GPa and 23,503 GPa with error percentage 14,49729% (Zn – 1%Mg) and 37,02932% (Zn – 5%Mg) which simulated by Morse potential, for C44 is 8,2219 GPa with error percentage 0,266362% (Zn – 3%Mg) which simulated by Stillinger – Weber potential. read less NOT USED (low confidence) J. Fernandez-Toledano, T. Blake, and J. D. Coninck, “Taking a closer look: A molecular-dynamics investigation of microscopic and apparent dynamic contact angles.,” Journal of colloid and interface science. 2020. link Times cited: 23 NOT USED (low confidence) W. Jian, S. Xu, and I. Beyerlein, “On the significance of model design in atomistic calculations of the Peierls stress in Nb,” Computational Materials Science. 2020. link Times cited: 15 NOT USED (low confidence) K. Huang et al., “An experimental study on atomic-level unified criterion for brittle fracture,” International Journal of Solids and Structures. 2020. link Times cited: 5 NOT USED (low confidence) L. Wan, “Excitations of atomic vibrations in amorphous solids,” Journal of Physics: Condensed Matter. 2020. link Times cited: 0 Abstract: We study excitations of atomic vibrations in the reciprocal … read moreAbstract: We study excitations of atomic vibrations in the reciprocal space for amorphous solids. There are two kinds of excitations we obtained, collective excitation and local excitation. The collective excitation is the collective vibration of atoms in the amorphous solids while the local excitation is stimulated locally by a single atom vibrating in the solids. We introduce a continuous wave vector for the study and transform the equations of atomic vibrations from the real space to the reciprocal space. We take the amorphous silicon as an example and calculate the structures of the excitations in the reciprocal space. Results show that an excitation is a wave packet composed of a collection of plane waves. We also find a periodical structure in the reciprocal space for the collective excitation with longitudinal vibrations, which is originated from the local order of the structure in the real space of the amorphous solid. For the local excitation, the wave vector is complex. The imaginary part of the wave vector is inversed to evaluate the decaying length of the local excitation. It is found that the decaying length is larger for the local excitation with a higher vibration frequency. read less NOT USED (low confidence) D. Dockar, L. Gibelli, and M. Borg, “Forced oscillation dynamics of surface nanobubbles.,” The Journal of chemical physics. 2020. link Times cited: 5 Abstract: Surface nanobubbles have potential applications in the manip… read moreAbstract: Surface nanobubbles have potential applications in the manipulation of nanoscale and biological materials, waste-water treatment, and surface cleaning. These spherically capped bubbles of gas can exist in stable diffusive equilibrium on chemically patterned or rough hydrophobic surfaces, under supersaturated conditions. Previous studies have investigated their long-term response to pressure variations, which is governed by the surrounding liquid's local supersaturation; however, not much is known about their short-term response to rapid pressure changes, i.e., their cavitation dynamics. Here, we present molecular dynamics simulations of a surface nanobubble subjected to an external oscillating pressure field. The surface nanobubble is found to oscillate with a pinned contact line, while still retaining a mostly spherical cap shape. The amplitude-frequency response is typical of an underdamped system, with a peak amplitude near the estimated natural frequency, despite the strong viscous effects at the nanoscale. This peak is enhanced by the surface nanobubble's high internal gas pressure, a result of the Laplace pressure. We find that accurately capturing the gas pressure, bubble volume, and pinned growth mode is important for estimating the natural frequency, and we propose a simple model for the surface nanobubble frequency response, with comparisons made to other common models for a spherical bubble, a constant contact angle surface bubble, and a bubble entrapped within a cylindrical micropore. This work reveals the initial stages of growth of cavitation nanobubbles on surfaces, common in heterogeneous nucleation, where classical models based on spherical bubble growth break down. read less NOT USED (low confidence) S. Wu, J. Wang, H. Xie, and Z. Guo, “Interfacial Thermal Conductance across Graphene/MoS2 van der Waals Heterostructures,” Energies. 2020. link Times cited: 9 Abstract: The thermal conductivity and interface thermal conductance o… read moreAbstract: The thermal conductivity and interface thermal conductance of graphene stacked MoS2 (graphene/MoS2) van der Waals heterostructure were studied by the first principles and molecular dynamics (MD) simulations. Firstly, two different heterostructures were established and optimized by VASP. Subsequently, we obtained the thermal conductivity (K) and interfacial thermal conductance (G) via MD simulations. The predicted Κ of monolayer graphene and monolayer MoS2 reached 1458.7 W/m K and 55.27 W/m K, respectively. The thermal conductance across the graphene/MoS2 interface was calculated to be 8.95 MW/m2 K at 300 K. The G increases with temperature and the interface coupling strength. Finally, the phonon spectra and phonon density of state were obtained to analyze the changing mechanism of thermal conductivity and thermal conductance. read less NOT USED (low confidence) S. Starikov, I. Gordeev, Y. Lysogorskiy, L. Kolotova, and S. Makarov, “Optimized interatomic potential for study of structure and phase transitions in Si-Au and Si-Al systems,” Computational Materials Science. 2020. link Times cited: 19 NOT USED (low confidence) K. Talaat, M. El-Genk, and B. Cowen, “Extrapolation of thermal conductivity in non-equilibrium molecular dynamics simulations to bulk scale,” International Communications in Heat and Mass Transfer. 2020. link Times cited: 2 NOT USED (low confidence) T. Albaret, F. Boioli, and D. Rodney, “Time-resolved shear transformations in the transient plastic regime of sheared amorphous silicon.,” Physical review. E. 2020. link Times cited: 2 Abstract: The accumulation of shear transformations (STs) in space and… read moreAbstract: The accumulation of shear transformations (STs) in space and time is responsible for plastic deformation in amorphous solids. Here we study the effect of finite strain rates on STs during simulations of athermal shear deformation in an atomistic model of amorphous silicon. We present a time-resolved analysis of STs by mapping the plastic events identified in the atomistic simulations on a collection of Eshelby inclusions, which are characterized in terms of number, effective volume, lifetime, and orientation. Our analysis led us to distinguish between small and large events. We find that the main effect of a lower strain rate is to allow for a larger number of small events, roughly identified by an effective volume γ_{0}V_{0}<20 Å^{3}, while the number and characteristics of larger events are surprisingly independent of the strain rate. We show that at low strains, the decrease of the stress observed at lower strain rates is mainly due to the excess of small events, while at larger strains, when the glass approaches the yield point where a shear band forms, larger events start to play a role and organize due to their elastic interactions. This phenomenology is compared with the predictions of mesoscale elastoplastic models. The technique developed here can be used as a systematic tool to analyze plasticity during molecular dynamics simulations. It can also give valuable information to develop physically grounded mesoscale models of plasticity, providing quantitative predictions of the mechanical properties of amorphous materials. read less NOT USED (low confidence) A. Rohskopf, S. Wyant, K. Gordiz, H. R. Seyf, M. G. Muraleedharan, and A. Henry, “Fast & accurate interatomic potentials for describing thermal vibrations,” Computational Materials Science. 2020. link Times cited: 7 NOT USED (low confidence) J. Harrison, S. Stuart, and D. Brenner, “Atomic-Scale Simulation of Tribological and Related Phenomena,” Handbook of Micro/Nano Tribology. 2020. link Times cited: 3 NOT USED (low confidence) E. Dontsova, R. Ballarini, and B. Yakobson, “Dimensionality effects in crystal plasticity, from 3D silicon to 2D silicene,” Extreme Mechanics Letters. 2020. link Times cited: 1 NOT USED (low confidence) X. Chu et al., “The role of nuclear charges in unifying the descriptions of neural networks (NN)-based force fields,” Materials Letters. 2020. link Times cited: 0 NOT USED (low confidence) M. C. Barry, K. Wise, S. Kalidindi, and S. Kumar, “Voxelized Atomic Structure Potentials: Predicting Atomic Forces with the Accuracy of Quantum Mechanics Using Convolutional Neural Networks.,” The journal of physical chemistry letters. 2020. link Times cited: 9 Abstract: This paper introduces Voxelized Atomic Structure (VASt) pote… read moreAbstract: This paper introduces Voxelized Atomic Structure (VASt) potentials as a machine learning (ML) framework for developing interatomic potentials. The VASt framework utilizes a voxelized representation of the atomic structure directly as the input to a convolutional neural network (CNN). This allows for high fidelity representations of highly complex and diverse spatial arrangements of the atomic environments of interest. The CNN implicitly establishes the low-dimensional features needed to correlate each atomic neighborhood to its net atomic force. The selection of the salient features of the atomic structure (i.e., feature engineering) in the VASt framework is implicit, comprehensive, automated, scalable, and highly efficient. The calibrated convolutional layers learn the complex spatial relationships and multibody interactions that govern the physics of atomic systems with remarkable fidelity. We show that VASt potentials predict highly accurate forces on two phases of silicon carbide and the thermal conductivity of silicon over a range of isotropic strain. read less NOT USED (low confidence) Y. Kan, F. Hong, Z. Wei, and K. Bi, “Interfacial coupling effects on the thermal conductivity of few-layer graphene,” Materials Research Express. 2020. link Times cited: 1 Abstract: The thermal conductivities of both suspended and supported f… read moreAbstract: The thermal conductivities of both suspended and supported few-layer graphene (FLG) were investigated via molecular dynamics simulations. The results indicate that the thermal conductivity of a suspended FLG sample decreases by 3.9% from 511.2 W m−1 K−1 upon an increase in the number of layers from 1 to 20 layers, whereas it increases by 5.5% to 486.8 W m−1 K−1 in the case of supported FLG specimens on a smooth crystalline silicon surface. Both trends converge when the number of layers is higher than five. The effects of the substrate roughness on the supported FLG samples were also investigated. The results show that their thermal conductivity on a rough silicon surface is lower than that on a smooth silicon surface. In order to demonstrate the importance of interfacial coupling on the phonon transport properties, the coupling strength parameter was enhanced by a factor of 3 or 10 to see the influence on the thermal conductivity. The simulations show that the thermal conductivity decreases with an increasing coupling strength. Lastly, the phonon dispersion of a two-layer graphene specimen was calculated by varying the interlayer coupling strength. The calculations show that the coupling strength is mainly influenced by the out-of-plane phonon dispersion relation. The frequency of flexural acoustic (ZA’) phonons around the center of the first Brillouin zone increases significantly from 2.14 to 6.78 THz when the interlayer coupling strength is enhanced by a factor of 10. This may decrease the phonon group velocity and provide more scattering channels, and thus reduce the thermal conductivity. read less NOT USED (low confidence) A. Krishnamoorthy et al., “Evolutionary multi-objective optimization and Pareto-frontal uncertainty quantification of interatomic forcefields for thermal conductivity simulations,” Comput. Phys. Commun. 2020. link Times cited: 8 NOT USED (low confidence) M. Guziewski, A. D. Banadaki, S. Patala, and S. Coleman, “Application of Monte Carlo techniques to grain boundary structure optimization in silicon and silicon-carbide,” Computational Materials Science. 2020. link Times cited: 13 NOT USED (low confidence) T. C. Sagar, V. Chinthapenta, and M. Horstemeyer, “Effect of defect guided out-of-plane deformations on the mechanical properties of graphene,” Fullerenes, Nanotubes and Carbon Nanostructures. 2020. link Times cited: 5 Abstract: In this paper, nanoscale mechanical properties and failure b… read moreAbstract: In this paper, nanoscale mechanical properties and failure behavior of graphene with Stone-Wales defect concentration were investigated using molecular dynamics simulations with the latest ReaxFFC-2013 potential that can accurately capture bond breakages of graphitic compounds. The choice of interatomic potential plays an essential role in capturing the deformation mechanism accurately. Stable configuration of two-dimensional graphene experiences out-of-plane deformation leading to ripples and wrinkles in graphene. It is observed that the mechanical properties such as Young’s modulus, ultimate tensile strength, and the fracture strain are dependent on the out-of-plane deformation, temperature, defect concentration, defect orientation, defect layout and loading configuration. It is observed that the post transient phase non-homogenous ripples and wrinkles influence the mechanical properties at low and high defect concentrations, respectively. read less NOT USED (low confidence) R. Kobayashi, Y. Miyaji, K. Nakano, and M. Nakayama, “High-throughput production of force-fields for solid-state electrolyte materials,” APL Materials. 2020. link Times cited: 11 Abstract: An automatic and high-throughput method to produce interatom… read moreAbstract: An automatic and high-throughput method to produce interatomic force-fields for solid-state electrolyte materials is proposed. The proposed method employs the cuckoo search algorithm with an automatic update of search space to optimize parameters in empirical potentials to reproduce radial and angular distribution functions and equilibrium volume obtained from the ab initio molecular dynamics simulation. The force-fields for LiZr2(PO4)3 and LaF3 systems parameterized using the present method well reproduce key physical properties required to study ion conductivity of solid-state electrolyte materials. The current approach takes only one or two days to produce a force-field including the ab initio calculation to create reference data, which will greatly enhance the speed of exploration and screening of candidate materials. read less NOT USED (low confidence) S. Gelin, A. Champagne-Ruel, and N. Mousseau, “Enthalpy-entropy compensation of atomic diffusion originates from softening of low frequency phonons,” Nature Communications. 2020. link Times cited: 16 NOT USED (low confidence) A. Akkerman, J. Barak, and M. Murat, “A Survey of the Analytical Methods of Proton-NIEL Calculations in Silicon and Germanium,” IEEE Transactions on Nuclear Science. 2020. link Times cited: 4 Abstract: The nonionizing energy loss (NIEL) concept has been used for… read moreAbstract: The nonionizing energy loss (NIEL) concept has been used for many years for qualitative estimation of the damage induced by radiation (particles and gamma rays). Different approaches, based on the physics of radiation interaction with the nuclear and electronic subsystems of the target atoms, are used for calculating NIEL values. The simplest model used is the binary collision approximation (BCA), which is applicable for energies larger than the threshold energy for Frenkel pair creation. In this article, we analyze the dependence of the calculated NIEL values (in silicon and germanium) on the basic interaction characteristics: the differential cross section (DCS) of energy transferred to the recoiling atoms and the partition factor between ionization and ion displacement. We estimate the differences between existing approaches and the possible scatter of the NIEL data for Coulomb, elastic, and inelastic nuclear scatterings. We also present new partition factors based on fits to experimental data. The contribution of low-energy cascade zones of displaced atoms (pockets) to the total damage is estimated using results of molecular dynamics (MD) calculation. We find for silicon a total increase of NIEL by 30%–40% relative to the original (BCA) NIEL value. The role of phonon excitations in the subthreshold cascades on the damage value is discussed. read less NOT USED (low confidence) H. Nobarani, N. Zhang, N. Zhang, and M. A. Zaeem, “Nanotwin-induced strengthening in silicon: A molecular dynamics study,” International Journal of Mechanical Sciences. 2020. link Times cited: 11 NOT USED (low confidence) C. Desgranges and J. Delhommelle, “Unraveling liquid polymorphism in silicon driven out-of-equilibrium.,” The Journal of chemical physics. 2020. link Times cited: 4 Abstract: Using nonequilibrium molecular dynamics simulations, we stud… read moreAbstract: Using nonequilibrium molecular dynamics simulations, we study the properties of supercooled liquids of Si under shear at T = 1060 K over a range of densities encompassing the low-density liquid (LDL) and high-density liquid (HDL) forms. This enables us to generate nonequilibrium steady-states of the LDL and HDL polymorphs that remain stabilized in their liquid forms for as long as the shear is applied. This is unlike the LDL and HDL forms at rest, which are metastable under those conditions and, when at rest, rapidly undergo a transition toward the crystal, i.e., the thermodynamically stable equilibrium phase. In particular, through a detailed analysis of the structural and energetic features of the liquids under shear, we identify the range of densities, as well as the range of shear rates, which give rise to the two forms. We also show how the competition between shear and tetrahedral order impacts the two-body entropy in steady-states of Si under shear. These results open the door to new ways of utilizing shear to stabilize forms that are metastable at rest and can exhibit unique properties, since, for instance, experiments on Si have shown that HDL is metallic with no bandgap, while LDL is semimetallic with a pseudogap. read less NOT USED (low confidence) H. Yanxon, D. Zagaceta, B. Tang, D. Matteson, and Q. Zhu, “PyXtal_FF: a python library for automated force field generation,” Machine Learning: Science and Technology. 2020. link Times cited: 15 Abstract: We present PyXtal_FF—a package based on Python programming l… read moreAbstract: We present PyXtal_FF—a package based on Python programming language—for developing machine learning potentials (MLPs). The aim of PyXtal_FF is to promote the application of atomistic simulations through providing several choices of atom-centered descriptors and machine learning regressions in one platform. Based on the given choice of descriptors (including the atom-centered symmetry functions, embedded atom density, SO4 bispectrum, and smooth SO3 power spectrum), PyXtal_FF can train MLPs with either generalized linear regression or neural network models, by simultaneously minimizing the errors of energy/forces/stress tensors in comparison with the data from ab-initio simulations. The trained MLP model from PyXtal_FF is interfaced with the Atomic Simulation Environment (ASE) package, which allows different types of light-weight simulations such as geometry optimization, molecular dynamics simulation, and physical properties prediction. Finally, we will illustrate the performance of PyXtal_FF by applying it to investigate several material systems, including the bulk SiO2, high entropy alloy NbMoTaW, and elemental Pt for general purposes. Full documentation of PyXtal_FF is available at https://pyxtal-ff.readthedocs.io. read less NOT USED (low confidence) M. Povarnitsyn, N. Shcheblanov, D. Ivanov, V. Timoshenko, and S. Klimentov, “Vibrational Analysis of Silicon Nanoparticles Using Simulation and Decomposition of Raman Spectra,” Physical review applied. 2020. link Times cited: 5 NOT USED (low confidence) M. Isaiev, X. Wang, K. Termentzidis, and D. Lacroix, “Thermal transport enhancement of hybrid nanocomposites; impact of confined water inside nanoporous silicon,” Applied Physics Letters. 2020. link Times cited: 2 Abstract: The thermal transport properties of porous silicon and nano-… read moreAbstract: The thermal transport properties of porous silicon and nano-hybrid “porous silicon/water” systems are presented here. The thermal conductivity was evaluated using the equilibrium molecular dynamics technique for porous systems made of spherical voids or water-filled cavities. We revealed large thermal conductivity enhancement in the nano-hybrid systems as compared to their dry porous counterparts, which cannot be captured by effective media theory. This rise of thermal conductivity is related to the increase in the specific surface area of the liquid/solid interface. We demonstrated that the significant difference, more than two folds, in thermal conductivity of pristine porous silicon and “porous silicon liquid–composite” is due to the liquid density fluctuation close to the “solid–liquid interface” (layering effect). This effect is getting more importance for the large specific surface of the interfacial area. Specifically, the enhancement of the effective thermal conductivity is 50% for a specific surface area of 0.3 (1/nm), and it increases further upon the increase in the surface to volume ratio. Our study provides valuable insights into the thermal properties of hybrid liquid/solid nanocomposites and into the importance of confined liquids within nanoporous materials. read less NOT USED (low confidence) H. Li et al., “Imaging moiré flat bands in three-dimensional reconstructed WSe2/WS2 superlattices,” Nature Materials. 2020. link Times cited: 114 NOT USED (low confidence) S. Yesudasan, R. D. Averett, and S. Chacko, “Machine Learned Coarse Grain Water Models for Evaporation Studies.” 2020. link Times cited: 6 Abstract: Evaporation studies of water using classical molecular dynam… read moreAbstract: Evaporation studies of water using classical molecular dynamics simulations are largely limited due to its high computational expense. We aim at addressing the computational issues by developing a coarse grain model for evaporation of water on solid surfaces by combining four water molecules into a single bead. Most commonly used mono atomic pair potentials like Lennard Jones, Morse, Mie and three body potential like Stillinger-Weber are optimized using a combination of Genetic algorithm and Nelder-Mead algorithm. Among them, Stillinger-Weber based model shows excellent agreement of density and Enthalpy of vaporization with experimental results for a wide range of temperatures. Further, the new water model is used to simulate contact angle of water and thin film evaporation from surfaces with different wettabilities. read less NOT USED (low confidence) M. Shi, N. Admal, and E. Tadmor, “Noise filtering in atomistic stress calculations for crystalline materials,” Journal of The Mechanics and Physics of Solids. 2020. link Times cited: 2 NOT USED (low confidence) L. Li, R. Lin, and T. Ng, “Contribution of nonlocality to surface elasticity,” International Journal of Engineering Science. 2020. link Times cited: 69 NOT USED (low confidence) V.-T. Pham and T. Fang, “Anisotropic mechanical strength, negative Poisson’s ratio and fracture mechanism of borophene with defects,” Thin Solid Films. 2020. link Times cited: 16 NOT USED (low confidence) K. Huang, T. Sumigawa, T. Shimada, and T. Kitamura, “An Atomic-Level Unified Criterion for Brittle Fracture.” 2020. link Times cited: 0 NOT USED (low confidence) H. Li, H. Xiang, H. Huang, Z. Zeng, and X. Peng, “Interface structure and deformation mechanisms of AlN/GaN multilayers,” Ceramics International. 2020. link Times cited: 14 NOT USED (low confidence) A. Gautam and A. Chandra, “A computational study of excess properties for mW potential model of water in supercooled region,” Physica A: Statistical Mechanics and its Applications. 2020. link Times cited: 0 NOT USED (low confidence) M. Razi, A. Narayan, R. Kirby, and D. Bedrov, “Force-field coefficient optimization of coarse-grained molecular dynamics models with a small computational budget,” Computational Materials Science. 2020. link Times cited: 5 NOT USED (low confidence) S. Uchida, K. Fujiwara, and M. Shibahara, “Molecular Dynamics Study of Interactions between the Water/ice Interface and a Nanoparticle in the Vicinity of a Solid Surface,” Nanoscale and Microscale Thermophysical Engineering. 2020. link Times cited: 4 Abstract: ABSTRACT In this study, non-equilibrium molecular dynamics s… read moreAbstract: ABSTRACT In this study, non-equilibrium molecular dynamics simulations were conducted for a coexistence system of water and ice on a wall surface with a single nanoparticle to reveal the effects of water solidification on the nanoparticle in the vicinity of a wall surface. We further investigated the effect of the presence and size of particles on the density profile of water in the vicinity of the wall surface and the force acting on particles from water molecules, when the solidification interface contacted the wall and the particles. The results revealed that a strong mutual influence exists between the solidification interface and the nanoparticle on the wall’s surface; the nanoparticle on the wall prevents water solidification in proximity to the wall. Moreover, the force acting on the nanoparticle from water molecules changes as the solidification interface approaches; the cooling temperature is shown to affect the direction of this force. It indicates that the solidification process is a key influential factor which affects nanoparticle movements on a wall surface at molecular scales. read less NOT USED (low confidence) G. G. Vogiatzis, L. V. Breemen, D. Theodorou, and M. Hütter, “Free energy calculations by molecular simulations of deformed polymer glasses,” Comput. Phys. Commun. 2020. link Times cited: 8 NOT USED (low confidence) J. Hickman and Y. Mishin, “Thermal conductivity and its relation to atomic structure for symmetrical tilt grain boundaries in silicon.,” Physical review materials. 2020. link Times cited: 9 Abstract: We perform a systematic study of thermal resistance/conducta… read moreAbstract: We perform a systematic study of thermal resistance/conductance of tilt grain boundaries (GBs) in Si using classical molecular dynamics. The GBs studied are naturally divided into three groups according to the structural units forming the GB core. We find that, within each group, the GB thermal conductivity strongly correlates with the excess GB energy. All three groups predict nearly the same GB conductivity extrapolated to the high-energy limit. This limiting value is close to the thermal conductivity of amorphous Si, suggesting similar heat transport mechanisms. While the lattice thermal conductivity decreases with temperature, the GB conductivity slightly increases. However, at high temperatures it turns over and starts decreasing if the GB structure undergoes a premelting transformation. Analysis of vibrational spectra of GBs resolved along different directions sheds light on the mechanisms of their thermal resistance. The existence of alternating tensile and compressive atomic environments in the GB core gives rise to localized vibrational modes, frequency gaps creating acoustic mismatch with lattice phonons, and anharmonic vibrations of loosely-bound atoms residing in open atomic environments. read less NOT USED (low confidence) Á. Jász, Á. Rák, I. Ladjánszki, and G. Cserey, “Classical molecular dynamics on graphics processing unit architectures,” Wiley Interdisciplinary Reviews: Computational Molecular Science. 2020. link Times cited: 6 Abstract: Molecular dynamics (MD) has experienced a significant growth… read moreAbstract: Molecular dynamics (MD) has experienced a significant growth in the recent decades. Simulating systems consisting of hundreds of thousands of atoms is a routine task of computational chemistry researchers nowadays. Thanks to the straightforwardly parallelizable structure of the algorithms, the most promising method to speed‐up MD calculations is exploiting the large‐scale processing power offered by the parallel hardware architecture of graphics processing units or GPUs. Programming GPUs is becoming easier with general‐purpose GPU computing frameworks and higher levels of abstraction. In the recent years, implementing MD simulations on graphics processors has gained a large interest, with multiple popular software packages including some form of GPU‐acceleration support. Different approaches have been developed regarding various aspects of the algorithms, with important differences in the specific solutions. Focusing on published works in the field of classical MD, we describe the chosen implementation methods and algorithmic techniques used for porting to GPU, as well as how recent advances of GPU architectures will provide even more optimization possibilities in the future. read less NOT USED (low confidence) M. Xiong, X. Zhao, N. Li, and H.-hua Xu, “General energy-strain scheme for accurate evaluation of the Born elasticity term for solid and liquid systems under finite temperature and pressure conditions,” Comput. Phys. Commun. 2020. link Times cited: 6 NOT USED (low confidence) T. Yokoi, Y. Noda, A. Nakamura, and K. Matsunaga, “Neural-network interatomic potential for grain boundary structures and their energetics in silicon,” Physical Review Materials. 2020. link Times cited: 11 Abstract: Artificial neural-network (ANN) interatomic potentials for s… read moreAbstract: Artificial neural-network (ANN) interatomic potentials for simulating atomic structures and energetics of grain boundaries (GBs) in silicon were constructed and integrated into structural optimization and molecular dynamics (MD) algorithms. A training dataset including various atomic environments of symmetric tilt GBs was generated by performing density-functional-theory (DFT) calculations. The ANN potential after training was found to be capable of approximating the potential-energy surface at GBs even with dangling bonds and large atomic displacements at high temperatures, which cannot be well reproduced with empirical interatomic potentials. Additionally, reliability of the ANN potential for molecular simulations was evaluated. GB structures optimized or equilibrated by the ANN molecular simulations were also energetically lower for DFT calculations, without significant errors. The ANN potential is therefore expected to greatly reduce structural-optimization iterations and required time steps to acquire stable or equilibrium GB structures in MD simulations, enabling us to address even large-scale systems of general GBs in silicon, with high accuracy and low computational cost. read less NOT USED (low confidence) A. Singh and Y. Li, “Uncertainty Management and Reduction of Machine Learning Potential,” AIAA Scitech 2021 Forum. 2020. link Times cited: 0 NOT USED (low confidence) R. Ma et al., “Molecular Insights into the Effect of a Solid Surface on the Stability of a Hydrate Nucleus,” Journal of Physical Chemistry C. 2020. link Times cited: 13 Abstract: Understanding and controlling hydrate formation are of vital… read moreAbstract: Understanding and controlling hydrate formation are of vital importance for the storage and transportation of natural gas. In this work, the influence of a solid surface on the stability of a hydrate nucleus is studied by molecular dynamics simulations. The surface with a strong affinity for guest molecules induces the decomposition of the hydrate nucleus because of competitive adsorption on guest molecules. Specifically, the competitive adsorption for guest molecules results in the transformation of interface structures of the hydrate nucleus, and this process can be divided into two steps: transformation from whole cages to semi-cages and aggregation of the isolated semi-cages. While the interaction between the guest molecules and the solid surface decreases to form a weakly affinitive surface, the hydrate nucleus can maintain its structure near the surface. Our research shows that not all surfaces facilitate hydrate nucleation, and the stability of the hydrate nucleus on the surface is closely related ... read less NOT USED (low confidence) T. Hori, “Verification of the phonon relaxation time approximation by probing the relaxation process of a single excited mode,” Physical Review B. 2019. link Times cited: 1 NOT USED (low confidence) I. Talyzin and V. Samsonov, “On the prospect of creating memory elements based on silicon nanoparticles,” Izvestiya Vysshikh Uchebnykh Zavedenii. Materialy Elektronnoi Tekhniki = Materials of Electronics Engineering. 2019. link Times cited: 0 Abstract: Phase-change memory is based on a change in the optical, ele… read moreAbstract: Phase-change memory is based on a change in the optical, electrical, or other properties of a substance during a phase transition, for example, transition from the amorphous to the crystalline state. Already realized and potential applications of such memory are associated with the use for this purpose of multicomponent alloys based on metals, semiconductors. However, single-component nanoparticles, including Si ones, are also of interest in view of the prospects for their use as nanoscale memory units. In particular, possibility of creating such memory units is confirmed by the fact that the bulk phase of the amorphous silicon has an optical absorption coefficient which is by an order of magnitude greater than that of the crystalline, although, it is difficult to release this effect for an individual nanoparticle whose size does not exceed the wavelength of light. In this work, using molecular dynamics (MD) and the Stillinger-Weber potential, we studied the laws of melting and conditions of crystallization for silicon nanoparticles containing up to 100,000 atoms. It has been shown that upon cooling a silicon nanodroplet at a rate of 0.2 TK/s and higher rates, its transition into the amorphous state takes place, whereas single-component metal nanodroplets crystallize even at cooling rates of 1 TK/s. Upon subsequent heating of amorphous silicon nanoparticles containing more than 50,000 atoms, they crystallize in the definite temperature range 1300—1400 K. It is concluded that it is principally possible to create memory units based on the above phase transitions. The transition of a nanoparticle to the amorphous state is achieved by its melting and subsequent cooling to the room temperature at a rate of 0.2 TK/s, and switching to the crystalline state is achieved by heating it to 1300—1400 K at a rate of 0.2 TK/s and subsequent cooling. On the basis of results of MD experiments, a conclusion is made that there exist a minimal size of silicon nanoparticles, for which producing memory units based on the change of the phase state, is not possible. It was found that for the temperature change rate of 0.2 TK/s, the minimal size in question 12.4 nm that corresponds to 50,000 atoms. read less NOT USED (low confidence) B. Seo, M. Y. Ha, J. W. Yu, and W. B. Lee, “Enhanced sampling of cylindrical microphase separation via a shell-averaged bond-orientational order parameter.,” Soft matter. 2019. link Times cited: 1 Abstract: The formation of a hexagonal phase from disordered phase is … read moreAbstract: The formation of a hexagonal phase from disordered phase is one of the typical order-disorder transitions (ODTs) observed in asymmetric diblock copolymer systems. In order to drive this transition in a particle-based simulation, we introduce a shell-based bond-orientational order parameter that selectively responds to the mesoscopic order of the hexagonal cylinder phase. From metadynamics simulations in a bond-free particle model system, the characteristic pathway involved with the underlying free energy surface is deduced for the disordered-to-hexagonal transition. It is shown consecutively that the transition pathway and the metastable state are reproduced in dissipative particle dynamics simulations for the corresponding transition in a bulk asymmetric block copolymer melt system. These agreements suggest that efficient strategies for enhanced sampling with particle-based simulations of block copolymer systems can be devised using coarse-grained pictures of the mesoscopic order. read less NOT USED (low confidence) S. Takamoto, S. Izumi, and J. Li, “TeaNet: universal neural network interatomic potential inspired by iterative electronic relaxations,” ArXiv. 2019. link Times cited: 29 NOT USED (low confidence) S. Shinzato, M. Wakeda, and S. Ogata, “An atomistically informed kinetic Monte Carlo model for predicting solid solution strengthening of body-centered cubic alloys,” International Journal of Plasticity. 2019. link Times cited: 26 NOT USED (low confidence) D. Olson, C. Ortner, Y. Wang, and L. Zhang, “Elastic Far-Field Decay from Dislocations in Multilattices,” Multiscale Modeling & Simulation. 2019. link Times cited: 2 Abstract: We precisely and rigorously characterise the decay of elasti… read moreAbstract: We precisely and rigorously characterise the decay of elastic fields generated by dislocations in crystalline materials, focusing specifically on the role of multilattices. Concretely, we establish that the elastic field generated by a dislocation in a multilattice can be decomposed into a continuum field predicted by a linearised Cauchy-Born elasticity theory, and a discrete and nonlinear core corrector representing the defect core. We demonstrate both analytically and numerically the consequences of this result for cell size effects in numerical simulations. read less NOT USED (low confidence) J. Lu et al., “Self-assembled monolayer for polymer-semiconductor interface with improved interfacial thermal management.,” ACS applied materials & interfaces. 2019. link Times cited: 23 Abstract: Reliability and lifespan of highly miniaturized and integrat… read moreAbstract: Reliability and lifespan of highly miniaturized and integrated devices will be effectively improved if excessive accumulated heat can be quickly transported to heat sinks. In this study, both molecular dynamics (MD) simulations and experiments were performed to demonstrate that self-assembled monolayers (SAMs) have high potential in interfacial thermal management and can enhance thermal transport across polystyrene (PS) / silicon (Si) interface, modelling the common polymer/semiconductor interfaces in actual devices. The influence of packing density and alkyl-chain length of SAMs are investigated. Firstly, MD simulations show that the interfacial thermal transport efficiency of SAM is higher with high packing density. The interfacial thermal conductance (ITC) between PS and Si can be improved up to 127 ± 9 MW m-2 K-1, close to the ITC across metal and semiconductor interface. At moderate packing density, the SAMs with less than 8 carbon atoms in alkyl-chain show superior improvements over those with more carbons due to the assembled structure variation. Secondly, time-domain thermoreflectance technique was employed to characterize the ITCs of a bunch of Al/PS/SAM/Si samples. C6-SAM enhances the ITC by 5 folds, from 11 ± 1 MW m-2 K-1 to 56 ± 17 MW m-2 K-1. The interfacial thermal management efficiency will weaken when alkyl-chain exceeds 8 carbon atoms, which agrees with the ITC trend from MD simulations at moderate packing density. The relationship between SAM morphology and interfacial thermal management efficiency is also discussed in detail. This study demonstrates the feasibility of molecular level design for interfacial thermal management from both theoretical calculation and experiment, and may provide a new idea for improving the heat dissipation efficiency of micro devices. read less NOT USED (low confidence) Y. Zhang, L. Wang, and J. Jiang, “Thermal vibration of MoS2/Black phosphorus Bi-layered heterostructure,” Physica E: Low-dimensional Systems and Nanostructures. 2019. link Times cited: 2 NOT USED (low confidence) P. Stoch, P. Goj, M. Ciecińska, and A. Stoch, “Structural features of 19Al2O3-19Fe2O3-62P2O5 glass from a theoretical and experimental point of view,” Journal of Non-Crystalline Solids. 2019. link Times cited: 20 NOT USED (low confidence) N. T. Brown, E. Martínez, and J. Qu, “Solid-liquid metal interface definition studies using capillary fluctuation method,” Computational Materials Science. 2019. link Times cited: 3 NOT USED (low confidence) E. Aifantis, “Gradient Extension of Classical Material Models: From Nuclear & Condensed Matter Scales to Earth & Cosmological Scales,” Springer Tracts in Mechanical Engineering. 2019. link Times cited: 9 NOT USED (low confidence) F. Huber, J. Berwanger, S. Polesya, S. Mankovsky, H. Ebert, and F. Giessibl, “Chemical bond formation showing a transition from physisorption to chemisorption,” Science. 2019. link Times cited: 57 Abstract: Imaging a chemisorption process At low temperatures, a molec… read moreAbstract: Imaging a chemisorption process At low temperatures, a molecule may adsorb to a surface only through weak forces (physisorption), and only upon heating and overcoming an energetic barrier does it form a strong covalent bond (chemisorption). Huber et al. imaged this transition for an atomic force microscopy tip terminating in a carbon monoxide molecule. Although the oxygen atom of the tip is normally considered to act like a rare gas atom, interacting only through van der Waals interactions, at short distances directly above a transition metal atom, it transitions to a strongly interacting chemisorption state. Science, this issue p. 235 The CO molecule that terminates an atomic force microscope tip transitions to a chemisorbed state when imaging metal atoms. Surface molecules can transition from physisorption through weak van der Waals forces to a strongly bound chemisorption state by overcoming an energy barrier. We show that a carbon monoxide (CO) molecule adsorbed to the tip of an atomic force microscope enables a controlled observation of bond formation, including its potential transition from physisorption to chemisorption. During imaging of copper (Cu) and iron (Fe) adatoms on a Cu(111) surface, the CO was not chemically inert but transited through a physisorbed local energy minimum into a chemisorbed global minimum, and an energy barrier was seen for the Fe adatom. Density functional theory reveals that the transition occurs through a hybridization of the electronic states of the CO molecule mainly with s-, pz-, and dz2-type states of the Fe and Cu adatoms, leading to chemical bonding. read less NOT USED (low confidence) J. Carrete et al., “Phonon transport across crystal-phase interfaces and twin boundaries in semiconducting nanowires.,” Nanoscale. 2019. link Times cited: 12 Abstract: We combine state-of-the-art Green's-function methods an… read moreAbstract: We combine state-of-the-art Green's-function methods and nonequilibrium molecular dynamics calculations to study phonon transport across the unconventional interfaces that make up crystal-phase and twinning superlattices in nanowires. We focus on two of their most paradigmatic building blocks: cubic (diamond/zinc blende) and hexagonal (lonsdaleite/wurtzite) polytypes of the same group-IV or III-V material. Specifically, we consider InP, GaP and Si, and both the twin boundaries between rotated cubic segments and the crystal-phase boundaries between different phases. We reveal the atomic-scale mechanisms that give rise to phonon scattering in these interfaces, quantify their thermal boundary resistance and illustrate the failure of common phenomenological models in predicting those features. In particular, we show that twin boundaries have a small but finite interface thermal resistance that can only be understood in terms of a fully atomistic picture. read less NOT USED (low confidence) Y. Zhao et al., “Kink effects on thermal transport in silicon nanowires,” International Journal of Heat and Mass Transfer. 2019. link Times cited: 14 NOT USED (low confidence) J. V. Michelin, L. G. Gonçalves, and J. Rino, “On the transferability of interaction potentials for condensed phases of silicon,” Journal of Molecular Liquids. 2019. link Times cited: 6 NOT USED (low confidence) J. Moon, R. Hermann, M. Manley, A. Alatas, A. Said, and A. Minnich, “Thermal acoustic excitations with atomic-scale wavelengths in amorphous silicon,” Physical Review Materials. 2019. link Times cited: 18 Abstract: The vibrational properties of glasses remain a topic of inte… read moreAbstract: The vibrational properties of glasses remain a topic of intense interest due to several unresolved puzzles, including the origin of the Boson peak and the mechanisms of thermal transport. Inelastic scattering measurements have revealed that amorphous solids support collective acoustic excitations with low THz frequencies despite the atomic disorder, but these frequencies are well below most of the thermal vibrational spectrum. Here, we report the observation of acoustic excitations with frequencies up to 10 THz in amorphous silicon. The excitations have atomic-scale wavelengths as short as 6 A and exist well into the thermal vibrational frequencies. Simulations indicate that these high-frequency waves are supported due to the high group velocity and monatomic composition of a-Si, suggesting that other glasses with these characteristics may also exhibit such excitations. Our findings demonstrate that a substantial portion of thermal vibrational modes in amorphous materials can still be described as a phonon gas despite the lack of atomic order. read less NOT USED (low confidence) G.-R. Han, T. Chang, and J.-W. Jiang, “Directional Motion of a Graphene Sheet on Graded MoS2–WSe2 Lateral Heterostructures,” Journal of Applied Mechanics. 2019. link Times cited: 3 Abstract: Directional motion is one of the most fundamental motions in… read moreAbstract: Directional motion is one of the most fundamental motions in the nature, which is driven by specific types of gradients. The transition metal dichalcogenides graded lateral heterostructure is a valuable semiconductor playing crucial roles in electronic and optoelectronic devices. This lateral heterostructure has a graded composition and is thus a promising candidate to drive possible directional motions. Here, we perform molecular dynamics simulations to demonstrate the directional motion of a graphene sheet on top of the MoS2–WSe2 graded lateral heterostructure. It is quite interesting that the direction for the diffusion is sensitive to the graphene sheet’s initial location, which is in two different regions. The graphene sheet diffuses in opposite directions for the initial location that falls in different regions. We derive an analytic formula for the interlayer coupling potential, which discloses the underlying mechanism for the dependence of the directional motion on the initial location of the graphene sheet. These results shall be varifiable by present experimental set ups and may be valuable for the application of the transition metal dichalcogenides graded lateral heterostructure in practical electronic devices. read less NOT USED (low confidence) T. Riedl and J. Lindner, “Stability of heteroepitaxial coherent growth modes on nanowire radial surfaces,” Physical Review Materials. 2019. link Times cited: 0 NOT USED (low confidence) S. Yao et al., “Nanofriction oscillation driven by sublayer indirect contact of silicon tip sliding on few-layer graphene,” AIP Advances. 2019. link Times cited: 0 Abstract: Nanofriction with few layers of graphene as lubrication is a… read moreAbstract: Nanofriction with few layers of graphene as lubrication is an interesting issue recently, and it provides a quite important guide for modeling the nanofriction properties of nanodevice. Based on the molecular dynamics (MD) simulations, nanofriction properties of a silicon tip sliding on different graphene layers with or without substrate were studied systemically. We revealed that the friction of these systems exhibits clearly the even-odd oscillations with different thickness of graphene, and we further demonstrated that such even-odd oscillations behavior is totally independent of the size of the silicon tips, as well as applying normal loadings. The underlying physics of this intriguing phenomenon is attributed to the oscillations of indirect-contact-atom-number between top and sublayers of suspended graphene. Furthermore, we showed that such indirect contact oscillations would be reflected by the direct contact oscillations between the tip and the top-layer graphene when graphene lubrication layers on a rigid substrate. Overall, our new findings not only enrich the nanofriction mechanism of graphene lubrication systems, but also introduce a new way to design the nanofriction systems with two-dimensional (2D) van der Waals materials as lubrications.Nanofriction with few layers of graphene as lubrication is an interesting issue recently, and it provides a quite important guide for modeling the nanofriction properties of nanodevice. Based on the molecular dynamics (MD) simulations, nanofriction properties of a silicon tip sliding on different graphene layers with or without substrate were studied systemically. We revealed that the friction of these systems exhibits clearly the even-odd oscillations with different thickness of graphene, and we further demonstrated that such even-odd oscillations behavior is totally independent of the size of the silicon tips, as well as applying normal loadings. The underlying physics of this intriguing phenomenon is attributed to the oscillations of indirect-contact-atom-number between top and sublayers of suspended graphene. Furthermore, we showed that such indirect contact oscillations would be reflected by the direct contact oscillations between the tip and the top-layer graphene when graphene lubrication layers on... read less NOT USED (low confidence) E. Minamitani, M. Ogura, and S. Watanabe, “Simulating lattice thermal conductivity in semiconducting materials using high-dimensional neural network potential,” Applied Physics Express. 2019. link Times cited: 27 Abstract: We demonstrate that a high-dimensional neural network potent… read moreAbstract: We demonstrate that a high-dimensional neural network potential (HDNNP) can predict the lattice thermal conductivity of semiconducting materials with an accuracy that is comparable to that of density functional theory (DFT) calculation. After a training procedure based on force, the root mean square error between the forces predicted by HDNNP and DFT is less than 40 meV Å−1. As typical examples, we present the results of Si and GaN bulk crystals. The deviation from the thermal conductivity calculated using DFT is within 1% at 200 to 500 K for Si and within 5.4% at 200 to 1000 K for GaN. read less NOT USED (low confidence) H. Nguyen, “Graphene layer of hybrid graphene/hexagonal boron nitride model upon heating,” Carbon Letters. 2019. link Times cited: 9 NOT USED (low confidence) V. V. Hoang and N. H. Giang, “Heating-induced phase transitions in confined amorphous tetra-silicene,” Materials Research Express. 2019. link Times cited: 2 Abstract: Heating-induced phase transitions of confined amorphous tetr… read moreAbstract: Heating-induced phase transitions of confined amorphous tetra-silicene (t-silicene) are studied via molecular dynamics (MD) simulations. Glassy models containing 6066 atoms interacted via Stillinger-Weber potential are heated up from 300 K to 5000 K at the heating rate of 1011 K s−1. We find glass-crystal-liquid phase transition indicated that amorphous t-silicene is a less stable glass. Crystallization of amorphous t-silicene occurs at around T X = 1290 K while subsequent melting of crystallized t-silicene appears at around T m = 1739 K. The latter is close to that of hexa-silicene. Thermodynamics and evolution of structure of models upon heating are analyzed in details. We find that crystallization of amorphous t-silicene occurs via homogeneous local rearrangements of atoms in the glassy matrix. Atomic mechanism of crystallization and subsequent melting of the obtained crystalline t-silicene is studied and the role of liquid-like atoms in this phase transition is clarified. read less NOT USED (low confidence) S. Smidstrup et al., “QuantumATK: an integrated platform of electronic and atomic-scale modelling tools,” Journal of Physics: Condensed Matter. 2019. link Times cited: 638 Abstract: QuantumATK is an integrated set of atomic-scale modelling to… read moreAbstract: QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented, the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals. The platform includes a long list of advanced modules, including Green’s-function methods for electron transport simulations and surface calculations, first-principles electron-phonon and electron-photon couplings, simulation of atomic-scale heat transport, ion dynamics, spintronics, optical properties of materials, static polarization, and more. Seamless integration of the different simulation engines into a common platform allows for easy combination of different simulation methods into complex workflows. Besides giving a general overview and presenting a number of implementation details not previously published, we also present four different application examples. These are calculations of the phonon-limited mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model simulation of lithium ion drift through a battery cathode in an external electric field, and electronic-structure calculations of the composition-dependent band gap of SiGe alloys. read less NOT USED (low confidence) O. Yenigun and M. Barisik, “Effect of nano-film thickness on thermal resistance at water/silicon interface,” International Journal of Heat and Mass Transfer. 2019. link Times cited: 16 NOT USED (low confidence) S. Hilke et al., “Analysis of medium-range order based on simulated segmented ring detector STEM-images: amorphous Si.,” Ultramicroscopy. 2019. link Times cited: 8 NOT USED (low confidence) V. V. Hoang, N. H. Giang, T. Q. Dong, and T. T. Hanh, “Tetra-SiC – New allotrope of 2D silicon carbide,” Computational Materials Science. 2019. link Times cited: 6 NOT USED (low confidence) M. Vohra and S. Mahadevan, “Discovering the active subspace for efficient UQ of molecular dynamics simulations of phonon transport in silicon,” International Journal of Heat and Mass Transfer. 2019. link Times cited: 8 NOT USED (low confidence) Q. Liu, Z. Jia, Z. Yaowu, L. Xiong, T. Shi, and Y. Long, “On the dynamic behaviors of silicon single crystal under nanosecond laser irradiation,” Computational Materials Science. 2019. link Times cited: 3 NOT USED (low confidence) J. Cao, Y. Wang, J. Chai, and J. Shi, “Nano-peapods from C60-encapsulated CNTs driving self-assembly of phosphorus nanotube: A molecular dynamics study,” Computational Materials Science. 2019. link Times cited: 5 NOT USED (low confidence) A. Krishnamoorthy et al., “Thermal conductivity of MoS2 monolayers from molecular dynamics simulations,” AIP Advances. 2019. link Times cited: 20 Abstract: Quantification of lattice thermal conductivity of two-dimens… read moreAbstract: Quantification of lattice thermal conductivity of two-dimensional semiconductors like MoS2 is necessary for the design of electronic and thermoelectric devices, but direct experimental measurements on free-standing samples is challenging. Molecular dynamics simulations, with appropriate corrections, can provide a reference value for thermal conductivity for these material systems. Here, we construct a new empirical forcefield of the Stillinger-Weber form, parameterized to phonon dispersion relations, lattice constants and elastic moduli and we use it to compute a material-intrinsic thermal conductivity of 38.1 W/m-K at room temperature and estimate a maximum thermal conductivity of 85.4 W/m-K at T = 200 K. We also identify that phonon scattering by the large isotopic mass distribution of Mo and S contributes a significant correction (>45%) to the thermal conductivity at low temperatures. read less NOT USED (low confidence) J. Lu, A. Barnett, and V. Molinero, “Effect of Polymer Architecture on the Nanophase Segregation, Ionic Conductivity, and Electro-Osmotic Drag of Anion Exchange Membranes,” The Journal of Physical Chemistry C. 2019. link Times cited: 27 Abstract: Anion exchange membranes (AEMs) are considered an attractive… read moreAbstract: Anion exchange membranes (AEMs) are considered an attractive alternative to proton exchange membranes in fuel cell applications because they can operate with nonprecious metal electrodes. However, widespread adoption of AEMs has been hampered by their insufficient ionic conductivity. Much of the growing body of research on AEMs focuses on designing new polymer chemistries and architectures that would increase their conductivity, while controlling the swelling of the membrane. It is, however, challenging to assess the separate effects of water content and polymer architecture on the phase segregation and molecular transport of the ions and water in the membrane because changes in the chemistry of the polymer also impact the equilibrium water uptake. Here, we use large-scale molecular simulations to study the distinct effects of water content and ionomer architecture on the nanophase segregation, anion and water diffusivity, ion conductivity, and water electro-osmotic drag coefficient of anion exchange memb... read less NOT USED (low confidence) P. Grammatikopoulos, M. Sowwan, and J. Kioseoglou, “Computational Modeling of Nanoparticle Coalescence,” Advanced Theory and Simulations. 2019. link Times cited: 68 Abstract: The coalescence of nanoclusters fabricated in the gas phase … read moreAbstract: The coalescence of nanoclusters fabricated in the gas phase is a fundamental growth mechanism determining cluster shapes, sizes, compositions, and structures, with resultant effects on practically all of their physical and chemical properties. Furthermore, coalescence can affect properties of larger structures that consist of nanoparticles as their elementary building blocks, such as the fractal dimension of cluster aggregates and the porosity and conductance of thin films. Therefore, it comes as no surprise that a great body of research, both experimental and theoretical, has focused on nanoparticle coalescence over the course of the past few decades. This review attempts to summarize the most important recent results from computational studies on nanoparticle coalescence and draw parallels between theoretical and experimental findings. The approach used here aspires to explain nanoparticle coalescence within the framework of a single intuitive narrative by integrating previous results obtained using various methods by the authors and others. Simultaneously, it is discussed where understanding and controlling (i.e., enhancing or inhibiting) nanoparticle coalescence can have great technological interest. read less NOT USED (low confidence) V. Diana and S. Casolo, “A bond-based micropolar peridynamic model with shear deformability: Elasticity, failure properties and initial yield domains,” International Journal of Solids and Structures. 2019. link Times cited: 69 NOT USED (low confidence) T. Juntunen, O. Vänskä, and I. Tittonen, “Anderson Localization Quenches Thermal Transport in Aperiodic Superlattices.,” Physical review letters. 2019. link Times cited: 51 Abstract: We show that aperiodic superlattices exhibit intriguing inte… read moreAbstract: We show that aperiodic superlattices exhibit intriguing interplay between phononic coherent wave interference effects and incoherent transport. In particular, broadband Anderson localization results in a drastic thermal conductivity reduction of 98% at room temperature, providing an ultralow value of 1.3 W m^{-1} K^{-1}, and further yields an anomalously large thermal anisotropy ratio of ∼10^{2} in aperiodic Si/Ge superlattices. A maximum in the thermal conductivity emerges as an unambiguous consequence of phonon Anderson localization at a system length scale bridging the extended and localized transport regimes. The frequency-resolved picture, combined with our lattice dynamical description of Anderson localization, elucidates the rich transport characteristics in these systems and the potential of correlated disorder for sub- to few-THz phononic engineering of heat transport in thermoelectric applications. read less NOT USED (low confidence) Z. Hossain, F. Elahi, and Z. Zhang, “Differential anharmonicity and thermal expansion coefficient in3C-SiC nanowires,” Physical Review B. 2019. link Times cited: 4 Abstract: Surface and core are two essential but distinct structural p… read moreAbstract: Surface and core are two essential but distinct structural parts of a nanowire---but their individual effects on overall thermal expansion coefficient of a nanowire have never been quantified. Here we present an average bond-length based framework to determine the effects of the surface and core regimes of $3C$-SiC nanowires on their effective volumetric thermal expansion coefficient over a wide range of temperatures. Our results suggest that the surface and core atoms exhibit differential anharmonic response at finite temperatures, which makes the surface regime exhibit disparate expansion behavior compared to the core. While at lower temperatures the differential anharmonicity is negligible, at temperatures higher than the room temperature there is a pronounced differential anharmonicity in the nanowire. Furthermore, temperature-dependent expansion coefficients of the nanowire and the surface and core regimes qualitatively follow the behavior of the bulk---but they vary substantially quantitatively, with the maximum coefficient exhibited by the surface at higher temperatures. The diameter-dependent expansion coefficients follow inverse power laws with their exponents varying from 0.95 to 2.5. In thinner nanowires the expansion coefficient is controlled by an intricate combination of mass inertia and bond stiffness at the surface and core, whereas the expansion of thicker nanowires is dominated by the anharmonic motion of the core atoms alone. The surface effects saturate with increasing diameter, but the core effects decay nonlinearly with increasing diameter and approaches the bulk value as $d\ensuremath{\rightarrow}\ensuremath{\infty}$. read less NOT USED (low confidence) M. French, “Thermal conductivity of dissociating water—an ab initio study,” New Journal of Physics. 2019. link Times cited: 12 Abstract: The thermal conductivity of partially dissociated and ionise… read moreAbstract: The thermal conductivity of partially dissociated and ionised water is calculated in a large-scale study using density functional theory (DFT)-based molecular dynamics (MD) simulations. In doing so, the required heat current of the nuclei is calculated by mapping the effective particle interactions from the DFT-MD simulations onto classical pair potentials. It is demonstrated that experimental and theoretical thermal conductivity data for liquid heavy water and for ice VII are well reproduced with this efficient procedure. Moreover, the approach also allows for an illustrative interpretation of the characteristics of the thermal conductivity in the dense chemically reacting fluid. The thermodynamic conditions investigated here range from densities between 0.2 and 6 g cm−3 and temperatures between 600 and 50 000 K, which includes states highly relevant for understanding the interiors of water-rich planets like Uranus and Neptune and exoplanets of similar composition. read less NOT USED (low confidence) X. Zhuang, B. He, B. Javvaji, and H. S. Park, “Intrinsic bending flexoelectric constants in two-dimensional materials,” Physical Review B. 2019. link Times cited: 45 Abstract: Flexoelectricity is a form of electromechanical coupling tha… read moreAbstract: Flexoelectricity is a form of electromechanical coupling that has recently emerged because, unlike piezoelectricity, it is theoretically possible in any dielectric material. Two-dimensional (2D) materials have also garnered significant interest because of their unusual electromechanical properties and high flexibility, but the intrinsic flexoelectric properties of these materials remain unresolved. In this work, using atomistic modeling accounting for charge-dipole interactions, we report the intrinsic flexoelectric constants for a range of two-dimensional materials, including graphene allotropes, nitrides, graphene analogs of group-IV elements, and the transition metal dichalcogenides (TMDCs). We accomplish this through a proposed mechanical bending scheme that eliminates the piezoelectric contribution to the total polarization, which enables us to directly measure the flexoelectric constants. While flat 2D materials like graphene have low flexoelectric constants due to weak π − σ interactions, buckling is found to increase the flexoelectric constants in monolayer group-IV elements. Finally, due to significantly enhanced charge transfer coupled with structural asymmetry due to bending, the TMDCs are found to have the largest flexoelectric constants, including MoS 2 having a flexoelectric constant ten times larger than graphene. read less NOT USED (low confidence) V. V. Hoang, N. H. Giang, and T. Q. Dong, “Confined tetra-silicene obtained by cooling from the melt,” Computational Materials Science. 2019. link Times cited: 12 NOT USED (low confidence) H. Nguyen and T. T. Hanh, “Melting process of zigzag boron nitride nanoribbon,” Physica E: Low-dimensional Systems and Nanostructures. 2019. link Times cited: 4 NOT USED (low confidence) B. Liu and K. Zhou, “Recent progress on graphene-analogous 2D nanomaterials: Properties, modeling and applications,” Progress in Materials Science. 2019. link Times cited: 208 NOT USED (low confidence) N. Hafsi, H. Bouridah, N. Boutaoui, and H. Haoues, “Structural characterization determination of silicon nanocrystals embedded in amorphous silicon nitride matrix from the effect of the light scattering,” Optik. 2019. link Times cited: 1 NOT USED (low confidence) J.-D. He and J.-W. Jiang, “Misfit strain-induced energy dissipation for graphene/MoS2 heterostructure nanomechanical resonators,” Nanotechnology. 2019. link Times cited: 8 Abstract: Misfit strain is inevitable in various heterostructures like… read moreAbstract: Misfit strain is inevitable in various heterostructures like the graphene/MoS2 van der Waals heterostructure. Although the misfit strain effect on electronic and other physical properties have been well studied, it is still unclear how the misfit strain will affect the performance of the nanomechanical resonator based on the graphene/MoS2 heterostructure. By performing molecular dynamics simulations, we disclose a misfit strain-induced decoupling phenomenon between the graphene layer and the MoS2 layer during the resonant oscillation of the heterostructure. A direct relationship between the misfit strain and the decoupling mechanism is successfully established through the retraction force analysis. We further suggest to use the graphene/MoS2/graphene sandwich heterostructure for the nanomechanical resonator application, which is able to prevent the misfit strain-related decoupling phenomenon. These results provide valuable information for the future application of the graphene/MoS2 heterostructure in the nanomechanical resonator field. read less NOT USED (low confidence) D. Fijan and M. Wilson, “Liquid state anomalies and the relationship to the crystalline phase diagram.,” Physical review. E. 2019. link Times cited: 5 Abstract: A relationship between the observation of a density anomaly … read moreAbstract: A relationship between the observation of a density anomaly and the underlying crystalline phase diagram is demonstrated. The crystal phase diagram and temperature of maximum density (TMD) lines are calculated over a range of parameter space using a Stillinger-Weber potential. Relationships between the loci of density maxima in the PT plane for the liquid state and the underlying crystalline phase diagram are investigated. Two key potential parameters are systematically varied in order to control the balance between the model two- and three-body interaction terms, and the relative effects of varying the potential parameters analyzed. The respective TMD lines diverge at extreme values with one set of lines showing a reentrant behavior. For each parameter set the TMD lines are extrapolated to T=0K. The corresponding pressures are related to the crystalline phase diagram and are found to lie on or near specific crystal-crystal coexistence lines for a wide range of potential parameters. The density anomaly is observed to vanish corresponding to regions in the crystal phase diagram which lack crystal-crystal coexistence lines potentially offering a new interpretation for the emergence of anomalous behavior. read less NOT USED (low confidence) R. Drautz, “Atomic cluster expansion for accurate and transferable interatomic potentials,” Physical Review B. 2019. link Times cited: 260 NOT USED (low confidence) Q. Wang, J. Chang, and H. Wang, “Thermophysical properties and atomic structure of liquid Si-Ge alloys,” Materials Chemistry and Physics. 2019. link Times cited: 8 NOT USED (low confidence) A. Gautam and A. Chandra, “A computational study of Stillinger–Weber silicon at 0.75 GPa in supercooled region,” International Journal of Modern Physics B. 2018. link Times cited: 0 Abstract: We studied the liquid-liquid transition in supercooled silic… read moreAbstract: We studied the liquid-liquid transition in supercooled silicon modeled by the Stillinger–Weber potential. The Isothermal Isobaric Monte Carlo (NPT-MC) simulation techniques were performed here to compute the free energy difference between the two liquid phases of silicon by Bennett Acceptance Ratio (BAR) method along with a reversible path at 0.75 GPa pressure and 970 K temperature. The thermodynamic properties as energy ([Formula: see text]) and density ([Formula: see text]) of the high-density liquid (HDL) phase have been computed here at different temperatures from 970–990 K. We also computed the entropy difference between the high-density liquid (HDL) and low-density liquid (LDL) phases which indicates that the glass transition temperature for the LDL phase is lower compared to the HDL phase. Further, by using the BAR method, we have computed the excess Gibbs free energy (G[Formula: see text]) of HDL phase with respect to the crystalline phase at different temperatures in the supercooled region of SW-Silicon potential model. Based on the slope of excess Gibbs free energy with respect to temperature (T), we found that the excess entropy (Se) of the HDL with respect to crystalline phase shows a nonmonotonic dependence on temperature at the liquid-liquid transition temperature of T[Formula: see text] = 970 K. Our results are in good agreement with the previous observation of a nonmonotonic dependence of the enthalpy on temperature in MD simulations, starting with the HDL phase at a temperature just above T[Formula: see text]. All these properties are useful to understand the phase behavior of supercooled silicon and can be applicable to identify the better quality of silicon for industrial uses. read less NOT USED (low confidence) L. Lindsay, C. Hua, X. Ruan, and S. Lee, “Survey of ab initio phonon thermal transport,” Materials Today Physics. 2018. link Times cited: 99 NOT USED (low confidence) F. Elahi, L. Ma, and Z. Hossain, “Heterogeneity governs diameter-dependent toughness and strength in SiC nanowires,” Physical Review B. 2018. link Times cited: 10 NOT USED (low confidence) M. Verdier, Y. Han, D. Lacroix, P. Chapuis, and K. Termentzidis, “Radial dependence of thermal transport in silicon nanowires,” Journal of Physics: Materials. 2018. link Times cited: 10 Abstract: A radial decomposition of the heat flux in a silicon crystal… read moreAbstract: A radial decomposition of the heat flux in a silicon crystalline nanowire is studied with molecular dynamics (MD) and Monte Carlo (MC) simulations. Less heat flux is carried in the external layer of nanowires than in the center. The difference between the center and the surface is of the order of 50% and 30% with MD and MC simulations, respectively. As a result, a heat flux close to the surface is 30% and 15% lower than the total axial heat flux in the structure. The physical mechanism behind is analyzed from partial contribution of each atom in each phonon mode calculated from lattice dynamics. The reduction of the flux close to the surface is related to back-scattering, the amorphous-like DOS of the external layer and flattened dispersion curves, thus lower phonon group velocities. Our study points to the need for cautions analysis of experimental determination of the thermal conductivity involving contact measurements, such as scanning thermal microscopy. read less NOT USED (low confidence) D. Limbu, R. Atta-Fynn, D. A. Drabold, S. Elliott, and P. Biswas, “Information-driven inverse approach to disordered solids: Applications to amorphous silicon,” Physical Review Materials. 2018. link Times cited: 7 Abstract: Diffraction data play an important role in the structural ch… read moreAbstract: Diffraction data play an important role in the structural characterizations of solids. While reverse Monte Carlo (RMC) and similar methods provide an elegant approach to (re)construct a three-dimensional model of noncrystalline solids, a satisfactory solution to the RMC problem is still not available. Following our earlier efforts, we present here an accurate structural solution of the inverse problem by developing an information-driven inverse approach (INDIA). The efficacy of the approach is illustrated by choosing amorphous silicon as an example, which is particularly difficult to model using total-energy-based relaxation methods. We demonstrate that, by introducing a subspace optimization technique that sequentially optimizes two objective functions (involving experimental diffraction data, a total-energy functional, and a few geometric constraints), it is possible to produce models of amorphous silicon with very little or no coordination defects and a pristine gap around the Fermi level in the electronic spectrum. The structural, electronic, and vibrational properties of the resulting INDIA models are shown to be fully compliant with experimental data from x-ray diffraction, Raman spectroscopy, differential scanning calorimetry, and inelastic neutron scattering measurements. A direct comparison of the models with those obtained from the Wooten-Winer-Weaire approach and from recent high-quality molecular-dynamics simulations is also presented. read less NOT USED (low confidence) X. Liu, J. Gao, G. Zhang, and Y.-W. Zhang, “Design of phosphorene/graphene heterojunctions for high and tunable interfacial thermal conductance.,” Nanoscale. 2018. link Times cited: 31 Abstract: Using density functional theory calculations and molecular d… read moreAbstract: Using density functional theory calculations and molecular dynamics simulations, we systematically explore various possible atomic structures of phosphorene/graphene in-plane heterojunctions and their effects on interfacial thermal conductance (ITC). Unlike the remarkable orientation-dependence of thermal conductivity in pure phosphorene, the ITC is much less orientation-dependent. In addition, the ITC is found to be high, comparable to those of graphene-MoS2 in-plane heterojunctions and chemically-bonded graphene-metal heterojunctions. Moreover, the ITC of armchair heterojunctions abnormally increases with tensile strain, while the zigzag heterojunctions simply follow the normal trend. To gain an in-depth understanding of these interesting observations, we further analyze the atomic topology and phonon vibrational spectrum and examine the nonlinear interfacial coupling in the heat transport, ITC anisotropy, and temperature effect on the ITC. Our findings suggest that phonon anharmonicity plays a critical role in the thermal transport behavior of two-dimensional in-plane heterojunctions. read less NOT USED (low confidence) R. Su and X. Zhang, “Size effect of thermal conductivity in monolayer graphene,” Applied Thermal Engineering. 2018. link Times cited: 27 NOT USED (low confidence) L. Zhang, D.-Y. Lin, H. Wang, R. Car, and E. Weinan, “Active Learning of Uniformly Accurate Inter-atomic Potentials for Materials Simulation,” ArXiv. 2018. link Times cited: 246 Abstract: An active learning procedure called Deep Potential Generator… read moreAbstract: An active learning procedure called Deep Potential Generator (DP-GEN) is proposed for the construction of accurate and transferable machine learning-based models of the potential energy surface (PES) for the molecular modeling of materials. This procedure consists of three main components: exploration, generation of accurate reference data, and training. Application to the sample systems of Al, Mg and Al-Mg alloys demonstrates that DP-GEN can produce uniformly accurate PES models with a minimal number of reference data. read less NOT USED (low confidence) L. Bonati and M. Parrinello, “Silicon Liquid Structure and Crystal Nucleation from Ab Initio Deep Metadynamics.,” Physical review letters. 2018. link Times cited: 10 Abstract: Studying the crystallization process of silicon is a challen… read moreAbstract: Studying the crystallization process of silicon is a challenging task since empirical potentials are not able to reproduce well the properties of both a semiconducting solid and metallic liquid. On the other hand, nucleation is a rare event that occurs in much longer timescales than those achievable by ab initio molecular dynamics. To address this problem, we train a deep neural network potential based on a set of data generated by metadynamics simulations using a classical potential. We show how this is an effective way to collect all the relevant data for the process of interest. In order to efficiently drive the crystallization process, we introduce a new collective variable based on the Debye structure factor. We are able to encode the long-range order information in a local variable which is better suited to describe the nucleation dynamics. The reference energies are then calculated using the strongly constrained and appropriately normed (SCAN) exchange-correlation functional, which is able to get a better description of the bonding complexity of the Si phase diagram. Finally, we recover the free energy surface with a density functional theory accuracy, and we compute the thermodynamics properties near the melting point, obtaining a good agreement with experimental data. In addition, we study the early stages of the crystallization process, unveiling features of the nucleation mechanism. read less NOT USED (low confidence) T. Zohdi, “Electrodynamic machine-learning-enhanced fault-tolerance of robotic free-form printing of complex mixtures,” Computational Mechanics. 2018. link Times cited: 15 NOT USED (low confidence) T. Zohdi, “Electrodynamic machine-learning-enhanced fault-tolerance of robotic free-form printing of complex mixtures,” Computational Mechanics. 2018. link Times cited: 0 NOT USED (low confidence) A. Bandura, S. I. Lukyanov, and R. Evarestov, “Temperature dependence of thermodynamic properties of MoS2 monolayer and single-wall nanotubes: Application of the developed three-body force field.,” Journal of molecular graphics & modelling. 2018. link Times cited: 4 NOT USED (low confidence) X. Zhuo and H. Beom, “Atomistic study of the bending properties of silicon nanowires,” Computational Materials Science. 2018. link Times cited: 13 NOT USED (low confidence) A. Gautam and A. Chandra, “A computational study of liquid–solid interfacial free energy (γ) for SW-Ge potential model,” Physica A: Statistical Mechanics and its Applications. 2018. link Times cited: 2 NOT USED (low confidence) J. Harrison, J. Schall, S. Maskey, P. Mikulski, M. T. Knippenberg, and B. Morrow, “Review of force fields and intermolecular potentials used in atomistic computational materials research,” Applied Physics Reviews. 2018. link Times cited: 99 Abstract: Molecular simulation is a powerful computational tool for a … read moreAbstract: Molecular simulation is a powerful computational tool for a broad range of applications including the examination of materials properties and accelerating drug discovery. At the heart of molecular simulation is the analytic potential energy function. These functions span the range of complexity from very simple functions used to model generic phenomena to complex functions designed to model chemical reactions. The complexity of the mathematical function impacts the computational speed and is typically linked to the accuracy of the results obtained from simulations that utilize the function. One approach to improving accuracy is to simply add more parameters and additional complexity to the analytic function. This approach is typically used in non-reactive force fields where the functional form is not derived from quantum mechanical principles. The form of other types of potentials, such as the bond-order potentials, is based on quantum mechanics and has led to varying levels of accuracy and transferability. When selecting a potential energy function for use in molecular simulations, the accuracy, transferability, and computational speed must all be considered. In this focused review, some of the more commonly used potential energy functions for molecular simulations are reviewed with an eye toward presenting their general forms, strengths, and weaknesses.Molecular simulation is a powerful computational tool for a broad range of applications including the examination of materials properties and accelerating drug discovery. At the heart of molecular simulation is the analytic potential energy function. These functions span the range of complexity from very simple functions used to model generic phenomena to complex functions designed to model chemical reactions. The complexity of the mathematical function impacts the computational speed and is typically linked to the accuracy of the results obtained from simulations that utilize the function. One approach to improving accuracy is to simply add more parameters and additional complexity to the analytic function. This approach is typically used in non-reactive force fields where the functional form is not derived from quantum mechanical principles. The form of other types of potentials, such as the bond-order potentials, is based on quantum mechanics and has led to varying levels of accuracy and transferabilit... read less NOT USED (low confidence) T. Sipkens and K. Daun, “Effect of Surface Interatomic Potential on Thermal Accommodation Coefficients Derived from Molecular Dynamics,” The Journal of Physical Chemistry C. 2018. link Times cited: 14 Abstract: This work investigates how the interatomic surface potential… read moreAbstract: This work investigates how the interatomic surface potential influences molecular dynamics (MD)-derived thermal accommodation coefficients (TACs). Iron, copper, and silicon surfaces are considered over a range of temperatures that include their melting points. Several classes of potentials are reviewed, including two-body, three-body, and bond-order force fields. MD-derived densities and visualization of the surfaces are used to explain the differences in the parameterizations of these potentials within the context of gas–surface scattering. Finally, TACs are predicted for a range of gas–surface combinations, and recommended values of the TAC are selected that take into account the robustness and uncertainties of each of the considered parameterizations. Further, it is observed that there is a significant change in the TAC about phase changes that must be taken into account for applications with a large range of surface temperatures. read less NOT USED (low confidence) X. Zhou and L. Chen, “Review on Multi-scale Simulation Methods,” IOP Conference Series: Materials Science and Engineering. 2018. link Times cited: 1 Abstract: It is by now widely recognized that not only natural but als… read moreAbstract: It is by now widely recognized that not only natural but also synthetic materials are inherently of hierarchical, multi-scale character important properties and material responses can arise at a myriad of length scales ranging from atomic to microscopic to mesoscopic to macroscopic. In this article, several multi-scale research methods were introduced, focusing on the basic principles of some comparatively advanced ones. Then their advantages and disadvantages were discussed. Finally, the future development of this method was predicted. read less NOT USED (low confidence) G. Lazzaroni and U. Stefanelli, “Chain-like ground states in three dimensions,” Transactions of Mathematics and Its Applications. 2018. link Times cited: 5 Abstract:
We investigate the minimization of configurational energie… read moreAbstract:
We investigate the minimization of configurational energies of Brenner type. These include two- and three-body interaction terms, which favor the alignment of first neighbors. In particular, such configurational energies arise in connection with the molecular-mechanical modeling of covalent$sp$-bonding in carbon. Ground states in three dimensions are characterized and the stability of chains and rings is discussed. The interaction energy is then augmented with terms corresponding to weaker interactions favoring the stratification of configurations. This gives rise to stratified structures, which are reminiscent of nanoscrolls and multi-wall nanotubes. Optimal stratified configurations are identified and their geometry is discussed. read less NOT USED (low confidence) A. K. Metya and J. Singh, “Ice Nucleation on a Graphite Surface in the Presence of Nanoparticles,” The Journal of Physical Chemistry C. 2018. link Times cited: 5 Abstract: In this work, we have carried out a systematic study of nucl… read moreAbstract: In this work, we have carried out a systematic study of nucleation of a supercooled nanofluid droplet on a graphite substrate using molecular dynamics simulations. In particular, the effect of nanoparticle (NP) loading (φs up to 12.0 vol %) in the supercooled liquid and the interaction strength between water and NP (ϵNP–W) on the behavior of ice nucleation is investigated. At lower ϵNP–W, the nucleation rate is indifferent, while at higher ϵNP–W, the nucleation rate is found to reduce with the addition of nanoparticles. We found the maximum rate of ice nucleation is at φs = 1.91% and ϵNP–W = 0.40 kcal/mol, which is approximately 45 times more than that seen in the bulk water. We present in detail the effect of nanoparticle and nanoparticle–water interactions on the structure and composition of ice. The results demonstrate that the number of ice-like water molecules in the nanofluid droplet decreases with increasing φs and ϵNP–W, which correlates well with the lowering of the rate of ice nucleation at high... read less NOT USED (low confidence) A. Vasin, F. Oliveira, M. Cerqueira, J. Schulze, and M. Vasilevskiy, “Structural and vibrational properties of SnxGe1-x: Modeling and experiments,” Journal of Applied Physics. 2018. link Times cited: 7 Abstract: The effects of the composition and macroscopic strain on the… read moreAbstract: The effects of the composition and macroscopic strain on the structural properties and lattice vibrations of SnxGe1-x solid solutions (SSs) are investigated numerically, employing Tersoff empirical inter-atomic potentials, and experimentally. The calculations provide statistical distributions of bond lengths, pair correlation function, and vibrational Raman spectra of the SSs. Using this approach, we are able to evaluate the tin-content-dependent shifts due to the local environment (i.e., changes in the atomic mass and bond stiffness) and strain effects in the calculated Raman spectra and compare them to experimental data. The relative importance of the composition dependent effects of the local environment and strain for epitaxial layers of GeSn solid solutions is analysed.The effects of the composition and macroscopic strain on the structural properties and lattice vibrations of SnxGe1-x solid solutions (SSs) are investigated numerically, employing Tersoff empirical inter-atomic potentials, and experimentally. The calculations provide statistical distributions of bond lengths, pair correlation function, and vibrational Raman spectra of the SSs. Using this approach, we are able to evaluate the tin-content-dependent shifts due to the local environment (i.e., changes in the atomic mass and bond stiffness) and strain effects in the calculated Raman spectra and compare them to experimental data. The relative importance of the composition dependent effects of the local environment and strain for epitaxial layers of GeSn solid solutions is analysed. read less NOT USED (low confidence) A. Hudait, D. R. Moberg, Y. Qiu, N. Odendahl, F. Paesani, and V. Molinero, “Preordering of water is not needed for ice recognition by hyperactive antifreeze proteins,” Proceedings of the National Academy of Sciences. 2018. link Times cited: 71 Abstract: Significance Antifreeze proteins have evolved to inhibit ice… read moreAbstract: Significance Antifreeze proteins have evolved to inhibit ice growth in organisms living at subfreezing temperatures; the mechanism by which these proteins recognize and bind ice is not understood. It has been proposed that antifreeze proteins recognize ice by preordering water at the ice-binding site already in solution. Here we use multiresolution molecular simulations to demonstrate that preordering of interfacial water is not needed for ice recognition by antifreeze proteins. We predict that preordering could emerge on the large ice-binding surfaces of aggregates of ice-nucleating proteins, where it may assist with ice nucleation. Antifreeze proteins (AFPs) inhibit ice growth in organisms living in cold environments. Hyperactive insect AFPs are particularly effective, binding ice through “anchored clathrate” motifs. It has been hypothesized that the binding of hyperactive AFPs to ice is facilitated by preordering of water at the ice-binding site (IBS) of the protein in solution. The antifreeze protein TmAFP displays the best matching of its binding site to ice, making it the optimal candidate to develop ice-like order in solution. Here we use multiresolution simulations to unravel the mechanism by which TmAFP recognizes and binds ice. We find that water at the IBS of the antifreeze protein in solution does not acquire ice-like or anchored clathrate-like order. Ice recognition occurs by slow diffusion of the protein to achieve the proper orientation with respect to the ice surface, followed by fast collective organization of the hydration water at the IBS to form an anchored clathrate motif that latches the protein to the ice surface. The simulations suggest that anchored clathrate order could develop on the large ice-binding surfaces of aggregates of ice-nucleating proteins (INP). We compute the infrared and Raman spectra of water in the anchored clathrate motif. The signatures of the OH stretch of water in the anchored clathrate motif can be distinguished from those of bulk liquid in the Raman spectra, but not in the infrared spectra. We thus suggest that Raman spectroscopy may be used to probe the anchored clathrate order at the ice-binding surface of INP aggregates. read less NOT USED (low confidence) A. Bourque and G. Rutledge, “Heterogeneous nucleation of an n-alkane on graphene-like materials,” European Polymer Journal. 2018. link Times cited: 17 NOT USED (low confidence) L. Wang and K. Cai, “Absorption and temperature effects on the tensile strength of a black phosphorus ribbon in argon environment,” Computational Materials Science. 2018. link Times cited: 6 NOT USED (low confidence) X. Duan, B. He, M. Guo, Z. Liu, Y. Wen, and B. Shan, “Lattice inversion modified embedded atom method for FCC metals,” Computational Materials Science. 2018. link Times cited: 8 NOT USED (low confidence) W. Smith, I. Nezbeda, J. Kolafa, and F. Moučka, “Recent progress in the molecular simulation of thermodynamic properties of aqueous electrolyte solutions,” Fluid Phase Equilibria. 2018. link Times cited: 55 NOT USED (low confidence) Y. Dai and X. Xu, “New Nanostructure in a Metastable Ice Phase,” The Journal of Physical Chemistry C. 2018. link Times cited: 2 Abstract: Hydrogen bonds between water molecules can form a polygonal … read moreAbstract: Hydrogen bonds between water molecules can form a polygonal structure, which determine the physical properties of different ice phases. Pure pentagonal rings are not stable in crystal ice. In this work, we discover a new nanostructure of ice in heterogeneous nucleation on metal surfaces by molecular dynamic simulation. In this nanostructure, pentagonal rings are connected by dodecahedrons and staggered hydrogen bonds. The presence of dodecahedrons could help the stability of ice structure with pentagons. This nanostructure serves as a skeleton unit in ice. Our results provide a new explanation for the existence of pentagonal rings in ice, which are helpful to understand the complex ice phase behaviors. read less NOT USED (low confidence) J. Guo, A. Haji-Akbari, and J. Palmer, “Hybrid Monte Carlo with LAMMPS,” Journal of Theoretical and Computational Chemistry. 2018. link Times cited: 9 Abstract: We describe a strategy for performing canonical and isotherm… read moreAbstract: We describe a strategy for performing canonical and isothermal-isobaric ensemble hybrid Monte Carlo (HMC) simulations with the widely-used Large-scale Atomic/Molecular Massively Parallel Simulator ... read less NOT USED (low confidence) A. Dasmahapatra and P. Kroll, “Modeling amorphous silicon nitride: A comparative study of empirical potentials,” Computational Materials Science. 2018. link Times cited: 12 NOT USED (low confidence) F. Krause, D. Bredemeier, M. Schowalter, T. Mehrtens, T. Grieb, and A. Rosenauer, “Using molecular dynamics for multislice TEM simulation of thermal diffuse scattering in AlGaN.,” Ultramicroscopy. 2018. link Times cited: 13 NOT USED (low confidence) F. González-Cataldo, F. Corvacho, and G. Gutiérrez, “Melting curve of Si by means of the Z-method,” Journal of Physics: Conference Series. 2018. link Times cited: 1 Abstract: The melting curve of silicon is investigated through classic… read moreAbstract: The melting curve of silicon is investigated through classical molecular dynamics simulations. We explore pressures from 0 to 20 GPa using the EDIP, Stillinger-Weber, and Tersoff interactomic potentials. Using the Z method, we demonstrate that the predicted melting temperature Tm can be significantly overestimated, depending on the potential chosen. Our results show that none of the potentials explored is able to reproduce the experimental melting curve of silicon by means of the Z-method. However, the EDIP potential does predict the change in the Clapeyron slope, associated with the diamond to β-tin phase transition. read less NOT USED (low confidence) T. Majdi, S. Pal, A. Hafreager, S. Murad, R. Sahu, and I. Puri, “Altering thermal transport by strained-layer epitaxy,” Applied Physics Letters. 2018. link Times cited: 4 Abstract: Since strain changes the interatomic spacing of matter and a… read moreAbstract: Since strain changes the interatomic spacing of matter and alters electron and phonon dispersion, an applied strain can modify the thermal conductivity k of a material. We show how the strain induced by heteroepitaxy is a passive mechanism to change k in a thin film. Molecular dynamics simulations of the deposition and epitaxial growth of ZnTe thin films provide insights into the role of interfacial strain in the conductivity of a deposited film. ZnTe films grow strain-free on lattice-matched ZnTe substrates, but similar thin films grown on a lattice-mismatched CdTe substrate exhibit ∼6% biaxial in-plane tensile strain and ∼7% uniaxial out-of-plane compressive strain. In the T = 700 K–1100 K temperature range, the conductivities of strained ZnTe layers decrease to ∼60% of their unstrained values. The resulting understanding of dk/dT shows that strain engineering can be used to alter the performance of a thermal rectifier and also provides a framework for enhancing thermoelectric devices. read less NOT USED (low confidence) N. T. Long, H. A. Huy, T. Q. Tuan, O. K. Le, V. V. Hoang, and N. H. Giang, “Crystallization of supercooled liquid and amorphous silicene,” Journal of Non-crystalline Solids. 2018. link Times cited: 5 NOT USED (low confidence) M. Radek, J.-G. Tenberge, S. Hilke, G. Wilde, and M. Peterlechner, “STEMcl-A multi-GPU multislice algorithm for simulation of large structure and imaging parameter series.,” Ultramicroscopy. 2018. link Times cited: 7 NOT USED (low confidence) G. Fugallo and L. Colombo, “Corrigendum: Calculating lattice thermal conductivity: a synopsis (2018 Phys. Scr. 93 043002),” Physica Scripta. 2018. link Times cited: 2 Abstract: visually comparing the bottom panel of the published version… read moreAbstract: visually comparing the bottom panel of the published version of fi gure 13 with the corresponding bottom panel of the same fi gure in the present corrigendum it is apparent that a graphical error occurred, whereby only the present version of the fi gure correctly reports the temperature pro fi le ( corresponding to the blue line in ( c )) found in the stationary state of thermal conduction consistent with the assigned boundary conditions. We remark that fi gure 13 ( c ) is not the output of any calculation, but just represents the graphical conceptualization of a given ther-modynamical situation. We fi nally state that the scien-ti fi c content discussed in the paper is not affected by this graphical error. read less NOT USED (low confidence) A. Cherala and S. Sreenivasan, “Molecular dynamics modeling framework for overcoming nanoshape retention limits of imprint lithography,” Microsystems & Nanoengineering. 2018. link Times cited: 4 NOT USED (low confidence) T. Zohdi, “Laser-induced heating of dynamic particulate depositions in additive manufacturing,” Computer Methods in Applied Mechanics and Engineering. 2018. link Times cited: 14 NOT USED (low confidence) Y. A. Kosevich, L. G. Potyomina, A. Darinskii, and I. Strelnikov, “Phonon interference control of atomic-scale metamirrors, meta-absorbers, and heat transfer through crystal interfaces,” Physical Review B. 2018. link Times cited: 5 NOT USED (low confidence) H. Dong, Z. Fan, L. Shi, A. Harju, and T. Ala-Nisilla, “Equivalence of the equilibrium and the nonequilibrium molecular dynamics methods for thermal conductivity calculations: From bulk to nanowire silicon,” Physical Review B. 2018. link Times cited: 43 Abstract: © 2018 American Physical Society. Molecular dynamics (MD) si… read moreAbstract: © 2018 American Physical Society. Molecular dynamics (MD) simulations play an important role in studying heat transport in complex materials. The lattice thermal conductivity can be computed either using the Green-Kubo formula in equilibrium MD (EMD) simulations or using Fourier's law in nonequilibrium MD (NEMD) simulations. These two methods have not been systematically compared for materials with different dimensions and inconsistencies between them have been occasionally reported in the literature. Here we give an in-depth comparison of them in terms of heat transport in three allotropes of Si: three-dimensional bulk silicon, two-dimensional silicene, and quasi-one-dimensional silicon nanowire. By multiplying the correlation time in the Green-Kubo formula with an appropriate effective group velocity, we can express the running thermal conductivity in the EMD method as a function of an effective length and directly compare it to the length-dependent thermal conductivity in the NEMD method. We find that the two methods quantitatively agree with each other for all the systems studied, firmly establishing their equivalence in computing thermal conductivity. read less NOT USED (low confidence) S. Prestipino, “The barrier to ice nucleation in monatomic water.,” The Journal of chemical physics. 2018. link Times cited: 19 Abstract: Crystallization from a supercooled liquid initially proceeds… read moreAbstract: Crystallization from a supercooled liquid initially proceeds via the formation of a small solid embryo (nucleus), which requires surmounting an activation barrier. This phenomenon is most easily studied by numerical simulation, using specialized biased-sampling techniques to overcome the limitations imposed by the rarity of nucleation events. Here, I focus on the barrier to homogeneous ice nucleation in supercooled water, as represented by the monatomic-water model, which in the bulk exhibits a complex interplay between different ice structures. I consider various protocols to identify solidlike particles on a computer, which perform well enough for the Lennard-Jones model, and compare their respective impact on the shape and height of the nucleation barrier. It turns out that the effect is stronger on the nucleus size than on the barrier height. As a by-product of the analysis, I determine the structure of the nucleation cluster, finding that the relative amount of ice phases in the cluster heavily depends on the method used for classifying solidlike particles. Moreover, the phase which is most favored during the earlier stages of crystallization may happen, depending on the nucleation coordinate adopted, to be different from the stable polymorph. Therefore, the quality of a reaction coordinate cannot be assessed simply on the basis of the barrier height obtained. I explain how this outcome is possible and why it just points out the shortcoming of collective variables appropriate to simple fluids in providing a robust method of particle classification for monatomic water. read less NOT USED (low confidence) D. Shen, G. Zou, L. Liu, A. Wu, W. Duley, and Y. Zhou, “Investigation of impact and spreading of molten nanosized gold droplets on solid surfaces.,” Applied optics. 2018. link Times cited: 5 Abstract: Understanding the impact dynamics and spreading of molten na… read moreAbstract: Understanding the impact dynamics and spreading of molten nanosized droplets on a solid surface is a crucial step towards the design and control of nano-fabrication in many novel applications of nanotechnology. In this context, molecular dynamic (MD) simulations have been conducted to compute temperature and dynamic contact angles of nano-droplets during impact. The evolution of the morphology of a molten metallic nano-droplet impacting on a substrate has been studied using a combination of experimental and simulation techniques. Femtosecond lasers have been used to transfer nanosized gold droplets. Droplet morphology calculated in MD simulations is found to be in good agreement with that seen in scanning electron microscopy (SEM) images. It is found that the spreading of nanoscale molten gold droplets upon impact is enhanced by increasing the droplet impact energy. As observed in experimental data, MD simulation results show that a high droplet-substrate heat transfer rate together with increased wettability of the substrate facilitates spreading and results in a thinner metal deposit after solidification. read less NOT USED (low confidence) R. Atta-Fynn and P. Biswas, “Nearly defect-free dynamical models of disordered solids: The case of amorphous silicon.,” The Journal of chemical physics. 2018. link Times cited: 17 Abstract: It is widely accepted in the materials modeling community th… read moreAbstract: It is widely accepted in the materials modeling community that defect-free realistic networks of amorphous silicon cannot be prepared by quenching from a molten state of silicon using classical or ab initio molecular-dynamics (MD) simulations. In this work, we address this long-standing problem by producing nearly defect-free ultra-large models of amorphous silicon, consisting of up to half a million atoms, using classical MD simulations. The structural, topological, electronic, and vibrational properties of the models are presented and compared with experimental data. A comparison of the models with those obtained from using the modified Wooten-Winer-Weaire bond-switching algorithm shows that the models are on par with the latter, which were generated via event-based total-energy relaxations of atomistic networks in the configuration space. The MD models produced in this work represent the highest quality of amorphous-silicon networks so far reported in the literature using MD simulations. read less NOT USED (low confidence) A. K. Ivanov-Schitz and G. Mazo, “Atomistic Simulation of Interfaces in Materials of Solid State Ionics,” Crystallography Reports. 2018. link Times cited: 2 NOT USED (low confidence) Z. Rashid, L. Zhu, and W. Li, “Effect of confinement on anharmonic phonon scattering and thermal conductivity in pristine silicon nanowires,” Physical Review B. 2018. link Times cited: 7 NOT USED (low confidence) R. S. DeFever and S. Sarupria, “Surface chemistry effects on heterogeneous clathrate hydrate nucleation: A molecular dynamics study,” The Journal of Chemical Thermodynamics. 2018. link Times cited: 16 NOT USED (low confidence) T. Gao et al., “Crystalline structures and defects in liquid GaN during rapid cooling processes,” Materials Science in Semiconductor Processing. 2018. link Times cited: 6 NOT USED (low confidence) A. Soleimani, H. Araghi, Z. Zabihi, and A. Alibakhshi, “A comparative study of molecular dynamics simulation methods for evaluation of the thermal conductivity and phonon transport in Si nanowires,” Computational Materials Science. 2018. link Times cited: 21 NOT USED (low confidence) K. Chu, J. Gruber, X. W. Zhou, R. Jones, S. R. Lee, and G. Tucker, “Molecular dynamics studies of InGaN growth on nonpolar (11 2 \xAF0 ) GaN surfaces,” Physical Review Materials. 2018. link Times cited: 8 NOT USED (low confidence) L. Sementa, G. Barcaro, S. Monti, and V. Carravetta, “Molecular dynamics simulations of melting and sintering of Si nanoparticles: a comparison of different force fields and computational models.,” Physical chemistry chemical physics : PCCP. 2018. link Times cited: 17 Abstract: Melting and sintering of silicon nanoparticles are investiga… read moreAbstract: Melting and sintering of silicon nanoparticles are investigated by means of classical molecular dynamics simulations to disclose the dependence of modelling on the system type, the simulation procedure and interaction potential. The capability of our parametrization of a reactive force field ReaxFF to describe such processes is assessed through a comparison with formally simpler Stillinger-Weber and Tersoff potentials, which are frequently used for simulating silicon-based materials. A substantial dependence of both the predicted melting point and its variation as a function of the nanoparticle size on the simulation model is also highlighted. The outcomes of the molecular dynamics simulations suggest that the trend of the nanoparticulate sintering/coalescence time vs. temperature could provide a valid tool to determine the melting points of nanoparticles theoretically/experimentally. read less NOT USED (low confidence) L. Rovigatti, G. Nava, T. Bellini, and F. Sciortino, “Self-Dynamics and Collective Swap-Driven Dynamics in a Particle Model for Vitrimers,” Macromolecules. 2018. link Times cited: 37 Abstract: We numerically investigate the self-dynamics and collective … read moreAbstract: We numerically investigate the self-dynamics and collective dynamics of a simple model for vitrimers—polymeric covalent networks that have the ability to dynamically rearrange the bond structure via exchange reactions, preserving the total connectivity. Specifically, we study a binary mixture of tetrafunctional and bifunctional particles by means of molecular dynamics simulations that naturally incorporate the bond-swapping mechanism. We specifically focus on the dynamics at small wavevector q by simulating 800 000 particles. We observe two distinct collective relaxation processes: (i) a fast vibrational damped mode and (ii) a slow network restructuring dynamics. Unexpectedly, the slow process is characterized by a wavevector-independent (q0) mode originating from the swap motion of the bonds. read less NOT USED (low confidence) L. Feng, T. Shiga, H. Han, S. Ju, Y. Kosevich, and J. Shiomi, “Phonon-interference resonance effects in nanoparticles embedded in a matrix,” arXiv: Computational Physics. 2017. link Times cited: 19 Abstract: We report an unambiguous phonon resonance effect originating… read moreAbstract: We report an unambiguous phonon resonance effect originating from germanium nanoparticles embedded in silicon matrix. Our approach features the combination of phonon wave-packet method with atomistic dynamics and finite element method rooted in continuum theory. We find that multimodal phonon resonance, caused by destructive interference of coherent lattice waves propagating through and around the nanoparticle, gives rise to sharp and significant transmittance dips, blocking the lower-end frequency range of phonon transport that is hardly diminished by other nanostructures. The resonance is sensitive to the phonon coherent length, where the finiteness of the wave packet width weakens the transmittance dip even when coherent length is longer than the particle diameter. Further strengthening of transmittance dips are possible by arraying multiple nanoparticles that gives rise to the collective vibrational mode. Finally, it is demonstrated that these resonance effects can significantly reduce thermal conductance in the lower-end frequency range. read less NOT USED (low confidence) T. Gao, Y. Li, Z. Yao, X. Hu, and Q. Xie, “Properties of tetrahedral clusters and medium range order in GaN during rapid solidification,” Superlattices and Microstructures. 2017. link Times cited: 3 NOT USED (low confidence) J. Jiang and L. Wang, “Timoshenko beam model for vibrational analysis of double-walled carbon nanotubes bridged on substrate,” Current Applied Physics. 2017. link Times cited: 9 NOT USED (low confidence) H. Xiang, H. Li, and X. Peng, “Comparison of different interatomic potentials for MD simulations of AlN,” Computational Materials Science. 2017. link Times cited: 21 NOT USED (low confidence) K. Huang et al., “A unified and universal Griffith-based criterion for brittle fracture,” International Journal of Solids and Structures. 2017. link Times cited: 33 NOT USED (low confidence) H. Dret and A. Raoult, “Hexagonal lattices with three-point interactions,” Journal de Mathématiques Pures et Appliquées. 2017. link Times cited: 4 NOT USED (low confidence) R. Frieling and H. Bracht, “Thermal transport across isotopic 28Si/mSi interfaces,” Computational Materials Science. 2017. link Times cited: 1 NOT USED (low confidence) E. Halac, M. Reinoso, and E. Burgos, “Study of bi-dimensional materials using a semi-empirical potential including a torsional term,” Chemical Physics Letters. 2017. link Times cited: 0 NOT USED (low confidence) J. Shi, K. Cai, L. Liu, and Q. Qin, “Self-assembly of a parallelogram black phosphorus ribbon into a nanotube,” Scientific Reports. 2017. link Times cited: 12 NOT USED (low confidence) I. Klett and B. Rethfeld, “Relaxation of a nonequilibrium phonon distribution induced by femtosecond laser irradiation,” Physical Review B. 2017. link Times cited: 11 Abstract: Ultrafast laser irradiation of solids leads to a thermodynam… read moreAbstract: Ultrafast laser irradiation of solids leads to a thermodynamic nonequilibrium within and between the electron and phonon subsystems of the material. Due to electron-electron and phonon-phonon collisions, both subsystems relax into respective new thermodynamic equilibria within a characteristic thermalization time, which is different for each one of them. Moreover, they equilibrate their temperatures by electron phonon coupling. The relaxation of the electronic nonequilibrium and its effect on the electron phonon coupling was subject to a number of studies and it is comparably well understood, while the nonequilibrium within the phononic subsystem is usually neglected and its influence of the nonequilibrium phonons on other relaxation processes is unclear. Our calculations show significant differences in the energy transfer rate between the electrons and the phonons depending whether a nonequilibrium distribution is assumed for the phonons or not. Here, we present a model to study the relaxation of the nonequilibrium phonon subsystem. Collisions between phonons are described within the frame of Boltzmann integrals. From this, an energy-dependent relaxation time can be extracted and inserted into a relaxation-time approach. Within the frame of this model, we study the thermalization of a phonon distribution induced by ultrafast laser irradiation. We show, that the thermalization time of such a distribution is of the order of some hundreds of picoseconds. Moreover, we discuss the energy transfer between Fermi-distributed electrons and nonequilibrium phonons and compare this to the energy transfer for equilibrium distributions in both subsystems. read less NOT USED (low confidence) C. Scherer and D. Andrienko, “Understanding three-body contributions to coarse-grained force fields.,” Physical chemistry chemical physics : PCCP. 2017. link Times cited: 22 Abstract: Coarse-graining is a systematic reduction of the number of d… read moreAbstract: Coarse-graining is a systematic reduction of the number of degrees of freedom used to describe a system of interest. Coarse-graining can be thought of as a projection on the coarse-grained degrees of freedom and is therefore dependent on the number and type of basis functions used to represent the coarse-grained force field. We show that many-body extensions of the coarse-grained force field can result in substantial changes of the two-body interactions, making them much more attractive at short distances. This interplay can be alleviated by first parametrizing the two-body potential and then fitting the additional three-body contribution to the residual forces. The approach is illustrated on liquid water where three-body interactions are essential to reproduce the structural properties, and liquid methanol where two-body interactions are sufficient to reproduce the main structural features of the atomistic system. Furthermore, we demonstrate that the structural and thermodynamic accuracy of the coarse-grained models can be controlled by varying the magnitude of the three-body interactions. Our findings motivate basis set extensions which separate the many-body contributions of different order. read less NOT USED (low confidence) Y. Wang, X. Zhou, W. Yuan, and Y. Shou, “A 3-D conjugated bond-pair-based peridynamic formulation for initiation and propagation of cracks in brittle solids,” International Journal of Solids and Structures. 2017. link Times cited: 250 NOT USED (low confidence) D. Fijan and M. Wilson, “The characterisation of the ‘X’ crystal structure in the Stillinger-Weber potential,” Chemical Physics Letters. 2017. link Times cited: 2 NOT USED (low confidence) L. Jaillet, S. Artemova, and S. Redon, “IM-UFF: Extending the universal force field for interactive molecular modeling.,” Journal of molecular graphics & modelling. 2017. link Times cited: 31 NOT USED (low confidence) A. Kumar and V. Molinero, “Self-Assembly of Mesophases from Nanoparticles.,” The journal of physical chemistry letters. 2017. link Times cited: 27 Abstract: A growing number of crystalline and quasi-crystalline struct… read moreAbstract: A growing number of crystalline and quasi-crystalline structures have been formed by coating nanoparticles with ligands, polymers, and DNA. The design of nanoparticles that assemble into mesophases, such as those formed by block copolymers, would combine the order, mobility, and stimuli responsive properties of mesophases with the electronic, magnetic, and optical properties of nanoparticles. Here we use molecular simulations to demonstrate that binary mixtures of unbound particles with simple short-ranged pair interactions produce the same mesophases as block copolymers and surfactants, including lamellar, hexagonal, gyroid, body-centered cubic, face-centered cubic, perforated lamellar, and semicrystalline phases. The key to forming the mesophases is the frustrated attraction between particles of different types, achieved through control over interparticle size and over strength and softness of the interaction. Experimental design of nanoparticles with effective interactions described by the potentials of this work would provide a distinct, robust route to produce ordered tunable liquid crystalline mesophases from nanoparticles. read less NOT USED (low confidence) A. Giri and P. Hopkins, “Role of interfacial mode coupling of optical phonons on thermal boundary conductance,” Scientific Reports. 2017. link Times cited: 15 NOT USED (low confidence) D. Niu, L. Guo, H. Hu, and G. Tang, “Dropwise condensation heat transfer model considering the liquid-solid interfacial thermal resistance,” International Journal of Heat and Mass Transfer. 2017. link Times cited: 42 NOT USED (low confidence) S.-Y. Xiong and G. Cao, “Continuum thin-shell model of the anisotropic two-dimensional materials: Single-layer black phosphorus,” Extreme Mechanics Letters. 2017. link Times cited: 13 NOT USED (low confidence) G. Giannopoulos and S. K. Georgantzinos, “Tensile behavior of gallium nitride monolayer via nonlinear molecular mechanics,” European Journal of Mechanics A-solids. 2017. link Times cited: 3 NOT USED (low confidence) F. Lehnert and S. G. Mayr, “Nanoporous amorphous Ge-Si alloys - unraveling the physics behind ion beam induced morphogenesis.,” Physical chemistry chemical physics : PCCP. 2017. link Times cited: 2 Abstract: Despite a high technical relevance and 35 years of observati… read moreAbstract: Despite a high technical relevance and 35 years of observation, self-organized morphogenesis of nanoporous sponge-like amorphous structures during exposure of selected covalent materials to energetic ions is still insufficiently understood. Due to the presence and absence of these effects in amorphous Ge and Si, respectively, the Ge-Si alloy system constitutes an ideal testbed to track down the underlying physics at the atomic scale. This is realized within the present study by a combination of tailored experiments and extensive molecular dynamics computer modeling. The swelling capabilities of a variety of interaction potentials for the Ge-Si system and its elemental constituents are scrutinized with respect to the experimental observations and related to relevant physical properties of the model systems. This allows to identify defect kinetics in combination with a moderate radiation induced fluidity as key ingredients for nanopore morphogenesis. Cast in a simple quantitative model, it enables to account for both experimental as well as computational results, thus paving the way for a design by understanding approach in synthesis. read less NOT USED (low confidence) N. Korobeishchikov, P. Stishenko, Y. Popenko, M. Roenko, and I. Nikolaev, “Interaction of accelerated argon cluster ions with a silicon dioxide surface.” 2017. link Times cited: 9 Abstract: Gas cluster ion beams bring new opportunities for diagnostic… read moreAbstract: Gas cluster ion beams bring new opportunities for diagnostics and modification of materials surfaces. In this work impact of argon clusters on silicon dioxide has been studied by molecular dynamics simulations and experimentally. We have obtained dependencies of crater size and the SiO2 sputtering yield on cluster size and specific energy. High reactive selectivity of sputtered products has been revealed for a high specific energy of clusters. It can cause modification of the target surface layer composition in case of long time irradiation. Peculiarities of experimental and computational data matching have been discussed.Gas cluster ion beams bring new opportunities for diagnostics and modification of materials surfaces. In this work impact of argon clusters on silicon dioxide has been studied by molecular dynamics simulations and experimentally. We have obtained dependencies of crater size and the SiO2 sputtering yield on cluster size and specific energy. High reactive selectivity of sputtered products has been revealed for a high specific energy of clusters. It can cause modification of the target surface layer composition in case of long time irradiation. Peculiarities of experimental and computational data matching have been discussed. read less NOT USED (low confidence) X. Zhou, Y. Wang, Y. Shou, and M. Kou, “A novel conjugated bond linear elastic model in bond-based peridynamics for fracture problems under dynamic loads,” Engineering Fracture Mechanics. 2017. link Times cited: 69 NOT USED (low confidence) Z.-Q. Ye and B. Cao, “Thermal rectification at the bimaterial nanocontact interface.,” Nanoscale. 2017. link Times cited: 17 Abstract: Thermal rectification can help develop modern thermal manipu… read moreAbstract: Thermal rectification can help develop modern thermal manipulation devices but has been rarely engineered. Here, we validated the nanoscale bimaterial interface-induced thermal rectification experimentally for the first time and investigated its underlying mechanism via molecular dynamics simulations. The thermal diode consists of polyamide (PA) and silicon (Si) nanowires in contact with each other. The thermal rectification ratio measured by a high-precision nanoscale experiment reached 4% with an uncertainty of <1%. The temperature has little influence on the ratio, while the decrease in contact length or increase in temperature differences can increase the ratio. The molecular dynamics simulations further confirmed the thermal rectification in the PA/Si nanowires. We found that the localized modes generally gather on the edge, and the higher extent of phonon localization is responsible for the lower thermal conductance in the thermal rectification. Our findings not only have guiding significance, but can also promote the development of interface-based solid-state thermal diodes. read less NOT USED (low confidence) 黄建平 and 唐婧, “硅晶体原子间相互作用力常数的计算与负热膨胀机制的研究 Calculations of the Interatomic Force Constants and Study on the Mechanism of Negative Thermal Expansion of Silicon Crystal,” Open Journal of Nature Science. 2017. link Times cited: 0 Abstract: 本文根据Rignanese等人基于第一性原理得到的硅晶体中原子间的力常数矩阵元,计算了两体和三体线性力常数,再将这些线性… read moreAbstract: 本文根据Rignanese等人基于第一性原理得到的硅晶体中原子间的力常数矩阵元,计算了两体和三体线性力常数,再将这些线性力常数对原子间距求导数得两体和三体非线性力常数,在此基础上运用硅晶体的热膨胀系数公式计算了其热膨胀系数。计算结果与实验结果很好地吻合,这表明硅晶体的各个线性和非线性力常数是正确的。计算结果还表明,硅晶体的两体非线性力常数为负,两体势引起了正热膨胀,而三体非线性力常数为正,三体势引起负热膨胀,且低温时负热膨胀效应大于正热膨胀效应,因而总体上呈现低温负热膨性质。 The two-body and three-body linear force constants in silicon crystal were calculated based on the interatomic force constant matrix elements obtained by Rignanese with the ab initio method, and then the two-body and three-body non-linear force constants were obtained by derivate the corresponding linear force constants with respect to bond length. Finally, the thermal expansion coefficients of silicon crystal were calculated based on these force constants and formula for thermal expansion coefficients of silicon crystal, and the calculated results are in good agreement with experimental results, it means that the results of all the linear and non-linear force constants are correct. It is also found that the thermal expansion caused by two-body potential is positive because of the negative two-body non-linear force constant, the thermal expansion caused by three-body potential is negative because of the positive three-body non-linear force constant, and at low temperature the total thermal expansion is negative because the absolute value of thermal expansion caused by three-body potential is greater than thermal expansion caused by two-body potential. read less NOT USED (low confidence) Y. Wang, X. Zhou, and Y. Shou, “The modeling of crack propagation and coalescence in rocks under uniaxial compression using the novel conjugated bond-based peridynamics,” International Journal of Mechanical Sciences. 2017. link Times cited: 187 NOT USED (low confidence) L. Zhang, J. Han, H. Wang, R. Car, and E. Weinan, “Deep Potential Molecular Dynamics: a scalable model with the accuracy of quantum mechanics,” Physical review letters. 2017. link Times cited: 785 Abstract: We introduce a scheme for molecular simulations, the deep po… read moreAbstract: We introduce a scheme for molecular simulations, the deep potential molecular dynamics (DPMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data. The neural network model preserves all the natural symmetries in the problem. It is first-principles based in the sense that there are no ad hoc components aside from the network model. We show that the proposed scheme provides an efficient and accurate protocol in a variety of systems, including bulk materials and molecules. In all these cases, DPMD gives results that are essentially indistinguishable from the original data, at a cost that scales linearly with system size. read less NOT USED (low confidence) J. Fu, B. Cao, S. H. Hamdar, and T. Li, “Towards Safer Pedestrian Traffic: Investigation of the Impact of Social Field Characteristic on Crowd Dynamics,” Traffic and Granular Flow ’17. 2017. link Times cited: 0 NOT USED (low confidence) A. Haji-Akbari and P. Debenedetti, “Perspective: Surface freezing in water: A nexus of experiments and simulations.,” The Journal of chemical physics. 2017. link Times cited: 18 Abstract: Surface freezing is a phenomenon in which crystallization is… read moreAbstract: Surface freezing is a phenomenon in which crystallization is enhanced at a vapor-liquid interface. In some systems, such as n-alkanes, this enhancement is dramatic and results in the formation of a crystalline layer at the free interface even at temperatures slightly above the equilibrium bulk freezing temperature. There are, however, systems in which the enhancement is purely kinetic and only involves faster nucleation at or near the interface. The first, thermodynamic, type of surface freezing is easier to confirm in experiments, requiring only the verification of the existence of crystalline order at the interface. The second, kinetic, type of surface freezing is far more difficult to prove experimentally. One material that is suspected of undergoing the second type of surface freezing is liquid water. Despite strong indications that the freezing of liquid water is kinetically enhanced at vapor-liquid interfaces, the findings are far from conclusive, and the topic remains controversial. In this perspective, we present a simple thermodynamic framework to understand conceptually and distinguish these two types of surface freezing. We then briefly survey fifteen years of experimental and computational work aimed at elucidating the surface freezing conundrum in water. read less NOT USED (low confidence) J. Lu, C. Miller, and V. Molinero, “Parameterization of a coarse-grained model with short-ranged interactions for modeling fuel cell membranes with controlled water uptake.,” Physical chemistry chemical physics : PCCP. 2017. link Times cited: 11 Abstract: The design of polymer electrolyte membranes with controlled … read moreAbstract: The design of polymer electrolyte membranes with controlled water uptake is of high importance for high-performance fuel cells, because the water content of the membranes modulates their conductivity, chemical stability and mechanical strength. The water activity aw controls the equilibrium water uptake of a system. Predicting aw of materials is currently a daunting challenge for molecular simulations, because calculations of water activity require grand canonical simulations that are extremely expensive even with classical non-polarizable force fields. Moreover, force fields do not generally reproduce aw of solutions. Here, we first present a general strategy to parameterize force fields that reproduce the experimental aw of solutions, and then implement that strategy to re-parameterize the interactions in FFcomp, a coarse-grained model for hydrated polyphenylene oxide/trimethylamine chloride (PPO/TMACl) membranes in which the TMA cation is attached to the PPO backbone and the Cl anion is in the mobile water nanophase. Coarse-grained models based on short-ranged potentials successfully model fuel cell membranes and other concentrated aqueous electrolyte solutions because electrostatic interactions are highly screened in these systems. The new force field, FFpvap, differs from the original FFcomp only in the parameters of the ion-ion interactions, yet it reproduces aw in TMACl solutions with accuracy within 0.5 and 3% of the experimental value in all the concentration range relevant to the operation of fuel cell membranes. We find that the heat needed to vaporize water in solutions with as little as five water molecules per ion pair is essentially the same as in pure water, despite the strong water-ion interactions and their impact on the water activity. We review the literature to demonstrate that this is independent of the model and a general feature of water solutions. FFpvap reproduces the radial distribution functions and captures well the relative diffusivities of water and ions in the ionic solution as predicted by the reference atomistic GAFF-TIP4P/2005 model, while providing a hundred-fold gain in computing efficiency with respect to the atomistic model. With the backbone fragments inherited from FFcomp, the new FFpvap force field can be used to model hydrated polymer electrolyte membranes and advance the design of fuel cell membranes with controlled water uptake and conductivity. read less NOT USED (low confidence) Q. Wang, X. Wang, R. Guo, and B. Huang, “Parametrization of Density Functional Tight-Binding Method for Thermal Transport in Bulk and Low-Dimensional Si Systems,” Journal of Physical Chemistry C. 2017. link Times cited: 6 Abstract: Understanding the thermal transport in different Si-based ma… read moreAbstract: Understanding the thermal transport in different Si-based materials is of both practical and academic importance because of the essential role of such materials in modern electronic and microelectromechanical applications and other areas. Conventional atomic modeling approaches such as density functional theory offer high accuracy but can hardly handle a large system, whereas the empirical potentials used in classical molecular dynamics often lack accuracy or transferability. We have thus developed a new parametrization of the Si–Si interaction of the density-functional-based tight-binding method for the atomic-scale investigation of thermal transport properties in various Si systems. We found that this parametrization can accurately predict many harmonic and anharmonic thermal transport properties in different silicon systems such as single-crystalline silicon, silicene, and silicene nanoribbons, showing excellent computational efficiency and transferability. Therefore, this Si–Si parameter set can contr... read less NOT USED (low confidence) T. Zohdi, “Computational modeling of electrically-driven deposition of ionized polydisperse particulate powder mixtures in advanced manufacturing processes,” J. Comput. Phys. 2017. link Times cited: 3 NOT USED (low confidence) H. Li, R. Xu, Z. Bi, X. Shen, and K. Han, “Melting Properties of Medium-Sized Silicon Nanoclusters:
A Molecular Dynamics Study,” Journal of Electronic Materials. 2017. link Times cited: 7 NOT USED (low confidence) G. Gyawali, S. Sternfield, R. Kumar, and S. Rick, “Coarse-Grained Models of Aqueous and Pure Liquid Alkanes.,” Journal of chemical theory and computation. 2017. link Times cited: 17 Abstract: A model for linear alkanes is presented in which interaction… read moreAbstract: A model for linear alkanes is presented in which interaction sites are only on the carbon atoms, and the range of the potential is reduced using the Stillinger-Weber potential. The model is optimized for aqueous and liquid alkane properties and can match thermodynamic and structural properties, including solvation free energies, liquid densities, and liquid/vapor and liquid/water surface tensions for alkanes over a range of lengths. The results for long alkanes indicate that such models can be useful as accurate, yet efficient, coarse-grained potentials for macromolecules in water and other environments. read less NOT USED (low confidence) E. Dontsova and R. Ballarini, “Atomistic modeling of the fracture toughness of silicon and silicon-silicon interfaces,” International Journal of Fracture. 2017. link Times cited: 6 NOT USED (low confidence) Z. Bažant and J. Le, “Probabilistic Mechanics of Quasibrittle Structures: Strength, Lifetime, and Size Effect.” 2017. link Times cited: 76 NOT USED (low confidence) N. Liu, J. Hong, X. Zeng, R. Pidaparti, and X. Wang, “Fracture mechanisms in multilayer phosphorene assemblies: from brittle to ductile.,” Physical chemistry chemical physics : PCCP. 2017. link Times cited: 8 Abstract: The outstanding mechanical performance of nacre has stimulat… read moreAbstract: The outstanding mechanical performance of nacre has stimulated numerous studies on the design of artificial nacres. Phosphorene, a new two-dimensional (2D) material, has a crystalline in-plane structure and non-bonded interaction between adjacent flakes. Therefore, multi-layer phosphorene assemblies (MLPs), in which phosphorene flakes are piled up in a staggered manner, may exhibit outstanding mechanical performance, especially exceptional toughness. Therefore, molecular dynamics simulations are performed to study the dependence of the mechanical properties on the overlap distance between adjacent phosphorene layers and the number of phosphorene flakes per layer. The results indicate that when the flake number is equal to 1, a transition of fracture patterns is observed by increasing the overlap distance, from a ductile failure controlled by interfacial friction to a brittle failure dominated by the breakage of covalent bonds inside phosphorene flakes. Moreover, the failure pattern can be tuned by changing the number of flakes in each phosphorene layer. The results imply that the ultimate strength follows a power law with the exponent -0.5 in terms of the flake number, which is in good agreement with our analytical model. Furthermore, the flake number in each phosphorene layer is optimized as 2 when the temperature is 1 K in order to potentially achieve both high toughness and strength. Moreover, our results regarding the relations between mechanical performance and overlap distance can be explained well using a shear-lag model. However, it should be pointed out that increasing the temperature of MLPs could cause the transition of fracture patterns from ductile to brittle. Therefore, the optimal flake number depends heavily on temperature to achieve both its outstanding strength and toughness. Overall, our findings unveil the fundamental mechanism at the nanoscale for MLPs as well as provide a method to design phosphorene-based structures with targeted properties via tunable overlap distance and flake number in phosphorene layers. read less NOT USED (low confidence) Y. Zhao et al., “Engineering the thermal conductivity along an individual silicon nanowire by selective helium ion irradiation,” Nature Communications. 2017. link Times cited: 62 NOT USED (low confidence) N. Zographos, C. Zechner, I. Martín-Bragado, K. Lee, and Y. Oh, “Multiscale modeling of doping processes in advanced semiconductor devices,” Materials Science in Semiconductor Processing. 2017. link Times cited: 12 NOT USED (low confidence) J.-W. Jiang and Y.-P. Zhou, “Parameterization of Stillinger-Weber Potential for Two- Dimensional Atomic Crystals,” arXiv: Materials Science. 2017. link Times cited: 51 Abstract: We parametrize the Stillinger-Weber potential for 156 two-di… read moreAbstract: We parametrize the Stillinger-Weber potential for 156 two-dimensional atomic crystals. Parameters for the Stillinger-Weber potential are obtained from the valence force field model following the analytic approach (Nanotechnology 26, 315706 (2015)), in which the valence force constants are determined by the phonon spectrum. The Stillinger-Weber potential is an efficient nonlinear interaction, and is applicable for numerical simulations of nonlinear physical or mechanical processes. The supplemental resources for all simulations in the present work are available online in Ref. 1, including a fortran code to generate crystals' structures, files for molecular dynamics simulations using LAMMPS, files for phonon calculations with the Stillinger-Weber potential using GULP, and files for phonon calculations with the valence force field model using GULP. read less NOT USED (low confidence) M. Wood, M. Cherukara, E. Antillon, and A. Strachan, “Molecular Dynamics Simulations of Shock Loading of Materials: A Review and Tutorial.” 2017. link Times cited: 14 NOT USED (low confidence) Q. Li and W. Ye, “An interfering Monte Carlo method for partially coherent phonon transport in superlattices,” International Journal of Heat and Mass Transfer. 2017. link Times cited: 9 NOT USED (low confidence) H. Garg and G. Singh, “Solution of two-parameter cohesive law using Chebyshev polynomials for singular integral equation,” Theoretical and Applied Fracture Mechanics. 2017. link Times cited: 1 NOT USED (low confidence) V. Kuryliuk and O. Korotchenkov, “Atomistic simulation of the thermal conductivity in amorphous SiO 2 matrix/Ge nanocrystal composites,” Physica E-low-dimensional Systems & Nanostructures. 2017. link Times cited: 5 NOT USED (low confidence) H. N. Pishkenari and S. Rezaei, “Characterization of silicon surface elastic constants based on different interatomic potentials,” Thin Solid Films. 2017. link Times cited: 7 NOT USED (low confidence) J. Zylberg, E. Lerner, Y. Bar-Sinai, and E. Bouchbinder, “Local thermal energy as a structural indicator in glasses,” Proceedings of the National Academy of Sciences. 2017. link Times cited: 62 Abstract: Significance When liquids are cooled sufficiently fast, they… read moreAbstract: Significance When liquids are cooled sufficiently fast, they fail to crystalize and form disordered solids—glasses. Understanding the physical properties of glasses remains a major challenge, in large part because of the lack of tools to characterize the emerging disordered structures and well-established structure–properties relations. In this work, we propose that fluctuational thermal energy reveals highly localized and soft structures in glasses. We show that the degree of softness of these “soft spots” follows a universal fat-tailed statistical distribution and relate it to the density of noncrystalline vibrational states. The softest spots are shown to predict the loci of irreversible plastic rearrangements in sheared glasses, thus offering a generic structure–properties approach to glassy materials. Identifying heterogeneous structures in glasses—such as localized soft spots—and understanding structure–dynamics relations in these systems remain major scientific challenges. Here, we derive an exact expression for the local thermal energy of interacting particles (the mean local potential energy change caused by thermal fluctuations) in glassy systems by a systematic low-temperature expansion. We show that the local thermal energy can attain anomalously large values, inversely related to the degree of softness of localized structures in a glass, determined by a coupling between internal stresses—an intrinsic signature of glassy frustration—anharmonicity and low-frequency vibrational modes. These anomalously large values follow a fat-tailed distribution, with a universal exponent related to the recently observed universal ω4 density of states of quasilocalized low-frequency vibrational modes. When the spatial thermal energy field—a “softness field”—is considered, this power law tail manifests itself by highly localized spots, which are significantly softer than their surroundings. These soft spots are shown to be susceptible to plastic rearrangements under external driving forces, having predictive powers that surpass those of the normal modes-based approach. These results offer a general, system/model-independent, physical/observable-based approach to identify structural properties of quiescent glasses and relate them to glassy dynamics. read less NOT USED (low confidence) A. Ciani, C. Grein, B. Irick, M. Miao, and N. Kioussis, “Molecular dynamics growth modeling of InAs1−xSbx-based type-II superlattice,” Optical Engineering. 2017. link Times cited: 10 Abstract: Abstract. Type-II strained-layer superlattices (T2SL) based … read moreAbstract: Abstract. Type-II strained-layer superlattices (T2SL) based on InAs1−xSbx are a promising photovoltaic detector material technology for thermal imaging; however, Shockley–Read–Hall recombination and generation rates are still too high for thermal imagers based on InAs1−xSbx T2SL to reach their ideal performance. Molecular dynamics simulations using the Stillinger–Weber (SW) empirical potentials are a useful tool to study the growth of tetrahedral coordinated crystals and the nonequilibrium formation of defects within them, including the long-range effects of strain. SW potentials for the possible atomic interactions among {Ga, In, As, Sb} were developed by fitting to ab initio calculations of elastically distorted zinc blende and diamond unit cells. The SW potentials were tested against experimental observations of molecular beam epitaxial (MBE) growth and then used to simulate the MBE growth of InAs/InAs0.5Sb0.5 T2SL on GaSb substrates over a range of processes parameters. The simulations showed and helped to explain Sb cross-incorporation into the InAs T2SL layers, Sb segregation within the InAsSb layers, and identified medium-range defect clusters involving interstitials and their induction of interstitial-vacancy pairs. Defect formation was also found to be affected by growth temperature and flux stoichiometry. read less NOT USED (low confidence) T. Min, T. Yoon, and T. Lim, “Molecular dynamics simulation of melting of silicene,” Materials Research Express. 2017. link Times cited: 8 Abstract: We report the melting temperature of free-standing silicene … read moreAbstract: We report the melting temperature of free-standing silicene by carrying out molecular dynamics (MD) simulation experiments using optimized Stillinger-Weber (SW) potential by Zhang et al (2014 Phys. Rev. B 89 054310). The melting scenario of a free-standing silicene is well captured visually in our MD simulations. The data are systematically analyzed using a few qualitatively different indicators, including caloric curve, radial distribution function and a numerical indicator known as global similarity index. The optimized SW potential consistently yields a melting temperature of 1500 K for the simulated free-standing, infinite silicene. read less NOT USED (low confidence) J. Jiang, L. Wang, and Y. Zhang, “Vibration of single-walled carbon nanotubes with elastic boundary conditions,” International Journal of Mechanical Sciences. 2017. link Times cited: 30 NOT USED (low confidence) S. Goel, S. Chavoshi, and A. Murphy, “Molecular dynamics simulation (MDS) to study nanoscale machining processes.” 2017. link Times cited: 2 Abstract: 1 Molecular dynamics simulation (MDS) to study nanoscale cut… read moreAbstract: 1 Molecular dynamics simulation (MDS) to study nanoscale cutting processes Saurav Goel1*, Saeed Zare Chavoshi2 and Adrian Murphy3 1Precision Engineering Institute, School of Aerospace, Transport and Manufacturing, Cranfield University, Cranfield, Bedfordshire, MK430AL, UK 2Mechanical Engineering Department, Imperial College London, London, SW7 2AZ, UK 3School of Mechanical and Aerospace Engineering, Queen’s University, Belfast, BT9 5AH, UK *Corresponding author Tel.: +44 1234754132, Email address: sgoel.diamond@gmail.com read less NOT USED (low confidence) C. Lemarchand, M. Couty, and B. Rousseau, “Coarse-grained simulations of cis- and trans-polybutadiene: A bottom-up approach.,” The Journal of chemical physics. 2017. link Times cited: 31 Abstract: We apply the dissipative particle dynamics strategy proposed… read moreAbstract: We apply the dissipative particle dynamics strategy proposed by Hijón et al. [Faraday Discuss. 144, 301-322 (2010)] and based on an exact derivation of the generalized Langevin equation to cis- and trans-1,4-polybutadiene. We prove that it is able to reproduce not only the structural but also the dynamical properties of these polymers without any fitting parameter. A systematic study of the effect of the level of coarse-graining is done on cis-1,4-polybutadiene. We show that as the level of coarse-graining increases, the dynamical properties are better and better reproduced while the structural properties deviate more and more from those calculated in molecular dynamics (MD) simulations. We suggest two reasons for this behavior: the Markovian approximation is better satisfied as the level of coarse-graining increases, while the pair-wise approximation neglects important contributions due to the relative orientation of the beads at large levels of coarse-graining. Finally, we highlight a possible limit of the Markovian approximation: the fact that in constrained simulations, in which the centers-of-mass of the beads are kept constant, the bead rotational dynamics become extremely slow. read less NOT USED (low confidence) D. Dhabal, K. T. Wikfeldt, L. Skinner, C. Chakravarty, and H. K. Kashyap, “Probing the triplet correlation function in liquid water by experiments and molecular simulations.,” Physical chemistry chemical physics : PCCP. 2017. link Times cited: 10 Abstract: Despite very significant developments in scattering experime… read moreAbstract: Despite very significant developments in scattering experiments like X-ray and neutron diffraction, it has been challenging to elucidate the nature of tetrahedral molecular configurations in liquid water. A key question is whether the pair correlation functions, which can be obtained from scattering experiments, are sufficient to describe the tetrahedral ordering of water molecules. In our previous study (Dhabal et al., J. Chem. Phys., 2014, 141, 174504), using data-sets generated from reverse Monte Carlo and molecular dynamics simulations, we showed that the triplet correlation functions contain important information on the tetrahedrality of water in the liquid state. In the present study, X-ray scattering experiments and molecular dynamics (MD) simulations are used to link the isothermal pressure derivative of the structure factor with the triplet correlation functions for water. Triplet functions are determined for water up to 3.3 kbar at 298 K to display the effect of pressure on the water structure. The results suggest that triplet functions (H[combining tilde](q)) obtained using a rigid-body TIP4P/2005 water model are consistent with the experimental results. The triplet functions obtained in experiment as well as in simulations evince that in the case of tetrahedral liquids, exertion of higher pressure leads to a better agreement with the Kirkwood superposition approximation (KSA). We further validate this observation using the triplet correlation functions (g(3)(r,s,t)) calculated directly from simulation trajectory, revealing that both H[combining tilde](q) in q-space and g(3)(r,s,t) in real-space contain similar information on the tetrahedrality of liquids. This study demonstrates that the structure factor, even though it has only pair correlation information of the liquid structure, can shed light on three-body correlations in liquid water through its isothermal pressure derivative term. read less NOT USED (low confidence) C. Wang, C. Zhang, and T. Rabczuk, “A Two-Dimensional Coarse-Grained Model for Molybdenum Disulphide,” Journal of Modeling in Mechanics and Materials. 2017. link Times cited: 2 Abstract: We parametrize a two-dimensional (2D) coarse-grained (CG) mo… read moreAbstract: We parametrize a two-dimensional (2D) coarse-grained (CG) model of molybdenum disulphide (MoS2) with Stillinger Weber (SW) potential in which all SW geometrical parameters are determined analytically from the equilibrium condition for each potential term, while the SW energy parameters are derived analytically based on the valence force field (VFF) model. This parametrization method transfers the accuracy of the VFF model to the SW potential. The uniqueness of the CG model is that the hexagonal lattice symmetry is maintained, and especially, the positions of Moi beads and Si beads in the CG model are the same as Mo atoms and S atoms, respectively, in the atomic SLMoS2, where the subscript i represent the ith order CG level. Owing to its simplicity, the CG model can be used to investigate the adsorption effect on the resonant frequency. We find that the resonant frequency of the oscillation is insensitive to the adsorbed effect. read less NOT USED (low confidence) V. Levitas, H. Chen, and L. Xiong, “Triaxial-Stress-Induced Homogeneous Hysteresis-Free First-Order Phase Transformations with Stable Intermediate Phases.,” Physical review letters. 2017. link Times cited: 43 Abstract: Starting with thermodynamic predictions and following with m… read moreAbstract: Starting with thermodynamic predictions and following with molecular dynamics simulations, special triaxial compression-tension states were found for which the stresses for the instability of the crystal lattice of silicon (Si) are the same for direct and reverse phase transformations (PTs) between semiconducting Si I and metallic Si II phases. This leads to unique homogeneous and hysteresis-free first-order PTs, for which each intermediate crystal lattice along the transformation path is in indifferent thermodynamic equilibrium and can be arrested and studied by fixing the strain in one direction. By approaching these stress states, a traditional two-phase system continuously transforms to homogenous intermediate phases. Zero hysteresis and homogeneous transformations are the optimal property for various PT applications, which drastically reduce damage and energy dissipation. read less NOT USED (low confidence) A. H. Nguyen, C. W. Rosenbrock, C. S. Reese, and G. Hart, “Robustness of the cluster expansion: Assessing the roles of relaxation and numerical error,” Physical Review B. 2017. link Times cited: 25 Abstract: Cluster expansion (CE) is effective in modeling the stabilit… read moreAbstract: Cluster expansion (CE) is effective in modeling the stability of metallic alloys, but sometimes cluster expansions fail. Failures are often attributed to atomic relaxation in the DFT-calculated data, but there is no metric for quantifying the degree of relaxation. Additionally, numerical errors can also be responsible for slow CE convergence. We studied over one hundred different Hamiltonians and identified a heuristic, based on a normalized mean-squared displacement of atomic positions in a crystal, to determine if the effects of relaxation in CE data are too severe to build a reliable CE model. Using this heuristic, CE practitioners can determine a priori whether or not an alloy system can be reliably expanded in the cluster basis. We also examined the error distributions of the fitting data. We find no clear relationship between the type of error distribution and CE prediction ability, but there are clear correlations between CE formalism reliability, model complexity, and the number of significant terms in the model. Our results show that the \emph{size} of the errors is much more important than their distribution. read less NOT USED (low confidence) N. Karkalos and A. Markopoulos, “Modeling Nano-Metric Manufacturing Processes with Molecular Dynamics Method: A Review,” Current Nanoscience. 2016. link Times cited: 9 NOT USED (low confidence) H. N. Pishkenari, E. Mohagheghian, and A. Rasouli, “Molecular dynamics study of the thermal expansion coefficient of silicon,” Physics Letters A. 2016. link Times cited: 23 NOT USED (low confidence) C. Bahr and B. Schulz, “Atomic force microscopy on liquid crystals.” 2016. link Times cited: 0 NOT USED (low confidence) S. Volz, “Relevant Semiempirical Potentials for Phonon Properties.” 2016. link Times cited: 1 NOT USED (low confidence) K. Miwa and H. Ohno, “Molecular dynamics study on β -phase vanadium monohydride with machine learning potential,” Physical Review B. 2016. link Times cited: 13 NOT USED (low confidence) Z. Wang and X. Ruan, “Uncertainties of Thermal Conductivities From Equilibrium Molecular Dynamics Simulations.” 2016. link Times cited: 0 NOT USED (low confidence) P.-Y. Yang, S. Ju, Z.-M. Lai, J. Hsieh, and J.-S. Lin, “The mechanical properties and thermal stability of ultrathin germanium nanowires,” RSC Advances. 2016. link Times cited: 8 Abstract: The most stable structures of four ultrathin germanium nanow… read moreAbstract: The most stable structures of four ultrathin germanium nanowires (GeNWs) were predicted by a simulated annealing basin-hopping method (SABH) with a Stillinger–Weber (SW) potential, including helix, pentagon, hexagon and 7-1 nanowires. The size and temperature dependence of the tensile behavior and mechanical properties are investigated to approach a real environment. The ultimate tensile strength, strain at failure and Young's modulus are evaluated. All the mechanical properties of nanowires are severely reduced when temperature increases from 20 K to 180 K, but become less severe at high temperature. At room temperature (300 K), the yielding stress and Young's modulus of all nanowires are higher than bulk, and the pentagonal NW exhibits the best mechanical properties among these three GeNWs. This study also demonstrates that the mechanical properties are not proportional to the size or radius of ultrathin GeNWs, a phenomenon different from that in the bulk. In addition, the phonon density of states and thermal stability of GeNWs are also discussed in this study. read less NOT USED (low confidence) M. Budnitzki and M. Kuna, “Stress induced phase transitions in silicon,” Journal of The Mechanics and Physics of Solids. 2016. link Times cited: 25 NOT USED (low confidence) K. Jolley and R. Smith, “Radiation tolerance of iron phosphate: a study of amorphous and crystalline structures,” Journal of Nuclear Materials. 2016. link Times cited: 11 NOT USED (low confidence) S. Jose et al., “Enhanced supercapacitor performance of a 3D architecture tailored using atomically thin rGO–MoS2 2D sheets,” RSC Advances. 2016. link Times cited: 35 Abstract: A 3D architecture is fabricated using 2D nano-sheets of GO a… read moreAbstract: A 3D architecture is fabricated using 2D nano-sheets of GO and MoS2 as the building blocks by a facile, one-pot chronoamperometry method to achieve a conductive additive free, binder free and scalable supercapacitor electrode. The superior electrochemical properties of the 3D PPy-rGO–MoS2 (PGMo) are due to its porous structure, thin wall, high surface area and high electrical conductivity that endow rapid transportation of electrolyte ions and electrons throughout the electrode matrix. The synergistic effect between the components in a proper ratio improves the supercapacitor performance and material stability of PGMo. The possible correlation of the structure and electrochemical performance of the 3D ternary composite is backed by a fully atomistic molecular dynamics (MD) simulation study. The high specific capacitance (387 F g−1) and impressive cycling stability (>1000 cycles) estimated for PGMo open up an opportunity to consider the 3D ternary nanostructures as cutting edge materials for energy storage solutions. read less NOT USED (low confidence) P. Tredak, W. Rudnicki, and J. Majewski, “Efficient implementation of the many-body Reactive Bond Order (REBO) potential on GPU,” J. Comput. Phys. 2016. link Times cited: 4 NOT USED (low confidence) A. Nobakht and S. Shin, “Anisotropic control of thermal transport in graphene/Si heterostructures,” Journal of Applied Physics. 2016. link Times cited: 39 Abstract: The cross-plane interaction across interface changes phonon … read moreAbstract: The cross-plane interaction across interface changes phonon kinetics and spectrum near the interface, and the interaction effects on both in-plane and cross-plane thermal transport are investigated in graphene/Si heterostructure. The interaction with substrates dramatically reduces the in-plane thermal conductivity of graphene by changing the behaviors of the out-of-plane phonons as well as adding phonon-substrate scatterings. Applying pressure up to 2.6 GPa to the sandwiched graphene reduces the cross-plane interfacial thermal resistance by 50% without altering the in-plane thermal conductivity in a significant way. The pressure increases the inter-layer coupling and creates a low-energy phonon transport channel between graphene and Si with minor effects on phonons propagating along the graphene. This study suggests the anisotropic control of thermal transport, and the physics and calculation results can be used to improve the thermal design and analysis in two-dimensional nano-electronic devices. read less NOT USED (low confidence) J. Godet, C. Furgeaud, L. Pizzagalli, and M. Demkowicz, “Uniform tensile elongation in Au–Si core–shell nanowires,” Extreme Mechanics Letters. 2016. link Times cited: 10 NOT USED (low confidence) B. Liu, J. Tao, X. Chen, Y. Zhang, Y. Jiang, and Y. Qian, “Numerical investigation of the effects of phosphorus on the mechanical responses of [1 1 0]-oriented silicon nano-wires,” Microelectron. Reliab. 2016. link Times cited: 1 NOT USED (low confidence) J. R. Choudhuri, D. Vanzo, P. Madden, M. Salanne, D. Bratko, and A. Luzar, “Dynamic Response in Nanoelectrowetting on a Dielectric.,” ACS nano. 2016. link Times cited: 30 Abstract: Droplet spreading at an applied voltage underlies the functi… read moreAbstract: Droplet spreading at an applied voltage underlies the function of tunable optical devices including adjustable lenses and matrix display elements. Faster response and the enhanced resolution motivate research toward miniaturization of these devices to nanoscale dimensions. The response of an aqueous nanodroplet to an applied field can differ significantly from macroscopic predictions. Understanding these differences requires characterization at the molecular level. We describe the equilibrium and nonequilibrium molecular dynamics simulations of nanosized aqueous droplets on a hydrophobic surface with the embedded concentric electrodes. Constant electrode potential is enforced by a rigorous account of the metal polarization. We demonstrate that the reduction of the equilibrium contact angle is commensurate to, and adjusts reversibly with, the voltage change. For a droplet with O(10) nm diameter, a typical response time to the imposition of the field is of O(10(2)) ps. Drop relaxation is about twice as fast when the field is switched off. The friction coefficient obtained from the rate of the drop relaxation on the nonuniform surface, decreases when the droplet approaches equilibrium from either direction, that is, by spreading or receding. The strong dependence of the friction on the surface hydrophilicity points to the dominance of the liquid-surface friction at the drop's perimeter as described in the molecular kinetic theory. This approach enables correct predictions of trends in dynamic responses associated with varied voltage or substrate material. read less NOT USED (low confidence) N. Liu, J. Hong, R. Pidaparti, and X. Wang, “Abnormality in fracture strength of polycrystalline silicene,” 2D Materials. 2016. link Times cited: 21 Abstract: Silicene, a silicon-based homologue of graphene, arouses gre… read moreAbstract: Silicene, a silicon-based homologue of graphene, arouses great interest in nano-electronic devices due to its outstanding electronic properties. However, its promising electronic applications are greatly hindered by lack of understanding in the mechanical strength of silicene. Therefore, in order to design mechanically reliable devices with silicene, it is necessary to thoroughly explore the mechanical properties of silicene. Due to current fabrication methods, graphene is commonly produced in a polycrystalline form; the same may hold for silicene. Here we perform molecular dynamics simulations to investigate the mechanical properties of polycrystalline silicene. First, an annealing process is employed to construct a more realistic modeling structure of polycrystalline silicene. Results indicate that a more stable structure is formed due to the breaking and reformation of bonds between atoms on the grain boundaries. Moreover, as the grain size decreases, the efficiency of the annealing process, which is quantified by the energy change, increases. Subsequently, biaxial tensile tests are performed on the annealed samples in order to explore the relation between grain size and mechanical properties, namely in-plane stiffness, fracture strength and fracture strain etc. Results indicate that as the grain size decreases, the fracture strain increases while the fracture strength shows an inverse trend. The decreasing fracture strength may be partly attributed to the weakening effect from the increasing area density of defects which acts as the reservoir of stress-concentrated sites on the grain boundary. The observed crack localization and propagation and fracture strength are well-explained by a defect-pileup model. read less NOT USED (low confidence) A. Lipnitskii and V. Saveliev, “Development of n-body expansion interatomic potentials and its application for V,” Computational Materials Science. 2016. link Times cited: 20 NOT USED (low confidence) X. W. Zhou, J. J. Chavez, and D. Zubia, “Molecular Dynamics Analysis of Nanostructures.” 2016. link Times cited: 0 NOT USED (low confidence) T. Sanyal and S. Shella, “Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation.,” The Journal of chemical physics. 2016. link Times cited: 75 Abstract: Bottom-up multiscale techniques are frequently used to devel… read moreAbstract: Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment. read less NOT USED (low confidence) O. Strickson, “Numerical constitutive modelling for continuum mechanics simulation.” 2016. link Times cited: 0 NOT USED (low confidence) Z. Zhang, A. Stukowski, and H. Urbassek, “Interplay of dislocation-based plasticity and phase transformation during Si nanoindentation,” Computational Materials Science. 2016. link Times cited: 28 NOT USED (low confidence) H. Hu, G.-H. Tang, and D. Niu, “Wettability modified nanoporous ceramic membrane for simultaneous residual heat and condensate recovery,” Scientific Reports. 2016. link Times cited: 59 NOT USED (low confidence) C. J. Choi and N. A. Roberts, “Simple model for effective thermal conductivity of bulk nanostructured materials,” International Journal of Thermal Sciences. 2016. link Times cited: 6 NOT USED (low confidence) G. Sosso et al., “Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations,” Chemical Reviews. 2016. link Times cited: 553 Abstract: The nucleation of crystals in liquids is one of nature’s mos… read moreAbstract: The nucleation of crystals in liquids is one of nature’s most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments. read less NOT USED (low confidence) X. Wang and A. Tabarraei, “Phonon thermal conductivity of monolayer MoS2,” Applied Physics Letters. 2016. link Times cited: 36 Abstract: We use nonequilibrium molecular dynamics modeling using Stil… read moreAbstract: We use nonequilibrium molecular dynamics modeling using Stillinger–Weber interatomic potential to investigate the thermal properties of monolayer molybdenum disulfide (MoS2) nanoribbons. We study the impact of factors such as length, edge chirality, monovacancies, and uniaxial stretching on the thermal conductivity of MoS2 nanoribbons. Our results show that longer ribbons have a higher thermal conductivity, and the thermal conductivity of infinitely long zigzag and armchair MoS2 nanoribbons is, respectively, 54 W/mK and 33 W/mK. This is significantly lower than the thermal conductivity of some other graphene-like two-dimensional materials such as graphene and boron nitride. While the presence of molybdenum or sulfur vacancies reduces the thermal conductivity of ribbons, molybdenum vacancies have a more deteriorating effect on thermal conductivities. We also have studied the impact of uniaxial stretching on the thermal conductivity of MoS2 nanoribbons. The results show that in contrast to three dimensional... read less NOT USED (low confidence) S. Mann and P. Rani, “Study of interaction in silica glass via model potential approach.” 2016. link Times cited: 0 Abstract: Silica is one of the most commonly encountered substances in… read moreAbstract: Silica is one of the most commonly encountered substances in daily life and in electronics industry. Crystalline SiO2 (in several forms: quartz, cristobalite, tridymite) is an important constituent of many minerals and gemstones, both in pure form and mixed with related oxides. Cohesive energy of amorphous SiO2 has been investigated via intermolecular potentials i.e weak Van der Waals interaction and Morse type short-range interaction.We suggest a simple atom-atom based Van der Waals as well as Morse potential to find cohesive energy of glass. It has been found that the study of silica structure using two different model potentials is significantly different. Van der Waals potential is too weak (P.E =0.142eV/molecule) to describe the interaction between silica molecules. Morse potential is a strong potential, earlier given for intramolecular bonding, but if applied for intermolecular bonding, it gives a value of P.E (=−21.92eV/molecule) to appropriately describe the structure of silica. read less NOT USED (low confidence) Y. Qiu, J. Ma, and Y. Chen, “Ionic Behavior in Highly Concentrated Aqueous Solutions Nanoconfined between Discretely Charged Silicon Surfaces.,” Langmuir : the ACS journal of surfaces and colloids. 2016. link Times cited: 22 Abstract: Through molecular dynamics simulations considering thermal v… read moreAbstract: Through molecular dynamics simulations considering thermal vibration of surface atoms, ionic behaviors in concentrated NaCl solutions confined between discretely charged silicon surfaces have been investigated. The electric double layer structure was found to be sensitive to the density and distribution of surface charges. Due to the discreteness of the surface charge, a slight charge inversion appeared which depended on the surface charge density, bulk concentration, and confinement. In the nanoconfined NaCl solutions concentrated from 0.2 to 4.0 M, the locations of accumulation layers for Na(+) and Cl(-) ions remained stable, but their peak values increased. The higher the concentration was, the more obvious the charge inversion appeared. In 4.0 M NaCl solution, Na(+) and Cl(-) ions show obvious alternating layered distributions which may correspond to the solidification found in experiments. By changing surface separation, the confinement had a large effect on the ionic distribution. As both surfaces approached each other, many ions and water molecules were squeezed out of the confined space. Two adjacent layers in ion or water distribution profiles can be forced closer to each other and merge together. From ionic hydration analysis, the coordination number of Na(+) ions in highly confined space was much lower than that in the bulk. read less NOT USED (low confidence) R. Raustin and H. Mohammadi, “TOWARD MULTISCALE MODELING OF WAVE PROPAGATION IN ARTERIES,” Journal of Mechanics in Medicine and Biology. 2016. link Times cited: 3 Abstract: In this study, we apply a novel numerical technique for mode… read moreAbstract: In this study, we apply a novel numerical technique for modeling the propagation of mechanical wave in the human arteries using the multiscale method. We define a particle region characterized by molecular dynamics (MD) method which is surrounded by a continuous region characterized by a finite element (FE) method. The interface between the two models are defined so as to minimize spurious reflections at the interface. This is a preliminary work for the modeling of the mechanical stability of atherosclerosis plaques using multiscale method. The model offered has extensive application in cell mechanics. read less NOT USED (low confidence) Z. Jiang, H. Fang, X. Luo, and J. Xu, “Numerical scheme analysis towards prediction of nanoscale fracture toughness of silicon at room temperature,” Engineering Fracture Mechanics. 2016. link Times cited: 7 NOT USED (low confidence) J. Al-Ghalith, Y. Ni, and T. Dumitricǎ, “Nanowires with dislocations for ultralow lattice thermal conductivity.,” Physical chemistry chemical physics : PCCP. 2016. link Times cited: 15 Abstract: Nanostructures grown by screw dislocations have been success… read moreAbstract: Nanostructures grown by screw dislocations have been successfully synthesized in a range of materials, including thermoelectric materials, but the impact of these extended crystallographic defects on thermal properties of these nanostructures is not known. We investigate thermal transport in PbSe and SiGe nanowires storing screw dislocations via equilibrium molecular dynamics simulations. The inherent one dimensionality and the combined presence of a reconstructed surface and dislocation yield ultralow thermal conductivity values. Our simulations suggest that the large dislocation strain field in nanowires may play a key role in suppressing the thermal conductivity of thermoelectric nanomaterials to increase their thermoelectric figure of merit. read less NOT USED (low confidence) E. Hernández, Y. Takada, and T. Yamamoto, “Mechanical Properties of Inorganic Nanostructures.” 2016. link Times cited: 0 NOT USED (low confidence) P. Nicolini and T. Polcar, “A comparison of empirical potentials for sliding simulations of MoS2,” Computational Materials Science. 2016. link Times cited: 37 NOT USED (low confidence) N. Liu, J. Hong, R. Pidaparti, and X. Wang, “Fracture patterns and the energy release rate of phosphorene.,” Nanoscale. 2016. link Times cited: 44 Abstract: Phosphorene, also known as monolayer black phosphorus, has b… read moreAbstract: Phosphorene, also known as monolayer black phosphorus, has been enjoying popularity in electronic devices due to its superior electrical properties. However, it's relatively low Young's modulus, low fracture strength and susceptibility to structural failure have limited its application in mechanical devices. Therefore, in order to design more mechanically reliable devices that utilize phosphorene, it is necessary to explore the fracture patterns and energy release rate of phosphorene. In this study, molecular dynamics simulations are performed to investigate phosphorene's fracture mechanism. The results indicate that fracture under uniaxial tension along the armchair direction is attributed to a break in the interlayer bond angles, while failure in the zigzag direction is triggered by the break in both intra-layer angles and bonds. Furthermore, we developed a modified Griffith criterion to analyze the energy release rate of phosphorene and its dependence on the strain rates and orientations of cracks. Simulation results indicate that phosphorene's energy release rate remains almost unchanged in the armchair direction while it fluctuates intensively in the zigzag direction. Additionally, the strain rate was found to play a negligible role in the energy release rate. The geometrical factor α in the Griffith's criterion is almost constant when the crack orientation is smaller than 45 degree, regardless of the crack orientation and loading direction. Overall, these findings provide helpful insights into the mechanical properties and failure behavior of phosphorene. read less NOT USED (low confidence) A. Portavoce, J. P. Toinin, K. Hoummada, L. Raymond, and G. Tréglia, “Stress influence on substitutional impurity segregation on dislocation loops in IV–IV semiconductors,” Computational Materials Science. 2016. link Times cited: 3 NOT USED (low confidence) N. Artrith and A. Urban, “An implementation of artificial neural-network potentials for atomistic materials simulations: Performance for TiO2,” Computational Materials Science. 2016. link Times cited: 350 NOT USED (low confidence) F. Agullo-lopez, A. Climent-Font, Á. Muñoz-Martín, J. Olivares, and A. Zucchiatti, “Ion beam modification of dielectric materials in the electronic excitation regime: Cumulative and exciton models,” Progress in Materials Science. 2016. link Times cited: 48 NOT USED (low confidence) K. Shimamura et al., “Crystalline anisotropy of shock-induced phenomena: Omni-directional multiscale shock technique,” Applied Physics Letters. 2016. link Times cited: 11 Abstract: We propose an omni-directional multiscale shock technique (O… read moreAbstract: We propose an omni-directional multiscale shock technique (OD-MSST) to study the shock waves in an arbitrary direction of crystalline materials, atomistically based on the molecular dynamics simulation method. Using OD-MSST, we found transitions from elastic to shear-banding to plastic behaviors for a model covalent crystal. In addition to such a shock “phase diagram,” a transition from inter-molecular to intra-molecular mechanochemical reaction pathways was found as a function of crystallographic orientation in an energetic van der Waals crystal. read less NOT USED (low confidence) N. Jakse and A. Pasturel, “Excess Entropy Scaling Law for Diffusivity in Liquid Metals,” Scientific Reports. 2016. link Times cited: 45 NOT USED (low confidence) A. Filipponi and P. D’Angelo, “XAS in Liquid Systems.” 2016. link Times cited: 7 NOT USED (low confidence) T. Zohdi, “A discrete element and ray framework for rapid simulation of acoustical dispersion of microscale particulate agglomerations,” Computational Mechanics. 2016. link Times cited: 0 NOT USED (low confidence) A. Kandemir, H. Yapicioglu, A. Kinaci, T. Çagin, and C. Sevik, “Thermal transport properties of MoS2 and MoSe2 monolayers,” Nanotechnology. 2016. link Times cited: 95 Abstract: The isolation of single- to few-layer transition metal dicha… read moreAbstract: The isolation of single- to few-layer transition metal dichalcogenides opens new directions in the application of two-dimensional materials to nanoelectronics. The characterization of thermal transport in these new low-dimensional materials is needed for their efficient implementation, either for general overheating issues or specific applications in thermoelectric devices. In this study, the lattice thermal conductivities of single-layer MoS2 and MoSe2 are evaluated using classical molecular dynamics methods. The interactions between atoms are defined by Stillinger–Weber-type empirical potentials that are developed to represent the structural, mechanical, and vibrational properties of the given materials. In the parameterization of the potentials, a stochastic optimization algorithm, namely particle swarm optimization, is utilized. The final parameter sets produce quite consistent results with density functional theory in terms of lattice parameters, bond distances, elastic constants, and vibrational properties of both single-layer MoS2 and MoSe2. The predicted thermal properties of both materials are in very good agreement with earlier first-principles calculations. The discrepancies between the calculations and experimental measurements are most probably caused by the pristine nature of the structures in our simulations. read less NOT USED (low confidence) A. Minnich, “Exploring the Extremes of Heat Conduction in Anisotropic Materials,” Nanoscale and Microscale Thermophysical Engineering. 2016. link Times cited: 17 Abstract: ABSTRACT Anisotropic solids possess thermal conductivities r… read moreAbstract: ABSTRACT Anisotropic solids possess thermal conductivities ranging from among the highest found in nature, as in the in-plane thermal conductivity of graphite, to the lowest, as in the cross-plane thermal conductivity of disordered layered crystals. Though these extremes of thermal conductivity make anisotropic materials attractive for diverse applications such as thermal management and thermal insulation, the microscopic physics of heat conduction in these materials remain poorly understood. In this review article, we discuss the recent advances in our understanding of thermal phonon transport in anisotropic solids obtained using new theoretical, computational, and experimental tools. read less NOT USED (low confidence) E. Malolepsza and T. Keyes, “Pathways through Equilibrated States with Coexisting Phases for Gas Hydrate Formation.,” The journal of physical chemistry. B. 2015. link Times cited: 20 Abstract: Under ambient conditions, water freezes to either hexagonal … read moreAbstract: Under ambient conditions, water freezes to either hexagonal ice or a hexagonal/cubic composite ice. The presence of hydrophobic guest molecules introduces a competing pathway: gas hydrate formation, with the guests in clathrate cages. Here, the pathways of the phase transitions are sought as sequences of states with coexisting phases, using a generalized replica exchange algorithm designed to sample them in equilibrium, avoiding nonequilibrium processes. For a dilute solution of methane in water under 200 atm, initializing the simulation with the full set of replicas leads to methane trapped in hexagonal/cubic ice, while gradually adding replicas with decreasing enthalpy produces the initial steps of hydrate growth. Once a small amount of hydrate is formed, water rearranges to form empty cages, eventually transforming the remainder of the system to metastable β ice, a scaffolding for hydrates. It is suggested that configurations with empty cages are reaction intermediates in hydrate formation when more guest molecules are available. Free energy profiles show that methane acts as a catalyst reducing the barrier for β ice versus hexagonal/cubic ice formation. read less NOT USED (low confidence) H. Wilson, “Efficient ab initio free energy calculations by classically assisted trajectory sampling,” Comput. Phys. Commun. 2015. link Times cited: 1 NOT USED (low confidence) J. Boer, “Theoretical studies of epitaxial graphene formation on metal surfaces.” 2015. link Times cited: 0 Abstract: In this thesis we develop a set of pheneomenological models … read moreAbstract: In this thesis we develop a set of pheneomenological models that we apply to the problem of epitaxial growth of graphene on metal substrates. The high temperature and typically low flux conditions under which graphene growth occurs are such that state of the art techniques such as kinetic Monte Carlo (kMC) are extremely difficult to apply to study the growth processes. Rather we utilise simpler theories based on rate equations and also develop a technique based on the phase-field method of island front tracking. The latter method may be considered to be an addition to the class of techniques known as "island dynamics" models [1]. We use rate equations to study the nucleation and growth of graphene [2] and to explore the dehydrogenation sequence of ethylene CH read less NOT USED (low confidence) M. Ganchenkova et al., “Influence of the ab-initio calculation parameters on prediction of energy of point defects in silicon,” Modern Electronic Materials. 2015. link Times cited: 7 NOT USED (low confidence) X. Cartoixà, L. Colombo, and R. Rurali, “Thermal Rectification by Design in Telescopic Si Nanowires.,” Nano letters. 2015. link Times cited: 65 Abstract: We show that thermal rectification by design is possible by … read moreAbstract: We show that thermal rectification by design is possible by joining/growing Si nanowires (SiNWs) with sections of appropriately selected diameters (i.e., telescopic nanowires). This is done, first, by showing that the heat equation can be applied at the nanoscale (NW diameters down to 5 nm). We (a) obtain thermal conductivity versus temperature, κ(T), curves from molecular dynamics (MD) simulations for SiNWs of three different diameters, then (b) we conduct MD simulations of a telescopic NW built as the junction of two segments with different diameters, and afterward (c) we verify that the MD results for thermal rectification in telescopic NWs are very well reproduced by the heat equation with κ(T) of the segments from MD. Second, we apply the heat equation to predict the amount of thermal rectification in a variety of telescopic SiNWs with segments made from SiNWs where κ(T) has been experimentally measured, obtaining r values up to 50%. This methodology can be applied to predict the thermal rectification of arbitrary heterojunctions as long as the κ(T) data of the constituents are available. read less NOT USED (low confidence) T. Hofer and A. O. Tirler, “Combining 2d-Periodic Quantum Chemistry with Molecular Force Fields: A Novel QM/MM Procedure for the Treatment of Solid-State Surfaces and Interfaces.,” Journal of chemical theory and computation. 2015. link Times cited: 17 Abstract: The feasibility of a novel approach for the hybrid quantum m… read moreAbstract: The feasibility of a novel approach for the hybrid quantum mechanical/molecular mechanical (QM/MM) treatment of solid-state surfaces without the requirement of artificially keeping atoms at fixed positions is explored. In order to avoid potential artifacts of the QM/MM transition near the surface, a 2d-periodic QM treatment of the system is employed. Thus, the only QM/MM interface between atoms of the solid is along the non-periodic z-dimension. It is shown for the metal oxide and metal systems MgO(100) and Be(0001) that a properly adjusted embedding potential supplemented by adequate non-Coulombic potentials (if required) enables the application of the QM/MM framework in all-atom structure optimization and molecular dynamics (MD) simulation. The commonly employed constraint to keep at least some of the embedding atoms at fixed position is not required. Two exemplary applications of H2O on MgO(100) and H2 on Be(0001) demonstrate the applicability of the framework in exemplary MD simulation studies. read less NOT USED (low confidence) N. S. Mikhaleva, M. Visotin, Z. Popov, A. Kuzubov, and A. Fedorov, “Ab initio and empirical modeling of lithium atoms penetration into silicon,” Computational Materials Science. 2015. link Times cited: 4 NOT USED (low confidence) H. N. Pishkenari, B. Afsharmanesh, and E. Akbari, “Surface elasticity and size effect on the vibrational behavior of silicon nanoresonators,” Current Applied Physics. 2015. link Times cited: 21 NOT USED (low confidence) B. Liu, H. Zhang, J. Tao, X. Chen, and Y.-A. Zhang, “Comparative investigation of a newly optimized modified embedded atom method potential with other potentials for silicon,” Computational Materials Science. 2015. link Times cited: 7 NOT USED (low confidence) M. M. Gianetti, A. Haji-Akbari, P. Longinotti, and P. Debenedetti, “Computational investigation of structure, dynamics and nucleation kinetics of a family of modified Stillinger-Weber model fluids in bulk and free-standing thin films.,” Physical chemistry chemical physics : PCCP. 2015. link Times cited: 24 Abstract: In recent years, computer simulations have found increasingl… read moreAbstract: In recent years, computer simulations have found increasingly widespread use as powerful tools for studying phase transitions in wide variety of systems. In the particular and very important case of aqueous systems, the commonly used force-fields tend to offer quite different predictions with respect to a wide range of thermodynamic and kinetic properties, including the ease of ice nucleation, the propensity to freeze at a vapor-liquid interface, and the existence of a liquid-liquid phase transition. It is thus of fundamental and practical interest to understand how different features of a given water model affect its thermodynamic and kinetic properties. In this work, we use the forward-flux sampling technique to study the crystallization kinetics of a family of modified Stillinger-Weber (SW) potentials with energy (ε) and length (σ) scales taken from the monoatomic water (mW) model, but with different tetrahedrality parameters (λ). By increasing λ from 21 to 24, we observe the nucleation rate increases by 48 orders of magnitude at a supercooling of ζ = T/Tm = 0.845. Using classical nucleation theory, we are able to demonstrate that this change can largely be accounted for by the increase in |Δμ|, the thermodynamic driving force. We also perform rate calculations in freestanding thin films of the supercooled liquid, and observe a crossover from surface-enhanced crystallization at λ = 21 to bulk-dominated crystallization for λ ≥ 22. read less NOT USED (low confidence) A. Giri, P. Hopkins, J. G. Wessel, and J. Duda, “Kapitza resistance and the thermal conductivity of amorphous superlattices,” Journal of Applied Physics. 2015. link Times cited: 50 Abstract: We report on the thermal conductivities of amorphous Stillin… read moreAbstract: We report on the thermal conductivities of amorphous Stillinger-Weber and Lennard-Jones superlattices as determined by non-equilibrium molecular dynamics simulations. Thermal conductivities decrease with increasing interface density, demonstrating that interfaces contribute a non-negligible thermal resistance. Interestingly, Kapitza resistances at interfaces between amorphous materials are lower than those at interfaces between the corresponding crystalline materials. We find that Kapitza resistances within the Stillinger-Webber based Si/Ge amorphous superlattices are not a function of interface density, counter to what has been observed in crystalline superlattices. Furthermore, the widely used thermal circuit model is able to correctly predict the interfacial resistance within the Stillinger-Weber based amorphous superlattices. However, we show that the applicability of this widely used thermal circuit model is invalid for Lennard-Jones based amorphous superlattices, suggesting that the assumptions made... read less NOT USED (low confidence) E. Hahn and M. Meyers, “Grain-size dependent mechanical behavior of nanocrystalline metals,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2015. link Times cited: 162 NOT USED (low confidence) Y. He et al., “Multilayer hexagonal silicon forming in slit nanopore,” Scientific Reports. 2015. link Times cited: 5 NOT USED (low confidence) E. Malolepsza, J. Kim, and T. Keyes, “Generalized ensemble method applied to study systems with strong first order transitions,” Journal of Physics: Conference Series. 2015. link Times cited: 2 Abstract: At strong first-order phase transitions, the entropy versus … read moreAbstract: At strong first-order phase transitions, the entropy versus energy or, at constant pressure, enthalpy, exhibits convex behavior, and the statistical temperature curve correspondingly exhibits an S-loop or back-bending. In the canonical and isothermal-isobaric ensembles, with temperature as the control variable, the probability density functions become bimodal with peaks localized outside of the S-loop region. Inside, states are unstable, and as a result simulation of equilibrium phase coexistence becomes impossible. To overcome this problem, a method was proposed by Kim, Keyes and Straub [1], where optimally designed generalized ensemble sampling was combined with replica exchange, and denoted generalized replica exchange method (gREM). This new technique uses parametrized effective sampling weights that lead to a unimodal energy distribution, transforming unstable states into stable ones. In the present study, the gREM, originally developed as a Monte Carlo algorithm, was implemented to work with molecular dynamics in an isobaric ensemble and coded into LAMMPS, a highly optimized open source molecular simulation package. The method is illustrated in a study of the very strong solid/liquid transition in water. read less NOT USED (low confidence) C. A. Krausse, T. Milek, and D. Zahn, “Molecular modeling of amorphous, non-woven polymer networks,” Journal of Molecular Modeling. 2015. link Times cited: 2 NOT USED (low confidence) J. Zhang, Y. Hong, Z. Tong, Z. Xiao, H. Bao, and Y. Yue, “Molecular dynamics study of interfacial thermal transport between silicene and substrates.,” Physical chemistry chemical physics : PCCP. 2015. link Times cited: 41 Abstract: In this work, the interfacial thermal transport across silic… read moreAbstract: In this work, the interfacial thermal transport across silicene and various substrates, i.e., crystalline silicon (c-Si), amorphous silicon (a-Si), crystalline silica (c-SiO2) and amorphous silica (a-SiO2) are explored by classical molecular dynamics (MD) simulations. A transient pulsed heating technique is applied in this work to characterize the interfacial thermal resistance in all hybrid systems. It is reported that the interfacial thermal resistances between silicene and all substrates decrease nearly 40% with temperature from 100 K to 400 K, which is due to the enhanced phonon couplings from the anharmonicity effect. Analysis of phonon power spectra of all systems is performed to interpret simulation results. Contradictory to the traditional thought that amorphous structures tend to have poor thermal transport capabilities due to the disordered atomic configurations, it is calculated that amorphous silicon and silica substrates facilitate the interfacial thermal transport compared with their crystalline structures. Besides, the coupling effect from substrates can improve the interface thermal transport up to 43.5% for coupling strengths χ from 1.0 to 2.0. Our results provide fundamental knowledge and rational guidelines for the design and development of the next-generation silicene-based nanoelectronics and thermal interface materials. read less NOT USED (low confidence) A. Arab and Q. Li, “Anisotropic thermoelectric behavior in armchair and zigzag mono- and fewlayer MoS2 in thermoelectric generator applications,” Scientific Reports. 2015. link Times cited: 58 NOT USED (low confidence) B. Cowen and M. El-Genk, “On force fields for molecular dynamics simulations of crystalline silica,” Computational Materials Science. 2015. link Times cited: 31 NOT USED (low confidence) Z. Zhang, Y. Yao, and X. Mao, “Modeling wave propagation induced fracture in rock with correlated lattice bond cell,” International Journal of Rock Mechanics and Mining Sciences. 2015. link Times cited: 16 NOT USED (low confidence) M. Caccin, Z. Li, J. Kermode, and A. Vita, “A framework for machine‐learning‐augmented multiscale atomistic simulations on parallel supercomputers,” International Journal of Quantum Chemistry. 2015. link Times cited: 35 Abstract: Recent advances in quantum mechanical (QM)-based molecular d… read moreAbstract: Recent advances in quantum mechanical (QM)-based molecular dynamics (MD) simulations have used machine-learning (ML) to predict, rather than recalculate, QM-accurate forces in atomic configurations sufficiently similar to previously encountered ones. Here, we discuss how ML approaches can be deployed within large-scale QM/MM materials simulations on massively parallel supercomputers, making QM zones of ≳1000 atoms routinely attainable. We argue that the ML approach allows computational effort to be concentrated on the most chemically active subregions of the QM zone, significantly improving the overall efficiency of the simulation. We thus propose a novel method to partition large QM regions into multiple subregions, which can be computed in parallel to achieve optimal scaling. Then we review a recently proposed QM/ML MD scheme (Z. Li, J.R. Kermode, A. De Vita Phys. Rev. Lett., 2015, 114, 096405), discussing how this could be efficiently combined with QM-zone partitioning. read less NOT USED (low confidence) J. Walton, L. Rivera-Rivera, R. Lucchese, and J. Bevan, “Canonical Potentials and Spectra within the Born-Oppenheimer Approximation.,” The journal of physical chemistry. A. 2015. link Times cited: 14 Abstract: A generalized formulation of canonical transformations and s… read moreAbstract: A generalized formulation of canonical transformations and spectra are used to investigate the concept of a canonical potential strictly within the Born-Oppenheimer approximation. Data for the most accurate available ground electronic state pairwise intermolecular potentials in H2, HD, D2, HeH(+), and LiH are used to rigorously evaluate such transformations. The corresponding potentials are generated explicitly using parameters calculated with algebraic functions from that of the single canonical potential of the simplest molecule, H2(+). The efficacy of this approach is further tested by direct comparison of the predicted eigenvalues of all vibrational states in the selected molecular systems considered with the corresponding most accurately known Born-Oppenheimer eigenvalues currently available. Deviations are demonstrated to be less than 2 cm(-1) for all vibrational states in H2, HD, D2, HeH(+), and LiH, with an average standard deviation of 0.27 cm(-1) for the 87 states considered. The implications of these results for molecular quantum chemistry are discussed. read less NOT USED (low confidence) X. Zhuo and H. Beom, “Size-dependent fracture properties of cracked silicon nanofilms,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2015. link Times cited: 19 NOT USED (low confidence) J. A. Rodríguez-Manzo, M. Puster, A. Nicolaï, V. Meunier, and M. Drndić, “DNA Translocation in Nanometer Thick Silicon Nanopores.,” ACS nano. 2015. link Times cited: 73 Abstract: Solid-state nanopores are single-molecule sensors that detec… read moreAbstract: Solid-state nanopores are single-molecule sensors that detect changes in ionic conductance (ΔG) when individual molecules pass through them. Producing high signal-to-noise ratio for the measurement of molecular structure in applications such as DNA sequencing requires low noise and large ΔG. The latter is achieved by reducing the nanopore diameter and membrane thickness. While the minimum diameter is limited by the molecule size, the membrane thickness is constrained by material properties. We use molecular dynamics simulations to determine the theoretical thickness limit of amorphous Si membranes to be ∼1 nm, and we designed an electron-irradiation-based thinning method to reach that limit and drill nanopores in the thinned regions. Double-stranded DNA translocations through these nanopores (down to 1.4 nm in thickness and 2.5 nm in diameter) provide the intrinsic ionic conductance detection limit in Si-based nanopores. In this regime, where the access resistance is comparable to the nanopore resistance, we observe the appearance of two conductance levels during molecule translocation. Considering the overall performance of Si-based nanopores, our work highlights their potential as a leading material for sequencing applications. read less NOT USED (low confidence) C. Taylor, J. Gale, H. Strehblow, and P. Marcus, “An Introduction to Corrosion Mechanisms and Models.” 2015. link Times cited: 4 NOT USED (low confidence) J. Walton, L. Rivera-Rivera, R. Lucchese, and J. Bevan, “A general transformation to canonical form for potentials in pairwise interatomic interactions.,” Physical chemistry chemical physics : PCCP. 2015. link Times cited: 11 Abstract: A generalized formulation of explicit force-based transforma… read moreAbstract: A generalized formulation of explicit force-based transformations is introduced to investigate the concept of a canonical potential in both fundamental chemical and intermolecular bonding. Different classes of representative ground electronic state pairwise interatomic interactions are referenced to a chosen canonical potential illustrating application of such transformations. Specifically, accurately determined potentials of the diatomic molecules H2, H2(+), HF, LiH, argon dimer, and one-dimensional dissociative coordinates in Ar-HBr, OC-HF, and OC-Cl2 are investigated throughout their bound potentials. Advantages of the current formulation for accurately evaluating equilibrium dissociation energies and a fundamentally different unified perspective on nature of intermolecular interactions will be emphasized. In particular, this canonical approach has significance to previous assertions that there is no very fundamental distinction between van der Waals bonding and covalent bonding or for that matter hydrogen and halogen bonds. read less NOT USED (low confidence) S. Ju and X.-gang Liang, “Detecting the phonon interference effect in Si/Ge nanocomposite by wave packets,” Applied Physics Letters. 2015. link Times cited: 13 Abstract: As the particle size in nanocomposites approaches the order … read moreAbstract: As the particle size in nanocomposites approaches the order of several nanometers that is comparable with the phonon wavelength, the phonon wave interference and particle scattering effect will lead to a much more complicated energy transport. This letter reports the investigation of phonon interference and scattering in Si/Ge nanocomposites by the phonon wave packet simulation. The particle size, particle layer number, and particle shape effects on the phonon transmission are considered. For both cubic and spherical particles, the phonon transmission coefficient fluctuates obviously with the increasing particle size and there are local peaks and valleys of transmission coefficient at certain particle sizes. The transmission decreases with the increasing layers of particle. The optical multi-layer transmission model can be applied to predict the transmission coefficient of Si/Ge nanocomposites with layered particles. The enhancement of thermal conductance is up to 19.1% due to the phonon interference effect. read less NOT USED (low confidence) X. Chen, Y.-W. Wang, X. Liu, X.-B. Wang, and Y.-Q. Zhao, “Study of structural and electronic properties of the silanone group as bulk defect in amorphous SiO2,” Journal of Non-crystalline Solids. 2015. link Times cited: 7 NOT USED (low confidence) A. Akimov and O. Prezhdo, “Large-Scale Computations in Chemistry: A Bird’s Eye View of a Vibrant Field.,” Chemical reviews. 2015. link Times cited: 171 NOT USED (low confidence) E. Gnecco and E. Meyer, “Elements of Friction Theory and Nanotribology.” 2015. link Times cited: 35 Abstract: Preface 1. Introduction 2. Dry friction and damped oscillato… read moreAbstract: Preface 1. Introduction 2. Dry friction and damped oscillators Part I. Elastic Contacts: 3. Elements of theory of elasticity 4. Normal contacts 5. Tangential contacts 6. Elastic rolling 7. Beams, plates and layered materials Part II. Advanced Contact Mechanics: 8. Rough contacts 9. Viscoelastic contacts 10. Adhesive contacts 11. Thermal and electric effects 12. Plastic contacts 13. Fracture 14. Stick-slip Part III. Nanotribology: 15. Atomic-scale stick-slip 16. Atomic-scale stick-slip in two dimensions 17. Instrumental and computational methods in nanotribology 18. Experimental results in nanotribology 19. Nanomanipulation 20. Wear on the nanoscale 21. Non-contact friction Part IV. Lubrication: 22. Drag in a viscous fluid 23. Lubrication 24. Viscous phenomena in confined or spreading liquids Appendix A Appendix B Appendix C Notes References Index. read less NOT USED (low confidence) Y. Jing, C. L. Zhang, Y. Liu, L. Guo, and Q. Meng, “Mechanical properties of kinked silicon nanowires,” Physica B-condensed Matter. 2015. link Times cited: 13 NOT USED (low confidence) T. Zushi, K. Ohmori, K. Yamada, and T. Watanabe, “Effect of aSiO2layer on the thermal transport properties of〈100〉Sinanowires: A molecular dynamics study,” Physical Review B. 2015. link Times cited: 2 Abstract: The presence of a ${\mathrm{SiO}}_{2}$ layer on Si nanowires… read moreAbstract: The presence of a ${\mathrm{SiO}}_{2}$ layer on Si nanowires (SiNWs) has been found through molecular dynamics simulation to reduce their thermal conductivity $(\ensuremath{\kappa})$, with $\ensuremath{\kappa}$ approaching the amorphous limit of Si as the oxide layer thickness is increased. Through analysis of the phonon energy dispersion and vibrational density of states (VDOS) spectrum, this decrease in $\ensuremath{\kappa}$ was attributed to dispersionless vibrational states that appear in the low energy range below 4 THz as a result of the lattice vibration of Si atoms near the ${\mathrm{SiO}}_{2}/\mathrm{Si}$ interface. The ${\mathrm{SiO}}_{2}$ layer also induced a low-frequency tail in the VDOS spectrum, the length of which was more closely correlated to the reduction in $\ensuremath{\kappa}$ than the frequency-integrated value of the VDOS spectrum. These findings provide a more refined explanation for the decrease in $\ensuremath{\kappa}$ than has been previously observed, and contribute to providing a greater understanding of the anomalistic vibration near the interface that is critical to determining the heat conductivity in nanoscale materials. read less NOT USED (low confidence) E. Lascaris, M. Hemmati, S. Buldyrev, H. Stanley, and C. Angell, “Diffusivity and short-time dynamics in two models of silica.,” The Journal of chemical physics. 2015. link Times cited: 17 Abstract: We discuss the dynamic behavior of two silica models, the BK… read moreAbstract: We discuss the dynamic behavior of two silica models, the BKS model (by van Beest, Kramer, and van Santen) and the WAC model (by Woodcock, Angell, and Cheeseman). Although BKS is considered the more realistic model for liquid silica, the WAC model has the unique property that it is very close to having a liquid-liquid critical point (LLCP), and this makes it particularly useful in studying the dynamics of models that do have a LLCP. We find that the diffusivity is a good indicator of how close a liquid is to criticality--the Si diffusivity shows a jump of 3-4 orders of magnitude when the pressure is reduced, which may be interpreted as an abrupt (though not first-order) transition from a high-density liquid state to a low-density liquid state. We show that this transition is captured by the Adam-Gibbs relation, which also allows us to estimate the configurational entropy of the system. read less NOT USED (low confidence) J. Zhang and S. Meguid, “On the piezoelectric potential of gallium nitride nanotubes,” Nano Energy. 2015. link Times cited: 45 NOT USED (low confidence) P. Süle and M. Szendrő, “Time-lapsed graphene moiré superlattices on Cu(1 1 1),” Modelling and Simulation in Materials Science and Engineering. 2015. link Times cited: 7 Abstract: We report classical molecular dynamics simulations (CMD) of … read moreAbstract: We report classical molecular dynamics simulations (CMD) of the moiré superlattice of graphene on Cu(1 1 1) using a new parameterized Abell–Tersoff potential for the graphene/Cu(1 1 1) interface fitted in this paper to nonlocal van der Waals density functional theory calculations. The interfacial force field with time-lapsed CMD provides superlattices in good quantitative agreement with the available experimental results. The long range coincidence supercells with nonequivalent moiré hills have also been identified and analyzed. Spot profile analysis reveals that the moiré spots are inequivalent over large areas, and their heights are randomly distributed. This result is in accordance with recent atomic force microscopy studies. Our simulations also shed light on the transient dynamics of the moiré superlattice in atomic detail. The moiré superlattice exhibits a pattern which is dynamical rather than statically pinned to the support, and can be observed mostly via time-lapsing. The instantaneous snapshots of the periodic moiré pattern at low temperature are already weakly disordered, lacking the apparent sharpness of the time-averaged pattern and of the scanning tunneling microscopy images. This suggests the existence of competition of orders—between a static (first-order) moiré superstructure and a dynamical (second-order) moiré superstructure. read less NOT USED (low confidence) X. Duan, B. Zhou, Y. Wen, R. Chen, H. Zhou, and B. Shan, “Lattice inversion modified embedded atom method for bcc transition metals,” Computational Materials Science. 2015. link Times cited: 14 NOT USED (low confidence) A. Bartók and G. Csányi, “Gaussian approximation potentials: A brief tutorial introduction,” International Journal of Quantum Chemistry. 2015. link Times cited: 432 Abstract: © 2015 Wiley Periodicals, Inc. We present a swift walk-throu… read moreAbstract: © 2015 Wiley Periodicals, Inc. We present a swift walk-through of our recent work that uses machine learning to fit interatomic potentials based on quantum mechanical data. We describe our Gaussian approximation potentials (GAP) framework, discuss a variety of descriptors, how to train the model on total energies and derivatives, and the simultaneous use of multiple models of different complexity. We also show a small example using QUIP, the software sandbox implementation of GAP that is available for noncommercial use. read less NOT USED (low confidence) J. Chen, G. Zhang, and B. Li, “Molecular Dynamics Simulations for Computing Thermal Conductivity of Nanomaterials: Molecular Dynamics Simulations for Computing Thermal Conductivity of Nanomaterials.” 2015. link Times cited: 2 NOT USED (low confidence) M. Ridgway, F. Djurabekova, and K. Nordlund, “Ion-solid interactions at the extremes of electronic energy loss: Examples for amorphous semiconductors and embedded nanostructures,” Current Opinion in Solid State & Materials Science. 2015. link Times cited: 22 NOT USED (low confidence) H. Chen, W. Y. Chen, Y. Chen, and K. Bi, “Out-of-Plane Thermal Conductivity of Silicon Thin Film Doped with Germanium,” Advanced Materials Research. 2014. link Times cited: 0 Abstract: The out-of-plane thermal conductivity of silicon thin film d… read moreAbstract: The out-of-plane thermal conductivity of silicon thin film doped with germanium is calculated by non-equilibrium molecular dynamics simulation using the Stillinger-Weber potential model. The silicon thin film is doped with germanium atoms in a random doping pattern with a doping density of 5% and 50% respectively. The effect of silicon thin film thickness on its thermal conductivity is investigated. The simulated thicknesses of silicon thin film doped with germanium range from 2.2 to 10.9 nm at an average temperature 300K. The simulation results indicate that the out-of-plane thermal conductivity of the silicon thin film doped with germanium decreases linearly with the decreasing film thickness. As for the film thickness of 9.8nm and the average temperature ranging from 250 to 1000 K, the investigation shows that the temperature dependence of the film thermal conductivity is not sensitive. read less NOT USED (low confidence) X. Duan, B. Zhou, R. Chen, H. Zhou, Y. Wen, and B. Shan, “Development of lattice inversion modified embedded atom method and its applications,” Current Applied Physics. 2014. link Times cited: 11 NOT USED (low confidence) S. Xiong, Y. Kosevich, K. Sääskilahti, Y. Ni, and S. Volz, “Tunable thermal conductivity in silicon twinning superlattice nanowires,” Physical Review B. 2014. link Times cited: 42 Abstract: Shiyun Xiong,1,2 Yuriy A. Kosevich,1,2,3 K. Saaskilahti,1,2,… read moreAbstract: Shiyun Xiong,1,2 Yuriy A. Kosevich,1,2,3 K. Saaskilahti,1,2,4 Yuxiang Ni,1,2,* and Sebastian Volz1,2,† 1CNRS, UPR 288 Laboratoire d’Energetique Moleculaire et Macroscopique, Combustion (EM2C), Grande Voie des Vignes, 92295 Châtenay-Malabry, France 2Ecole Centrale Paris, Grande Voie des Vignes, 92295 Châtenay-Malabry, France 3Semenov Institute of Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia 4Department of Biomedical Engineering and Computational Science, Aalto University, FI-00076 Aalto, Finland (Received 17 September 2014; revised manuscript received 29 October 2014; published 24 November 2014) read less NOT USED (low confidence) Y. Wang and K. Chang, “Continuum shape sensitivity analysis and what-if study for two-dimensional multi-scale crack propagation problems using bridging scale decomposition,” Structural and Multidisciplinary Optimization. 2014. link Times cited: 0 NOT USED (low confidence) Q. Lu, J. Kim, J. Farrell, D. Wales, and J. Straub, “Investigating the solid-liquid phase transition of water nanofilms using the generalized replica exchange method.,” The Journal of chemical physics. 2014. link Times cited: 9 Abstract: The generalized Replica Exchange Method (gREM) was applied t… read moreAbstract: The generalized Replica Exchange Method (gREM) was applied to study a solid-liquid phase transition in a nanoconfined bilayer water system using the monatomic water (mW) model. Exploiting optimally designed non-Boltzmann sampling weights with replica exchanges, gREM enables an effective sampling of configurations that are metastable or unstable in the canonical ensemble via successive unimodal energy distributions across phase transition regions, often characterized by S-loop or backbending in the statistical temperature. Extensive gREM simulations combined with Statistical Temperature Weighted Histogram Analysis Method (ST-WHAM) for nanoconfined mW water at various densities provide a comprehensive characterization of diverse thermodynamic and structural properties intrinsic to phase transitions. Graph representation of minimized structures of bilayer water systems determined by the basin-hopping global optimization revealed heterogeneous ice structures composed of pentagons, hexagons, and heptagons, consistent with an increasingly ordered solid phase with decreasing density. Apparent crossover from a first-order solid-liquid transition to a continuous one in nanoconfined mW water with increasing density of the system was observed in terms of a diminishing S-loop in the statistical temperature, smooth variation of internal energies and heat capacities, and a characteristic variation of lateral radial distribution functions, and transverse density profiles across transition regions. read less NOT USED (low confidence) Z. Yang, R. Feng, F. Su, D. Hu, and X. Ma, “Isotope and strain effects on thermal conductivity of silicon thin film,” Physica E-low-dimensional Systems & Nanostructures. 2014. link Times cited: 9 NOT USED (low confidence) B. Liu et al., “INTERFACE THERMAL CONDUCTANCE AND RECTIFICATION IN HYBRID GRAPHENE/SILICENE MONOLAYER,” Carbon. 2014. link Times cited: 110 NOT USED (low confidence) L. Yang, N. Yang, and B. Li, “Thermoelectric Properties of Nanoscale three dimensional Si Phononic Crystal,” arXiv: Materials Science. 2014. link Times cited: 21 NOT USED (low confidence) R. Guo and B. Huang, “Thermal transport in nanoporous Si: Anisotropy and junction effects,” International Journal of Heat and Mass Transfer. 2014. link Times cited: 23 NOT USED (low confidence) X. Zhao and Y. Shin, “Ablation enhancement of silicon by ultrashort double-pulse laser ablation,” Applied Physics Letters. 2014. link Times cited: 45 Abstract: In this study, the ultrashort double-pulse ablation of silic… read moreAbstract: In this study, the ultrashort double-pulse ablation of silicon is investigated. An atomistic simulation model is developed to analyze the underlying physics. It is revealed that the double-pulse ablation could significantly increase the ablation rate of silicon, compared with the single pulse ablation with the same total pulse energy, which is totally different from the case of metals. In the long pulse delay range (over 1 ps), the enhancement is caused by the metallic transition of melted silicon with the corresponding absorption efficiency. At ultrashort pulse delay (below 1 ps), the enhancement is due to the electron excitation by the first pulse. The enhancement only occurs at low and moderate laser fluence. The ablation is suppressed at high fluence due to the strong plasma shielding effect. read less NOT USED (low confidence) Z. Zhang and Y. Chen, “Modeling nonlinear elastic solid with correlated lattice bond cell for dynamic fracture simulation,” Computer Methods in Applied Mechanics and Engineering. 2014. link Times cited: 38 NOT USED (low confidence) H. Zhou, N. D. Duan, and B. Wang, “Synergistic and Strengthening Mechanism of Twin Boundaries under Nanoindentations for Cadmium Telluride Semiconductors,” Advanced Materials Research. 2014. link Times cited: 1 Abstract: In this study, eight nanotwinned cadmium telluride (CdTe or … read moreAbstract: In this study, eight nanotwinned cadmium telluride (CdTe or CZ) models were employed to investigate the synergistic and strengthening mechanism of twin boundaries under nanoindentations, using molecular dynamics (MD) simulations. Twin thickness between adjacent boundaries of 16 nm exhibited the maximum hardness during unloading conditions, among eight MD models with twin thickness varied from 4 to 23 nm. The maximum hardness was formed by the synergistic and strengthening effect induced by the stress fields between upper and lower twin boundaries under nanoindentations. When the twin thickness was less than 16 nm, the hardness increased with increasing twin thickness. Whereas, when the twin thickness was more than 16 nm, the hardness decreased with increasing twin thickness. read less NOT USED (low confidence) O. Sharia, J. Holzgrafe, N. Park, and G. Henkelman, “Rare event molecular dynamics simulations of plasma induced surface ablation.,” The Journal of chemical physics. 2014. link Times cited: 2 Abstract: The interaction of thermal Ar plasma particles with Si and W… read moreAbstract: The interaction of thermal Ar plasma particles with Si and W surfaces is modeled using classical molecular dynamics (MD) simulations. At plasma energies above the threshold for ablation, the ablation yield can be calculated directly from MD. For plasma energies below threshold, the ablation yield becomes exponentially low, and direct MD simulations are inefficient. Instead, we propose an integration method where the yield is calculated as a function of the Ar incident kinetic energy. Subsequent integration with a Boltzmann distribution at the temperature of interest gives the thermal ablation yield. At low plasma temperatures, the ablation yield follows an Arrhenius form in which the activation energy is shown to be the threshold energy for ablation. Interestingly, equilibrium material properties, including the surface and bulk cohesive energy, are not good predictors of the threshold energy for ablation. The surface vacancy formation energy is better, but is still not a quantitative predictor. An analysis of the trajectories near threshold shows that ablation occurs by different mechanisms on different material surfaces, and both the mechanism and the binding of surface atoms determine the threshold energy. read less NOT USED (low confidence) Y. Fu and J. H. Song, “On computing stress in polymer systems involving multi-body potentials from molecular dynamics simulation.,” The Journal of chemical physics. 2014. link Times cited: 14 Abstract: Hardy stress definition has been restricted to pair potentia… read moreAbstract: Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifies the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems. read less NOT USED (low confidence) T. Zohdi, “Additive particle deposition and selective laser processing-a computational manufacturing framework,” Computational Mechanics. 2014. link Times cited: 111 NOT USED (low confidence) H. Nguyen, V. V. Hoang, and L. N. T. Minh, “Melting of crystalline silicon thin films,” Computational Materials Science. 2014. link Times cited: 9 NOT USED (low confidence) D. V. Singh, C. Cassidy, P. Grammatikopoulos, F. Djurabekova, K. Nordlund, and M. Sowwan, “Heterogeneous Gas-Phase Synthesis and Molecular Dynamics Modeling of Janus and Core–Satellite Si–Ag Nanoparticles,” Journal of Physical Chemistry C. 2014. link Times cited: 73 Abstract: Heterogeneous gas-phase condensation is a promising method o… read moreAbstract: Heterogeneous gas-phase condensation is a promising method of producing hybrid multifunctional nanoparticles with tailored composition and microstructure but also intrinsically introduces greater complexity to the nucleation process and growth kinetics. Herein, we report on the synthesis and growth modeling of silicon–silver (Si–Ag) hybrid nanoparticles using gas-aggregated cosputtering from elemental Si and Ag source targets. The final Si–Ag ensemble size was manipulated in the range 5–15 nm by appropriate tuning of the deposition parameters, while variations in the Si–Ag sputtering power ratio, from 1.8 to 2.25, allowed distinctive Janus and core–satellite structures, respectively, to be produced. Molecular dynamics simulations indicate that the individual species first form independent clusters of Si and Ag without significant intermixing. Collisions between unlike species are unstable in the early stages of growth (<100 ns), with large temperature differences resulting in rapid energy exchange and sep... read less NOT USED (low confidence) K. F. Murphy, B. Piccione, M. B. Zanjani, J. Lukes, and D. Gianola, “Strain- and defect-mediated thermal conductivity in silicon nanowires.,” Nano letters. 2014. link Times cited: 76 Abstract: The unique thermal transport of insulating nanostructures is… read moreAbstract: The unique thermal transport of insulating nanostructures is attributed to the convergence of material length scales with the mean free paths of quantized lattice vibrations known as phonons, enabling promising next-generation thermal transistors, thermal barriers, and thermoelectrics. Apart from size, strain and defects are also known to drastically affect heat transport when introduced in an otherwise undisturbed crystalline lattice. Here we report the first experimental measurements of the effect of both spatially uniform strain and point defects on thermal conductivity of an individual suspended nanowire using in situ Raman piezothermography. Our results show that whereas phononic transport in undoped Si nanowires with diameters in the range of 170-180 nm is largely unaffected by uniform elastic tensile strain, another means of disturbing a pristine lattice, namely, point defects introduced via ion bombardment, can reduce the thermal conductivity by over 70%. In addition to discerning surface- and core-governed pathways for controlling thermal transport in phonon-dominated insulators and semiconductors, we expect our novel approach to have broad applicability to a wide class of functional one- and two-dimensional nanomaterials. read less NOT USED (low confidence) G. Copie et al., “Atomic Scale Modeling of Two-Dimensional Molecular Self-Assembly on a Passivated Si Surface,” Journal of Physical Chemistry C. 2014. link Times cited: 25 Abstract: The self-assembly of two-dimensional (2D) molecular structur… read moreAbstract: The self-assembly of two-dimensional (2D) molecular structures on a solid surface relies on the subtle balance between noncovalent intermolecular and molecule–surface forces. The energetics of 2D molecular lattices forming different patterns on a passivated semiconductor surface are here investigated by a combination of atomistic simulation methods. Density-functional theory provides structure and charges of the molecules, while metadynamics with empirical forces provides a best guess for the lowest-energy adsorption sites of single molecules and dimers. Subsequently, molecular dynamics simulations of extended molecular assemblies with empirical forces yield the most favorable lattice structures at finite temperature and pressure. The theoretical results are in good agreement with scanning tunneling microscopy observations of self-assembled molecular monolayers on a B-doped Si(111) surface, thus allowing to rationalize the competition of long-range dispersion forces between the molecules and the surface. ... read less NOT USED (low confidence) M. C. Nguyen, X. Zhao, C. Wang, and K. Ho, “sp3-hybridized framework structure of group-14 elements discovered by genetic algorithm,” Physical Review B. 2014. link Times cited: 21 Abstract: Group-14 elements, including C, Si, Ge, and Sn, can form var… read moreAbstract: Group-14 elements, including C, Si, Ge, and Sn, can form various stable and metastable structures. Finding new metastable structures of group-14 elements with desirable physical properties for new technological applications has attracted a lot of interest. Using a genetic algorithm, we discovered a new low-energy metastable distorted sp3-hybridized framework structure of the group-14 elements. It has P42/mnm symmetry with 12 atoms per unit cell. The void volume of this structure is as large as 139.7A3 for Si P42/mnm, and it can be used for gas or metal-atom encapsulation. Band-structure calculations show that P42/mnm structures of Si and Ge are semiconducting with energy band gaps close to the optimal values for optoelectronic or photovoltaic applications. With metal-atom encapsulation, the P42/mnm structure would also be a candidate for rattling-mediated superconducting or used as thermoelectric materials. read less NOT USED (low confidence) S. Goel, “The current understanding on the diamond machining of silicon carbide,” Journal of Physics D: Applied Physics. 2014. link Times cited: 139 Abstract: The Glenn Research Centre of NASA, USA (www.grc.nasa.gov/WWW… read moreAbstract: The Glenn Research Centre of NASA, USA (www.grc.nasa.gov/WWW/SiC/, silicon carbide electronics) is in pursuit of realizing bulk manufacturing of silicon carbide (SiC), specifically by mechanical means. Single point diamond turning (SPDT) technology which employs diamond (the hardest naturally-occurring material realized to date) as a cutting tool to cut a workpiece is a highly productive manufacturing process. However, machining SiC using SPDT is a complex process and, while several experimental and analytical studies presented to date aid in the understanding of several critical processes of machining SiC, the current knowledge on the ductile behaviour of SiC is still sparse. This is due to a number of simultaneously occurring physical phenomena that may take place on multiple length and time scales. For example, nucleation of dislocation can take place at small inclusions that are of a few atoms in size and once nucleated, the interaction of these nucleations can manifest stresses on the micrometre length scales. The understanding of how these stresses manifest during fracture in the brittle range, or dislocations/phase transformations in the ductile range, is crucial to understanding the brittle–ductile transition in SiC. Furthermore, there is a need to incorporate an appropriate simulation-based approach in the manufacturing research on SiC, owing primarily to the number of uncertainties in the current experimental research that includes wear of the cutting tool, poor controllability of the nano-regime machining scale (effective thickness of cut), and coolant effects (interfacial phenomena between the tool, workpiece/chip and coolant), etc. In this review, these two problems are combined together to posit an improved understanding on the current theoretical knowledge on the SPDT of SiC obtained from molecular dynamics simulation. read less NOT USED (low confidence) J. Behler, “Representing potential energy surfaces by high-dimensional neural network potentials,” Journal of Physics: Condensed Matter. 2014. link Times cited: 293 Abstract: The development of interatomic potentials employing artifici… read moreAbstract: The development of interatomic potentials employing artificial neural networks has seen tremendous progress in recent years. While until recently the applicability of neural network potentials (NNPs) has been restricted to low-dimensional systems, this limitation has now been overcome and high-dimensional NNPs can be used in large-scale molecular dynamics simulations of thousands of atoms. NNPs are constructed by adjusting a set of parameters using data from electronic structure calculations, and in many cases energies and forces can be obtained with very high accuracy. Therefore, NNP-based simulation results are often very close to those gained by a direct application of first-principles methods. In this review, the basic methodology of high-dimensional NNPs will be presented with a special focus on the scope and the remaining limitations of this approach. The development of NNPs requires substantial computational effort as typically thousands of reference calculations are required. Still, if the problem to be studied involves very large systems or long simulation times this overhead is regained quickly. Further, the method is still limited to systems containing about three or four chemical elements due to the rapidly increasing complexity of the configuration space, although many atoms of each species can be present. Due to the ability of NNPs to describe even extremely complex atomic configurations with excellent accuracy irrespective of the nature of the atomic interactions, they represent a general and therefore widely applicable technique, e.g. for addressing problems in materials science, for investigating properties of interfaces, and for studying solvation processes. read less NOT USED (low confidence) Y. Zou, J. Cai, X. Huai, F. Xin, and Z. Guo, “Molecular dynamics simulation of heat conduction in Si nano-films induced by ultrafast laser heating,” Thin Solid Films. 2014. link Times cited: 7 NOT USED (low confidence) R. Malek and K. Kassmi, “Monte Carlo simulations of thin semiconductor films deposition. Case of InAs/GaAs,” 2014 International Conference on Multimedia Computing and Systems (ICMCS). 2014. link Times cited: 0 Abstract: Monte Carlo simulation of heteroepitaxial growth with large … read moreAbstract: Monte Carlo simulation of heteroepitaxial growth with large mismatch is reported. The simulation model combines Monte Carlo method with an energetic model derived from the Valence Force Field (VFF). The energetic model is needed to determine stress and strain in the deposited film. Through the use of Monte Carlo method, it was possible to handle the random nature of the heteroepitaxial growth based on Arrhenius law and Poisson process. The results concern (1) the morphology of the surface, particularly the formation of islands defined by the (111) facets, (2) the growth mode as well as the formation of cavities in the deposited layers defined by these facets, (3) the strain relaxation in the deposited film. The case of In/As/GaAs transition (8% lattice mismatch) is investigated. read less NOT USED (low confidence) P. A. Apte et al., “The freezing tendency towards 4-coordinated amorphous networks causes an increase in the heat capacity of supercooled Stillinger–Weber silicon,” RSC Advances. 2014. link Times cited: 7 Abstract: Supercooled liquid silicon (Si), modeled by the Stillinger–W… read moreAbstract: Supercooled liquid silicon (Si), modeled by the Stillinger–Weber (SW) potential, has been shown to undergo transition to low density amorphous phases at 1060 K in previous studies. Furthermore, the constant pressure heat capacity Cp has been found to exhibit a large increase as the liquid is cooled to 1060 K. In this work, we examine the nature of the equilibrium and the relaxation process of supercooled SW Si in the temperature range of 1060 K to 1070 K at zero pressure. We find that the relaxation of the supercooled liquid leads to a sharp irreversible decrease in the fluctuation of the two body energy of the largest connected network of 4-coordinated particles. Such a process implies a tightening of the bonds (i.e. freezing or jamming) of the network, and is accompanied by a sharp increase in the fraction of the 4-coordinated particles in the system. We find that the jamming (or freezing) process shows a sudden acceleration across a dynamical instability point that occurs at a unique potential energy state of the network. Further, we find that the occurrence of the dynamical instability is associated with the appearance of a straight line region in the cumulative potential energy distributions with a configurational temperature close to 1060 K. We conclude that the supercooled liquid state must be regarded as a constrained equilibrium state, since the accessible microstates are constrained by the inherent tendency of the system to approach the dynamical instability point. Thus all properties of supercooled liquid SW-Si, including the rise in Cp at 1060 K, can be attributed to the freezing tendency of the 4-coordinated particle network. read less NOT USED (low confidence) W. Paul, D. Oliver, and P. Grütter, “Indentation-formed nanocontacts: an atomic-scale perspective.,” Physical chemistry chemical physics : PCCP. 2014. link Times cited: 15 Abstract: One-to-one comparisons between indentation experiments and a… read moreAbstract: One-to-one comparisons between indentation experiments and atomistic modelling have until recently been hampered by the discrepancy in length scales of the two approaches. Here, we review progress in atomic-scale nanoindentation experiments employing scanning probe techniques to achieve depth-sensing indentation and field ion microscopy to permit detailed indenter characterization. This perspective addresses both mechanical (dislocation nucleation, defect structures, adhesion, indenter effects) and electronic (interface, disorder, and vacancy scattering) properties of indentation-formed contacts. read less NOT USED (low confidence) T. Ichiye, “Water in the Liquid State: A Computational Viewpoint.” 2014. link Times cited: 6 NOT USED (low confidence) H. Xie, M. Hu, and H. Bao, “Thermal conductivity of silicene from first-principles,” Applied Physics Letters. 2014. link Times cited: 148 Abstract: Silicene, as a graphene-like two-dimensional material, now r… read moreAbstract: Silicene, as a graphene-like two-dimensional material, now receives exceptional attention of a wide community of scientists and engineers beyond graphene. Despite extensive study on its electric property, little research has been done to accurately calculate the phonon transport of silicene so far. In this paper, thermal conductivity of monolayer silicene is predicted from first-principles method. At 300 K, the thermal conductivity of monolayer silicene is found to be 9.4 W/mK and much smaller than bulk silicon. The contributions from in-plane and out-of-plane vibrations to thermal conductivity are quantified, and the out-of-plane vibration contributes less than 10% of the overall thermal conductivity, which is different from the results of the similar studies on graphene. The difference is explained by the presence of small buckling, which breaks the reflectional symmetry of the structure. The flexural modes are thus not purely out-of-plane vibration and have strong scattering with other modes. read less NOT USED (low confidence) Z. Zhang, Y. Chen, and H. Zheng, “A modified Stillinger–Weber potential-based hyperelastic constitutive model for nonlinear elasticity,” International Journal of Solids and Structures. 2014. link Times cited: 25 NOT USED (low confidence) G. Barinovs, A. Sabanskis, and A. Muiznieks, “Study of silicon crystal surface formation based on molecular dynamics simulation results,” Journal of Crystal Growth. 2014. link Times cited: 6 NOT USED (low confidence) Y. He, X.-Y. Li, H. Li, Y. Jiang, and X. Bian, “Layering transition in confined silicon.,” Nanoscale. 2014. link Times cited: 12 Abstract: The structure of quasi-2D liquid silicon confined to slit na… read moreAbstract: The structure of quasi-2D liquid silicon confined to slit nanopores has been investigated using molecular dynamics (MD) simulations. An obvious structural change from a low-density low-coordinated liquid to a high-density highly coordinated liquid has been found in the confined silicon with the increase of the slit size. This kind of structural transition results from layering in the confined silicon, which disappears with the increase of temperature. In the process of layering transition, the coordination distribution of quasi-2D liquid undergoes an evolutionary process from the initial non-uniform distribution to the final uniform distribution. In addition, our results also indicate that the increase of pressure will also induce a layering transition in the confined silicon. read less NOT USED (low confidence) G. Opletal and S. Russo, “Atomistic Modeling and Simulations of Chalcogenide Glasses.” 2014. link Times cited: 1 NOT USED (low confidence) T. Frolov, W. C. Carter, and M. Asta, “Capillary instability in nanowire geometries.,” Nano letters. 2014. link Times cited: 12 Abstract: In this study, we present atomistic simulations and theoreti… read moreAbstract: In this study, we present atomistic simulations and theoretical analyses that reveal a capillary instability that is intrinsic to wetting geometries characteristic of the vapor-liquid-solid mechanism for nanowire growth. The analysis establishes a transition between axisymmetric and tilted wetting configurations that occurs when the triple line geometry satisfies Young's force-balance condition. The intrinsic nature of the instability is anticipated to be linked to the phenomenon of nanowire kinking in response to changes in environmental conditions, such that the current results may have broad implications for the design of experimental strategies for controlled growth of crystalline nanowires with complex geometries. read less NOT USED (low confidence) M. C. Nguyen, X. Zhao, Y. Wang, C. Wang, and K. Ho, “Genetic algorithm prediction of crystal structure of metastable Si-IX phase,” Solid State Communications. 2014. link Times cited: 7 NOT USED (low confidence) N. V. Hung, C. S. Thang, N. C. Toan, and H. Hieu, “Temperature dependence of Debye–Waller factors of semiconductors,” Vacuum. 2014. link Times cited: 2 NOT USED (low confidence) A. Portavoce and G. Tréglia, “Theoretical investigation of Cottrell atmosphere in silicon,” Acta Materialia. 2014. link Times cited: 11 NOT USED (low confidence) Z. Zhang, B. Wang, and X. Zhang, “A maximum in the hardness of nanotwinned cadmium telluride,” Scripta Materialia. 2014. link Times cited: 12 NOT USED (low confidence) T. Gao, W. Yan, X. Guo, X. Qin, and Q. Xie, “STRUCTURAL EVOLUTIONS AND PROPERTIES OF GERMANIUM CLUSTERS DURING RAPID COOLING PROCESSES,” Modern Physics Letters B. 2013. link Times cited: 0 Abstract: In this paper, structural evolutions of germanium cluster ar… read moreAbstract: In this paper, structural evolutions of germanium cluster are studied by molecular dynamics simulations during quenching processes. Three-dimensional atomic configurations of germanium cluster are established. Our simulation results are in good agreement with the experimental ones. The structural properties of germanium are described in detail by means of several structural analysis methods. It is obtained that the 〈2, 3, 0, 0 〉 and 〈4, 0, 0, 0 〉 polyhedra play different roles in the course of liquid-to-amorphous transition. 〈4, 0, 0, 0〉 tend to be gathered together to form single crystal regions. However, 〈2, 3, 0, 0 〉 has five neighboring atoms that destroy the translational symmetry of the crystal structure, and enhances the transition barrier to crystals. Consequently, it is difficult for 〈4, 0, 0, 0 〉 to form crystal germanium at the cooling rate of 1.0 × 1010 °C/s. read less NOT USED (low confidence) W. M. Brown and M. Yamada, “Implementing molecular dynamics on hybrid high performance computers - Three-body potentials,” Comput. Phys. Commun. 2013. link Times cited: 106 NOT USED (low confidence) S. Cajahuaringa, M. de Koning, and A. Antonelli, “Revisiting dynamics near a liquid-liquid phase transition in Si and Ga: the fragile-to-strong transition.,” The Journal of chemical physics. 2013. link Times cited: 6 Abstract: Using molecular dynamics simulations we analyze the dynamics… read moreAbstract: Using molecular dynamics simulations we analyze the dynamics of two atomic liquids that display a liquid-liquid phase transition (LLPT): Si described by the Stillinger-Weber potential and Ga as modeled by the modified embedded-atom model. In particular, our objective is to investigate the extent to which the presence of a dip in the self-intermediate scattering function is a manifestation of an excess of vibrational states at low frequencies and may be associated with a fragile-to-strong transition (FTST) across the LLPT, as suggested recently. Our results suggest a somewhat different picture. First, in the case of Ga we observe the appearance of an excess of vibrational states at low frequencies, even in the absence of the appearance of a dip in the self-intermediate scattering function across the LLPT. Second, studying the behavior of the shear viscosities traversing the LLPTs we find that both substances are fragile in character above and below their respective LLPT temperatures. Instead of a FTST in an absolute sense these findings are more in line with a view in which the LLPTs are accompanied by a transition from a more fragile to a less fragile liquid. Furthermore, we do not find this transition to correlate with the presence of a dip in the intermediate scattering function. read less NOT USED (low confidence) Y. Umeno, W. Nöhring, A. Iskandarov, and E. Bitzek, “Atomistic Model Analysis of Local and Global Instabilities in Crystals at Finite Temperature,” Key Engineering Materials. 2013. link Times cited: 0 Abstract: There have been a lot of studies dedicated to structural ins… read moreAbstract: There have been a lot of studies dedicated to structural instability in solids. For local instability, theoretical (ideal) strength of crystals has been extensively studied with ab initio calculations. Global instability taking into account the collective motion of atoms involved in deformation has also been investigated. However, these studies have usually been done at 0 K and little has been understood about the effect of temperature. In this study, we demonstrate computational approaches to the effect of temperature on local and global instabilities. Ideal shear strength (ISS) of silicon at finite temperatures is calculated by molecular dynamics (MD) simulations with an empirical potential. ISS is obtained as a function of temperature. Our results imply that, unlike metals, the reduction in ISS by temperature cannot be estimated simply by taking into account thermal expansion of volume. In addition, global instability for dislocation nucleation in a Cu thin film model under tension is investigated. We first evaluated instability modes at 0 K with increasing strain, and then performed MD simulations at 50 K. After the nucleation of a partial dislocation, the second dislocation can be one to create a twin or one to create another partial dislocation. These different deformations can be understood as the competition of latent instability modes that have relatively small eigenvalues. read less NOT USED (low confidence) H. Hieu and V. Hùng, “ISOTOPIC EFFECT IN DEBYE–WALLER FACTOR OF CRYSTALLINE GERMANIUM,” Modern Physics Letters B. 2013. link Times cited: 0 Abstract: The statistical moment method has been used to study the eff… read moreAbstract: The statistical moment method has been used to study the effect of isotopic mass difference on extended X-ray absorption fine structure (EXAFS) Debye–Waller factor of crystalline germanium. The effects on the parallel mean-square relative displacement and the atomic mean square displacements have been considered. This research also exposed that isotopic effect is noticeable where the correlated atomic motion is concerned. Numerical calculations have been performed for two isotopes 70Ge and 76Ge in range of temperature from 0 K to 600 K. Our results are compared with available experimental EXAFS data [J. Purans et al., Phys. Rev. Lett.100 (2008) 055901] as well as with lattice dynamics calculations [A. Sanson, Solid State Sci.12 (2010) 1988] and the good agreements are found. read less NOT USED (low confidence) T. Ichinomiya, “Temporal coarse-graining method to simulate the movement of atoms,” J. Comput. Phys. 2013. link Times cited: 0 NOT USED (low confidence) Y. Wang et al., “Antimony-mediated control of misfit dislocations and strain at the highly lattice mismatched GaSb/GaAs interface.,” ACS applied materials & interfaces. 2013. link Times cited: 8 Abstract: Determining the atomic structure of misfit dislocations at h… read moreAbstract: Determining the atomic structure of misfit dislocations at highly lattice mismatched interface is essential to optimize the quality of the epitaxial layer. Here, with aberration corrected scanning transmission electron microscopy at sub-Angstrom resolution and molecular dynamics simulation, we investigated the atomic structure of misfit dislocations at GaSb/GaAs interface. New types of Lomer misfit dislocation formed on an Sb wetting monolayer were observed, in contrast to a conventional misfit dislocation whose core is located at interface. These Sb-mediated dislocations have highly localized cores and offer more capability to confine the mismatch strain at the interface. The low strain atomic configuration of Sb-mediated dislocations is driven by minimization of the core energy. This unveiled mechanism may pave the way to the growth of high quality hetero-epitaxial layers. read less NOT USED (low confidence) S. D. Nath, “Study of the effect of sizes on the structural properties of SiO2 glass by molecular dynamics simulations,” Journal of Non-crystalline Solids. 2013. link Times cited: 8 NOT USED (low confidence) M. L. Nietiadi and H. Urbassek, “Influence of local curvature on sputtering,” Applied Physics Letters. 2013. link Times cited: 19 Abstract: Sputtering depends on the local surface curvature; it is hig… read moreAbstract: Sputtering depends on the local surface curvature; it is higher for convex and lower for concave surfaces than for a flat reference target. We analyze this dependence theoretically and show that the sputter yield primarily depends on a dimension-free curvature parameter, and second on the relative variance of the deposited-energy distribution in the direction along the ion beam. Using molecular dynamics, we study the effects in an exemplary way for 500 eV Ar impact on an a-Si target; here, we compare a wire and a valley structure (radii of curvature 2.5 nm) with a planar target. Our findings demonstrate that the sputter yield, the crater function, and the angular distribution of sputtered particles strongly depend on the curvature. read less NOT USED (low confidence) P. Guo, Y. Luo, M. Li, P. Yuan, Q. Sun, and Y. Jia, “Atomistic Views of Dynamical Fracture Instabilities in Silicon: Molecular Dynamics Studies,” Modern Physics Letters B. 2013. link Times cited: 0 Abstract: This study investigates the crystallographic orientations mo… read moreAbstract: This study investigates the crystallographic orientations most widely known to exhibit fractures in silicon, such as those on the (111) plane cracks travelling along the $[\bar 211]$ direction (${\rm Si}(111)~[\bar 211]$ cracks). The (111) crack plane is believed to be the most stable fracture plane. However, fracture instabilities caused by brittle crack jumps remain on (111) the crack plane in a discontinuous manner. In this study, molecular dynamics simulations were performed to investigate the atomistic-level studies of fracture properties under a uniaxial tensile load (mode I load) in the (111) $[\bar 211]$Si system. Our simulation results suggest that the formation of untypical-membered Si atomic rings in the vicinity of the crack tip, which can be induced by atomic stress near the crack tip, has an important role in the behavior of crack propagation instabilities. The presence of untypical-membered Si atomic rings acts as a self-protecting mechanism that contribute in maintaining the crack on the (... read less NOT USED (low confidence) W. Noid, “Perspective: Coarse-grained models for biomolecular systems.,” The Journal of chemical physics. 2013. link Times cited: 673 Abstract: By focusing on essential features, while averaging over less… read moreAbstract: By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems. read less NOT USED (low confidence) T. Liang et al., “Classical atomistic simulations of surfaces and heterogeneous interfaces with the charge-optimized many body (COMB) potentials,” Materials Science & Engineering R-reports. 2013. link Times cited: 207 NOT USED (low confidence) N. Podolska and A. I. Zhmakin, “Semiconductor nanostructure properties. Molecular Dynamic Simulations,” Journal of Physics: Conference Series. 2013. link Times cited: 0 Abstract: The need for research is based on the fact that development … read moreAbstract: The need for research is based on the fact that development of non-planar semiconductor nanosystems and nanomaterials with controlled properties is an important scientific and industrial problem. So, final scientific and technological problem is the creation of adequate modern methods and software for growth and properties simulation and optimization of various III-V (GaAs, InAs, InP, InGaAs etc.) nanostructures (e.g. nanowires) with controlled surface morphology, crystal structure, optical, transport properties etc. Accordingly, now we are developing a specialized computer code for atomistic simulation of structural (distribution of atoms and impurities, elastic and force constants, strain distribution etc.) and thermodynamic (mixing energy, interaction energy, surface energy etc.) properties of the nanostructures. Some simulation results are shown too. read less NOT USED (low confidence) E. Bylaska, J. Weare, and J. Weare, “Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations.,” The Journal of chemical physics. 2013. link Times cited: 13 Abstract: Parallel in time simulation algorithms are presented and app… read moreAbstract: Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0[ellipsis (horizontal)]tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup (serial execution/timeparallel execution time) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step. read less NOT USED (low confidence) G. Opletal, T. Petersen, I. Snook, and S. Russo, “HRMC_2.0: Hybrid Reverse Monte Carlo method with silicon, carbon and germanium potentials,” Comput. Phys. Commun. 2013. link Times cited: 24 NOT USED (low confidence) Z. Li, D. Chen, J. Wang, and L. Shao, “Molecular dynamics simulation of Coulomb explosion and structural changes in silicon,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2013. link Times cited: 4 NOT USED (low confidence) L. Lu, J. Dama, and G. Voth, “Fitting coarse-grained distribution functions through an iterative force-matching method.,” The Journal of chemical physics. 2013. link Times cited: 73 Abstract: An iterative coarse-graining method is developed for systema… read moreAbstract: An iterative coarse-graining method is developed for systematically converting an atomistic force field to a model at lower resolution that is able to accurately reproduce the distribution functions defined in the coarse-grained potential. The method starts from the multiscale coarse-graining (MS-CG) approach, and it iteratively refines the distribution functions using repeated applications of the MS-CG algorithm. It is justified on the basis of the force matching normal equation, which can be considered a discrete form of the Yvon-Born-Green equation in liquid state theory. Numerical results for molecular systems involving pairwise nonbonded and three-body bonded interactions are obtained, and comparison with other approaches in literature is provided. read less NOT USED (low confidence) T. Liang et al., “Reactive Potentials for Advanced Atomistic Simulations,” Materials Research-ibero-american Journal of Materials. 2013. link Times cited: 180 Abstract: This article reviews recent advances in the development of r… read moreAbstract: This article reviews recent advances in the development of reactive empirical force fields or potentials. In particular, we compare two widely used reactive potentials with variable-charge schemes that are desirable for multicomponent or multifunctional systems: the ReaxFF (reactive force field) and charge-optimized many-body (COMB) potentials. Several applications of these approaches in atomistic simulations that involve metal-based heterogeneous systems are also discussed. read less NOT USED (low confidence) I. Szlufarska, K. Ramesh, and D. Warner, “Simulating Mechanical Behavior of Ceramics Under Extreme Conditions,” Annual Review of Materials Research. 2013. link Times cited: 14 Abstract: The mechanical behavior of ceramics in extreme environments … read moreAbstract: The mechanical behavior of ceramics in extreme environments can be qualitatively different from that observed at ambient conditions and at typical loading rates. For instance, during shock loading the fracture of ceramics is not controlled by the largest flaw. Computer simulations play an increasingly important role in understanding and predicting material behavior, in particular under conditions in which experiments might be challenging or expensive. Here, we review the strengths and limitations of simulation techniques that are most commonly used to model the mechanical behavior of ceramics. We discuss specific application areas of simulations, focusing on the effects of high strain rate, confined deformation volume, altered material chemistry, and high temperature. We conclude by providing examples of future opportunities for modeling studies in this field. read less NOT USED (low confidence) J. N. Sarma, R. Chowdhury, and R. Jayaganthan, “Mechanical behavior of gallium nitride nanosheets using molecular dynamics,” Computational Materials Science. 2013. link Times cited: 13 NOT USED (low confidence) G. Norman and V. Stegailov, “Stochastic theory of the classical molecular dynamics method,” Mathematical Models and Computer Simulations. 2013. link Times cited: 0 NOT USED (low confidence) T. Gao, W. Yan, X. Guo, Y. Qin, and Q. Xie, “Structural properties in liquid Si during rapid cooling processes,” Physica B-condensed Matter. 2013. link Times cited: 5 NOT USED (low confidence) C. Li, W. Huang, C. Hou, and W. Ge, “Multi-Scale Simulation of Grain Boundary Structure Effects in POLY-Si Thin Film Solar Cell,” International Journal of Modern Physics C. 2013. link Times cited: 5 Abstract: The atomic structures of grain boundary (GB) and their effec… read moreAbstract: The atomic structures of grain boundary (GB) and their effect on the performance of poly-Si thin film solar cell are studied by multi-scale simulations. First, the atomic structures of various GBs are calculated using molecular dynamics. Subsequently, the energy band diagram are obtained by ab-initio calculations. Then, finite difference method is performed to obtain solar cell performance. The results show that the Σ5 (twist) GB can greatly enhance the carriers recombination and results in small short-circuit current density (JSC) and open-circuit voltage (VOC). However, the Σ17 (twist and tilt) GBs have little influence on the cell performance. Also revealed in the simulations is that the GB near the p–n junction leads to very small JSC and VOC. When the distance between GB and p–n junction increases from about 1.10 μm to 3.65 μm, the conversion efficiency increases by about 29%. The thickness effect of solar cell containing the Σ5 (twist) GB on the cell performance is also studied. The results show that the conversion efficiency and JSC increase rapidly as the thickness increases from about 5.2 μm to 40 μm. When the thickness ranges from about 40 μm to 70 μm, the efficiency and the JSC both increase gradually and reach their own peak values at about 70 μm. When the thickness exceeds 70 μm, the efficiency and JSC both decrease gradually. However, the VOC keeps increasing with increase in thickness. The effects of GB on the carrier transport and recombination processes are discussed to understand the above results. read less NOT USED (low confidence) M. L. Nietiadi, Y. Rosandi, Y. Rosandi, J. Lorincik, and H. Urbassek, “Sputtering of a silicon surface: Preferential sputtering of surface impurities,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2013. link Times cited: 4 NOT USED (low confidence) D. Nagai, K. Miyazaki, and H. Tsukamoto, “Molecular dynamics simulations on heat conduction in nano‐porous Si,” Heat Transfer Research. 2013. link Times cited: 1 Abstract: We investigated heat conduction in a nano-porous silicon by … read moreAbstract: We investigated heat conduction in a nano-porous silicon by molecular-dynamics simulations (MDs). We calculated the phonon dispersion curves of the nano-structured Si to understand the effects of nano-structures on phonon properties, such as phonon group velocity and phonon density of states. The dispersion curves were calculated from MD's results by using the 2D time–space Fourier transformation. Frequency gaps in phonon dispersion curves reduce the phonon group velocity in the periodic nano-porous structures. Moreover the group velocity of phonon was reduced due to new phonon modes even though the nano-porous was random. The results showed that nano-porous structures reduce the thermal conductivity as well as super lattices. © 2011 Wiley Periodicals, Inc. Heat Trans Asian Res; Published online in Wiley Online Library (wileyonlinelibrary.com/journal/htj). DOI 10.1002/htj.20370 read less NOT USED (low confidence) C. Hou, J. Xu, P. Wang, W. Huang, and X. Wang, “Efficient GPU-accelerated molecular dynamics simulation of solid covalent crystals,” Comput. Phys. Commun. 2013. link Times cited: 28 NOT USED (low confidence) Y. Azdoud, F. Han, and G. Lubineau, “A Morphing framework to couple non-local and local anisotropic continua,” International Journal of Solids and Structures. 2013. link Times cited: 71 NOT USED (low confidence) V. Tomar, “Timescaling in Multiscale Mechanics of Nanowires and Nanocrystalline Materials.” 2013. link Times cited: 0 NOT USED (low confidence) N. Giovambattista, “The Liquid–Liquid Phase Transition, Anomalous Properties, and Glass Behavior of Polymorphic Liquids.” 2013. link Times cited: 3 NOT USED (low confidence) R. Ruberto, G. Pastore, and M. Tosi, “An interionic force law for HgCl2 from first-principles molecular calculations,” Physics Letters A. 2013. link Times cited: 4 NOT USED (low confidence) J.-W. Jiang, J. Zhao, and T. Rabczuk, “Size-sensitive Young’s modulus of kinked silicon nanowires,” Nanotechnology. 2013. link Times cited: 7 Abstract: We perform both classical molecular dynamics simulations and… read moreAbstract: We perform both classical molecular dynamics simulations and beam model calculations to investigate the Young’s modulus of kinked silicon nanowires (KSiNWs). The Young’s modulus is found to be highly sensitive to the arm length of the kink and is essentially inversely proportional to the arm length. The mechanism underlying the size dependence is found to be the interplay between the kink angle potential and the arm length potential, where we obtain an analytic relationship between the Young’s modulus and the arm length of the KSiNW. Our results provide insight into the application of this novel building block in nanomechanical devices. read less NOT USED (low confidence) V. Brázdová and D. Bowler, “Calculating Energies and Forces.” 2013. link Times cited: 0 NOT USED (low confidence) C. Ciobanu, C. Wang, and K. Ho, “Crystal Structure Prediction.” 2013. link Times cited: 3 NOT USED (low confidence) C. Ciobanu, C. Wang, and K. Ho, “Other Methodologies for Investigating Atomic Structure.” 2013. link Times cited: 0 NOT USED (low confidence) X. Liu, W. Seider, and T. Sinno, “A general method for spatially coarse-graining Metropolis Monte Carlo simulations onto a lattice.,” The Journal of chemical physics. 2013. link Times cited: 3 Abstract: A recently introduced method for coarse-graining standard co… read moreAbstract: A recently introduced method for coarse-graining standard continuous Metropolis Monte Carlo simulations of atomic or molecular fluids onto a rigid lattice of variable scale [X. Liu, W. D. Seider, and T. Sinno, Phys. Rev. E 86, 026708 (2012)] is further analyzed and extended. The coarse-grained Metropolis Monte Carlo technique is demonstrated to be highly consistent with the underlying full-resolution problem using a series of detailed comparisons, including vapor-liquid equilibrium phase envelopes and spatial density distributions for the Lennard-Jones argon and simple point charge water models. In addition, the principal computational bottleneck associated with computing a coarse-grained interaction function for evolving particle positions on the discretized domain is addressed by the introduction of new closure approximations. In particular, it is shown that the coarse-grained potential, which is generally a function of temperature and coarse-graining level, can be computed at multiple temperatures and scales using a single set of free energy calculations. The computational performance of the method relative to standard Monte Carlo simulation is also discussed. read less NOT USED (low confidence) D. T. Limmer and D. Chandler, “The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water. II.,” The Journal of chemical physics. 2013. link Times cited: 21 Abstract: This paper extends our earlier studies of free energy functi… read moreAbstract: This paper extends our earlier studies of free energy functions of density and crystalline order parameters for models of supercooled water, which allows us to examine the possibility of two distinct metastable liquid phases [D. T. Limmer and D. Chandler, J. Chem. Phys. 135, 134503 (2011) and preprint arXiv:1107.0337 (2011)]. Low-temperature reversible free energy surfaces of several different atomistic models are computed: mW water, TIP4P/2005 water, Stillinger-Weber silicon, and ST2 water, the last of these comparing three different treatments of long-ranged forces. In each case, we show that there is one stable or metastable liquid phase, and there is an ice-like crystal phase. The time scales for crystallization in these systems far exceed those of structural relaxation in the supercooled metastable liquid. We show how this wide separation in time scales produces an illusion of a low-temperature liquid-liquid transition. The phenomenon suggesting metastability of two distinct liquid phases is actually coarsening of the ordered ice-like phase, which we elucidate using both analytical theory and computer simulation. For the latter, we describe robust methods for computing reversible free energy surfaces, and we consider effects of electrostatic boundary conditions. We show that sensible alterations of models and boundary conditions produce no qualitative changes in low-temperature phase behaviors of these systems, only marginal changes in equations of state. On the other hand, we show that altering sampling time scales can produce large and qualitative non-equilibrium effects. Recent reports of evidence of a liquid-liquid critical point in computer simulations of supercooled water are considered in this light. read less NOT USED (low confidence) Y. Dong, Q. Li, and A. Martini, “Molecular dynamics simulation of atomic friction: A review and guide,” Journal of Vacuum Science and Technology. 2013. link Times cited: 158 Abstract: This paper reviews recent progress in molecular dynamics sim… read moreAbstract: This paper reviews recent progress in molecular dynamics simulation of atomic-scale friction measured by an atomic force microscopy. Each section of the review focuses on an individual condition or parameter that affects atomic friction including materials, surfaces, compliance, contact area, normal load, temperature, and velocity. The role each parameter plays is described in the context of both experimental measurements and simulation predictions. In addition, the discussion includes an overview of the research community's current understanding of observed effects, guidelines for implementation of those effects in an atomistic simulation, and suggestions for future research to address open questions. Taken together, this review conveys the message that friction at the atomic scale is affected by many interrelated parameters and that the use of molecular dynamics simulation as a predictive tool can be accomplished only through careful model design. read less NOT USED (low confidence) C. Y. Chuang, Q. Li, D. Leonhardt, S. Han, and T. Sinno, “Atomistic analysis of Ge on amorphous SiO2 using an empirical interatomic potential,” Surface Science. 2013. link Times cited: 14 NOT USED (low confidence) M. H. Khadem and A. Wemhoff, “Comparison of Green–Kubo and NEMD heat flux formulations for thermal conductivity prediction using the Tersoff potential,” Computational Materials Science. 2013. link Times cited: 57 NOT USED (low confidence) Y. Gan and J. K. Chen, “Atomic-level modeling of a silicon nanofilm irradiated by ultrashort-pulsed laser bursts,” International Journal of Thermal Sciences. 2013. link Times cited: 4 NOT USED (low confidence) J. Thibault, J. Rouviere, and A. Bourret, “Grain Boundaries in Semiconductors,” Materials Science and Technology. 2013. link Times cited: 2 Abstract: The sections in this article are
Introduction
Grain Bo… read moreAbstract: The sections in this article are
Introduction
Grain Boundary Structure: Concepts and Tools
Grain Boundary Definitions
Geometrical Concepts
Dislocation Model
Primary Dislocation Network
Secondary Dislocation Network
Stress Field Associated with Grain Boundaries
Structural Unit Descriptions
Stick and Ball Structural Units
Energetic Structural Units
Algebraic Structural Units
Structural Units and Dislocations/Disclinations
The Limits of the Structural Unit Descriptions
Computer Simulation Techniques
Methods
Boundary Conditions
Interaction Laws
Experimental Techniques
Grain Boundary Structure: Experience and Simulation Results
Silicon and Germanium
Tilt Grain Boundaries
Twist Grain Boundaries
Diamond
SiC
GaAs
GaN
AlN
NiO
Comments on Grain Boundary Structures
Electrical Properties of Grain Boundaries
Introduction
Electrical Effects Induced by Grain Boundaries
Electronic States Associated with a Grain Boundary
Potential Barrier and Transport Properties
Dynamic Properties and Recombination Properties
Experimental Methods for Measuring the Grain Boundary Electrical Activity
Methods Based on Transport
Transient Methods
Correlation Between Electrical Activity and Structure
Transport Experiments in Bicrystals
Transient Properties Measured on Bicrystals
Emission and Capture Properties of Silicon and Germanium Grain Boundaries
Polycrystalline Silicon
Intrinsic or Extrinsic Origin of Electrical Activity of Grain Boundaries
Impurity Segregation and Precipitation Induced by Grain Boundaries
Introduction
Dopant Elements
Oxygen and Sulfur
Transition Elements
Copper
Nickel
Iron
Conclusions
Mechanical Properties of Grain Boundaries in Semiconductors
Introduction
Interaction Between Dislocations and Grain Boundaries
Dislocation Absorption
Dislocation Transmission Across Grain Boundaries
Grain Boundaries as a Dislocation Source
Grain Boundary Dislocation Movement
Physical Consequences
Grain Boundary Migration
Recovery of the Grain Boundary Structure and Cavitation
Deformation Modelling
Conclusions read less NOT USED (low confidence) X. W. Zhou, R. Jones, J. Duda, and P. Hopkins, “Molecular dynamics studies of material property effects on thermal boundary conductance.,” Physical chemistry chemical physics : PCCP. 2013. link Times cited: 38 Abstract: Thermal boundary resistance (inverse of conductance) between… read moreAbstract: Thermal boundary resistance (inverse of conductance) between different material layers can dominate the overall thermal resistance in nanostructures and therefore impact the performance of the thermal property limiting nano devices. Because relationships between material properties and thermal boundary conductance have not been fully understood, optimum devices cannot be developed through a rational selection of materials. Here we develop generic interatomic potentials to enable material properties to be continuously varied in extremely large molecular dynamics simulations to explore the dependence of thermal boundary conductance on the characteristic properties of materials such as atomic mass, stiffness, and interfacial crystallography. To ensure that our study is not biased to a particular model, we employ different types of interatomic potentials. In particular, both a Stillinger-Weber potential and a hybrid embedded-atom-method + Stillinger-Weber potential are used to study metal-on-semiconductor compound interfaces, and the results are analyzed considering previous work based upon a Lennard-Jones (LJ) potential. These studies, therefore, reliably provide new understanding of interfacial transport phenomena particularly in terms of effects of material properties on thermal boundary conductance. Our most important finding is that thermal boundary conductance increases with the overlap of the vibrational spectra between metal modes and the acoustic modes of the semiconductor compound, and increasing the metal stiffness causes a continuous shift of the metal modes. As a result, the maximum thermal boundary conductance occurs at an intermediate metal stiffness (best matched to the semiconductor stiffness) that maximizes the overlap of the vibrational modes. read less NOT USED (low confidence) A. Rimola, D. Costa, M. Sodupe, J. Lambert, and P. Ugliengo, “Silica surface features and their role in the adsorption of biomolecules: computational modeling and experiments.,” Chemical reviews. 2013. link Times cited: 499 Abstract: Silica Surface Features and Their Role in the Adsorption of … read moreAbstract: Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments / Albert Rimola;Dominique Costa;Mariona Sodupe;Jean-François Lambert;Piero Ugliengo. In: CHEMICAL REVIEWS. ISSN 0009-2665. STAMPA. 113:6(2013), pp. 4216-4313. Original Citation: Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments read less NOT USED (low confidence) Y. Gan and J. K. Chen, “Numerical Analysis of Ultrashort Pulse Laser-Induced Thermomechanical Response of Germanium Thin Films,” Nanoscale and Microscale Thermophysical Engineering. 2012. link Times cited: 4 Abstract: Ultrashort pulse laser heating of a germanium nanofilm was s… read moreAbstract: Ultrashort pulse laser heating of a germanium nanofilm was simulated using a combined continuum–atomistic method that couples the molecular dynamics and a self-consistent energy model for ultrafast laser–semiconductor interaction. Both a single pulse and a pulse burst were considered. To accurately describe laser energy deposition, the transient optical properties were computed based on the Drude formula. It was found that for a single pulse at low fluence (e.g., 0.02 J/cm2), the pulse duration had little impact on the lattice temperature response. In contrast, a higher lattice temperature could be obtained for a longer pulse (e.g., 5 ps) at higher fluences (e.g., 0.06 J/cm2) due to lower surface reflectivity. A strong thermal stress wave could be induced by the laser heating, with its maximum compression and tension occurring in the front and rear film regions, respectively. The investigations of laser burst heating revealed that a laser burst not only can retain the advantages of ultrashort pulse lasers but can enhance the photon efficiency for material melting as well. read less NOT USED (low confidence) K. Zhong, Q. Meng, and Z. Yang, “Theoretical Study on the Interaction between Shuffle 60° Dislocation and Hexavacancy in Silicon,” Advanced Materials Research. 2012. link Times cited: 0 Abstract: The interaction of the shuffle 60° dislocation with a regula… read moreAbstract: The interaction of the shuffle 60° dislocation with a regular chain of hexavacancies was investigated via the molecular dynamics simulation with Stillinger-Weber potential. The results show that an attraction exists between the shuffle 60° dislocation and hexavacany. The attraction energy is dependent obviously upon the hexavacancy concentration. The dislocation can overcome the pinning of vacancies under a critical resolved shear stress, and a linear relationship is found between the critical stress and hexavacancy concentration. read less NOT USED (low confidence) S.-W. Ren, J. Sun, and Y. Hao, “Simulation of the Growth, Structure and Crystallization of the Amorphous Silicon Thin Film,” Advanced Materials Research. 2012. link Times cited: 3 Abstract: In this paper, using classical molecular dynamics, the growt… read moreAbstract: In this paper, using classical molecular dynamics, the growth of the amorphous silicon thin film deposited on the single crystal silicon is simulated and studied by Stillinger-Weber potential. The radial distribution functions of particles are calculated and the Voronoi diagrams of the films are given. The regular and irregular structures in the film are analyzed and the part crystallization condition is discussed. It is found that the features of the film are related with the ratio of the substrate temperature and the temperature of the incident atoms. The density of the deposited silicon film is obtained. The value of the density is about 2.2515g/cm3 which is consistent with the experiment data. read less NOT USED (low confidence) T. Besmann et al., “Modeling Deep Burn TRISO particle nuclear fuel,” Journal of Nuclear Materials. 2012. link Times cited: 17 NOT USED (low confidence) M. Wang, X. Shan, and N. Yang, “Understanding length dependences of effective thermal conductivity of nanowires,” Physics Letters A. 2012. link Times cited: 24 NOT USED (low confidence) M. L. Nietiadi, Y. Rosandi, M. Kopnarski, and H. Urbassek, “Sputtering of dimers off a silicon surface,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2012. link Times cited: 5 NOT USED (low confidence) A. Dongare, B. Lamattina, and A. Rajendran, “Strengthening Behavior and Tension–Compression Strength–Asymmetry in Nanocrystalline Metal–Ceramic Composites,” Journal of Engineering Materials and Technology-transactions of The Asme. 2012. link Times cited: 10 NOT USED (low confidence) C.-ying Wang, Z. Wang, G. Li, and Q. Meng, “INTERACTION BETWEEN THE 30° PARTIAL DISLOCATION AND HEX-VACANCY IN SILICON,” Modern Physics Letters B. 2012. link Times cited: 3 Abstract: The molecular dynamics (MD) method is used to investigate th… read moreAbstract: The molecular dynamics (MD) method is used to investigate the interaction between the 30° partial dislocation and hex-vacancy (V6) in Si. The interaction processes are described in detail and compared with the prior results of mono-vacancy (V1) and di-vacancy (V2). It is found that dislocations are pinned by V6 when the shear stresses are smaller than a definite critical value τc. It illustrates that the encountered two segments beside vacant sites parallel each other or annihilate. Moreover, it is shown that the critical shear stress τc is mainly determined by both the migration barrier of kink and the volume of vacancy. Although V6 cannot make dislocations move faster due to the present small models, it may lower the dislocation density in certain conditions due to the pinning effect. read less NOT USED (low confidence) K. Bi et al., “The thermal conductivity of SiGe heterostructure nanowires with different cores and shells,” Physics Letters A. 2012. link Times cited: 14 NOT USED (low confidence) T. Ito et al., “Si Damage Due to Oblique-Angle Ion Impact Relevant for Vertical Gate Etching Processes,” Japanese Journal of Applied Physics. 2012. link Times cited: 11 Abstract: In reactive ion etching (RIE) processes of vertical metal ox… read moreAbstract: In reactive ion etching (RIE) processes of vertical metal oxide semiconductor (MOS) devices, damages caused by ion bombardment at oblique incidence may affect the device performance. In this study, damage formation on Si surfaces by energetic hydrogen and halogen ions has been examined for different angles of incidence with the use of a multi-beam system. The beam experiments and molecular dynamics simulations have shown that the depth of a Si damage layer caused by H+ ion injections has weak dependence on the angle of incidence. It is also found experimentally that the Cl+ or Br+ ion etching yield of a Si substrate that is damaged by energetic hydrogen ions prior to Cl+ or Br+ ion injections is essentially the same as that of the undamaged Si substrate. The results indicate that, in the etching process of vertical MOS gate structures, surface bombardment by energetic hydrogen ions even at oblique incidence may cause several-nanometer deep damages to the Si channels but etching yields for the gate fabrication are unlikely to be altered by the surface damages. read less NOT USED (low confidence) B. D. Jensen, A. Bandyopadhyay, K. Wise, and G. Odegard, “Parametric Study of ReaxFF Simulation Parameters for Molecular Dynamics Modeling of Reactive Carbon Gases.,” Journal of chemical theory and computation. 2012. link Times cited: 35 Abstract: The development of innovative carbon-based materials can be … read moreAbstract: The development of innovative carbon-based materials can be greatly facilitated by molecular modeling techniques. Although the Reax Force Field (ReaxFF) can be used to simulate the chemical behavior of carbon-based systems, the simulation settings required for accurate predictions have not been fully explored. Using the ReaxFF, molecular dynamics (MD) simulations are used to simulate the chemical behavior of pure carbon and hydrocarbon reactive gases that are involved in the formation of carbon structures such as graphite, buckyballs, amorphous carbon, and carbon nanotubes. It is determined that the maximum simulation time step that can be used in MD simulations with the ReaxFF is dependent on the simulated temperature and selected parameter set, as are the predicted reaction rates. It is also determined that different carbon-based reactive gases react at different rates, and that the predicted equilibrium structures are generally the same for the different ReaxFF parameter sets, except in the case of the predicted formation of large graphitic structures with the Chenoweth parameter set under specific conditions. read less NOT USED (low confidence) T. Liang, B. Devine, S. Phillpot, and S. Sinnott, “Variable charge reactive potential for hydrocarbons to simulate organic-copper interactions.,” The journal of physical chemistry. A. 2012. link Times cited: 89 Abstract: A variable charge reactive empirical potential for carbon-ba… read moreAbstract: A variable charge reactive empirical potential for carbon-based materials, hydrocarbons, organometallics, and their interfaces is developed within the framework of charge optimized many-body (COMB) potentials. The resulting potential contains improved expressions for the bond order and self-energy, which gives a flexible, robust, and integrated treatment of different bond types in multicomponent and multifunctional systems. It furthermore captures the dissociation and formation of the chemical bonds and appropriately and dynamically determines the associated charge transfer, thus providing a powerful method to simulate the complex chemistry of many-atom systems in changing environments. The resulting COMB potential is used in a classical molecular dynamics simulation of the room temperature, low energy deposition of ethyl radicals on the Cu (111) surface (a system with ∼5000 atoms) to demonstrate its capabilities at describing organic-metal interactions in a dynamically changing environment. read less NOT USED (low confidence) B. S. Jabes, D. Nayar, D. Dhabal, V. Molinero, and C. Chakravarty, “Water and other tetrahedral liquids: order, anomalies and solvation,” Journal of Physics: Condensed Matter. 2012. link Times cited: 45 Abstract: In order to understand the common features of tetrahedral li… read moreAbstract: In order to understand the common features of tetrahedral liquids with water-like anomalies, the relationship between local order and anomalies has been studied using molecular dynamics simulations for three categories of such liquids: (a) atomistic rigid-body models for water (TIP4P, TIP4P/2005, mTIP3P, SPC/E), (b) ionic melts, BeF2 (TRIM model) and SiO2 (BKS potential) and (c) Stillinger–Weber liquids parametrized to model water (mW) and silicon. Rigid-body, atomistic models for water and the Stillinger–Weber liquids show a strong correlation between tetrahedral and pair correlation order and the temperature for the onset of the density anomaly is close to the melting temperature. In contrast, the ionic melts show weaker and more variable degrees of correlation between tetrahedral and pair correlation metrics, and the onset temperature for the density anomaly is more than twice the melting temperature. In the case of water, the relationship between water-like anomalies and solvation is studied by examining the hydration of spherical solutes (Na+, Cl−, Ar) in water models with different temperature regimes of anomalies (SPC/E, TIP4P and mTIP3P). For both ionic and nonpolar solutes, the local structure and energy of water molecules is essentially the same as in bulk water beyond the second-neighbour shell. The local order and binding energy of water molecules are not perturbed by the presence of a hydrophobic solute. In the case of ionic solutes, the perturbation is largely localized within the first hydration shell. The binding energies for the ions are strongly dependent on the water models and clearly indicate that the geometry of the partial charge distributions, and the associated multipole moments, play an important role. However the anomalous behaviour of the water network has been found to be unimportant for polar solvation. read less NOT USED (low confidence) T. Aoki, T. Seki, and J. Matsuo, “Molecular dynamics study of crater formation by core-shell structured cluster impact,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2012. link Times cited: 6 NOT USED (low confidence) H. Park et al., “Ab initio based empirical potential used to study the mechanical properties of molybdenum,” Physical Review B. 2012. link Times cited: 70 Abstract: Density-functional theory energies, forces, and elastic cons… read moreAbstract: Density-functional theory energies, forces, and elastic constants determine the parametrization of an empirical, modified embedded-atom method potential for molybdenum. The accuracy and transferability of the potential are verified by comparison to experimental and density-functional data for point defects, phonons, thermal expansion, surface and stacking fault energies, and ideal shear strength. Searching the energy landscape predicted by the potential using a genetic algorithm verifies that it reproduces not only the correct bcc ground state of molybdenum but also all low-energy metastable phases. The potential is also applicable to the study of plastic deformation and used to compute energies, core structures, and Peierls stresses of screw and edge dislocations. Molybdenum's high strength and high-temperature stability make this refractory metal very attractive for use in advanced process technologies. The motion of dislocations is generally accepted to be responsible for the complex deformation behavior of this transition metal. 1-8 In recent years progress has been made on the description of the properties of screw dislocations using density-functional theory (DFT), tight- binding calculations, and empirical potentials. 9-19 However, DFT and tight-binding techniques are limited to small system sizes, which is problematic due to the long-range strain field of dislocations, and current empirical potentials lack the required accuracy for the description of the dislocation structure. Simulations of dislocation motion and interactions require efficient interatomic potentials which accurately describe the dislocation energies, core structures, and motion. In this work we develop an empirical potential for Mo which predicts the ideal shear strength, generalized stacking fault en- ergies, energies of dislocations, and the Peierls stress and core structure of the � 111� /2 screw dislocation. The potential form is given by the modified embedded-atom method (MEAM) and the potential parameters are optimized usingabinitio energies, lattice parameters, forces, and elastic constants. Section II describes the calculations for the DFT database, the functional form of the MEAM potential, and the optimization of the potential parameters to the DFT database. The accuracy of the potential for structural, elastic, and defect properties is verified in Sec. III by comparison to DFT results and experiments. A genetic algorithm search of the energy landscape of the MEAM potential confirms that the potential reproduces the correct bcc ground state and predicts several low-energy metastable structures whose energies agree well with DFT results. Results of the MEAM potential for formation energies of point defects, phonon dispersion, thermal expansion, surface energies, ideal shear strength, and generalized stacking faults for the MEAM potential closely match DFT results and available experimental data. In Sec. IV we apply the potential to determine energies and Peierls stresses of the screw and edge dislocation in bcc Mo. The results show that the MEAM potential accurately describes the structural and mechanical properties of Mo and should be applicable to simulate the motion of dislocations and the plastic deformation of Mo. read less NOT USED (low confidence) H. Lai, S. Cea, H. Kennel, and S. Dunham, “Molecular dynamics modeling of solid phase epitaxial regrowth,” Journal of Applied Physics. 2012. link Times cited: 3 Abstract: Solid phase epitaxial regrowth (SPER) is of great technologi… read moreAbstract: Solid phase epitaxial regrowth (SPER) is of great technological importance in semiconductor device fabrication. A better understanding and accurately modeling of its behavior are vital to the design of fabrication processes and the improvement of the device performance. In this paper, SPER was modeled by molecular dynamics (MD) with Tersoff potential. Extensive MD simulations were conducted to study the dependence of SPER rate on temperature, growth orientation, pressure, and uniaxial stress. The simulation data were fitted to empirical formula, and the results were compared with experimental data. It was concluded that MD with Tersoff potential can qualitatively describe the SPER process. For a more quantitatively accurate model, larger simulation systems and a better interatomic potential are needed. read less NOT USED (low confidence) Y. Lü and M. Chen, “Surface layering-induced crystallization of Ni–Si alloy drops,” Acta Materialia. 2012. link Times cited: 15 NOT USED (low confidence) U. Monteverde, M. Migliorato, and D. Powell, “Empirical interatomic potential for the mechanical, vibrational and thermodynamic properties of semiconductors,” Journal of Physics: Conference Series. 2012. link Times cited: 12 Abstract: Empirical models are widely used to simulate large atomic st… read moreAbstract: Empirical models are widely used to simulate large atomic structures where instead ab initio methods are not practical because of computational limitations. However models such as Tersoff potential [8], [9], Valence Force Field [13], [14] or Stillinger- Weber potential [15] have some restrictions in correctly predicting simultaneously both elastic and vibrational properties of the crystals [18]. Thus, extension of the functional form of the potentials by including further atomic interactions [20] [21] compared to the simple 2- and 3-body terms, is required. An empirical interatomic potential is proposed which represents a substantial improvement of the Tersoff potential for semiconductors modelling. The new model includes multi-bond interactions and the volume dependency by considering the tetrahedron distortions of the covalent crystal. read less NOT USED (low confidence) E. K. Lee et al., “Large thermoelectric figure-of-merits from SiGe nanowires by simultaneously measuring electrical and thermal transport properties.,” Nano letters. 2012. link Times cited: 175 Abstract: The strongly correlated thermoelectric properties have been … read moreAbstract: The strongly correlated thermoelectric properties have been a major hurdle for high-performance thermoelectric energy conversion. One possible approach to avoid such correlation is to suppress phonon transport by scattering at the surface of confined nanowire structures. However, phonon characteristic lengths are broad in crystalline solids, which makes nanowires insufficient to fully suppress heat transport. Here, we employed Si-Ge alloy as well as nanowire structures to maximize the depletion of heat-carrying phonons. This results in a thermal conductivity as low as ∼1.2 W/m-K at 450 K, showing a large thermoelectric figure-of-merit (ZT) of ∼0.46 compared with those of SiGe bulks and even ZT over 2 at 800 K theoretically. All thermoelectric properties were "simultaneously" measured from the same nanowires to facilitate accurate ZT measurements. The surface-boundary scattering is prominent when the nanowire diameter is over ∼100 nm, whereas alloying plays a more important role in suppressing phonon transport for smaller ones. read less NOT USED (low confidence) S. Sinnott and D. Brenner, “Three decades of many-body potentials in materials research,” MRS Bulletin. 2012. link Times cited: 45 Abstract: A brief history of atomic simulation as it was used in chemi… read moreAbstract: A brief history of atomic simulation as it was used in chemistry, physics, and materials science is presented starting with seminal work by Eyring in the 1930s through to current work and future challenges. This article provides the background and perspective needed to understand the ways in which reactive many-body potentials developed over the last three decades and have impacted materials research. It also explains the way in which this substantial impact on the field has been facilitated by increases in computational resources and traces the development of reactive potentials, which have steadily increased in complexity and sophistication over time. Together with the other contributions in this issue of MRS Bulletin , this article will help guide and inspire the next generation of computational materials scientists and engineers as they build on current capabilities to expand atomic simulation into new and exciting areas of materials research. read less NOT USED (low confidence) K. Esfarjani, G. Chen, Y. Chalopin, A. Henry, and S. Volz, “Thermal interface conductance in Si/Ge superlattices by equilibrium molecular dynamics.” 2012. link Times cited: 133 Abstract: Gesuperlattices.Thermalconductancecalculationsofsuperlattice… read moreAbstract: Gesuperlattices.Thermalconductancecalculationsofsuperlatticeswithperiodthicknessesrangingfrom0.5to60nmarepresentedaswellasthetemperaturedependence.ResultshavebeencomparedtocomplementaryGreen-Kubothermalconductivitycalculationsdemonstratingthatthermalconductivityofperfectsuperlatticescanbedirectlydeduced from interfacial conductance in the investigated period range. This confirms the predominant role ofinterfaces in materials with large phonon mean free paths.DOI: 10.1103/PhysRevB.85.195302 PACS number(s): 65 read less NOT USED (low confidence) K. Miyazaki, S. Tanaka, and D. Nagai, “Heat Conduction of a Porous Material,” Journal of Heat Transfer-transactions of The Asme. 2012. link Times cited: 11 Abstract: In this study we introduce our numerical and experimental wo… read moreAbstract: In this study we introduce our numerical and experimental works for the thermal conductivity reduction by using a porous material. Recently thermal conductivity reduction has been one of the key technologies to enhance the figure of merit (ZT) of a thermoelectric material. We carry out numerical calculations of heat conduction in porous materials, such as, phonon Boltzmann transport (BTE), molecular dynamics simulations (MD), in order to investigate the mechanism of the thermal conductivity reduction of a porous material. In the BTE, we applied the periodic boundary conditions with constant heat flux to calculate the effective thermal conductivity of porous materials. In the MD simulation, we calculated phonon properties of Si by using the Stillinger-Weber potential at constant temperature with periodic boundary conditions in the x, y and z directions. Phonon dispersion curves of single crystal of Si calculated from MD results by time-space 2D FFT are agreed well with reference data. Moreover, the effects of nano-porous structures on both the phonon group velocity and the phonon density of states (DOS) are discussed. At last, we made a porous p-type Bi2 Te3 by nano-particles prepared by a beads milling method. The thermal conductivity is one-fifth of that of a bulk material as well as keeping the same Seebeck coefficient as the bulk value. However electrical conductivity was much reduced, and the ZT was only 0.048.Copyright © 2009 by ASME read less NOT USED (low confidence) J. Welker and F. Giessibl, “Revealing the Angular Symmetry of Chemical Bonds by Atomic Force Microscopy,” Science. 2012. link Times cited: 118 Abstract: Working the Angles on Chemical Bonding The forces exerted by… read moreAbstract: Working the Angles on Chemical Bonding The forces exerted by chemical bonds depend not only on the distances between atoms but also upon the angles between them. Welker and Giessibl (p. 444; see the cover) probed the angular dependence of the CO molecule adsorbed on top of a copper atom on an atomically flat Cu(111) surface using both atomic force microscopy and scanning tunneling microscopy (STM). Probe tips with three different tip-atom-symmetry environments were used. All three tips delivered similar STM images, but force probes revealed the angular dependence of the CO bond to the surface and provided data for a model of the changes in bond energy. The angular dependence of chemical bonding forces was determined for carbon monoxide adsorbed on a copper surface atom. We have measured the angular dependence of chemical bonding forces between a carbon monoxide molecule that is adsorbed to a copper surface and the terminal atom of the metallic tip of a combined scanning tunneling microscope and atomic force microscope. We provide tomographic maps of force and current as a function of distance that revealed the emergence of strongly directional chemical bonds as tip and sample approach. The force maps show pronounced single, dual, or triple minima depending on the orientation of the tip atom, whereas tunneling current maps showed a single minimum for all three tip conditions. We introduce an angular dependent model for the bonding energy that maps the observed experimental data for all observed orientations and distances. read less NOT USED (low confidence) A. Fedorov, Z. Popov, A. Kuzubov, and S. Ovchinnikov, “Theoretical study of the diffusion of lithium in crystalline and amorphous silicon,” JETP Letters. 2012. link Times cited: 16 NOT USED (low confidence) A. Oluwajobi, “Molecular Dynamics Simulation of Nanoscale Machining.” 2012. link Times cited: 6 Abstract: Product miniaturization is a major motivation for the develo… read moreAbstract: Product miniaturization is a major motivation for the development of ultra-precision technologies and processes which can achieve high form and excellent surface finish. Of all the available manufacturing approaches, mechanical nanometric machining is still a good option for machining complex 3D devices in a controllable way (Jackson, 2008). As the dimension goes down to the nanoscale, the machining phenomena take place in a limited region of tool-workpiece interface. At this length scale and interface, the material removal mechanisms are not fully understood, so more insight is needed, which on the long run will help to achieve high precision manufacturing with predictability, repeatability and productivity (Luo, 2004). At present, it is very difficult to observe the diverse microscopic physical phenomena occurring through experiments at the nanoscale (Rentsch, 2008). Subsequently, the other alternative is to explore available simulation techniques. Continuum mechanics approach is not adequate, as the point of interest/interface cannot be assumed to be homogeneous, but rather discrete, so, atomistic simulation methods are the suitable techniques for modelling at the nanoscale. read less NOT USED (low confidence) D. A. Cheney and J. Lukes, “Excitation of Single Phonon Modes in Nanoscale Waveguides,” Journal of Heat Transfer-transactions of The Asme. 2012. link Times cited: 2 Abstract: We present a new computational method that excites guided ph… read moreAbstract: We present a new computational method that excites guided phonon modes in nanoscale waveguides at a specific frequency and wavenumber. The method uses nonequilibrium molecular dynamics and Fourier analysis of particle displacements to extract mode shapes from single frequency excitations consisting of superposed spatial modes. These mode shapes are used to excite the waveguide inlet boundary so that single phonon modes are generated in the structure. Mode shapes and phonon spectra for a silicon planar waveguide with rigid wall boundaries are calculated to demonstrate the viability of the technique. This method improves upon molecular dynamics techniques that activate all possible phonon modes and are thus not able to isolate the contribution of any single phonon excitation. Application of our method will enable the computational investigation of single phonon mode propagation in nanostructures of varying geometry.Copyright © 2011 by ASME read less NOT USED (low confidence) S. Murad and I. Puri, “Thermal rectification in a fluid reservoir,” Applied Physics Letters. 2012. link Times cited: 16 Abstract: An organized nonuniform mass distribution in solids leads to… read moreAbstract: An organized nonuniform mass distribution in solids leads to a monotonically varying thermal conductivity in a nanomaterial so that the heat flux is directionally dependent. We investigate through molecular dynamics simulations if the influence of an organized mass distribution in a fluid also leads to thermal rectification. Heat transfer is monitored in a water reservoir placed between two (hot and cold) silicon walls. The distribution of the fluid in the reservoirs is organized by applying an external force to each water molecule in a specified direction, creating a density gradient. This external force is smaller than the intermolecular forces in water, in most cases by much more than an order of magnitude. The simulations reveal that mass graded fluid-containing nanosystems can be engineered to possess an asymmetric axial thermal conductance that leads to greater heat flow in the direction of decreasing mass density. The rectification improves as the thermal conductivity is enhanced by increasing the ... read less NOT USED (low confidence) J. Adhikari, “Design of Compound Semiconductor Alloys Using Molecular Simulations.” 2012. link Times cited: 0 NOT USED (low confidence) D. A. Cheney and J. Lukes, “Comparison of Atomistic and Continuum Methods for Calculating Ballistic Phonon Transmission in Nanoscale Waveguides,” Journal of Heat Transfer-transactions of The Asme. 2012. link Times cited: 7 Abstract: We compare two methods for the calculation of mode dependent… read moreAbstract: We compare two methods for the calculation of mode dependent ballistic phonon transmission in nanoscale waveguides. The first method is based on continuum acoustic waveguide theory and uses an eigenmode expansion to solve for phonon transmission coefficients. The second method is an atomistic, lattice dynamics (LD)-molecular dynamics (MD) hybrid that uses LD computed mode shapes to excite guided phonon wavepackets in a nonequilibrium MD simulation and calculates phonon transmission from the final distribution of system energy. The two methods are compared for a planar waveguide with a t-stub irregularity, a geometry which has been proposed for the tuning of phonon transmission and nanostructure thermal conductance. Our comparison highlights advantages and disadvantages of the two methods and illustrates regimes when atomistic effects are prominent and continuum approaches are not appropriate.Copyright © 2012 by ASME read less NOT USED (low confidence) T. T. Hanh, V. V. Hoang, and T. P. Duy, “Structural properties of simulated liquid GanAsm,” Computational Materials Science. 2012. link Times cited: 0 NOT USED (low confidence) L. J. Lewis and D. Perez, “Computer Models of Laser Ablation in Liquids.” 2012. link Times cited: 3 NOT USED (low confidence) A. McGaughey and A. Jain, “Nanostructure thermal conductivity prediction by Monte Carlo sampling of phonon free paths,” Applied Physics Letters. 2012. link Times cited: 81 Abstract: We propose a method by which the thermal conductivity of a n… read moreAbstract: We propose a method by which the thermal conductivity of a nanostructure with arbitrary geometry can be predicted through Monte Carlo sampling of the free paths associated with phonon-phonon and phonon-boundary scattering. The required inputs are the nanostructure geometry and the bulk phonon frequencies, group velocities, and mean free paths. The method is applied to a thin film in the in-plane and cross-plane directions and to a polycrystalline bulk material. For the film, a faster approach to the bulk thermal conductivity is found compared to predictions made using the Matthiessen rule with the bulk mean free path and an average phonon-boundary scattering length. read less NOT USED (low confidence) Y. Zhen and C. Chu, “A deformation-fluctuation hybrid method for fast evaluation of elastic constants with many-body potentials,” Comput. Phys. Commun. 2012. link Times cited: 18 NOT USED (low confidence) H. Whitlow and S. Nakagawa, “Ordering effects in extreme high-resolution depth profiling with MeV ion beams,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2012. link Times cited: 0 NOT USED (low confidence) A. Trejo, Á. Miranda, L. N. D. Rivera, A. Díaz-Méndez, and M. Cruz‐Irisson, “Phonon optical modes and electronic properties in diamond nanowires,” Microelectronic Engineering. 2012. link Times cited: 9 NOT USED (low confidence) L. Lu and G. Voth, “The Multiscale Coarse‐Graining Method.” 2012. link Times cited: 102 NOT USED (low confidence) E. Tadmor and R. E. Miller, “Modeling Materials: Continuum, Atomistic and Multiscale Techniques.” 2011. link Times cited: 395 Abstract: 1. Introduction Part I. Continuum Mechanics and Thermodynami… read moreAbstract: 1. Introduction Part I. Continuum Mechanics and Thermodynamics: 2. Essential continuum mechanics and thermodynamics Part II. Atomistics: 3. Lattices and crystal structures 4. Quantum mechanics of materials 5. Empirical atomistic models of materials 6. Molecular statics Part III. Atomistic Foundations of Continuum Concepts: 7. Classical equilibrium statistical mechanics 8. Microscopic expressions for continuum fields 9. Molecular dynamics Part IV. Multiscale Methods: 10. What is multiscale modeling? 11. Atomistic constitutive relations for multilattice crystals 12. Atomistic/continuum coupling: static methods 13. Atomistic/continuum coupling: finite temperature and dynamics Appendix References Index. read less NOT USED (low confidence) H. Hieu and V. Hùng, “STUDY OF THERMODYNAMIC PROPERTIES OF ZINC-BLENDE-TYPE SEMICONDUCTORS: TEMPERATURE AND PRESSURE DEPENDENCES,” Modern Physics Letters B. 2011. link Times cited: 11 Abstract: Using the statistical moment method (SMM), the temperature a… read moreAbstract: Using the statistical moment method (SMM), the temperature and pressure dependences of thermodynamic quantities of zinc-blende-type semiconductors have been investigated. The analytical expressions of the nearest-neighbor distances, the change of volumes and the mean-square atomic displacements (MSDs) have been derived. Numerical calculations have been performed for a series of zinc-blende-type semiconductors: GaAs, GaP, GaSb, InAs, InP and InSb. The agreement between our calculations and both earlier other theoretical results and experimental data is a support for our new theory in investigating the temperature and pressure dependences of thermodynamic quantities of semiconductors. read less NOT USED (low confidence) A. Urban, M. Reese, M. Mrovec, C. Elsasser, and B. Meyer, “Parameterization of tight-binding models from density functional theory calculations,” Physical Review B. 2011. link Times cited: 25 NOT USED (low confidence) W. Ge et al., “Meso-scale oriented simulation towards virtual process engineering (VPE)-The EMMS Paradigm,” Chemical Engineering Science. 2011. link Times cited: 126 NOT USED (low confidence) X. Yang, A. To, and M. Kırca, “Thermal conductivity of periodic array of intermolecular junctions of silicon nanowires,” Physica E-low-dimensional Systems & Nanostructures. 2011. link Times cited: 6 NOT USED (low confidence) Y. Du, T. Lenosky, R. Hennig, S. Goedecker, and J. Wilkins, “Energy landscape of silicon tetra‐interstitials using an optimized classical potential,” physica status solidi (b). 2011. link Times cited: 20 Abstract: Mobile single interstitials can grow into extended interstit… read moreAbstract: Mobile single interstitials can grow into extended interstitial defect structures during thermal anneals following ion implantation. The silicon tetra‐interstitials present an important intermediate structure that can either provide a chain‐like nucleation site for extended structures or form a highly stable compact interstitial cluster preventing further growth. In this paper, dimer searches using the tight‐binding (TB) model by Lenosky et al. and density functional calculations show that the compact ground‐state $I_{4}^{a} $ and the I4‐chain are surrounded by high‐lying neighboring local minima. read less NOT USED (low confidence) P. Kroll, “Modeling Amorphous Ceramic Structures.” 2011. link Times cited: 2 NOT USED (low confidence) E. G. Solveyra, E. de la Llave, D. Scherlis, and V. Molinero, “Melting and crystallization of ice in partially filled nanopores.,” The journal of physical chemistry. B. 2011. link Times cited: 68 Abstract: We investigate the melting and formation of ice in partially… read moreAbstract: We investigate the melting and formation of ice in partially filled hydrophilic and hydrophobic nanopores of 3 nm diameter using molecular dynamics simulations with the mW water model. Above the melting temperature, the partially filled nanopores contain two water phases in coexistence: a condensed liquid plug and a surface-adsorbed phase. It has been long debated in the literature whether the surface-adsorbed phase is involved in the crystallization. We find that only the liquid plug crystallizes on cooling, producing ice I with stacks of hexagonal and cubic layers. The confined ice is wetted by a premelted liquid layer that persists in equilibrium with ice down to temperatures well below its melting point. The liquid-ice transition is first-order-like but rounded. We determine the temperature and enthalpy of melting as a function of the filling fraction of the pore. In agreement with experiments, we find that the melting temperature of the nanoconfined ice is strongly depressed with respect to the bulk T(m), it depends weakly on the filling fraction and is insensitive to the hydrophobicity of the pore wall. The state of water in the crystallized hydrophilic and hydrophobic pores, however, is not the same: the hydrophobic pore has a negligible density of the surface-adsorbed phase and higher fraction of water in the ice phase than the hydrophilic pore. The widths of the ice cores are nevertheless comparable for the hydrophobic and hydrophilic pores, and this may explain their almost identical melting temperatures. The enthalpy of melting ΔH(m), when normalized by the actual amount of ice in the pore, is indistinguishable for the hydrophobic and hydrophilic pores, insensitive to the filling fraction, and within the error bars, the same as the difference in enthalpy between bulk liquid and bulk ice evaluated at the temperature of melting of ice in the nanopores. read less NOT USED (low confidence) A. M. Nieves and T. Sinno, “An enthalpy landscape view of homogeneous melting in crystals.,” The Journal of chemical physics. 2011. link Times cited: 10 Abstract: A detailed analysis of homogeneous melting in crystalline ma… read moreAbstract: A detailed analysis of homogeneous melting in crystalline materials modeled by empirical interatomic potentials is presented using the theory of inherent structures. We show that the homogeneous melting of a perfect, infinite crystalline material can be inferred directly from the growth exponent of the inherent structure density-of-states distribution expressed as a function of formation enthalpy. Interestingly, this growth is already established by the presence of very few homogeneously nucleated point defects in the form of Frenkel pairs. This finding supports the notion that homogeneous melting is appropriately defined in terms of a one-phase theory and does not require detailed consideration of the liquid phase. We then apply this framework to the study of applied hydrostatic compression on homogeneous melting and show that the inherent structure analysis used here is able to capture the correct pressure-dependence for two crystalline materials, namely silicon and aluminum. The coupling between the melting temperature and applied pressure arises through the distribution of formation volumes for the various inherent structures. read less NOT USED (low confidence) Y. Wang et al., “Investigation of the anisotropic strain relaxation in GaSb islands on GaP,” Journal of Applied Physics. 2011. link Times cited: 13 Abstract: The strain relaxation at the initial stages of highly mismat… read moreAbstract: The strain relaxation at the initial stages of highly mismatched (11.8%) GaSb grown on a GaP substrate following a Ga-rich surface treatment by molecular beam epitaxy has been investigated. High resolution transmission electron microscopy and moire fringe analysis were used to determine the relaxation state in these GaSb islands in the [110] and [1–10] directions. The measurements revealed an anisotropic strain relaxation in these two directions; there is a higher misfit strain relaxation along the [110] direction where the islands are elongated, which is in agreement with a higher density of misfit dislocations. By combining molecular dynamics simulations and TEM results, the anisotropy in the strain relaxation is shown to be related to the asymmetry in the formation of interface misfit dislocations. The P-core glide set 60° dislocations (α type) and the Ga-core shuffle set Lomer dislocations serve as the primary misfit dislocation which contributes to the strain relaxation in the (1–10) interface, and t... read less NOT USED (low confidence) D. Chrobak, N. Tymiak, A. Beaber, O. Ugurlu, W. Gerberich, and R. Nowak, “Deconfinement leads to changes in the nanoscale plasticity of silicon.,” Nature nanotechnology. 2011. link Times cited: 136 NOT USED (low confidence) Q. Cao, X.-S. Kong, Y. D. Li, X. Wu, and C. Liu, “Revisiting scaling laws for the diffusion coefficients in simple melts based on the structural deviation from hard-sphere-like case,” Physica B-condensed Matter. 2011. link Times cited: 14 NOT USED (low confidence) T. Aoki, T. Seki, and J. Matsuo, “Molecular dynamics simulations of large fluorine cluster impact on silicon with supersonic velocity,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2011. link Times cited: 6 NOT USED (low confidence) P. Wochner, M. Castro-colin, S. Bogle, and V. Bugaev, “Of fluctuations and cross-correlations: finding order in disorder,” International Journal of Materials Research. 2011. link Times cited: 13 Abstract: We present an overview of several diffraction-based techniqu… read moreAbstract: We present an overview of several diffraction-based techniques used to study disordered systems, with an emphasis on accessing information on higher-order correlations. Appropriately const... read less NOT USED (low confidence) S. Zhang et al., “The study of melting stage of bulk silicon using molecular dynamics simulation,” Physica B-condensed Matter. 2011. link Times cited: 13 NOT USED (low confidence) L. Berthier, H. Jacquin, and F. Zamponi, “Microscopic theory of the jamming transition of harmonic spheres.,” Physical review. E, Statistical, nonlinear, and soft matter physics. 2011. link Times cited: 69 Abstract: We develop a microscopic theory to analyze the phase behavio… read moreAbstract: We develop a microscopic theory to analyze the phase behavior and compute correlation functions of dense assemblies of soft repulsive particles both at finite temperature, as in colloidal materials, and at vanishing temperature, a situation relevant for granular materials and emulsions. We use a mean-field statistical mechanical approach which combines elements of liquid state theory to replica calculations to obtain quantitative predictions for the location of phase boundaries, macroscopic thermodynamic properties, and microstructure of the system. We focus, in particular, on the derivation of scaling properties emerging in the vicinity of the jamming transition occurring at large density and zero temperature. The new predictions we obtain for pair correlation functions near contact are tested using computer simulations. Our work also clarifies the conceptual nature of the jamming transition and its relation to the phenomenon of the glass transition observed in atomic liquids. read less NOT USED (low confidence) I. Saika-Voivod, F. Romano, and F. Sciortino, “Nucleation barriers in tetrahedral liquids spanning glassy and crystallizing regimes.,” The Journal of chemical physics. 2011. link Times cited: 26 Abstract: Crystallization and vitrification of tetrahedral liquids are… read moreAbstract: Crystallization and vitrification of tetrahedral liquids are important both from a fundamental and a technological point of view. Here, we study via extensive umbrella sampling Monte Carlo computer simulations the nucleation barriers for a simple model for tetrahedral patchy particles in the regime where open tetrahedral crystal structures (namely, cubic and hexagonal diamond and their stacking hybrids) are thermodynamically stable. We show that by changing the angular bond width, it is possible to move from a glass-forming model to a readily crystallizing model. From the shape of the barrier we infer the role of surface tension in the formation of the crystalline clusters. Studying the trends of the nucleation barriers with the temperature and the patch width, we are able to identify an optimal value of the patch size that leads to easy nucleation. Finally, we find that the nucleation barrier is the same, within our numerical precision, for both diamond crystals and for their stacking forms. read less NOT USED (low confidence) K. Varga and J. A. Driscoll, “Computational Nanoscience: Applications for Molecules, Clusters, and Solids.” 2011. link Times cited: 23 Abstract: Preface Part I. 1D Problems: 1. Variational solution of the … read moreAbstract: Preface Part I. 1D Problems: 1. Variational solution of the Schrodinger equation 2. Solution of bound state problems using a grid 3. Solution of the Schrodinger equation for scattering states 4. Periodic potentials: band structure in 1D 5. Solution of time-dependent problems in quantum mechanics 6. Solution of Poisson's equation Part II. 2D and 3D Systems: 7. 3D real space approach: from quantum dots to Bose-Einstein condensates 8. Variational calculations in 2D: quantum dots 9. Variational calculations in 3D: atoms and molecules 10. Monte Carlo calculations 11. Molecular dynamics simulations 12. Tight binding approach to electronic structure calculations 13. Plane wave density functional calculations 14. Density functional calculations with atomic orbitals 15. Real-space density functional calculations 16. Time-dependent density functional calculations 17. Scattering and transport in nanostructures 18. Numerical linear algebra Appendix: code descriptions References Index. read less NOT USED (low confidence) N. Admal and E. Tadmor, “Stress and heat flux for arbitrary multibody potentials: a unified framework.,” The Journal of chemical physics. 2011. link Times cited: 44 Abstract: A two-step unified framework for the evaluation of continuum… read moreAbstract: A two-step unified framework for the evaluation of continuum field expressions from molecular simulations for arbitrary interatomic potentials is presented. First, pointwise continuum fields are obtained using a generalization of the Irving-Kirkwood procedure to arbitrary multibody potentials. Two ambiguities associated with the original Irving-Kirkwood procedure (which was limited to pair potential interactions) are addressed in its generalization. The first ambiguity is due to the nonuniqueness of the decomposition of the force on an atom as a sum of central forces, which is a result of the nonuniqueness of the potential energy representation in terms of distances between the particles. This is in turn related to the shape space of the system. The second ambiguity is due to the nonuniqueness of the energy decomposition between particles. The latter can be completely avoided through an alternate derivation for the energy balance. It is found that the expressions for the specific internal energy and the heat flux obtained through the alternate derivation are quite different from the original Irving-Kirkwood procedure and appear to be more physically reasonable. Next, in the second step of the unified framework, spatial averaging is applied to the pointwise field to obtain the corresponding macroscopic quantities. These lead to expressions suitable for computation in molecular dynamics simulations. It is shown that the important commonly-used microscopic definitions for the stress tensor and heat flux vector are recovered in this process as special cases (generalized to arbitrary multibody potentials). Several numerical experiments are conducted to compare the new expression for the specific internal energy with the original one. read less NOT USED (low confidence) T. Desai, “Thermal transport in nanoclusters,” Applied Physics Letters. 2011. link Times cited: 25 Abstract: Nonequilibrium and equilibrium molecular dynamics simulation… read moreAbstract: Nonequilibrium and equilibrium molecular dynamics simulations are employed to study the thermal transport in sintered silicon nanoclusters made of 15 nm diameter nanoparticles arranged on a simple cubic lattice. Both simulation techniques indicate a reduction in the thermal conductivity from ∼120 W/m K (bulk) to 1.5 W/m K (nanoclusters) at 500 K. This dramatic reduction is attributed to the reduced thermal conductivity of nanoparticle (15 W/m K) and most prominently to the nanosized constriction resistance due to necking between the two nanoparticles. Comparison with the existing models, radial distribution function and vibrational analysis show that the phonon transport in the nanosized neck region is ballistic rather than diffusive. read less NOT USED (low confidence) J. Templeton, R. Jones, J. W. Lee, J. Zimmerman, and B. M. Wong, “A Long-Range Electric Field Solver for Molecular Dynamics Based on Atomistic-to-Continuum Modeling.,” Journal of chemical theory and computation. 2011. link Times cited: 18 Abstract: Understanding charge transport processes at a molecular leve… read moreAbstract: Understanding charge transport processes at a molecular level is currently hindered by a lack of appropriate models for incorporating nonperiodic, anisotropic electric fields in molecular dynamics (MD) simulations. In this work, we develop a model for including electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and the algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. Our model represents the electric potential on a FE mesh satisfying a Poisson equation with source terms determined by the distribution of the atomic charges. Boundary conditions can be imposed naturally using the FE description of the potential, which then propagate to each atom through modified forces. The method is verified using simulations where analytical solutions are known or comparisons can be made to existing techniques. In addition, a calculation of a salt water solution in a silicon nanochannel is performed to demonstrate the method in a target scientific application in which ions are attracted to charged surfaces in the presence of electric fields and interfering media. read less NOT USED (low confidence) C.-J. Huang, C.-J. Wu, H. Teng, and K. Chiang, “A robust nano-mechanics approach for tensile and modal analysis using atomistic–continuum mechanics method,” Computational Materials Science. 2011. link Times cited: 1 NOT USED (low confidence) E. C. D. Rocha and C. R. da Cunha, “The transition from fracton to phonon states in a Sierpinski triangle lattice,” Chaos Solitons & Fractals. 2011. link Times cited: 6 NOT USED (low confidence) L. Trandinh, Y.-M. Ryu, W. Kang, and S. Cheon, “A molecular dynamics simulation on the defect structure in silicon under indentation.” 2011. link Times cited: 0 Abstract: ,In this paper, the symmetric axis parameter method, which w… read moreAbstract: ,In this paper, the symmetric axis parameter method, which was proposed to identify defects, dislocations and stacking fault, with perfect structures in the zinc-blende materials, was introduced as a way to distinguish between elastic and plastic deformation. LAMMPS, a molecular dynamics programme of Sandia National Laboratories, was used to perform nanoindentation simulation on silicon, a zinc-blende material. Defects in silicon (111) under spherical indentation showed the threefold pattern and the slip system in the form of ring crack. Also simulation results show good agreement with experimental results and existing theoretical analyses. read less NOT USED (low confidence) J. Dolado, M. Griebel, J. Hamaekers, and F. Heber, “The nano-branched structure of cementitious calcium–silicate–hydrate gel,” Journal of Materials Chemistry. 2011. link Times cited: 75 Abstract: Manipulation of concrete at the nanoscale is severely limite… read moreAbstract: Manipulation of concrete at the nanoscale is severely limited by the lack of precise knowledge on the nanostructure of calcium–silicate–hydrate gel, the main binding phase of cement-based materials. Here we report a computational description of C–S–H, which for the first time reconciles the existing structural and colloidal/gel-like models. Our molecular dynamic simulations predict the formation of a branched three-dimensional C–S–H solid network where the segmental branches (SB) are ∼3 × 3 × 6 nm-sized. The presented simulations account well for the features observed through Small Angle Neutron Scattering (SANS) experiments as well with various observations made by synchrotron X-ray, Nuclear Magnetic Resonance (NMR), and Inelastic Neutron Spectroscopy (INS) measurements and lead to a better understanding of the cementitious nanostructure formation and morphology. read less NOT USED (low confidence) C.-ying Wang, Z. Wang, and Q. Meng, “Comparative study of the empirical interatomic potentials and density-functional simulations of divacancy and hexavacancy in silicon,” Physica B-condensed Matter. 2011. link Times cited: 3 NOT USED (low confidence) J. Rabier and L. Pizzagalli, “Dislocation dipole annihilation in diamond and silicon,” Journal of Physics: Conference Series. 2011. link Times cited: 5 Abstract: The mechanism of dislocation dipole annihilation has been in… read moreAbstract: The mechanism of dislocation dipole annihilation has been investigated in C and Si using atomistic calculations with the aim of studying their annihilation by-products. It is shown, in C as well as in Si, that dipole annihilation yields debris that can be depicted as a cluster of vacancies, or alternately by two internal free surfaces. These defects have no strain field and can hardly be seen using usual TEM techniques. This suggests that the brown colouration of diamond could be due to microstructures resulting from deformation mechanisms associated with dipole formation and their annihilation rather than to a climb mechanism and vacancy aggregation. In silicon where a number of dipoles have been evidenced by TEM when dislocation trails are found, such debris could be the missing link responsible for the observation of strong chemical reactivity and electrical activity in the wake of moving dislocations. read less NOT USED (low confidence) L. Pizzagalli, J. Godet, J. Guénolé, and S. Brochard, “Dislocation cores in silicon: new aspects from numerical simulations,” Journal of Physics: Conference Series. 2011. link Times cited: 9 Abstract: Recent theoretical investigations of the properties of dislo… read moreAbstract: Recent theoretical investigations of the properties of dislocation cores in silicon are reviewed. New results, obtained from numerical simulations for the non-dissociated screw and 60° dislocations, are presented and discussed in relation with experiments. read less NOT USED (low confidence) J. Guénolé, J. Godet, and S. Brochard, “Investigation of Plasticity in Silicon Nanowires by Molecular Dynamics Simulations,” Key Engineering Materials. 2011. link Times cited: 3 Abstract: We have performed molecular dynamics simulations on silicon … read moreAbstract: We have performed molecular dynamics simulations on silicon nanowires (Si-NW) with [001] axis and square section. The forces are modeled by well-tested semi-empirical potentials. First we investigated the edge reconstruction of Si nanowires. Then, we studied the behavior of the NW when submitted to compression stresses along its axis. At low temperature (300K), we observed the formation of dislocation loops with a Burgers vector 1/2 [10-1]. These dislocations slip in the unexpected {101} planes having the largest Schmid factor. read less NOT USED (low confidence) J. Lukes, “Development of a Research Plan to Minimize Thermal Conductivity in Low Temperature Thermoelectric Materials.” 2010. link Times cited: 0 NOT USED (low confidence) M. Marder, “Cohesion of Solids.” 2010. link Times cited: 1 NOT USED (low confidence) D. Wales, “Energy Landscapes and Structure Prediction Using Basin‐Hopping.” 2010. link Times cited: 9 NOT USED (low confidence) D. Nagai, K. Miyazaki, and H. Tsukamoto, “分子動力学法を用いたナノポーラス構造Siにおける熱伝導解析(熱工学,内燃機関,動力など),” Transactions of the Japan Society of Mechanical Engineers. B. 2010. link Times cited: 0 NOT USED (low confidence) A. Oluwajobi and X. Chen, “The fundamentals of modelling abrasive machining using molecular dynamics,” International Journal of Abrasive Technology. 2010. link Times cited: 17 Abstract: The development of ultra-precision processes which can achie… read moreAbstract: The development of ultra-precision processes which can achieve excellent surface finish and tolerance at the nanometre level is now a critical requirement for many industrial applications. At present, it is very difficult to observe the diverse microscopic physical phenomena occurring in nanometric machining through experiments. The use of molecular dynamics (MD) simulation has proved to be an effective tool for the prediction and the analysis of these processes at the nanometre scale. The crucial task in a MD simulation is the selection of the potential function. The lack of clear understanding about the scope and the limitations of a given potential function may lead to nonsensical results. This article presents the backgrounds of popular potentials used in the modelling of materials processes and the algorithms for the solution of the equations encountered in the simulation. Current applications of MD in abrasive machining are reviewed. read less NOT USED (low confidence) G. Moras, R. Choudhury, J. Kermode, G. Csányi, M. Payne, and A. Vita, “Hybrid Quantum/Classical Modeling of Material Systems: The ‘Learn on the Fly’ Molecular Dynamics Scheme,” Springer US. 2010. link Times cited: 3 NOT USED (low confidence) S. Hamaguchi, “Plasma-surface Interactions in Material Processing,” Journal of Physics: Conference Series. 2010. link Times cited: 5 Abstract: In plasma processes such as reactive ion etching and thin fi… read moreAbstract: In plasma processes such as reactive ion etching and thin film deposition for microelectronics device fabrication, atomic-level control of surface morphologies and compositions of processed materials has become increasingly important as the device sizes diminish to the nano-meter range. While various species such as ions, neutral radicals, electrons and photons simultaneously hit the material surface in a plasma, the plasma-surface interactions can be best understood if individual elementary processes such as interaction of specific species with the surface at specific incident energy are studied separately under well controlled conditions. In this article, a molecular dynamics (MD) simulation technique is reviewed as a means to analyse plasma-surface interactions in such a manner and some sample simulation results for polymer etching and diamond-like carbon (DLC) deposition are presented. read less NOT USED (low confidence) C. Zhu and Q. Xie, “Simulation Study of Microstructure Transition of Liquid Ge during Rapid Cooling Solidification,” Materials Science Forum. 2010. link Times cited: 0 Abstract: Structural and dynamical properties of the rapid solidificat… read moreAbstract: Structural and dynamical properties of the rapid solidification process of liquid Ge have been investigated by molecular-dynamics calculations based on the Stillinger-Weber potential. The variations of microstructures during the solidification process are analyzed by the self-diffusion coefficient D(T), pair correlation function g(r) curves and the HA bond-type index method. The melting point implicated in D(T) is about 2100 K. The pair correlation function g(r) obtained by the simulated in liquid Ge is good agreement with experiment, the fist-peak of g(r) gradually becomes higher and sharper with the temperature decreasing, when temperature drops to 1400 K, the second-peak of g(r) begins to split. The change of HA bond-type indicated that the most important structural change occurs in the temperature range 1400 K-700 K. read less NOT USED (low confidence) E. S. Zijlstra and M. E. Garcia, “Laser‐Induced Softening of Lattice Vibrations.” 2010. link Times cited: 5 NOT USED (low confidence) S. Giordano, A. Mattoni, and L. Colombo, “Brittle Fracture: From Elasticity Theory to Atomistic Simulations,” Reviews in Computational Chemistry. 2010. link Times cited: 13 Abstract: Understanding the mechanical properties of materials with th… read moreAbstract: Understanding the mechanical properties of materials with theory traditionally has been done by using continuum methods, ranging from elastic theory (in both linear and nonlinear regimes), to plastic theory, and to fracture mechanics. The computational counterpart of continuum modeling is represented by finite element analysis. Continuum theories have been extremely successful, as proved by the tremendous achievements reached in structural design of buildings, ships, bridges, air-/space crafts, nuclear reactors, and so on. Overall this represents the core of theoretical and computational solid mechanics. In the last 20 years or so, the technological rush toward nano-sized systems has forced researchers to investigate mechanical phenomena at a length scale in which matter no longer can be considered as a continuum. This is the case, for instance, of investigating the crack-related features in a material displaying elastic or structural complexity (or, equivalently, inhomogeneity or disorder) at the nanoscale. This problem of atomic-scale granularity immediately seems to be prohibitive for (standard) solid mechanics. To better elaborate on this read less NOT USED (low confidence) L. Nasdala, A. Kempe, and R. Rolfes, “The Molecular Dynamic Finite Element Method (MDFEM),” Cmc-computers Materials & Continua. 2010. link Times cited: 31 Abstract: In order to understand the underlying mechanisms of inelasti… read moreAbstract: In order to understand the underlying mechanisms of inelastic material behavior and nonlinear surface interactions, which can be observed on macroscale as damping, softening, fracture, delamination, frictional contact etc., it is necessary to examine the molecular scale. Force fields can be applied to simulate the rearrangement of chemical and physical bonds. However, a simulation of the atomic interactions is very costly so that classical molecular dynamics (MD) is restricted to structures containing a low number of atoms such as carbon nanotubes. The objective of this paper is to show how MD simulations can be integrated into the finite element method (FEM) which is used to simulate engineering structures such as an aircraft panel or a vehicle chassis. A new type of finite element is required for force fields that include multi-body potentials. These elements take into account not only bond stretch but also bending, torsion and inversion without using rotational degrees of freedom. Since natural lengths and angles are implemented as intrinsic material parameters, the developed molecular dynamic finite element method (MDFEM) starts with a conformational analysis. By means of carbon nanotubes and elastomeric material it is demonstrated that this pre-step is needed to find an equilibrium configuration before the structure can be deformed in a succeeding loading step. read less NOT USED (low confidence) S. Kapur and T. Sinno, “Detailed Microscopic Analysis of Self-interstitial Aggregation in Silicon. I. Direct Molecular Dynamics Simulations of Aggregation,” Physical Review B. 2010. link Times cited: 25 Abstract: A comprehensive atomistic study of self-interstitial aggrega… read moreAbstract: A comprehensive atomistic study of self-interstitial aggregation in crystalline silicon is presented. Here, large-scale parallel molecular dynamics simulations are used to generate time-dependent views into the self-interstitial clustering process, which is important during post-implant damage annealing. The effects of temperature and pressure on the aggregation process are studied in detail and found to generate a variety of qualitatively different interstitial cluster morphologies and growth behavior. In particular, it is found that the self-interstitial aggregation process is strongly affected by hydrostatic pressure. {111}-oriented planar defects are found to be dominant under stress-free or compressive conditions while {113} rodlike and planar defects are preferred under tensile conditions. Moreover, the aggregation pathways for forming the different types of planar defect structures are found to be qualitatively different. In each case, the various cluster morphologies generated in the simulations are found to be in excellent agreement with structures previously predicted from electronic-structure calculations and observed experimentally by electron microscopy. Multiple empirical interatomic potential models were employed and found to generally provide similar results leading to a fairly consistent picture of self-interstitial aggregation. In a companion article, a detailed thermodynamic analysis of various cluster configurations is employed to probe the mechanistic origins of these observations. read less NOT USED (low confidence) V. Haxha and M. Migliorato, “Calculating strain using atomistic simulations: A review.” 2010. link Times cited: 0 Abstract: We present a short review of methods of evaluating of strain… read moreAbstract: We present a short review of methods of evaluating of strain from atomistic models in the context of linear elasticity. read less NOT USED (low confidence) J. A. Porter, N. Ashcroft, and G. Chester, “Pair potentials for simple metallic systems: Beyond linear response,” Physical Review B. 2010. link Times cited: 3 NOT USED (low confidence) T. Sinno, “Multiscale Modeling of Nanoscale Aggregation Phenomena: Applications in Semiconductor Materials Processing.” 2010. link Times cited: 0 NOT USED (low confidence) W. Miller, I. Rasin, and D. Stock, “Evolution of cellular structures during Ge 1-x Si x single-crystal growth by means of a modified phase-field method.,” Physical review. E, Statistical, nonlinear, and soft matter physics. 2010. link Times cited: 11 Abstract: We have studied the evolution of cellular structures in Ge 1… read moreAbstract: We have studied the evolution of cellular structures in Ge 1-x Si x single-crystal growth as a function of process parameters. Because these structures are much larger than those occurring during the solidification of metals, we developed a modified phase-field method, which is able to handle these structure within reasonable computer times using the real material parameters. The model has been tested for computing equilibrium shapes of crystals, dendritic growth, and cellular growth of Ni x Cu 1-x. We also performed classical molecular dynamics calculations in order to compute the diffusion coefficients of Si and Ge in melts of various compositions. read less NOT USED (low confidence) Y. Jing and Q. Meng, “Molecular dynamics simulations of the mechanical properties of crystalline/amorphous silicon core/shell nanowires,” Physica B-condensed Matter. 2010. link Times cited: 32 NOT USED (low confidence) M. Timonova and B. Thijsse, “Thermodynamic properties and phase transitions of silicon using a new MEAM potential,” Computational Materials Science. 2010. link Times cited: 13 NOT USED (low confidence) A. Matsuda, Y. Nakakubo, Y. Takao, K. Eriguchi, and K. Ono, “Modeling of ion-bombardment damage on Si surfaces for in-line analysis,” Thin Solid Films. 2010. link Times cited: 41 NOT USED (low confidence) Y. Wang and N. Chen, “Atomistic study of misfit dislocation in metal/SiC(111) interfaces,” Journal of Physics: Condensed Matter. 2010. link Times cited: 7 Abstract: The interatomic potentials across metal/SiC(111) interfaces … read moreAbstract: The interatomic potentials across metal/SiC(111) interfaces are derived from ab initio adhesive energies by an inversion method. We use these potentials to investigate the structures, energies and Burgers vectors of misfit dislocations in metal/SiC(111) interfaces. Two kinds of interfacial dislocations are found in M/SiC(111) (M = Au, Ag, Al, Pt) interfaces, where the M/SiC(111) (M = Au, Al) system has partial dislocations and the M/SiC(111) (M = Ag, Pt) system has perfect dislocations. The former has a coherent interface while the latter corresponds to a semi-coherent interface. read less NOT USED (low confidence) A. Krasheninnikov and K. Nordlund, “Ion and electron irradiation-induced effects in nanostructured materials,” Journal of Applied Physics. 2010. link Times cited: 877 Abstract: A common misconception is that the irradiation of solids wit… read moreAbstract: A common misconception is that the irradiation of solids with energetic electrons and ions has exclusively detrimental effects on the properties of target materials. In addition to the well-known cases of doping of bulk semiconductors and ion beam nitriding of steels, recent experiments show that irradiation can also have beneficial effects on nanostructured systems. Electron or ion beams may serve as tools to synthesize nanoclusters and nanowires, change their morphology in a controllable manner, and tailor their mechanical, electronic, and even magnetic properties. Harnessing irradiation as a tool for modifying material properties at the nanoscale requires having the full microscopic picture of defect production and annealing in nanotargets. In this article, we review recent progress in the understanding of effects of irradiation on various zero-dimensional and one-dimensional nanoscale systems, such as semiconductor and metal nanoclusters and nanowires, nanotubes, and fullerenes. We also consider the t... read less NOT USED (low confidence) N. Kastelowitz, J. C. Johnston, and V. Molinero, “The anomalously high melting temperature of bilayer ice.,” The Journal of chemical physics. 2010. link Times cited: 76 Abstract: Confinement of water usually depresses its melting temperatu… read moreAbstract: Confinement of water usually depresses its melting temperature. Here we use molecular dynamics simulations to determine the liquid-crystal equilibrium temperature for water confined between parallel hydrophobic or mildly hydrophilic plates as a function of the distance between the surfaces. We find that bilayer ice, an ice polymorph in which the local environment of each water molecule strongly departs from the most stable tetrahedral structure, has the highest melting temperature (T(m)) of the series of l-layer ices. The melting temperature of bilayer ice is not only unusually high compared to the other confined ices, but also above the melting point of bulk hexagonal ice. Recent force microscopy experiments of water confined between graphite and a tungsten tip reveal the formation of ice at room temperature [K. B. Jinesh and J. W. M. Frenken, Phys. Rev. Lett. 101, 036101 (2008)]. Our results suggest that bilayer ice, for which we compute a T(m) as high as 310 K in hydrophobic confinement, is the crystal formed in those experiments. read less NOT USED (low confidence) C. Tomaras, B. Schmid, and W. Schirmacher, “Anharmonic elasticity theory for sound attenuation in disordered solids with fluctuating elastic constants,” Physical Review B. 2010. link Times cited: 17 NOT USED (low confidence) A. Dalton, Y. Kondratenko, and E. Seebauer, “Diffusion mechanisms on amorphous silicon surfaces,” Chemical Engineering Science. 2010. link Times cited: 6 NOT USED (low confidence) A. Pedersen and H. Jónsson, “Distributed implementation of the adaptive kinetic Monte Carlo method,” Math. Comput. Simul. 2010. link Times cited: 18 NOT USED (low confidence) Y. Park, Y. Zhou, J. Jhaveri, and A. Strachan, “Molecular Dynamics Simulations of Strain Engineering and Thermal Transport in Nanostructured Materials,” Computing in Science & Engineering. 2010. link Times cited: 1 Abstract: Given the large surface-to-volume ratio of nanoscale and nan… read moreAbstract: Given the large surface-to-volume ratio of nanoscale and nanostructured materials and devices, their performance is often dominated by processes occurring at free surfaces or interfaces. By connecting a material's atomic structure and thermo-mechanical response, molecular dynamics is helping researchers better understand and quantify these processes. read less NOT USED (low confidence) D. Camacho and Y. Niquet, “Application of Keating’s valence force field model to non-ideal wurtzite materials,” Physica E-low-dimensional Systems & Nanostructures. 2010. link Times cited: 52 NOT USED (low confidence) P. Ganster, G. Tréglia, F. Lançon, and P. Pochet, “Molecular dynamics simulation of silicon oxidization,” Thin Solid Films. 2010. link Times cited: 5 NOT USED (low confidence) N. Yang, G. Zhang, and B. Li, “Violation of Fourier’s Law and Anomalous Heat Diffusion in Silicon,” arXiv: Materials Science. 2010. link Times cited: 205 NOT USED (low confidence) C. Jin, W. Ren, and Y. Xiang, “Computing transition rates of thermally activated events in dislocation dynamics,” Scripta Materialia. 2010. link Times cited: 9 NOT USED (low confidence) J. Turney, A. McGaughey, and C. Amon, “In-plane phonon transport in thin films,” Journal of Applied Physics. 2010. link Times cited: 114 Abstract: The in-plane phonon thermal conductivities of argon and sili… read moreAbstract: The in-plane phonon thermal conductivities of argon and silicon thin films are predicted from the Boltzmann transport equation under the relaxation time approximation. We model the thin films using bulk phonon properties obtained from harmonic and anharmonic lattice dynamics calculations. The input required for the lattice dynamics calculations is obtained from interatomic potentials: Lennard-Jones for argon and Stillinger–Weber for silicon. The effect of the boundaries is included by considering only phonons with wavelengths that fit within the film and adjusting the relaxation times to account for mode-dependent, diffuse boundary scattering. Our model does not rely on the isotropic approximation or any fitting parameters. For argon films thicker than 4.3 nm and silicon films thicker than 17.4 nm, the use of bulk phonon properties is found to be appropriate and the predicted reduction in the in-plane thermal conductivity is in good agreement with results obtained from molecular dynamics simulation and ex... read less NOT USED (low confidence) F. Cleri, “Surface ordering of molecular structures by dispersion forces,” Physical Review B. 2009. link Times cited: 8 NOT USED (low confidence) Y. Xu and G. Li, “Strain effect analysis on phonon thermal conductivity of two-dimensional nanocomposites,” Journal of Applied Physics. 2009. link Times cited: 51 Abstract: In this paper, we present a model that combines lattice dyna… read moreAbstract: In this paper, we present a model that combines lattice dynamics and the phonon Boltzmann transport equation (BTE) to analyze strain effect on the cross-plane phonon thermal conductivity of silicon wire-germanium host nanocomposites. For a given strain condition, mechanical strain is translated to crystal lattice deformation by using the Cauchy–Born rule. Strain-dependent phonon thermal properties of Si and Ge obtained from lattice dynamics with Tersoff empirical interatomic potential are then incorporated into the BTE, in which ballistic transport within one material and diffuse scattering between Si–Ge interface are employed. The strain-dependent BTE is solved numerically on an unstructured triangular mesh by using a finite volume method. Nanocomposites with different Si nanowire cross sections are also investigated. The results show that the phonon thermal conductivity of the nanocomposites can be significantly decreased (or increased) by a tensile (or compressive) strain. With the same length change, ... read less NOT USED (low confidence) N. Peev, “Particle collision frequency and particle density at equilibrium. I,” Physica Scripta. 2009. link Times cited: 0 Abstract: The subject of the present paper is the formation of multiat… read moreAbstract: The subject of the present paper is the formation of multiatomic particles such as clusters and nanoparticles. The probability for collision of two particles in an amorphous medium at equilibrium is derived and the particle frequency of collision per unit volume per unit time has been evaluated. Within the frame of given assumptions and approximations, the equilibrium density of two- and three-atomic particles in the medium has been assessed. This approach may be significant in the investigation of the process of new phase nuclei formation. The existence of a limit value of the particle size for coalescence is supposed by this approach. read less NOT USED (low confidence) O. H. Duparc, “On the origins of the Finnis–Sinclair potentials,” Philosophical Magazine. 2009. link Times cited: 10 Abstract: I trace back the origins of the famous Finnis-Sinclair poten… read moreAbstract: I trace back the origins of the famous Finnis-Sinclair potentials. These potentials mimic the results of tight binding theory through their use of the square root embedding function. From the tentative beginnings of tight binding in the 1930s up to 1984 or so, some of the famous names involved are Bloch, Seitz, Montroll, Friedel, Cyrot-Lackmann, Ducastelle, to name just a few. The application of the method of moments to the description of densities of states and its connexion to the physics of closed paths linking nearest neighbours interacting atoms helped to formalize Friedel's rectangular band model for the d electrons in transition metals. Extension from perfectly periodic structures to defective ones could not be but a slow process due to the change of paradigm for solid state scientists and to the necessary caution to be paid to self-consistency. The British scientists school also contributed significantly in the 80s. Computer progress and pragmatism helped to go from mainly analytical developments to numerical experiments (another change of paradigm). I also digress on various not so well known historical points of interest to this story. read less NOT USED (low confidence) T. Haxhimali, D. Buta, M. Asta, P. Voorhees, and J. Hoyt, “Size-dependent nucleation kinetics at nonplanar nanowire growth interfaces.,” Physical review. E, Statistical, nonlinear, and soft matter physics. 2009. link Times cited: 17 Abstract: In nanowire growth, kinetic processes at the growth interfac… read moreAbstract: In nanowire growth, kinetic processes at the growth interface can play an important role in governing wire compositions, morphologies, and growth rates. Molecular-dynamics simulations have been undertaken to probe such processes in a system featuring a solid-liquid interface shape characterized by a facet bounded by rough orientations. Simulated growth rates display a dependence on nanowire diameter consistent with a size-dependent barrier for facet nucleation. A theory for the interface mobility is developed, establishing a source for size-dependent growth rates that is an intrinsic feature of systems possessing growth interfaces with faceted and rough orientations. read less NOT USED (low confidence) C. Wang, Y. Zhang, and Y. Jia, “New tetramer structures in the initial process of Si homoepitaxial growth on Si (0 0 1),” Applied Surface Science. 2009. link Times cited: 0 NOT USED (low confidence) L. Pelaz, L. Marqués, M. Aboy, P. López, and I. Santos, “Front-end process modeling in silicon,” The European Physical Journal B. 2009. link Times cited: 32 NOT USED (low confidence) S. Ghasemi et al., “The energy landscape of silicon systems and its description by force fields, tight binding schemes, density functional methods and Quantum Monte Carlo methods,” arXiv: Computational Physics. 2009. link Times cited: 27 Abstract: The accuracy of the energy landscape of silicon systems obta… read moreAbstract: The accuracy of the energy landscape of silicon systems obtained from various density functional methods, a tight binding scheme and force fields is studied. Quantum Monte Carlo results serve as quasi exact reference values. In addition to the well known accuracy of DFT methods for geometric ground states and metastable configurations we find that DFT methods give a similar accuracy for transition states and thus a good overall description of the energy landscape. On the other hand, force fields give a very poor description of the landscape that are in most cases too rugged and contain many fake local minima and saddle points or ones that have the wrong height. read less NOT USED (low confidence) S. Yoo, S. Xantheas, and X. Zeng, “The melting temperature of bulk silicon from ab initio molecular dynamics simulations,” Chemical Physics Letters. 2009. link Times cited: 19 NOT USED (low confidence) H. Kariyazaki, T. Aoki, K. Izunome, and K. Sueoka, “Molecular Simulation on Interfacial Structure and Gettering Efficiency of Si (110)/(100) Directly Bonded Hybrid Crystal Orientation Substrates,” Solid State Phenomena. 2009. link Times cited: 0 Abstract: Hybrid crystal orientation technology (HOT) substrates compr… read moreAbstract: Hybrid crystal orientation technology (HOT) substrates comprised of Si (100) and (110) surface orientation paralleling each <110> direction attract considerable attentions as one of the promising technology for high performance bulk CMOS technology. Although HOT substrates are fabricated by wafer bonding of Si (110) and Si (100) surfaces, it is not clear the atomic configuration of interfacial structure. Furthermore, the possibility for the interface to be an effective gettering source of impurity metals was not well studied. In this paper, we studied the interfacial structure and gettering efficiency of the atomic bonded interface by molecular simulations. The results indicate that the simulated atomic configuration and gettering efficiency of the bonded interface agreed well with the experimental results. read less NOT USED (low confidence) N. Fazouan, E. Atmani, M. Rouhani, and A. Estève, “A Monte Carlo investigation of growth and characterization of heteroepitaxial thin films,” Thin Solid Films. 2009. link Times cited: 5 NOT USED (low confidence) T. Aoki, T. Seki, and J. Matsuo, “Study of density effect of large gas cluster impact by molecular dynamics simulations,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2009. link Times cited: 14 NOT USED (low confidence) C. Wang, Y. Zhang, and Y. Jia, “A new Si tetramer structure on Si (001),” Solid State Sciences. 2009. link Times cited: 4 NOT USED (low confidence) T.-M. Chang, C. Weng, M. Liu, and C.-K. Yu, “The Temperature-Quantum-Correction Effect on the MD-Calculated Thermal Conductivity of Silicon Thin Films,” Cmes-computer Modeling in Engineering & Sciences. 2009. link Times cited: 1 Abstract: We employ the non-equilibrium molecular dynamics (NEMD) simu… read moreAbstract: We employ the non-equilibrium molecular dynamics (NEMD) simulation to calculate the in-plane thermal conductivity of silicon thin films of thickness 2.2nm and 11nm. To eliminate the finite-size effect, samples of various lengths are simulated and an extrapolation technique is applied. To perform the quantum correction which is necessary as the MD simulation temperature is lower than Debye temperature, the confined phonon spectra are obtained in advance via the EMD simulations. The investigation shows the thermal conductivities corrected based on the bulk and thin-film phonon densities of states are very close and they agree excellently with the theoretical predictions of a certain surface roughness. Those uncorrected or corrected by the Debye DOS on the other hand fail in capturing the variation trend of the thermal conductivity against the temperature. read less NOT USED (low confidence) E. Winsberg, “A tale of two methods,” Synthese. 2009. link Times cited: 486 NOT USED (low confidence) S. Murad and I. Puri, “Thermal transport through a fluid-solid interface,” Chemical Physics Letters. 2009. link Times cited: 32 NOT USED (low confidence) Jos, P. Rino, G. O. Cardozo, and A. Picinin, “Atomistic Modeling of the Structural and Thermal Conductivity of the InSb,” Cmc-computers Materials & Continua. 2009. link Times cited: 6 Abstract: A new parametrization for the previous empirical interatomic… read moreAbstract: A new parametrization for the previous empirical interatomic potential for indium antimonite is presented. This alternative parametrization is designed to correct the energetic sequence of structures. The effective empirical interatomic potential proposed consists of two and three body interactions which has the same functional form of the interatomic potential proposed by Vashishta et. al. to study other semiconductors (Branicio et al., 2003; Ebbsjo et al., 2000; Shimojo et al., 2000; Vashishta et al., 2008). Molecular dynamics simulations (MD) are performed to study high pressure phases of InSb up to 70 GPa and its thermal conductivity as a function of temperature. The rock-salt to cesium chloride, expected to occur at high pressures, is observed with the proposed interatomic potential. read less NOT USED (low confidence) S. H. Lee, J. Kang, Y.-H. Hong, H. Oh, and D. H. Kim, “Vacancy behavior in Czochralski silicon growth,” Journal of Crystal Growth. 2009. link Times cited: 2 NOT USED (low confidence) J. Turney, A. McGaughey, and C. Amon, “Assessing the applicability of quantum corrections to classical thermal conductivity predictions,” Physical Review B. 2009. link Times cited: 161 Abstract: The validity of the commonly used quantum corrections for ma… read moreAbstract: The validity of the commonly used quantum corrections for mapping a classically predicted thermal conductivity onto a corresponding quantum value are assessed by self-consistently predicting the classical and quantum thermal conductivities of a crystalline silicon system via lattice-dynamics calculations. Applying the quantum corrections to the classical predictions, with or without the zero-point energy, does not bring them into better agreement with the quantum predictions compared to the uncorrected classical values above temperatures of 200 K. By examining the mode dependence of the phonon properties, we demonstrate that thermal conductivity cannot be quantum corrected on a system level. We explore the source of the differences in the quantum and classical phonon relaxation times on a mode-by-mode basis. read less NOT USED (low confidence) P. A. Apte, “Efficient computation of free energy of crystal phases due to external potentials by error-biased Bennett acceptance ratio method.,” The Journal of chemical physics. 2009. link Times cited: 7 Abstract: Free energy of crystal phases is commonly evaluated by therm… read moreAbstract: Free energy of crystal phases is commonly evaluated by thermodynamic integration along a reversible path that involves an external potential. However, this method suffers from the hysteresis caused by the differences in the center of mass position of the crystal phase in the presence and absence of the external potential. To alleviate this hysteresis, a constraint on the translational degrees of freedom of the crystal phase is imposed along the path and subsequently a correction term is added to the free energy to account for such a constraint. The estimation of the correction term is often computationally expensive. In this work, we propose a new methodology, termed as error-biased Bennett acceptance ratio method, which effectively solves this problem without the need to impose any constraint. This method is simple to implement and it does not require any modification to the path. We show the applicability of this method in the computation of crystal-melt interfacial energy by cleaving wall method [R. L. Davidchack and B. B. Laird, J. Chem. Phys. 118, 7651 (2003)] and bulk crystal-melt free energy difference by constrained fluid lambda-integration method [G. Grochola, J. Chem. Phys. 120, 2122 (2004)] for a model potential of silicon. read less NOT USED (low confidence) N. Rajabbeigi, B. Elyassi, T. Tsotsis, and M. Sahimi, “Molecular pore-network model for nanoporous materials. I: Application to adsorption in silicon-carbide membranes,” Journal of Membrane Science. 2009. link Times cited: 21 NOT USED (low confidence) D. Kovač and G. Hobler, “Amorphous pocket model based on the modified heat transport equation and local lattice collapse,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2009. link Times cited: 2 NOT USED (low confidence) H. Kim, “Supercooled Liquid, Glass and Glass Transition,” Journal of The Korean Chemical Society. 2009. link Times cited: 1 Abstract: Characteristics of supercooled liquid and glass, which are t… read moreAbstract: Characteristics of supercooled liquid and glass, which are the states involved in glass transition, are reviewed. These states are non-equilibrium states, therefore, the glass transition is different from the usual phase transitions. Theories of glass transition and related experimental methods are briefly summarized. read less NOT USED (low confidence) Y. Chen, “Reformulation of microscopic balance equations for multiscale materials modeling.,” The Journal of chemical physics. 2009. link Times cited: 99 Abstract: In this paper we present a new formalism that analytically l… read moreAbstract: In this paper we present a new formalism that analytically links atomic variables to continuously distributed local properties and that leads to a concurrent two-level representation of balance laws for atomistic systems with general lattice structure. The new component of this formulation is an explicit decomposition of associated fluxes in multiatomic lattices into components representing the distortions of lattice cells and the rearrangement of atoms within the lattice cells. New formulation of balance laws is obtained in a form that is suitable for a direct atomistic analysis at fine scale to a continuum analysis in coarse scales. The results of this work will provide a new continuum field representation of classical N-body dynamics that can fully reproduce phonon dispersion relations of multiatomic crystalline materials and will enable coupled atomistic and continuum simulations within a single theoretical framework. read less NOT USED (low confidence) H.-C. Cheng, Y.-L. Liu, Y. Hsu, and W.-H. Chen, “Atomistic-continuum modeling for mechanical properties of single-walled carbon nanotubes,” International Journal of Solids and Structures. 2009. link Times cited: 78 NOT USED (low confidence) A. Pedersen, L. Pizzagalli, and H. Jónsson, “Finding mechanism of transitions in complex systems: formation and migration of dislocation kinks in a silicon crystal,” Journal of Physics: Condensed Matter. 2009. link Times cited: 21 Abstract: We demonstrate how a saddle point search method can be used … read moreAbstract: We demonstrate how a saddle point search method can be used to study dislocation mobility in a covalent material—a non-trivial transition mechanism in a complex system. Repeated saddle point searches have been carried out by using the minimum mode following algorithm and dimer method in combination with several empirical potential functions for silicon in order to determine the mechanisms for the creation and migration of kinks on a non-dissociated screw dislocation in a silicon crystal. For the environment-dependent interatomic potential, three possible kink migration processes have been identified with activation energies of 0.17, 0.25, and 0.33 eV. The Lenosky potential gives a single, low energy migration mechanism with an activation energy of 0.07 eV, in good agreement with density functional theory results. The kink formation mechanism determined using this potential has an activation barrier of 1.2 eV. Calculations were also carried out with the Tersoff potential, Stillinger–Weber potential and Bolding–Andersen potential. The various potential functions give quite different results for the kink structure and the mechanism of transition. read less NOT USED (low confidence) N. Dugan and S. Erkoç, “Genetic Algorithm Application to the Structural Properties of Si–Ge Mixed Clusters,” Materials and Manufacturing Processes. 2009. link Times cited: 12 Abstract: Optimum geometries of silicon–germanium (Si–Ge) clusters are… read moreAbstract: Optimum geometries of silicon–germanium (Si–Ge) clusters are found using a single parent genetic algorithm. 100 atom and 150 atom clusters are studied with some variety of compositions and initial geometries. Total interaction energies, distances of Si and Ge atoms to the cluster centers, and average bond lengths are calculated. Si-core Ge-shell geometry is found to be favorable compared to other geometries. read less NOT USED (low confidence) J. G. Swadener and S. T. Picraux, “Strain distributions and electronic property modifications in Si/Ge axial nanowire heterostructures,” Journal of Applied Physics. 2009. link Times cited: 27 Abstract: Molecular dynamics simulations were carried out for Si/Ge ax… read moreAbstract: Molecular dynamics simulations were carried out for Si/Ge axial nanowire heterostructures using modified effective atom method (MEAM) potentials. A Si–Ge MEAM interatomic cross potential was developed based on available experimental data and was used for these studies. The atomic distortions and strain distributions near the Si/Ge interfaces are predicted for nanowires with their axes oriented along the [111] direction. The cases of 10 and 25 nm diameter Si/Ge biwires and of 25 nm diameter Si/Ge/Si axial heterostructures with the Ge disk 1 nm thick were studied. Substantial distortions in the height of the atoms adjacent to the interface were found for the biwires but not for the Ge disks. Strains as high as 3.5% were found for the Ge disk and values of 2%–2.5% were found at the Si and Ge interfacial layers in the biwires. Deformation potential theory was used to estimate the influence of the strains on the band gap, and reductions in band gap to as small as 40% of bulk values are predicted for the Ge disks. The localized regions of increased strain and resulting energy minima were also found within the Si/Ge biwire interfaces with the larger effects on the Ge side of the interface. The regions of strain maxima near and within the interfaces are anticipated to be useful for tailoring band gaps and producing quantum confinement of carriers. These results suggest that nanowire heterostructures provide greater design flexibility in band structure modification than is possible with planar layer growth. read less NOT USED (low confidence) S. Shenogin, A. Bodapati, P. Keblinski, and A. McGaughey, “Predicting the thermal conductivity of inorganic and polymeric glasses: The role of anharmonicity,” Journal of Applied Physics. 2009. link Times cited: 92 Abstract: The thermal conductivity of several amorphous solids is nume… read moreAbstract: The thermal conductivity of several amorphous solids is numerically evaluated within the harmonic approximation from Kubo linear-response theory following the formalism developed by Allen and Feldman [Phys. Rev. B 48, 12581 (1993)]. The predictions are compared to the results of molecular dynamics (MD) simulations with realistic anharmonic potentials and to experimental measurements. The harmonic theory accurately predicts the thermal conductivity of amorphous silicon, a model Lennard-Jones glass, and a bead-spring Lennard-Jones glass. For polystyrene and amorphous silica at room temperature, however, the harmonic theory underestimates the thermal conductivity by a factor of about 2. This result can be explained by the existence of additional thermal transport via anharmonic energy transfer. More surprisingly, the thermal conductivity of polystyrene and amorphous silica at low temperature (MD and experimental) are significantly below the predictions of the harmonic theory. Potential reasons for the failur... read less NOT USED (low confidence) J. Godet, P. Hirel, S. Brochard, and L. Pizzagalli, “Evidence of two plastic regimes controlled by dislocation nucleation in silicon nanostructures,” Journal of Applied Physics. 2009. link Times cited: 48 Abstract: We performed molecular dynamics simulations of silicon nanos… read moreAbstract: We performed molecular dynamics simulations of silicon nanostructures submitted to various stresses and temperatures. For a given stress orientation, a transition in the onset of silicon plasticity is revealed depending on the temperature and stress magnitude. At high temperature and low stress, partial dislocation loops are nucleated in the {111} glide set planes. But at low temperature and very high stress, perfect dislocation loops are formed in the other set of {111} planes called shuffle. This result confirmed by three different classical potentials suggests that plasticity in silicon nanostructures could be controlled by dislocation nucleation. read less NOT USED (low confidence) F. Tavazza, L. Levine, and A. Chaka, “Hybrid Methods for Atomic‐Level Simulations Spanning Multiple–Length Scales in the Solid State.” 2009. link Times cited: 0 NOT USED (low confidence) S. Murad and I. Puri, “Molecular simulation of thermal transport across hydrophilic interfaces,” Chemical Physics Letters. 2008. link Times cited: 54 NOT USED (low confidence) E. Sawardecker, M. Sales-Pardo, and L. A. Amaral, “Detection of node group membership in networks with group overlap,” The European Physical Journal B. 2008. link Times cited: 56 NOT USED (low confidence) T. Li, D. Donadio, L. Ghiringhelli, and G. Galli, “Surface-induced crystallization in supercooled tetrahedral liquids.,” Nature materials. 2008. link Times cited: 79 NOT USED (low confidence) L. Yuan, M. Wang, and K. J. Chen, “Atomistic modeling of fluorine implantation and diffusion in III-nitride semiconductors,” 2008 IEEE International Electron Devices Meeting. 2008. link Times cited: 8 Abstract: A hybrid molecular dynamics (MD)/kinetic Monte Carlo (KMC) m… read moreAbstract: A hybrid molecular dynamics (MD)/kinetic Monte Carlo (KMC) model is developed for atomistic modeling of fluorine ion implantation and diffusion in AlGaN/GaN heterostructures. The MD simulation reveals the F distribution profiles and the corresponding defect profiles, and most importantly, the potential energies of fluorine ions in the III-nitride material system. Using the results from the MD simulation, the diffusion process is simulated with KMC method, and the modeling results are validated by the secondary-ion-mass-spectrum (SIMS) measurement. The surface effect on the fluorine's stability and its improvement by passivation are also successfully modeled. read less NOT USED (low confidence) P. Schelling, “Phase behavior and kinetics of a new bond-order potential for silicon,” Computational Materials Science. 2008. link Times cited: 24 NOT USED (low confidence) D. Bandyopadhyay and M. Kumar, “The electronic structures and properties of transition metal-doped silicon nanoclusters: A density functional investigation,” Chemical Physics. 2008. link Times cited: 28 NOT USED (low confidence) A. Chroneos, H. Bracht, C. Jiang, B. Uberuaga, and R. Grimes, “Nonlinear stability of E centers in Si 1- x Ge x : electronic structure calculations,” Physical Review B. 2008. link Times cited: 56 Abstract: Electronic structure calculations are used to investigate th… read moreAbstract: Electronic structure calculations are used to investigate the binding energies of defect pairs composed of lattice vacancies and phosphorus or arsenic atoms ( E centers) in silicon-germanium alloys. To describe the local environment surrounding the E center we have generated special quasirandom structures that represent random silicon-germanium alloys. It is predicted that the stability of E centers does not vary linearly with the composition of the silicon-germanium alloy. Interestingly, we predict that the nonlinear behavior does not depend on the donor atom of the E center but only on the host lattice. The impact on diffusion properties is discussed in view of recent experimental and theoretical results. read less NOT USED (low confidence) R. D. Nyilas and R. Spolenak, “Orientation-dependent ductile-to-brittle transitions in nanostructured materials,” Acta Materialia. 2008. link Times cited: 4 NOT USED (low confidence) W. Cai, W. Fong, E. Elsen, and C. Weinberger, “Torsion and bending periodic boundary conditions for modeling the intrinsic strength of nanowires,” Journal of The Mechanics and Physics of Solids. 2008. link Times cited: 37 NOT USED (low confidence) H. Ohta, T. Watanabe, and I. Ohdomari, “Potential energy landscape of an interstitial O2 molecule in a SiO2 film near the SiO2/Si(001) interface,” Physical Review B. 2008. link Times cited: 10 NOT USED (low confidence) H. Ohta, A. Iwakawa, K. Eriguchi, and K. Ono, “An interatomic potential model for molecular dynamics simulation of silicon etching by Br+-containing plasmas,” Journal of Applied Physics. 2008. link Times cited: 22 Abstract: An interatomic potential model for Si–Br systems has been de… read moreAbstract: An interatomic potential model for Si–Br systems has been developed for performing classical molecular dynamics (MD) simulations. This model enables us to simulate atomic-scale reaction dynamics during Si etching processes by Br+-containing plasmas such as HBr and Br2 plasmas, which are frequently utilized in state-of-the-art techniques for the fabrication of semiconductor devices. Our potential form is based on the well-known Stillinger–Weber potential function, and the model parameters were systematically determined from a database of potential energies obtained from ab initio quantum-chemical calculations using GAUSSIAN03. For parameter fitting, we propose an improved linear scheme that does not require any complicated nonlinear fitting as that in previous studies [H. Ohta and S. Hamaguchi, J. Chem. Phys. 115, 6679 (2001)]. In this paper, we present the potential derivation and simulation results of bombardment of a Si(100) surface using a monoenergetic Br+ beam. read less NOT USED (low confidence) Z. Wang, D. Cheng, Z. Li, and X. Zu, “Atomistic simulation of the torsional buckling of single-crystalline GaN nanotubes,” Physica E-low-dimensional Systems & Nanostructures. 2008. link Times cited: 7 NOT USED (low confidence) M. Ghazisaeidi, J. Freund, and H. Johnson, “Statistical characterization of surface defects created by Ar ion bombardment of crystalline silicon,” Journal of Applied Physics. 2008. link Times cited: 1 Abstract: Ion bombardment of crystalline silicon targets induces patte… read moreAbstract: Ion bombardment of crystalline silicon targets induces pattern formation by the creation of mobile surface species that participate in forming nanometer-scale structures. The formation of these mobile species on a Si(001) surface, caused by sub-keV argon ion bombardment, is investigated through molecular dynamics simulation of Stillinger-Weber [Phys. Rev. B 31, 5262 (1985)] silicon. Specific criteria for identifying and classifying these mobile atoms based on their energy and coordination number are developed. The mobile species are categorized based on these criteria and their average concentrations are calculated. read less NOT USED (low confidence) X. Liu, J. Hu, and B. Pan, “The composition-dependent mechanical properties of Ge/Si core-shell nanowires,” Physica E-low-dimensional Systems & Nanostructures. 2008. link Times cited: 25 NOT USED (low confidence) M. Kaviany, “Heat Transfer Physics: Abbreviations.” 2008. link Times cited: 179 Abstract: 1. Introduction and preliminaries 2. Molecular orbitals/pote… read moreAbstract: 1. Introduction and preliminaries 2. Molecular orbitals/potentials/dynamics and quantum energy states 3. Carrier energy transport and transformation theories 4. Phonon energy storage, transport, and transformation kinetics 5. Electron energy storage, transport, and transformation kinetics 6. Fluid particle energy storage, transport, and transformation kinetics 7. Photon energy storage, transport, and transformation kinetics Appendices A-I. read less NOT USED (low confidence) S. Aubry, C. Kimmer, A. Skye, and P. Schelling, “Comparison of theoretical and simulation-based predictions of grain-boundary Kapitza conductance in silicon,” Physical Review B. 2008. link Times cited: 47 Abstract: We present a comparison between molecular-dynamics (MD) simu… read moreAbstract: We present a comparison between molecular-dynamics (MD) simulation and theoretical calculations using input from wave-packet simulations of the Kapitza conductance of two different grain boundaries in silicon. We find that for a $\ensuremath{\Sigma}3(111)$ twin boundary with minimal disruption of the lattice, the Kapitza conductance is extremely high in contrast to previous results obtained for the $\ensuremath{\Sigma}29(001)$ grain boundary. Theoretical predictions based on input from wave-packet simulations appear to show reasonable agreement with MD results for the $\ensuremath{\Sigma}29(001)$ grain boundary but disagreement by a factor of about ten for the $\ensuremath{\Sigma}3(111)$ boundary. The origin of the apparent discrepancies is analogous to previously noted difficulties in comparing theoretical predictions to experimental measurements of the Kapitza conductance. We show why the apparent discrepancies are large when the interface phonon transmission is high and relatively small when the phonon transmission is low. We demonstrate how the theoretical predictions and MD simulation results can be compared in a consistent and meaningful way, thereby removing the apparent contradictions. These questions also are discussed in the important context of relating MD results to experimental observations. read less NOT USED (low confidence) M. Yao, T. Watanabe, P. Schelling, P. Keblinski, D. Cahill, and S. Phillpot, “Phonon-defect scattering in doped silicon by molecular dynamics simulation,” Journal of Applied Physics. 2008. link Times cited: 13 Abstract: Molecular dynamics simulations are used to study the scatter… read moreAbstract: Molecular dynamics simulations are used to study the scattering of phonon wave packets of well-defined frequency and polarization from individual point defects and from a field of point defects in Si. The relative amounts of energy in the transmitted and reflected phonon fields are calculated and the parameters that influence the phonon scattering process are determined. The results show that the fractions of transmitted and reflected energies strongly depend on the frequency of the incident phonons and on the mass and concentration of the defects. These results are compared with the classic formula for the scattering strength for point defects derived by Klemens, which we find to be valid when each phonon-defect scattering event is independent. The Klemens formula fails when coupled multiple scattering dominates. The phonon density of states is used to characterize the effects of point defects on mode mixing. read less NOT USED (low confidence) Z. Wang, F. Gao, X. Zu, and W. J. Weber, “Physical Properties of GaN Nanotubes as Revealed by Computer Simulation.” 2008. link Times cited: 1 NOT USED (low confidence) M. Posselt, F. Gao, and H. Bracht, “Correlation between self-diffusion in Si and the migration mechanisms of vacancies and self-interstitials: An atomistic study,” Physical Review B. 2008. link Times cited: 28 Abstract: The migration of point defects in silicon and the correspond… read moreAbstract: The migration of point defects in silicon and the corresponding atomic mobility are investigated by classical molecular dynamics simulations using the Stillinger-Weber potential and the Tersoff potential. In contrast to most of the previous studies both the point defect diffusivity and the self-diffusion coefficient per defect are calculated separately so that the diffusion-correlation factor can be determined. Simulations with both the Stillinger-Weber and the Tersoff potential show that vacancy migration is characterized by the transformation of the tetrahedral vacancy to the split vacancy and vice versa and the diffusion-correlation factor is about 0.5. This value was also derived by the statistical diffusion theory under the assumption of the same migration mechanism. The mechanisms of self-interstitial migration are more complex. The detailed study, including a visual analysis and investigations with the nudged elastic band method, reveals a variety of transformations between different self-interstitial configurations. Molecular dynamics simulations using the Stillinger-Weber potential show, that the self-interstitial migration is dominated by a dumbbell mechanism, whereas the interstitialcy mechanism prevails with the Tersoff potental. The corresponding values of the correlation factor are different, namely 0.59 and 0.69 for the dumbbell and the interstitialcy mechanism, respectively. The latter value is nearly equal to that obtainedmore » by the statistical theory which assumes the interstitialcy mechanism. Recent analysis of experimental results demonstrated, that in the framework of state-of-the-art diffusion and reaction models the best interpretation of point defect data can be given by assuming . The comparison with the present atomistic study leads to the conclusion that a dumbbell mechanism governs the self-interstitial migration in Si. Simulations using the Stillinger-Weber potential reveal two dominating migration paths which are characterized by transformation between the extended dumbbell and the dumbbell and vice versa. This process occurs either in a single {110} plane or includes a change into an equivalent {110} plane.« less read less NOT USED (low confidence) E. Holmström, A. Kuronen, and K. Nordlund, “Threshold defect production in silicon determined by density functional theory molecular dynamics simulations,” Physical Review B. 2008. link Times cited: 140 Abstract: We studied threshold displacement energies for creating stab… read moreAbstract: We studied threshold displacement energies for creating stable Frenkel pairs in silicon using density functional theory molecular dynamics simulations. The average threshold energy over all lattice directions was found to be $36\ifmmode\pm\else\textpm\fi{}{2}_{\text{ST}\text{ }\text{AT}}\ifmmode\pm\else\textpm\fi{}{2}_{\text{SY}\text{ }\text{ST}}\text{ }\text{eV}$, and thresholds in the directions $⟨100⟩$ and $⟨111⟩$ were found to be $20\ifmmode\pm\else\textpm\fi{}{2}_{\text{SY}\text{ }\text{ST}}\text{ }\text{eV}$ and $12.5\ifmmode\pm\else\textpm\fi{}{1.5}_{\text{SY}\text{ }\text{ST}}\text{ }\text{eV}$, respectively. Moreover, we found that in most studied lattice directions, a bond defect complex is formed with a lower threshold than a Frenkel pair. The average threshold energy for producing either a bond defect or a Frenkel pair was found to be $24\ifmmode\pm\else\textpm\fi{}{1}_{\text{ST}\text{ }\text{AT}}\ifmmode\pm\else\textpm\fi{}{2}_{\text{SY}\text{ }\text{ST}}\text{ }\text{eV}$. read less NOT USED (low confidence) P. Tian, “Molecular dynamics simulations of nanoparticles.” 2008. link Times cited: 37 Abstract: A review of molecular dynamics simulation studies of nanopar… read moreAbstract: A review of molecular dynamics simulation studies of nanoparticles is presented. While research on nanoparticles and their usage in industries, healthcare, and biomedical sciences has been very active, real time observation and analysis of some dynamical and thermodynamic properties and physical mechanisms underlying many of the special characteristics of various nanoparticles are not easily achieved experimentally. Due to the rapid development of the computational algorithms and available computational resources to scientific researchers and relatively small sizes of nanoparticles, molecular dynamics (MD) simulations, together with other computational methods, occupy an increasingly important niche in this rapidly developing and expanding field. As part of the Annual Reports, the focus of this review is on the research published during the last year. A brief survey of fundamentals of MD simulations is given first, followed by how various MD methodologies are utilized for the investigations of the nucleation and melting behavior of various metallic nanoparticles, for the understanding of structural and physiochemical properties of metal oxide and semiconductor nanoparticles; and for the studies of interactions of nanoparticles with their surrounding materials and among themselves. The role of multiscale modeling, involving both methods and applications, in nanoparticle research is discussed. The challenges and opportunities in the future are briefly discussed at the end. read less NOT USED (low confidence) P. A. Apte and X. Zeng, “Anisotropy of crystal-melt interfacial free energy of silicon by simulation,” Applied Physics Letters. 2008. link Times cited: 58 Abstract: We extend the cleaving wall method to a nonpairwise additive… read moreAbstract: We extend the cleaving wall method to a nonpairwise additive potential. Using this method, we compute the anisotropy of crystal-melt interfacial free energy γ for Stillinger–Weber potential of silicon [F. H. Stillinger and T. A. Weber, Phys. Rev. B 31, 5262 (1985)]. The calculated γ for (100), (111), and (110) orientations are 0.42±0.02, 0.34±0.02, and 0.35±0.03J∕m2, respectively. The anisotropy in γ we found is consistent with the experimental observation that Si(100)-melt interface develops (111) facets and also helps in explaining a higher undercooling observed for Si(111)-melt interface in Czochralski method. read less NOT USED (low confidence) M. Buehler, A. Cohen, and D. Sen, “Multi-Paradigm Modeling of Fracture of a Silicon Single Crystal under Mode II Shear Loading,” Journal of Algorithms and Computational Technology. 2008. link Times cited: 4 Abstract: We report a novel multi-paradigm multi-scale approach based … read moreAbstract: We report a novel multi-paradigm multi-scale approach based on a combination of the first principles ReaxFF force field with an empirical Tersoff potential. Our hybrid multi-scale simulation model is computationally efficient and capable of treating thousands of atoms with QM accuracy, extending our ability to simulate the dynamical behavior of a wider range of chemically complex materials such as silicon, silica and metal-organic compounds. It is implemented in the Python based Computational Materials Design Facility (CMDF). We exemplify our method in a study focused on a systematic comparison of the fracture dynamics in silicon under mode II shear versus mode I tensile loading. We find that the mode II crack tends to branch at an angle of approximately 45 degrees once the crack speed approaches 38% of the Rayleigh-wave speed. In contrast, the mode I crack continuously propagates in the direction of the initial crack, and only makes a slight change of direction towards 10 degrees once fracture instabilities occur. Our results reveal fundamental differences of fracture dynamics under mode I versus mode II loading. read less NOT USED (low confidence) J. R. Morris, R. Aga, V. A. Levashov, and T. Egami, “Many-body effects in bcc metals: An embedded atom model extension of the modified Johnson pair potential for iron,” Physical Review B. 2008. link Times cited: 8 Abstract: In this work, we generalize a many-body extension of pairwis… read moreAbstract: In this work, we generalize a many-body extension of pairwise interatomic potentials originally proposed by Baskes, in particular, showing how a pair potential interacting with multiple near neighbor shells may be extended to an embedded atom form without changing the cohesive energy or lattice constant. This is important for parametric studies of interatomic potentials, particularly how elastic constants affect other properties. Specifically, we apply this to the modified Johnson potential, a pair potential for Fe that has been used extensively for understanding liquid and amorphous metals. read less NOT USED (low confidence) G. Opletal, T. Petersen, B. O’Malley, I. Snook, D. McCulloch, and I. Yarovsky, “HRMC: Hybrid Reverse Monte Carlo method with silicon and carbon potentials,” Comput. Phys. Commun. 2008. link Times cited: 21 NOT USED (low confidence) S. Kitamura, “Analysis of Strained Island Energetics in Ge/Si(001) Growth(Condensed matter : structure and mechanical and thermal properties),” Journal of the Physical Society of Japan. 2008. link Times cited: 0 Abstract: The numerical calculation for Ge/Si(001) heteroepitaxial gro… read moreAbstract: The numerical calculation for Ge/Si(001) heteroepitaxial growth is performed. We adopt the most widely used Stillinger–Weber potential, and the island energies of the three types, two-dimensional island, pyramid and dome, are explored as a function of the lateral size. These island energies are compared with each other to find the island morphology which has the lowest energy. Then, a growth history of the most stable growth mode is searched. Although the result reproduces qualitatively the Stranski–Krastanov growth as observed in the experiments, quantitative differences between our result and experiments in the critical wet layer thickness and the island morphology are found. read less NOT USED (low confidence) E. Webb, J. Zimmerman, and S. Seel, “Reconsideration of Continuum Thermomechanical Quantities in Atomic Scale Simulations,” Mathematics and Mechanics of Solids. 2008. link Times cited: 64 Abstract: As motivation builds to consider mechanics of nanometer scal… read moreAbstract: As motivation builds to consider mechanics of nanometer scale objects, it is increasingly advantageous to implement models with finer resolution than standard continuum approaches. For such exercises to prove fruitful, these models must be able to quantify continuum thermomechanical quantities; furthermore, it may be necessary to do so on a sub-system level in order to assess gradients or distributions in a given property. Herein we review the calculation of stress, heat flux, and temperature in atomic scale numerical simulations such as the molecular dynamics method. read less NOT USED (low confidence) Z. Wang, X. Zu, L. Yang, F. Gao, and W. J. Weber, “Buckling of GaN nanotubes under uniaxial compression,” Solid State Communications. 2008. link Times cited: 9 NOT USED (low confidence) T. Kouno and S. Ogata, “Activation Energy for Oxygen Diffusion in Strained Silicon : A Hybrid Quantum-Classical Simulation Study with the Nudged Elastic Band Method(Condensed matter : electronic structure and electrical, magnetic, and optical properties),” Journal of the Physical Society of Japan. 2008. link Times cited: 7 Abstract: The activation energy for oxygen diffusion in strained silic… read moreAbstract: The activation energy for oxygen diffusion in strained silicon crystal is investigated using the hybrid quantum-classical simulation scheme in combination with the nudged elastic band method. The electronic density-functional theory is applied to a local region containing the oxygen atom, while the classical inter-atomic potential, to the rest of the system. The system is stretched to three mutually perpendicular directions at a wide range of degree between -2 and 9%. We thereby find that the activation energy changes by between -0.4 and 0.2 eV depending sensitively on both direction and degree of the stretch, and that the peripheral atoms located far from the oxygen atom in the system contribute little to the change. Microscopic mechanisms of the strain-dependence of the activation energy are elucidated through combined analyses about the atomic and electronic structures. read less NOT USED (low confidence) N. Kalyanasundaram, M. Ghazisaeidi, J. Freund, and H. Johnson, “Single impact crater functions for ion bombardment of silicon,” Applied Physics Letters. 2008. link Times cited: 58 Abstract: The average effect of a single 500eV incident argon ion on a… read moreAbstract: The average effect of a single 500eV incident argon ion on a silicon surface is studied using molecular dynamics simulations. More than 103 ion impacts at random surface points are averaged for each of seven incidence angles, from 0° to 28° off normal, to determine a local surface height change function, or a crater function. The crater shapes are mostly determined by mass rearrangement; sputtering has a relatively small effect. Analytical fitting functions are provided for several cases, and may serve as input into kinetic Monte Carlo calculations or stability analyses for surfaces subjected to ion bombardment. read less NOT USED (low confidence) B. Cox, “Mathematical modelling of nano-scaled structures, devices and materials,” Bulletin of the Australian Mathematical Society. 2008. link Times cited: 1 Abstract: Problems from three specific areas of nanotechnology are exa… read moreAbstract: Problems from three specific areas of nanotechnology are examined in this thesis. Firstly, new models for nanostructures of carbon are presented. The structures of primary interest are carbon nanotubes and related nanoscale toroidal molecules of pure carbon. Following this, the mechanics of carbon nanotubes interacting with atoms and fullerenes is examined. Acted on by van der Waals forces alone, a fullerene can oscillate at high frequencies inside an open-ended carbon nanotube. The frequencies obtained are predicted to be in the gigahertz range and these so-called “gigahertz oscillators” provide the primary motivation for this part of the thesis. Lastly, the electrostatic problem of uncharged particles at close interstice subject to an external applied electric field is explored. This is a problem of interest for a class of material called “electrorheological fluids” and various aspects of particle geometry are examined. In this thesis the conventional theory which prescribes the geometric parameters of carbon nanotubes is examined and it is found that it does not adequately account for the curvature inherent in the structure of nanotubes. By considering three postulates and then applying geometry and trigonometry, a polyhedral model is proposed and new formulae are derived which provide more precise expressions for geometric parameters such as the chiral angle, radius and unit length. Asymptotic expansions of these expressions are also shown to produce the conventional formulae as the leading order terms. Following this, approximately toroidal molecules are described which are formed from carbon nanotubes which have defects that cause a bend in an otherwise straight nanotube. The angle of the bend is determined and then expressions are derived giving the dimensions for tori formed from a number of these bend defects. Representative formulae for the ideal tori parameters, of generating radius and tube radius, are determined from integral expressions for the circumference and surface area of the ideal surface. The part of this thesis concerned with the mechanics of carbon nanotubes and fullerenes is primarily focussed on the van der Waals interactions between these types of molecules. The particular application of fullerenes oscillating inside of carbon nanotubes is examined in detail and the terms “suction energy” and “acceptance energy” are introduced here for the first time to describe the general behaviour of read less NOT USED (low confidence) M. Matsukuma and S. Hamaguchi, “Molecular dynamics simulation of microcrystalline Si deposition processes by silane plasmas,” Thin Solid Films. 2008. link Times cited: 5 NOT USED (low confidence) N. Deladerrière, J. Delaye, F. Augereau, G. Despaux, and S. Peuget, “Molecular dynamics study of acoustic velocity in silicate glass under irradiation,” Journal of Nuclear Materials. 2008. link Times cited: 16 NOT USED (low confidence) J. Schall, G. Gao, and J. Harrison, “Elastic constants of silicon materials calculated as a function of temperature using a parametrization of the second-generation reactive empirical bond-order potential,” Physical Review B. 2008. link Times cited: 48 Abstract: A parametrization for silicon is presented that is based on … read moreAbstract: A parametrization for silicon is presented that is based on the second-generation reactive empirical bondorder REBO formalism Brenner, Shenderova, Harrison, Stuart, Ni, and Sinnott J. Phys.: Condens. Matter 14, 783 2002 . Because it shares the same analytic form as Brenner’s second-generation REBO, this new potential is a step toward a single potential that can model many atom systems that contain C, Si, and H, where bond breaking and bond making are important. The widespread use of Brenner’s REBO potential, its ability to model both zero-Kelvin elastic constants of diamond and the temperature dependence of the elastic constants, and the existence of parameters for many atom types were the motivating factors for obtaining this parametrization for Si. While Si-C-H classical bond-order potentials do exist, they are based on Brenner’s original formalism. This new parametrization is validated by examining the structure and stability of a large number of crystalline silicon structures, by examining the relaxation energies of point defects, the energies of silicon surfaces, the effects of adatoms on surface energies, and the structures of both liquid silicon and amorphous silicon. Finally, the elastic constants of diamond-cubic and amorphous silicon between 0 and 1100 K are calculated with this new parametrization and compared to values calculated using a previously published potential. read less NOT USED (low confidence) T. Hawa and M. Zachariah, “Development of a Simple Sintering Law for Fractal Aggregates Composed of Unequal Sized Primary Particles,” Bulletin of the American Physical Society. 2008. link Times cited: 0 NOT USED (low confidence) E.-H. Kim, Y.-H. Shin, and B.-J. Lee, “A modified embedded-atom method interatomic potential for Germanium,” Calphad-computer Coupling of Phase Diagrams and Thermochemistry. 2008. link Times cited: 86 NOT USED (low confidence) G. Parisi and F. Zamponi, “Mean-field theory of hard sphere glasses and jamming,” Reviews of Modern Physics. 2008. link Times cited: 494 Abstract: Hard spheres are ubiquitous in condensed matter: they have b… read moreAbstract: Hard spheres are ubiquitous in condensed matter: they have been used as models for liquids, crystals, colloidal systems, granular systems, and powders. Packings of hard spheres are of even wider interest, as they are related to important problems in information theory, such as digitalization of signals, error correcting codes, and optimization problems. In three dimensions the densest packing of identical hard spheres has been proven to be the FCC lattice, and it is conjectured that the closest packing is ordered (a regular lattice, e.g, a crystal) in low enough dimension. Still, amorphous packings have attracted a lot of interest, because for polydisperse colloids and granular materials the crystalline state is not obtained in experiments for kinetic reasons. We review here a theory of amorphous packings, and more generally glassy states, of hard spheres that is based on the replica method: this theory gives predictions on the structure and thermodynamics of these states. In dimensions between two and six these predictions can be successfully compared with numerical simulations. We will also discuss the limit of large dimension where an exact solution is possible. Some of the results we present here have been already published, but others are original: in particular we improved the discussion of the large dimension limit and we obtained new results on the correlation function and the contact force distribution in three dimensions. We also try here to clarify the main assumptions that are beyond our theory and in particular the relation between our static computation and the dynamical procedures used to construct amorphous packings. read less NOT USED (low confidence) N. Takahashi, Y. Nakamura, J. Nara, Y. Tateyama, T. Uda, and T. Ohno, “Theoretical study of the initial oxidation processes on the Si(0 0 1) surface,” Surface Science. 2008. link Times cited: 11 NOT USED (low confidence) C. Li, Q. Meng, K. Zhong, and C.-ying Wang, “Computer simulation of the 60° dislocation interaction with vacancy cluster in silicon,” Physical Review B. 2008. link Times cited: 11 Abstract: In the current work, the interaction of the 60\ifmmode^\circ… read moreAbstract: In the current work, the interaction of the 60\ifmmode^\circ\else\textdegree\fi{} shuffle dislocation with the vacancy cluster under applied shear stress in silicon crystal is studied via the molecular dynamics method. Stillinger-Weber (SW) potential and environment-dependent interatomic potential (EDIP) are used to calculate the interatomic forces. Simulation results show that at low shear stress, the dislocation is pinned by a vacancy cluster. With the stress level increased to a certain critical value ${\ensuremath{\sigma}}_{l}$, the dislocation can overcome the pinning and get through. It is found that ${\ensuremath{\sigma}}_{l}$ reaches its maximum at a transition temperature, which is about $350\phantom{\rule{0.3em}{0ex}}\mathrm{K}$. Also revealed in the simulations is a generalized dislocation dissociation that a 60\ifmmode^\circ\else\textdegree\fi{} dislocation, while interacting with a vacancy cluster, can result in 30\ifmmode^\circ\else\textdegree\fi{} and 90\ifmmode^\circ\else\textdegree\fi{} partial dislocations when the applied shear stress reaches another critical value ${\ensuremath{\sigma}}_{h}$. The two resultant partial dislocations are separated by an intrinsic stacking fault. Unlike ${\ensuremath{\sigma}}_{l}$, ${\ensuremath{\sigma}}_{h}$ keeps decreasing at temperatures higher than $400\phantom{\rule{0.3em}{0ex}}\mathrm{K}$ and remains a constant at lower temperatures. read less NOT USED (low confidence) J. Sumanth, D. Swanson, and H. Jiang, “A Novel Force Matrix Transformation with Optimal Load-Balance for 3-Body Potential Based Parallel Molecular Dynamics Using Atom-Decomposition in a Heterogeneous Cluster Environment,” International Conference on High Performance Computing. 2007. link Times cited: 1 NOT USED (low confidence) D. Broido, M. Malorny, G. Birner, N. Mingo, and D. Stewart, “Intrinsic lattice thermal conductivity of semiconductors from first principles,” Applied Physics Letters. 2007. link Times cited: 698 Abstract: The original version of this article may be found at the App… read moreAbstract: The original version of this article may be found at the Applied Physics Letters website:
http://dx.doi.org/10.1063/1.2822891
Copyright (2007) American Institute of Physics read less NOT USED (low confidence) D. Alfé, “Theory and Practice – The Ab Initio Treatment of High-Pressure and -Temperature Mineral Properties and Behavior.” 2007. link Times cited: 1 NOT USED (low confidence) J. Mauro and R. Loucks, “Selenium glass transition : A model based on the enthalpy landscape approach and nonequilibrium statistical mechanics,” Physical Review B. 2007. link Times cited: 59 NOT USED (low confidence) U. M. E. Christmas, D. Faux, and N. Cowern, “Elastic interaction energy between a silicon interstitial and a carbon substitutional in a silicon crystal,” Physical Review B. 2007. link Times cited: 1 Abstract: The strain interaction energy between a silicon interstitial… read moreAbstract: The strain interaction energy between a silicon interstitial and a carbon substitutional in a silicon crystal was modeled by a continuum Green’s function method and by atomistic simulation. The interaction energy is proportional to d−3, where d is separation distance between the defects. The pair interaction energy was found to be less than 0.04 meV for d 6 nm increasing to more than about 0.1 meV for d 3 nm. The energies are unlikely to influence the diffusional behavior of the defects except at distances of one or two unit cells. The potential between the point defects is repulsive if they are oriented along the 100 crystal axis, but attractive if they are positioned along 110 or 111 . read less NOT USED (low confidence) Y. Sasajima, T. Akabane, T. Nakazawa, and A. Iwase, “Computer simulation of high-energy-beam irradiation of single-crystalline silicon,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2007. link Times cited: 8 NOT USED (low confidence) P. McMillan et al., “Metastable phase transitions and structural transformations in solid-state materials at high pressure,” Phase Transitions. 2007. link Times cited: 14 Abstract: We use a combination of diamond anvil cell techniques and la… read moreAbstract: We use a combination of diamond anvil cell techniques and large volume (multi-anvil press, piston cylinder) devices to study the synthesis, structure and properties of new materials under high pressure conditions. The work often involves the study of structural and phase transformations occurring in the metastable regime, as we explore the phase space determined as a function of the pressure, temperature and chemical composition. The experimental studies are combined with first principles calculations and molecular dynamics simulations, as we determine the structures and properties of new phases and the nature of the transformations between them. Problems currently under investigation include structural studies of transition metal and main group nitrides, oxides and oxynitrides at high pressure, exploration of new solid-state compounds that are formed within the C-N-O system, polyamorphic low- to high-density transitions among amorphous semiconductors such as a-Si, and transformations into metastable forms of the element that occur when its “expanded” clathrate polymorph is compressed. read less NOT USED (low confidence) N. Dugan and S. Erkoç, “Monte Carlo geometry optimization of Sin (n ≤ 71) clusters,” J. Comput. Methods Sci. Eng. 2007. link Times cited: 1 Abstract: Optimum geometries of silicon clusters up to 71 atoms have b… read moreAbstract: Optimum geometries of silicon clusters up to 71 atoms have been found by a recently developed Monte Carlo based global optimization method. Structural properties of these clusters have been investigated and the results have been compared with available results obtained by other methods. Radial distribution of atoms of Si$_{71}$ have been compared with the silicon crystal structure. read less NOT USED (low confidence) T. Aoki and J. Matsuo, “Molecular dynamics study of glancing angle gas cluster irradiation on irregular-structured surfaces,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2007. link Times cited: 15 NOT USED (low confidence) Y. Nakamura, N. Takahashi, M. Okamoto, T. Uda, and T. Ohno, “Link molecule method for quantum mechanical/molecular mechanical hybrid simulations,” J. Comput. Phys. 2007. link Times cited: 6 NOT USED (low confidence) S. Ogata and T. Kouno, “Hybrid Simulations for Desinging of Nano-Interfacial Structures,” Solid State Phenomena. 2007. link Times cited: 0 Abstract: There is growing demand to perform dynamic, atomistic comput… read moreAbstract: There is growing demand to perform dynamic, atomistic computer-simulation of nano-scaled interfaces. For dynamic simulation of interesting processes at the nano-interfaces, we have been developing the hybrid simulation schemes by concurrently coupling the quantum description as the electronic density-functional theory and the classical description as the classical molecular dynamics. A quantum (QM) region composed of a relatively small number of atoms, is embedded with the novel buffered-cluster method in a classical (CL) region of atoms interacting through an empirical inter-atomic potential. The hybrid QM-CL simulation scheme is applied to various kinds of nano-processes including implantation of oxygen atoms to a Si slab relating to SIMOX technology. read less NOT USED (low confidence) H. Whitlow and S. Nakagawa, “Low-energy primary knock on atom damage distributions near MeV proton beams focused to nanometre dimensions,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2007. link Times cited: 14 NOT USED (low confidence) R. Hennig, T. Lenosky, D. Trinkle, S. Rudin, and J. Wilkins, “Classical potential describes martensitic phase transformations between the α, β, and ω titanium phases,” Physical Review B. 2007. link Times cited: 160 Abstract: A description of the martensitic transformations between the… read moreAbstract: A description of the martensitic transformations between the , , and phases of titanium that includes nucleation and growth requires an accurate classical potential. Optimization of the parameters of a modified embedded atom potential to a database of density-functional calculations yields an accurate and transferable potential as verified by comparison to experimental and density-functional data for phonons, surface and stacking fault energies, and energy barriers for homogeneous martensitic transformations. Molecular-dynamics simulations map out the pressure-temperature phase diagram of titanium. For this potential the martensitic phase transformation between and appears at ambient pressure and 1200 K, between and at ambient conditions, between and at 1200 K and pressures above 8 GPa, and the triple point occurs at 8 GPa and 1200 K. Molecular-dynamics explorations of the kinetics of the martensitic - transformation show a fast moving interface with a low interfacial energy of 30 meV/A 2 . The potential is applicable to the study of read less NOT USED (low confidence) H. Lei, X. J. Jiang, J. Chen, I. Belabbas, P. Ruterana, and G. Nouet, “InN clusters in InxGa1-xN quantum wells: analysis of bond lengths,” Physica Status Solidi (c). 2007. link Times cited: 2 Abstract: 1 Introduction III-V nitride semiconductors (GaN, AlN, InN) … read moreAbstract: 1 Introduction III-V nitride semiconductors (GaN, AlN, InN) are characterized by a direct band gap in the range 0.7-6.2 eV making them excellent candidates for a large domain of optoelectronic applica- tions: blue light emitting diodes and lasers (1). The first blue laser was based on an InxGa1-xN quantum well structure. InxGa1-xN alloys are random alloys in which the cation sites are occupied by Ga or In. However, during the growth of these alloys, defects such as inverted pyramids can be formed on the top surface of the layers, and different phenomena: In chemical non homogeneity, phase separation, partial ordering may take place. The properties of the In, Ga, N phase system have been previously investigated by empirical valence force field methods and confirmed by density functional theory (2-6). Moreover, for the GaN/InxGa1-xN/GaN quantum wells, the mechanisms of light emission are still controversial: the formation of clusters due to the indium segregation should result in the localisation of the carriers and be a centre for radiative recombination. One approach consists in measuring in HREM images the local deformation field in order to determine the chemical composition (7), but InN clustering artefacts due to the electron beam damage have been reported (8). Simulation of these heterostructures needs the calculation of the atomic structure and strain en- ergy. The size of the clusters can be large, the cell must contain tens of thousand of atoms and only em- pirical potentials are suitable. The Stillinger-Weber potential (9) was previously modified for the analysis of extended defects in GaN (10), and more recently for the analysis of InN clusters (11). In order to gen- eralize its use to ternary and quaternary alloys, the parameters for the three nitrides are presented. This empirical potential was previously applied for the III-V compound semiconductors to calculate the criti- cal thickness of InAs/GaAs heterostructures (12). Since the cations, Al, Ga, and In of these compounds are common with those of III-V nitride semiconductors, the parameters of Stillinger-Weber potential for the nitrides, GaN, and InN, are compared with those of the following compounds: Al(P,As,Sb), Ga(P,As,Sb), and In(P,As,Sb). In the second part, bond lengths in an InxGa1-xN quantum well containing an InGaN cluster are analyzed. read less NOT USED (low confidence) T. Kawamura, Y. Kangawa, and K. Kakimoto, “Molecular dynamics simulation of thermal conductivity of GaN/AlN quantum dot superlattices,” Physica Status Solidi (c). 2007. link Times cited: 6 Abstract: We calculated thermal conductivity of GaN/AlN quantum dot su… read moreAbstract: We calculated thermal conductivity of GaN/AlN quantum dot superlattices by molecular dynamics simulation. The results of investigation of the effect of quantum dots on thermal conductivity as a function of superlattice period are presented in this paper. An empirical potential function of Stillinger-Weber potential was used for simulations. Thermal conductivity was obtained by Green-Kubo's equation. The results show that the values of thermal conductivity parallel to the wetting layers decreased due to the effect of quantum dots. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) read less NOT USED (low confidence) P. Śpiewak et al., “Molecular dynamics simulation of intrinsic point defects in germanium,” Journal of Crystal Growth. 2007. link Times cited: 14 NOT USED (low confidence) T. Sinno, “A bottom-up multiscale view of point-defect aggregation in silicon,” Journal of Crystal Growth. 2007. link Times cited: 32 NOT USED (low confidence) Z. Insepov, J. Norem, D. Swenson, A. Hassanein, and M. Terasawa, “Surface erosion and modification by ions studied by computer simulation,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2007. link Times cited: 7 NOT USED (low confidence) M. Taguchi and S. Hamaguchi, “MD simulations of amorphous SiO2 thin film formation in reactive sputtering deposition processes,” Thin Solid Films. 2007. link Times cited: 33 NOT USED (low confidence) J. Matsuo, S. Ninomiya, Y. Nakata, K. Ichiki, T. Aoki, and T. Seki, “Size effect in cluster collision on solid surfaces,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2007. link Times cited: 23 NOT USED (low confidence) T. Kumagai, S. Izumi, S. Hara, and S. Sakai, “Development of bond-order potentials that can reproduce the elastic constants and melting point of silicon for classical molecular dynamics simulation,” Computational Materials Science. 2007. link Times cited: 148 NOT USED (low confidence) S. Munetoh, T. Motooka, K. Moriguchi, and A. Shintani, “Interatomic potential for Si–O systems using Tersoff parameterization,” Computational Materials Science. 2007. link Times cited: 382 NOT USED (low confidence) R. Kühn, J. van Mourik, M. Weigt, and A. Zippelius, “Finitely coordinated models for low-temperature phases of amorphous systems,” Journal of Physics A: Mathematical and Theoretical. 2007. link Times cited: 59 Abstract: We introduce models of heterogeneous systems with finite con… read moreAbstract: We introduce models of heterogeneous systems with finite connectivity defined on random graphs to capture finite-coordination effects on the low-temperature behaviour of finite-dimensional systems. Our models use a description in terms of small deviations of particle coordinates from a set of reference positions, particularly appropriate for the description of low-temperature phenomena. A Born–von Karman-type expansion with random coefficients is used to model effects of frozen heterogeneities. The key quantity appearing in the theoretical description is a full distribution of effective single-site potentials which needs to be determined self-consistently. If microscopic interactions are harmonic, the effective single-site potentials turn out to be harmonic as well, and the distribution of these single-site potentials is equivalent to a distribution of localization lengths used earlier in the description of chemical gels. For structural glasses characterized by frustration and anharmonicities in the microscopic interactions, the distribution of single-site potentials involves anharmonicities of all orders, and both single-well and double-well potentials are observed, the latter with a broad spectrum of barrier heights. The appearance of glassy phases at low temperatures is marked by the appearance of asymmetries in the distribution of single-site potentials, as previously observed for fully connected systems. Double-well potentials with a broad spectrum of barrier heights and asymmetries would give rise to the well-known universal glassy low-temperature anomalies when quantum effects are taken into account. read less NOT USED (low confidence) C. Wang and K. Ho, “Tight‐Binding Molecular Dynamics Studies of Covalent Systems.” 2007. link Times cited: 3 NOT USED (low confidence) V. Smirnov, A. V. Sten’gach, K. G. Gaynullin, V. Pavlovsky, S. Rauf, and P. Ventzek, “A molecular dynamics model for the interaction of energetic ions with SiOCH low-κ dielectric,” Journal of Applied Physics. 2007. link Times cited: 26 Abstract: A molecular dynamics model is used to investigate the intera… read moreAbstract: A molecular dynamics model is used to investigate the interaction of energetic ions with fluorocarbon passivated Si, O, C, and H (SiOCH) based low-κ dielectrics. The model includes a set of interatomic potentials required for the SiOCH–CFx interaction system, where the two- and three-body pseudopotentials have either been obtained from published literature or computed using ab initio techniques. The test structure used for the ion interaction simulations is put together through deposition of low energy SiOx+, CHy+, and H+ ions on a crystalline Si substrate. A thin fluorocarbon passivation layer is grown on the low-κ test structures by bombarding them with moderate energy CFx+ ions. Simulations of CF2+ ion interaction with the fluorocarbon passivated SiOCH samples show that the sputter yield of sample constituents (Si, O, and H) increases with ion energy and peaks at about 60°. H sputters more easily compared to other species, and the surface layer is expected to become H deficient over time. Sputtered H a... read less NOT USED (low confidence) D. Powell, M. Migliorato, and A. Cullis, “Optimized Tersoff potential parameters for tetrahedrally bonded III-V semiconductors,” Physical Review B. 2007. link Times cited: 64 Abstract: We address the issue of accurate parametrization for the Abe… read moreAbstract: We address the issue of accurate parametrization for the Abell-Tersoff empirical potential applied to tetrahedrally bonded semiconductor materials. Empirical potential methods for structural relaxation are widely used for group IV semiconductors while, with few notable exceptions, work on III-V materials has not been extensive. In the case of the Abell-Tersoff potential parametrizations exist only for III-As and III-N, and are designed to correctly predict only a limited number of cohesive and elastic properties. In this work we show how by fitting to a larger set of cohesive and elastic properties calculated from density functional theory, we are able to obtain parameters for III-As, III-N, III-P, and III-Sb zinc blende semiconductors, which can also correctly predict important nonlinear effects in the strain. read less NOT USED (low confidence) A. Ramasubramaniam, M. P. Ariza, and M. Ortiz, “A discrete mechanics approach to dislocation dynamics in BCC crystals,” Journal of The Mechanics and Physics of Solids. 2007. link Times cited: 18 NOT USED (low confidence) J. Yu, S. Sinnott, and S. Phillpot, “Charge optimized many-body potential for the Si/SiO2 system,” Physical Review B. 2007. link Times cited: 151 Abstract: A dynamic-charge, many-body potential for the Si/SiO{sub 2} … read moreAbstract: A dynamic-charge, many-body potential for the Si/SiO{sub 2} system, based on an extended Tersoff potential for semiconductors, is proposed and implemented. The validity of the potential function is tested for both pure silicon and for five polymorphs of silica, for which good agreement is found between the calculated and experimental structural parameters and energies. The dynamic charge transfer intrinsic to the potential function allows the interface properties to be captured automatically, as demonstrated for the silicon/{beta}-cristobalite interface. read less NOT USED (low confidence) K. Tsuruta, A. Uchida, C. Totsuji, and H. Totsuji, “Multiscale Molecular Dynamics Simulations of Nanostructured Materials,” Materials Science Forum. 2007. link Times cited: 1 Abstract: We present some attempts to simulate nanoscale phenomena, wh… read moreAbstract: We present some attempts to simulate nanoscale phenomena, which involve different length-scales and time-scales, using multiscale molecular-dynamics approaches. To simulate realistically an impurity-segregated nanostructure, we have developed the hybrid quantum/classical approach. The method can describe seamlessly both dynamical changes of local chemical bonding and nanoscale atomic relaxations. We apply the method to hydrogen diffusion in Si grain boundary. We find that the hydrogen is strongly trapped in (001)Σ5 twist boundary below 1000K, whereas it starts diffusing along the grain boundary above 1000K. For long-time processes in nanostructure formation, we apply the stochastic-difference-equation method to accelerate the simulations for microstructure evolution. The method bridges the states separated by high-energy barriers in a configuration space by optimizing an action, defined as an error accumulation along a reaction pathway. As an example, a SDE simulation is performed for Cu thin-film formation via nanocluster deposition. We show that the method can be applied effectively to search for the long-time process which involves a rare event due to a large potential barrier between two atomic configurations. read less NOT USED (low confidence) W. E and P. Ming, “Cauchy–Born Rule and the Stability of Crystalline Solids: Static Problems,” Archive for Rational Mechanics and Analysis. 2007. link Times cited: 216 NOT USED (low confidence) M. Cai, X. Li, and M. Rahman, “Molecular dynamics modelling and simulation of nanoscale ductile cutting of silicon,” Int. J. Comput. Appl. Technol. 2007. link Times cited: 22 Abstract: A simulation system for nanoscale ductile mode cutting of mo… read moreAbstract: A simulation system for nanoscale ductile mode cutting of monocrystalline silicon has been developed in thi study using the Molecular Dynamics (MD) method for better understanding of the ductile mode cutting mechanism. In the model of this simulation system, the initial atom positions of silicon workpiece material are arranged according to the crystal lattice structure, the atomic interactive actions of silicon are based on the Tersoff potential, the diamond cutting tool is assumed to be undeformable, the tool cutting edge is realistically modelled to have a finite radius, and the motions of the atoms in the chip formation zone are determined by Newton's equations of motion. The simulated variation of the cutting forces with the tool cutting edge radius is compared with the results of experimental cutting tests to substantiate the developed simulation system and the results show a good agreement with analytical findings. read less NOT USED (low confidence) D. Brenner, O. Shenderova, and D. Areshkin, “Quantum‐Based Analytic Interatomic Forces and Materials Simulation.” 2007. link Times cited: 21 NOT USED (low confidence) A. Bodapati, P. Schelling, S. Phillpot, and P. Keblinski, “Vibrations and thermal transport in nanocrystalline silicon,” Physical Review B. 2006. link Times cited: 92 NOT USED (low confidence) S. Bukkapatnam, M. Malshe, P. Agrawal, L. Raff, and R. Komanduri, “Parametrization of interatomic potential functions using a genetic algorithm accelerated with a neural network,” Physical Review B. 2006. link Times cited: 17 NOT USED (low confidence) W. Zenghui and L. Zhixin, “Research on the Out-of-plane thermal conductivity of nanometer silicon film,” Thin Solid Films. 2006. link Times cited: 14 NOT USED (low confidence) E. Winsberg, “Handshaking Your Way to the Top: Simulation at the Nanoscale,” Philosophy of Science. 2006. link Times cited: 42 Abstract: Should philosophers of science be paying attention to develo… read moreAbstract: Should philosophers of science be paying attention to developments in “nanoscience”? Undoubtedly, it is too early to tell for sure. The goal of this paper is to take a preliminary look. In particular, I look at the use of computational models in the study of nano‐sized solid‐state materials. What I find is that there are features of these models that appear on their face to be at odds with some basic philosophical intuitions about the relationships between different theories and between theories and their models. My conclusion is that developments in nanoscience are not an unlikely place for novel insights in the philosophy of science to emerge. read less NOT USED (low confidence) G. Otto, G. Hobler, P. Pongratz, and L. Palmetshofer, “Is there an influence of ion-beam-induced interfacial amorphization on the a/c-interface depth in silicon at common implantation energies?,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2006. link Times cited: 0 NOT USED (low confidence) Z. Wang and Z. Li, “Lattice dynamics analysis of thermal conductivity in silicon nanoscale film,” Applied Thermal Engineering. 2006. link Times cited: 22 NOT USED (low confidence) S. Wang et al., “THE CALCULATION OF THE SURFACE ENERGY OF HIGH-INDEX SURFACES OF SILICON AT ZERO TEMPERATURE,” Surface Review and Letters. 2006. link Times cited: 1 Abstract: We used the molecular dynamics simulation based on the Still… read moreAbstract: We used the molecular dynamics simulation based on the Stillinger–Weber (SW) interatomic potential to calculate the high-index surface energies of surfaces containing any of the stereographic surfaces of silicon at zero temperature. An empirical formula based on the structural unit model was generalized for high-index surfaces. Our simulated results show that the generalized formula can give a good estimation of the surface energy and structural feature of the high-index surfaces not only on the edge of stereographic but also within it. Our simulation and empirical formula results reveal that the closest surface has the lowest energy, so the closest (101) surface has the lowest surface energy and the (101), (111) and (001) surfaces are the extremum on the curve of surface energy versus orientation angle. Both the theoretical simulation results and the empirical formula calculation results are consistent with the available first-principles theoretical data. read less NOT USED (low confidence) Y. Yoshimoto, “Extended multicanonical method combined with thermodynamically optimized potential: application to the liquid-crystal transition of silicon.,” The Journal of chemical physics. 2006. link Times cited: 12 Abstract: A novel method is proposed to study first-order phase transi… read moreAbstract: A novel method is proposed to study first-order phase transition in real materials. It is applied to the liquid-crystal transition of silicon successfully. It consists of two parts: a direct simulation of the transition by an extended multicanonical ensemble with an order parameter defined with structure factors that characterize the transition, and optimization of a model interatomic potential in terms of the ensemble from an accurate one. These provide a principle to project a first-principles approach on a model-based approach conserving thermodynamic properties of multiple phases. read less NOT USED (low confidence) V. Zenou, A. Kiv, D. Fuks, V. Ezerski, and N. Moiseenko, “The microscopic mechanism of silicon precipitation in Al/Si system,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2006. link Times cited: 11 NOT USED (low confidence) M. Aly, E. Ng, S. Veldhuis, and M. Elbestawi, “Prediction of cutting forces in the micro-machining of silicon using a ‘hybrid molecular dynamic-finite element analysis’ force model,” International Journal of Machine Tools & Manufacture. 2006. link Times cited: 31 NOT USED (low confidence) J. Dziedzic, E. Principi, and J. Rybicki, “Analysis of the mixing rules for the Stillinger–Weber potential: a case-study of Ge–Si interactions in the liquid phase,” Journal of Non-crystalline Solids. 2006. link Times cited: 6 NOT USED (low confidence) F. S. A. Muriefah, F. Luca, and A. Togbé, “Computational Methods.” 2006. link Times cited: 171 NOT USED (low confidence) C. Ciobanu, “Global Optimization of 1- and 2-Dimensional Nanoscale Structures.” 2006. link Times cited: 0 NOT USED (low confidence) T. Morishita, “How does tetrahedral structure grow in liquid silicon upon supercooling?,” Physical review letters. 2006. link Times cited: 53 Abstract: We present an extensive set of isothermal-isobaric first-pri… read moreAbstract: We present an extensive set of isothermal-isobaric first-principles molecular-dynamics simulations of liquid silicon over a temperature range of 950-1700 K. We find that the tetrahedral order gradually grows upon cooling to approximately 1200 K, but that the growth accelerates significantly below approximately 1200 K. This growth process gives rise to anomalous changes in density and liquid structure upon supercooling. In particular, we find that the atomic coordination number remains constant to approximately 1200 K and then begins to decrease below approximately 1200 K, which resolves the existing controversy regarding liquid structure in the supercooled regime [T. H. Kim, Phys. Rev. Lett. 95, 085501 (2005)10.1103/PhysRevLett.95.085501]. read less NOT USED (low confidence) T. Eberlein, R. Jones, and A. Blumenau, “Theory of Dislocations in SiC: The Effect of Charge on Kink Migration,” Materials Science Forum. 2006. link Times cited: 1 Abstract: Under forward bias bipolar 4H- and 6H-SiC devices are known … read moreAbstract: Under forward bias bipolar 4H- and 6H-SiC devices are known to degrade rapidly through stacking fault formation and expansion in the basal plane. It is believed that the ob- served rapid stacking fault growth is due to a recombination-enhanced dislocation glide (REDG) mechanism at the bordering partial dislocations. This degradation phenomenon has generated considerable interest in the involved dislocations — in particular in their atomic and electronic structure, but also in the mechanisms of their glide motion. Fortunately, nowadays advances in computing power and in theoretical methodology allow the ab initio based modelling of some aspects of the problem. This paper therefore gives a brief review of recent activities in this field, and further discusses some general problems of ab initio based modelling of dislocations in compound semiconductors. read less NOT USED (low confidence) J. Rino, P. S. Branicio, and D. Borges, “Classical Molecular Dynamics Simulation of Structural and Dynamical Properties of II-VI and III-V Semiconductors,” Defect and Diffusion Forum. 2006. link Times cited: 2 Abstract: An effective inter-atomic potential is proposed in order to … read moreAbstract: An effective inter-atomic potential is proposed in order to describe structural and dynamical properties of II-VI and III-V semiconductors. The interaction potential consists of twoand three-body interactions. The two-body term takes into account steric repulsion, charge-induce dipole interaction due to the electronic polarizability of ions, Coulomb interaction due to charge transfer between ions, and dipole-dipole (van der Waals) interactions. The three-body term, which has a modified Stillinger-Weber form, describes bond-bending as well as bond-stretching effects. Here we report the fitting and the application of this interaction potential for InP in the crystalline phase and for CdTe in the crystalline and liquid phases. The structural correlations are discussed through pair distribution, coordination number and bond-angle functions. Vibrational density of states for InP and CdTe as well as the static structure factor for liquid CdTe are in very good agreement with experimental data. read less NOT USED (low confidence) H. Wilson, S. Prawer, P. Spizzirri, D. Jamieson, N. Stavrias, and D. Mckenzie, “P-2 dimer implantation in silicon: A molecular dynamics study,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2006. link Times cited: 11 NOT USED (low confidence) H. Lei, J. Chen, S. Petit, P. Ruterana, X. Jiang, and G. Nouet, “Stillinger-Weber parameters for In and N atoms,” Superlattices and Microstructures. 2006. link Times cited: 18 NOT USED (low confidence) A. Chehaidar and H. Khelifi, “Microstructural analysis of paracrystalline atomistic models of amorphous silicon,” Journal of Non-crystalline Solids. 2006. link Times cited: 1 NOT USED (low confidence) M. Finnis and M. Rühle, “Structures of Interfaces in Crystalline Solids,” Materials Science and Technology. 2006. link Times cited: 3 Abstract: Interfaces in materials may be grain boundaries between like… read moreAbstract: Interfaces in materials may be grain boundaries between like crystals or phase boundaries between unlike crystals. Experimental approaches for the determination of the atomic structures of the interfaces are reviewed with emphasis on high-resolution electron microscopy (HREM). It will be shown that information on orientation relationship between the adjacent grains, the translation state and atomic relaxations can be elaborated with high precision. In a case study, the structures of one specific grain boundary in Al2O3 will be discussed in detail. Such experimental studies have provided a mass of structural information in recent years. read less NOT USED (low confidence) P. Gaskell, “Models for the Structure of Amorphous Solids,” Materials Science and Technology. 2006. link Times cited: 12 NOT USED (low confidence) Y. Nakamura, N. Takahashi, T. Uda, and T. Ohno, “Multiregional hybrid method and its application: formation of an atomic protrusion at an atomic force microscope tip apex.,” Physical review letters. 2006. link Times cited: 1 Abstract: We present a multiregional hybrid scheme which incorporates … read moreAbstract: We present a multiregional hybrid scheme which incorporates first-principles (FP), tight-binding (TB), and molecular mechanical calculations. The key to this hybrid scheme is to find an explicit description of the FP-TB region coupling. We apply it to the atomic structure of a clean silicon atomic force microscope tip, and find the formation of a distinct atomic protrusion at the tip apex. The present study gives the reason why the atomic protrusion exits at the apex despite the fact that the atomic geometry of the very end of the tip is practically uncontrollable in the tip preparation. read less NOT USED (low confidence) P. Śpiewak et al., “Simulation of intrinsic point defect properties and vacancy clustering during Czochralski germanium crystal growth,” Materials Science in Semiconductor Processing. 2006. link Times cited: 8 NOT USED (low confidence) Y.-L. Bai, X.-rong Chen, X.-lin Zhou, X. Cheng, and X.-dong Yang, “First-Principles Calculations for Structures and Melting Temperature of Si 6 Clusters,” Chinese Physics Letters. 2006. link Times cited: 2 Abstract: We investigate the structures and the melting temperature of… read moreAbstract: We investigate the structures and the melting temperature of the Si6 cluster by using the first-principles pseudopotential method in real space and Langevin molecular dynamics. It is shown that the ground structure of the Si6 cluster is a square bipyramid, and the corresponding melting temperature is about 1923 K. In the heating procedure, the structures of the Si6 cluster change from high symmetry structures containing 5–8 bonds, via prolate structures containing 3–4 bonds, to oblate structures containing 1–2 bonds. read less NOT USED (low confidence) Z. Huang, Z. N. Guo, X. Chen, T. Yue, S. To, and W. Lee, “Molecular Dynamics Simulation for Ultrafine Machining,” Materials and Manufacturing Processes. 2006. link Times cited: 20 Abstract: This article surveys the advances of molecular dynamics (MD)… read moreAbstract: This article surveys the advances of molecular dynamics (MD) simulation in the research of ultrafine machining and related technologies. Modeling methods, including interatomic potentials and boundary conditions, are addressed. Algorithm strategies for MD simulations are discussed. By applying simulations with Tersoff potential, a case study of the material removal mechanism of the polishing based on coupling vibrations of liquid (PCVL) is presented. read less NOT USED (low confidence) Y. Tang, J. Wang, and X. Zeng, “Molecular simulations of solid-liquid interfacial tension of silicon.,” The Journal of chemical physics. 2006. link Times cited: 24 Abstract: Using the superheating method [Luo et al., Phys. Rev. B68, 1… read moreAbstract: Using the superheating method [Luo et al., Phys. Rev. B68, 134206 (2003)], we deployed classical molecular dynamics (MD) simulation to compute solid-liquid interfacial tension of silicon. We performed isobaric-isothermal MD simulation on two silicon models, the Stillinger-Weber [Phys. Rev. B31, 5262 (1985)] and Tersoff-89 [Phys. Rev. B38, 5565 (1989)], and applied heating rates of 1×1011 and 5×1011K∕s to the system. The calculated average value of solid-liquid surface tension of silicon is 0.413J∕m2, which is in good agreement with the measured values (0.34–0.40J∕m2). read less NOT USED (low confidence) I. Belabbas, P. Ruterana, J. Chen, and G. Nouet, “The atomic and electronic structure of dislocations in Ga-based nitride semiconductors,” Philosophical Magazine. 2006. link Times cited: 18 Abstract: The atomic and electronic properties of dislocations in III–… read moreAbstract: The atomic and electronic properties of dislocations in III–N semiconductor layers, especially GaN, are presented. The atomic structure of the edge threading dislocation is now well established with three different cores (8 or full core, 5/7 or open core, and 4-atom ring). The use of atomistic simulations has confirmed these atomic structures and has given a good understanding of the electronic structure of the screw dislocation. Partial dislocations which are mostly confined in the area close to the substrate are now also being investigated. It is becoming clear that the electrical activity of all these defects is dependent on the layer quality, which is governed by the growth conditions. read less NOT USED (low confidence) D. S. Krupskii, O. Subbotin, and V. Belosludov, “Account of three-body interactions in the lattice dynamics method,” Computational Materials Science. 2006. link Times cited: 1 NOT USED (low confidence) I. Chung, R. Walkup, H. Wen, and H. Yu, “A study of MPI performance analysis tools on Blue Gene/L,” Proceedings 20th IEEE International Parallel & Distributed Processing Symposium. 2006. link Times cited: 21 Abstract: Applications on today's massively parallel supercompute… read moreAbstract: Applications on today's massively parallel supercomputers rely on performance analysis tools to guide them toward scalable performance on thousands of processors. However, conventional tools for parallel performance analysis have serious problems due to the large data volume that may be required. In this paper, we discuss the scalability issue for MPI performance analysis on Blue Gene/L, the world's fastest supercomputing platform. We present an experimental study of existing MPI performance tools that were ported to BG/L from other platforms. These tools can be classified into two categories: profiling tools that collect timing summaries, and tracing tools that collect a sequence of time-stamped events. Profiling tools produce small data volumes and can scale well, but tracing tools tend to scale poorly. The experimental study discusses the advantages and disadvantages for the tools in the two categories and will be helpful in the future performance tools design read less NOT USED (low confidence) S. Billeter, A. Curioni, D. Fischer, and W. Andreoni, “Ab initio derived augmented Tersoff potential for silicon oxynitride compounds and their interfaces with silicon,” Physical Review B. 2006. link Times cited: 42 Abstract: Coordination-dependent interatomic potentials are proposed f… read moreAbstract: Coordination-dependent interatomic potentials are proposed for silicon oxides and oxynitrides\char22{}also hydrogenated ones\char22{}with a functional form based on the widely used Tersoff silicon potential. They are intended for an accurate sampling of the configurational space of realistic silicon oxynitride systems and their interfaces with silicon, including defects and changes of oxidation states. The parameters, which are given in the text, are obtained by simultaneously mapping forces and energies onto the results of density-functional-theory calculations performed for a set of diverse systems and configurations and a wide composition range. Application to a larger set of systems and configurations shows the transferability of these augmented Tersoff potentials and their validity in predicting bulk lattice parameters, energetics of defect relaxation, and vibrational spectra. read less NOT USED (low confidence) J. Xu, S. Kjelstrup, and D. Bedeaux, “Molecular dynamics simulations of a chemical reaction; conditions for local equilibrium in a temperature gradient.,” Physical chemistry chemical physics : PCCP. 2006. link Times cited: 27 Abstract: We have examined a simple chemical reaction in a temperature… read moreAbstract: We have examined a simple chemical reaction in a temperature gradient; 2F <==> F2. A mechanical model was used, based on Stillinger and Weber's 2- and 3-body potentials. Equilibrium and non-equilibrium molecular dynamics simulations showed that the chemical reaction is in local thermodynamic as well as in local chemical equilibrium (delta(r)G = 0) in the supercritical fluid, for temperature gradients up to 10(12) K m(-1). The reaction is thus diffusion-controlled. The velocity distributions of both components were everywhere close to being Maxwellian. The peak distributions were shifted slightly up or down from the average velocity of all particles. The shift depended on the magnitude of the temperature gradient. The results support the assumption that the entropy production of the reacting mixture can be written as a product sum of fluxes and forces. The temperature gradient promotes interdiffusion of components in the stationary state, a small reaction rate and an accumulation of the molecule in the cold region and the atom in the hot region. read less NOT USED (low confidence) J. Lauwaert et al., “Simulation of point defect diffusion in germanium,” Physica B-condensed Matter. 2006. link Times cited: 10 NOT USED (low confidence) G. Moras, G. Csányi, M. Payne, and A. Vita, “A novel molecular dynamics approach to large semiconductor systems,” Physica B-condensed Matter. 2006. link Times cited: 7 NOT USED (low confidence) P. Klein and J. Zimmerman, “Coupled atomistic-continuum simulations using arbitrary overlapping domains,” J. Comput. Phys. 2006. link Times cited: 81 NOT USED (low confidence) J. Zhao, X. Zhou, X. Chen, J. Wang, and J. Jellinek, “Density-functional study of small and medium-sizedAsnclusters up ton=28,” Physical Review B. 2006. link Times cited: 23 NOT USED (low confidence) J. Dai, W. Seider, and T. Sinno, “Lattice kinetic Monte Carlo simulations of defect evolution in crystals at elevated temperature,” Molecular Simulation. 2006. link Times cited: 22 Abstract: A lattice kinetic Monte Carlo (LKMC) model for vacancy diffu… read moreAbstract: A lattice kinetic Monte Carlo (LKMC) model for vacancy diffusion and aggregation in crystalline silicon at elevated temperature is developed and analyzed in detail by comparing predicted cluster aggregation, thermodynamics, structures and diffusivities with properties obtained from molecular dynamics (MD) simulations. The lattice KMC model is based on a long-range bond-counting scheme in which the bond energies are determined by regression to a single non-equilibrium MD simulation of vacancy aggregation. It is shown that the resulting KMC model is able to capture important high temperature entropic contributions by coarse-graining off-lattice relaxations around defect clusters. read less NOT USED (low confidence) H. Noguchi and G. Gompper, “Meshless membrane model based on the moving least-squares method.,” Physical review. E, Statistical, nonlinear, and soft matter physics. 2006. link Times cited: 81 Abstract: A meshless particle-based membrane model is proposed. The pa… read moreAbstract: A meshless particle-based membrane model is proposed. The particles possess no internal degree of freedom and interact via a potential, which has three different contributions: a short-range repulsive pair potential, an attractive multibody potential, and a curvature potential based on the moving least-squares method. Brownian dynamics simulations are employed to demonstrate that the particles self-assemble into a membrane and to study equilibrium properties, such as bending rigidity, surface tension, line tension, and diffusion constant. The bending rigidity and line tension are shown to depend on different potential parameters and can therefore be varied independently. The finite-size effects of nearly planar membranes are investigated. This model is well suited to study the membrane dynamics with topological changes. read less NOT USED (low confidence) Y. Chen, “Local stress and heat flux in atomistic systems involving three-body forces.,” The Journal of chemical physics. 2006. link Times cited: 123 Abstract: Local densities of fundamental physical quantities, includin… read moreAbstract: Local densities of fundamental physical quantities, including stress and heat flux fields, are formulated for atomistic systems involving three-body forces. The obtained formulas are calculable within an atomistic simulation, in consistent with the conservation equations of thermodynamics of continuum, and can be applied to systems with general two- and three-body interaction forces. It is hoped that this work may correct some misuse of inappropriate formulas of stress and heat flux in the literature, may clarify the definition of site energy of many-body potentials, and may serve as an analytical link between an atomistic model and a continuum theory. Physical meanings of the obtained formulas, their relation with virial theorem and heat theorem, and the applicability are discussed. read less NOT USED (low confidence) J. Delaye and D. Ghaleb, “Damage inhomogeneity in the core region of displacement cascades in simplified nuclear glasses,” Journal of Nuclear Materials. 2006. link Times cited: 14 NOT USED (low confidence) Z. V. Guo and W. Yang, “MPM/MD handshaking method for multiscale simulation and its application to high energy cluster impacts,” International Journal of Mechanical Sciences. 2006. link Times cited: 16 NOT USED (low confidence) X. W. Zhou, D. Murdick, B. Gillespie, and H. Wadley, “Atomic assembly during GaN film growth : Molecular dynamics simulations,” Physical Review B. 2006. link Times cited: 44 Abstract: Molecular dynamics simulations using a recently developed Ga… read moreAbstract: Molecular dynamics simulations using a recently developed Ga-N Tersoff type bond order interatomic potential have been used to investigate the growth mechanisms of 0001 wurtzite GaN films from thermalized atomic gallium and nitrogen fluxes. The crystallinity and stoichiometry of the deposited wurtzite lattice structures were determined as a function of growth temperature and N:Ga flux ratio. The lattice perfection was found to improve as the growth temperature was increased to 500 K. At a fixed growth temperature, the lattice quality and stoichiometry both reached optimum as the N:Ga ratio approached a value between two and three. The optimum flux ratio increased with increasing growth temperature. These three observations are consistent with experimental studies of growth on wurtzite phase promoting substrates. The atomic assembly mechanisms responsible for these effects have been explored using time-resolved atom position images. The analysis revealed that high quality crystalline growth only occurred when off-lattice atoms which are usually associated with amorphous embryos or defect complexes formed during deposition were able to move to unoccupied lattice sites by thermally activated diffusion processes. The need for a high N:Ga flux ratio to synthesize stochiometric films arises because many of the nitrogen adatoms that impact N-rich 0001 GaN surfaces are re-evaporated. Reductions of the substrate temperature reduce this reevaporation and as a result, the optimum N:Ga ratio for the stoichiometric film formation and best lattice perfection was reduced as the growth temperature was decreased. read less NOT USED (low confidence) V. Hùng, J. Lee, K. Masuda-Jindo, and P. T. L. Hong, “Study of Self-Diffusion in Silicon at High Pressure(Condensed Matter : Structure, Mechanical and Thermal Properties),” Journal of the Physical Society of Japan. 2006. link Times cited: 6 Abstract: The process of self-diffusion in semiconductors at high pres… read moreAbstract: The process of self-diffusion in semiconductors at high pressure is studied using the statistical moment method including the anharmonicity effects of the lattice vibration. The activation energy, Q , and pre-exponential factor, D 0 , of the self-diffusion coefficient are given in an explicit form. The thermodynamic relationships so obtained permit the direct calculation of the activation energy, Q , and pre-exponential factor, D 0 , in Si at high pressure, both in the high temperature region near the melting temperature, and at low (room temperature) temperatures. The calculated results are shown to be in good agreement with the experimental data. read less NOT USED (low confidence) D. Murdick, X. W. Zhou, H. Wadley, D. Nguyen-Manh, R. Drautz, and D. Pettifor, “Analytic bond-order potential for the gallium arsenide system,” Physical Review B. 2006. link Times cited: 56 Abstract: An analytic, bond-order potential BOP is proposed and parame… read moreAbstract: An analytic, bond-order potential BOP is proposed and parametrized for the gallium arsenide system. The potential addresses primary and secondary bonding and the valence-dependent character of heteroatomic bonding, and it can be combined with an electron counting potential to address the distribution of electrons on the GaAs surface. The potential was derived from a tight-binding description of covalent bonding by retaining the first two levels of an expanded Green’s function for the and bond-order terms. Predictions using the potential were compared with independent estimates for the structures and binding energy of small clusters dimers, trimers, and tetramers and for various bulk lattices with coordinations varying from 4 to 12. The structure and energies of simple point defects and melting transitions were also investigated. The relative stabilities of the 001 surface reconstructions of GaAs were well predicted, especially under high-arsenicoverpressure conditions. The structural and binding energy trends of this GaAs BOP generally match experimental observations and ab initio calculations. read less NOT USED (low confidence) M. Demkowicz and A. Argon, “Liquidlike atomic environments act as plasticity carriers in amorphous silicon,” Physical Review B. 2005. link Times cited: 88 NOT USED (low confidence) M. Demkowicz and A. Argon, “Autocatalytic avalanches of unit inelastic shearing events are the mechanism of plastic deformation in amorphous silicon,” Physical Review B. 2005. link Times cited: 54 NOT USED (low confidence) P. Tomson and G. Greenwood, “Using ant colony optimization to find low energy atomic cluster structures,” 2005 IEEE Congress on Evolutionary Computation. 2005. link Times cited: 1 Abstract: Over the past 20 years atomic cluster structures have been i… read moreAbstract: Over the past 20 years atomic cluster structures have been intensively studied because of their importance in physics, chemistry and recently material science. Unfortunately finding the lowest energy structure, which is the most stable configuration, is NP-hard. In this paper, we present preliminary results on an ant colony optimization algorithm used in conjunction with a Monte Carlo sampling method to find low energy configurations of small silicon atomic clusters. read less NOT USED (low confidence) J. Los, L. Ghiringhelli, E. Meijer, and A. Fasolino, “Improved long-range reactive bond-order potential for carbon. I. Construction (Correction on vol 72, pg 214102, 2005),” Acta Crystallographica Section B-structural Science. 2005. link Times cited: 181 Abstract: We present LCBOPII, an improvement of the long-range carbon … read moreAbstract: We present LCBOPII, an improvement of the long-range carbon bond-order potential (LCBOP) by Los and Fasolino [Phys. Rev. B 68, 024107 (2003)]. LCBOPII contains a coordination dependent medium range term for bond distances between 1.7 and $4\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}$, meant to reproduce the dissociation energy curves for single, double, and triple bonds and improve the reactive properties as well as the description of the liquid and of low coordinated phases. Other features of LCBOPII are a coordination dependent angular correlation, a correction for antibonding states, and a conjugation dependent torsional interaction based on ab initio calculations of the torsional barriers for a set of molecular configurations. We present results for the geometry and energetics of the graphite-to-diamond transformation and of the vacancy in diamond and graphite as well as the prediction of the energy barrier of the 5-77-5 defect in graphite and graphene for which ab initio results are available only for unsuitably small samples. In the accompanying paper (Ghiringhelli et al., Phys. Rev. B 72, 214103 (2005) we use LCBOPII to evaluate several properties, including the equation of state, of liquid carbon. read less NOT USED (low confidence) X. Zhang and P. Sharma, “Impact of size-dependent non-local elastic strain on the electronic band structure of embedded quantum dots,” Proceedings of the Institution of Mechanical Engineers, Part N: Journal of Nanoengineering and Nanosystems. 2005. link Times cited: 2 Abstract: The effect of mechanical strain on the quantum confinement p… read moreAbstract: The effect of mechanical strain on the quantum confinement properties of quantum dots is appreciable and both qualitative and quantitative description of the electronic band structure of quantum dots requires proper incorporation of its effect. Although atomistic calculations such as tight binding or pseudopotential approaches are viable options, the typical and ‘standard’ practice is to employ the coarse-grained multiband envelope function method to compute the band structure of both strained and unstrained quantum dots. The typical recipe involves calculation of strain based on classical continuum elasticity and a subsequent link to the aforementioned eight-band envelope function model. The mechanical strain predicted by classical elasticity is not only size-independent but also departs qualitatively from the actual (atomistic) field owing to neglect of non-local effects that are prevalent at the nanoscale. In the present work, the authors employ the strain as calculated from a size-dependent non-local theory of elasticity (presented in work previously published by the current authors) and assess the qualitative and quantitative effects on the electronic band structure of an InAs-GaAs quantum dot system. Quantitatively, deviations of band gaps in the range of 100 meV are found when compared to classical elasticity-based estimates, while no significant qualitative differences were found. The non-local elastic effects, however, are appreciable only for very small quantum dots and certain materials (such as the InAs-GaAs system discussed in the present work). read less NOT USED (low confidence) A. Tekin and B. Hartke, “GLOBAL GEOMETRY OPTIMIZATION OF SILICON CLUSTERS EMPLOYING EMPIRICAL POTENTIALS, DENSITY FUNCTIONALS, AND AB INITIO CALCULATIONS,” Journal of Theoretical and Computational Chemistry. 2005. link Times cited: 13 Abstract: Sin clusters in the size range n = 4–30 have been investigat… read moreAbstract: Sin clusters in the size range n = 4–30 have been investigated using a combination of global structure optimization methods with DFT and ab initio calculations. One of the central aims is to provide explanations for the structural transition from prolate to spherical outer shapes at about n = 25, as observed in ion mobility measurements. Firstly, several existing empirical potentials for silicon and a newly generated variant of one of them were better adapted to small silicon clusters, by global optimization of their parameters. The best resulting empirical potentials were then employed in global cluster structure optimizations. The most promising structures from this stage were relaxed further at the DFT level with the hybrid B3LYP functional. For the resulting structures, single point energies have been calculated at the LMP2 level with a reasonable medium-sized basis set, cc-pVTZ. These DFT and LMP2 calculations were also carried out for the best structures proposed in the literature, including the most recent ones, to obtain the currently best and most complete overall picture of the structural preferences of silicon clusters. In agreement with recent findings, results obtained at the DFT level do support the shape transition from prolate to spherical structures, beginning with Si26 (albeit not completely without problems). In stark contrast, at the LMP2 level, the dominance of spherical structures after the transition region could not be confirmed. Instead, just as below the transition region, prolate isomers are obtained as the lowest-energy structures for n ≤ 29. We conclude that higher (probably multireference) levels of theoretical treatments are needed before the puzzle of the silicon cluster shape transition at n = 25 can safely be considered as explained. read less NOT USED (low confidence) Z. Insepov, A. Hassanein, D. Swenson, and M. Terasawa, “Computer simulation of surface modification with ion beams,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2005. link Times cited: 6 NOT USED (low confidence) D. Murdick, X. W. Zhou, and H. Wadley, “Assessment of interatomic potentials for molecular dynamics simulations of GaAs deposition,” Physical Review B. 2005. link Times cited: 22 Abstract: Computational studies of atomic assembly processes during Ga… read moreAbstract: Computational studies of atomic assembly processes during GaAs vapor deposition require interatomic potentials that are able to reasonably predict the structures and energies of a molecular arsenic vapor, a variety of elemental gallium and arsenic lattices, binary GaAs lattices, GaAs lattice defects, and 001 GaAs surfaces. These properties were systematically evaluated and compared to ab initio and experimental data for one Tersoff and two Stillinger-Weber SW GaAs interatomic potentials. It was observed that bulk and arsenic molecular properties calculated by the Tersoff parametrization matched density functional predictions and experimental observations significantly better than either of the SW parametrizations. These trends can be related to the bonding physics included in each potential format. Surface free energy calculations indicate that none of these potentials correctly predict the low-energy surface reconstructions of the GaAs 001 surface. Simulated As2 molecular bonding with gallium-rich GaAs 001 surfaces indicate a high sticking probability for SW potentials, which is in good agreement with experimental observations at low growth temperatures. However, the Tersoff parametrization resulted in an unphysically high desorption probability for As2 over a wide range of surface temperatures. read less NOT USED (low confidence) N. Skoulidis and H. Polatoglou, “STREL: A versatile computational environment for the study and design of nanostructures,” International Journal of Nanotechnology. 2005. link Times cited: 4 Abstract: Fabrication techniques have advanced greatly and many nanost… read moreAbstract: Fabrication techniques have advanced greatly and many nanostructures have been produced, studied and have found technological application. The study of the nanostructures, both experimentally and theoretically is very demanding, as many degrees of freedom are important in determining their properties. In order to meet these complex tasks, we have prepared a computational environment to facilitate the study of the structural, electronic and optical properties of nanostructures. In this environment, it is possible to tailor the properties of specific nanostructures. read less NOT USED (low confidence) K. C. Huang, T. Wang, and J. Joannopoulos, “Nanoscale properties of melting at the surface of semiconductors,” Physical Review B. 2005. link Times cited: 6 NOT USED (low confidence) T. Zhu, J. Li, and S. Yip, “Nanomechanics of Crack Front Mobility,” Journal of Applied Mechanics. 2005. link Times cited: 3 Abstract: Minimum energy paths for unit advancement of a crack front a… read moreAbstract: Minimum energy paths for unit advancement of a crack front are determined by reaction pathway sampling, thus providing the reaction coordinates for the analysis of crack tip mechanics in ductile and brittle materials. We compare results on activation energy barrier and atomic displacement distributions for a atomically sharp crack in Cu, where one observes the emission of a partial dislocation loop, and in Si, where crack front extension evolves in a kink-like fashion. read less NOT USED (low confidence) K. Volokh and H. Gao, “On the Modified Virtual Internal Bond Method,” Journal of Applied Mechanics. 2005. link Times cited: 23 Abstract: The virtual internal bond (VIB) method was developed for the… read moreAbstract: The virtual internal bond (VIB) method was developed for the numerical simulation of fracture processes. In contrast to the traditional approach of fracture mechanics where stress analysis is separated from a description of the actual process of material failure, the VIB method naturally allows for crack nucleation, branching, kinking, and arrest. The idea of the method is to use atomic-like bond potentials in combination with the Cauchy-Born rule for establishing continuum constitutive equations which allow for the material separation-strain localization. While the conventional VIB formulation stimulated successful computational studies with applications to structural and biological materials, it suffers from the following theoretical inconsistency. When the constitutive relations of the VIB model are linearized for an isotropic homogeneous material, the Poisson ratio is found equal to 1/4 so that there is only one independent elastic constant-Young's modulus. Such restriction is not suitable for many materials. In this paper, we propose a modified VIB (MVIB) formulation, which allows for two independent linear elastic constants. It is also argued that the discrepancy of the conventional formulation is a result of using only two-body interaction potentials in the microstructural setting of the VIB method. When many-body interactions in bond bending are accounted for, as in the MVIB approach, the resulting formulation becomes consistent with the classical theory of isotropic linear elasticity. read less NOT USED (low confidence) R. Drautz, D. Murdick, D. Nguyen-Manh, X. W. Zhou, H. Wadley, and D. Pettifor, “Analytic bond-order potential for predicting structural trends across the sp-valent elements,” Physical Review B. 2005. link Times cited: 48 Abstract: An analytic interatomic bond-order potential BOP is derived … read moreAbstract: An analytic interatomic bond-order potential BOP is derived that depends explicitly on the group number of the sp-valent element. This is achieved by generalizing the previously published BOP for group-IV elements by extrapolating from half-full occupancy using a simple envelope function for the upper bound of the bond order. This interatomic potential predicts the structural trends across the sp-valent elements that are found by our tight-binding reference calculations and observed by experiment. Unlike empirical interatomic potentials this theoretically derived BOP includes the valence-dependent character of the bonding naturally within its remit. read less NOT USED (low confidence) T. Kawamura, Y. Kangawa, and K. Kakimoto, “Investigation of thermal conductivity of GaN by molecular dynamics,” Journal of Crystal Growth. 2005. link Times cited: 26 NOT USED (low confidence) K. Nordlund et al., “Measurement of Si 311 defect properties using x-ray scattering,” Journal of Applied Physics. 2005. link Times cited: 4 Abstract: The 311 defects play a crucial role in the damage healing an… read moreAbstract: The 311 defects play a crucial role in the damage healing and dopant redistribution which occurs during the annealing of an ion-beam-doped Si. Using grazing-incidence x-ray scattering we measure the type, length, and width of the 311 defects created with different annealing times. In particular, we show that measurements around (1.3 1.3 0) in reciprocal space can be used to determine all these quantities without the need for pristine reference samples. The results agree well with computer simulation predictions and transmission-electron-microscopy measurements, demonstrating that x-ray methods can be used as a nondestructive, rapid method to characterize the 311 defects. read less NOT USED (low confidence) N. Kalyanasundaram, J. Freund, and H. Johnson, “Atomistic Determination of Continuum Mechanical Properties of Ion-Bombarded Silicon,” Journal of Engineering Materials and Technology-transactions of The Asme. 2005. link Times cited: 9 Abstract: Highly disordered, ion-processed silicon is studied using a … read moreAbstract: Highly disordered, ion-processed silicon is studied using a molecular dynamics simulation with empirical interatomic potentials. The surface free energy density, stress-strain relations, and continuum surface features of silicon, bombarded in the simulations to relatively high fluence by medium energy argon ions, are computed statistically by preparing multiple randomized ion-bombarded specimens. The surface-free energy per unit area for the ion-bombarded silicon is about 1.76 J/m 2 , much lower than the 2.35 J/m 2 corresponding to a (001) unrelaxed, crystalline silicon surface. A stress-strain curve is obtained computationally by performing a constant strain test on the ion-bombarded specimens and by calculating stresses from the interatomic forces acting across different cross sections in the sample. The resulting tensile elastic modulus of the material, while slightly elevated due to the prominence of the free surface in the thin layer, is in good agreement with available experimental data. The surface is characterized using an interatomic potential-based C 2 continuous sampling method. read less NOT USED (low confidence) J. Vanhellemont et al., “Recent Progress in Understanding of Lattice Defects in Czochralski-Grown Germanium: Catching-up with Silicon,” Solid State Phenomena. 2005. link Times cited: 12 Abstract: Recent progress is presented in the understanding of grown-i… read moreAbstract: Recent progress is presented in the understanding of grown-in defects in Czochralskigrown germanium crystals with special emphasis on intrinsic point defects, on vacancy clustering and on interstitial oxygen. Whenever useful the results are compared with those obtained for silicon. read less NOT USED (low confidence) S. Brochard, J. Godet, L. Pizzagalli, P. Beauchamp, and J. Soler, “A Theoretical Study of Dislocation Formation at Surfaces in Covalent Materials: Effect of Step Geometry and Reactivity,” Solid State Phenomena. 2005. link Times cited: 0 Abstract: Atomistic simulations using both semi-empirical potential an… read moreAbstract: Atomistic simulations using both semi-empirical potential and first principles calculation have been performed to study the initiation of plasticity near surface steps in silicon. A comparison of both techniques on a prototypic case shows qualitative and quantitative agreement. Then each method has been used to analyze in detail some characteristics of the surface step: the step geometry thanks to semi-empirical potential calculations, and the step reactivity with ab initio techniques. read less NOT USED (low confidence) M. Bachlechner, J. Y. Zhang, Y.-F. Wang, J. Schiffbauer, S. Knudsen, and D. Korakakis, “Molecular dynamics simulations of the mechanical strength of Si/ Si 3 N 4 interfaces,” Physical Review B. 2005. link Times cited: 8 Abstract: Molecular dynamics simulations are performed on parallel com… read moreAbstract: Molecular dynamics simulations are performed on parallel computers to investigate the crystalline $\mathrm{Si}(111)∕{\mathrm{Si}}_{3}{\mathrm{N}}_{4}(0001)$ interface that is modeled as an eight-component system. The average total energy per particle and the average kinetic energy per particle of the subsystems are monitored during the preparation of the system. The Young's modulus of the interface is compared with that of the silicon part alone and that of the silicon-nitride film, respectively. The results for one extended simulation feature a crack in the silicon-nitride film and dislocated atoms in silicon below the crack. Simulations at rates of strain ranging from $0.00125\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}0.05\phantom{\rule{0.3em}{0ex}}{\mathrm{ps}}^{\ensuremath{-}1}$ show that for lower strain rates, the systems stretched faster reach their ultimate strength at a higher strain value than those that were stretched more slowly. At the highest strain rates, however, the failure mechanisms change qualitatively indicative of a more ductile behavior. read less NOT USED (low confidence) M. Payne, G. Csányi, and A. Vita, “Hybrid atomistic modelling of materials processes.” 2005. link Times cited: 4 NOT USED (low confidence) C. P. Massen and J. Doye, “Power-law distributions for the areas of the basins of attraction on a potential energy landscape.,” Physical review. E, Statistical, nonlinear, and soft matter physics. 2005. link Times cited: 42 Abstract: Energy landscape approaches have become increasingly popular… read moreAbstract: Energy landscape approaches have become increasingly popular for analyzing a wide variety of chemical physics phenomena. Basic to many of these applications has been the inherent structure mapping, which divides up the potential energy landscape into basins of attraction surrounding the minima. Here, we probe the nature of this division by introducing a method to compute the basin area distribution and applying it to some archetypal supercooled liquids. We find that this probability distribution is a power law over a large number of decades with the lower-energy minima having larger basins of attraction. Interestingly, the exponent for this power law is approximately the same as that for a high-dimensional Apollonian packing, providing further support for the suggestion that there is a strong analogy between the way the energy landscape is divided into basins, and the way that space is packed in self-similar, space-filling hypersphere packings, such as the Apollonian packing. These results suggest that the basins of attraction provide a fractal-like tiling of the energy landscape, and that a scale-free pattern of connections between the minima is a general property of energy landscapes. read less NOT USED (low confidence) Q. Lu and B. Bhattacharya, “The role of atomistic simulations in probing the small-scale aspects of fracture—a case study on a single-walled carbon nanotube,” Engineering Fracture Mechanics. 2005. link Times cited: 71 NOT USED (low confidence) P. McMillan, M. Wilson, D. Daisenberger, and D. Machon, “A density-driven phase transition between semiconducting and metallic polyamorphs of silicon,” Nature Materials. 2005. link Times cited: 204 NOT USED (low confidence) D. Vanderbilt, X. Zhao, and D. Ceresoli, “Structural and dielectric properties of crystalline and amorphous ZrO2,” Thin Solid Films. 2005. link Times cited: 149 NOT USED (low confidence) X. Li, S. Hassan, and E. Mehler, “Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: Calculation of structural and dynamic properties,” Proteins: Structure. 2005. link Times cited: 51 Abstract: Long dynamics simulations were carried out on the B1 immunog… read moreAbstract: Long dynamics simulations were carried out on the B1 immunoglobulin‐binding domain of streptococcal protein G (ProtG) and bovine pancreatic trypsin inhibitor (BPTI) using atomistic descriptions of the proteins and a continuum representation of solvent effects. To mimic frictional and random collision effects, Langevin dynamics (LD) were used. The main goal of the calculations was to explore the stability of tens‐of‐nanosecond trajectories as generated by this molecular mechanics approximation and to analyze in detail structural and dynamical properties. Conformational fluctuations, order parameters, cross correlation matrices, residue solvent accessibilities, pKa values of titratable groups, and hydrogen‐bonding (HB) patterns were calculated from all of the trajectories and compared with available experimental data. The simulations comprised over 40 ns per trajectory for ProtG and over 30 ns per trajectory for BPTI. For comparison, explicit water molecular dynamics simulations (EW/MD) of 3 ns and 4 ns, respectively, were also carried out. Two continuum simulations were performed on each protein using the CHARMM program, one with the all‐atom PAR22 representation of the protein force field (here referred to as PAR22/LD simulations) and the other with the modifications introduced by the recently developed CMAP potential (CMAP/LD simulations). The explicit solvent simulations were performed with PAR22 only. Solvent effects are described by a continuum model based on screened Coulomb potentials (SCP) reported earlier, i.e., the SCP‐based implicit solvent model (SCP–ISM). For ProtG, both the PAR22/LD and the CMAP/LD 40‐ns trajectories were stable, yielding Cα root mean square deviations (RMSD) of about 1.0 and 0.8 Å respectively along the entire simulation time, compared to 0.8 Å for the EW/MD simulation. For BPTI, only the CMAP/LD trajectory was stable for the entire 30‐ns simulation, with a Cα RMSD of ≈1.4 Å, while the PAR22/LD trajectory became unstable early in the simulation, reaching a Cα RMSD of about 2.7 Å and remaining at this value until the end of the simulation; the Cα RMSD of the EW/MD simulation was about 1.5 Å. The source of the instabilities of the BPTI trajectories in the PAR22/LD simulations was explored by an analysis of the backbone torsion angles. To further validate the findings from this analysis of BPTI, a 35‐ns SCP–ISM simulation of Ubiquitin (Ubq) was carried out. For this protein, the CMAP/LD simulation was stable for the entire simulation time (Cα RMSD of ≈1.0 Å), while the PAR22/LD trajectory showed a trend similar to that in BPTI, reaching a Cα RMSD of ≈1.5 Å at 7 ns. All the calculated properties were found to be in agreement with the corresponding experimental values, although local deviations were also observed. HB patterns were also well reproduced by all the continuum solvent simulations with the exception of solvent‐exposed side chain–side chain (sc–sc) HB in ProtG, where several of the HB interactions observed in the crystal structure and in the EW/MD simulation were lost. The overall analysis reported in this work suggests that the combination of an atomistic representation of a protein with a CMAP/CHARMM force field and a continuum representation of solvent effects such as the SCP–ISM provides a good description of structural and dynamic properties obtained from long computer simulations. Although the SCP–ISM simulations (CMAP/LD) reported here were shown to be stable and the properties well reproduced, further refinement is needed to attain a level of accuracy suitable for more challenging biological applications, particularly the study of protein–protein interactions. Proteins 2005. © 2005 Wiley‐Liss, Inc. read less NOT USED (low confidence) S. Ogata and T. Igarashi, “Concurrent Coupling of Electronic-Density-Functional, Molecular Dynamics, and Coarse-Grained Particles Schemes for Multiscale Simulation of Nanostructured Materials,” Materials Science Forum. 2005. link Times cited: 3 Abstract: Feature sizes of useful electronic devices are becoming smal… read moreAbstract: Feature sizes of useful electronic devices are becoming smaller and reaching nanometer ranges. There is increasing demand to perform dynamic simulations of such nano-devices with realistic sizes. To date, various kinds of simulation methods have been used for materials and devices including the density-functional theory (DFT) and the molecular dynamics (MD) for atomistic mechanics and the finite element method for continuum mechanics. We review recent progresses in our multiscale, hybrid simulation schemes that combine those methods. The coarse-grained particles (CG) method originally proposed by Rudd and Broughton [Phys. Rev. B58 (1998), p. R5893] has features suitable to such hybridization. We improve the CG method so that it is applicable to realistic nanostructured materials with large deformations. A novel hybridization scheme that couples the DFT method with the MD method is presented, which is applicable to virtually any selection of the DFT region in a wide range of materials. Hybrid DFT-MD simulations of the H2O reaction with nanostructured Si and alumina systems under stresses are performed, to demonstrate significant effects of stress on the chemical reaction. read less NOT USED (low confidence) H. Koizumi and T. Suzuki, “Motion of dislocation kinks in a simple model crystal,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2005. link Times cited: 9 NOT USED (low confidence) Z. Wang and E. Seebauer, “Temperature-dependent energy thresholds for ion-stimulated defect formation in solids.,” Physical review letters. 2005. link Times cited: 9 NOT USED (low confidence) D. Landau, F. Tavazza, and J. Adler, “Monte Carlo simulations of a compressible Ising ferromagnet at constant volume,” Comput. Phys. Commun. 2005. link Times cited: 1 NOT USED (low confidence) H. Xin, J.-min Zhang, X. Wei, and K. Xu, “Anisotropy analysis of energy in Ag/Si twist interface,” Surface and Interface Analysis. 2005. link Times cited: 16 Abstract: The energies in three combinations of Ag(001)/Si(111), Ag(01… read moreAbstract: The energies in three combinations of Ag(001)/Si(111), Ag(011)/Si(111) and Ag(111)/Si(111) twist boundaries have been calculated using the modified embedded atom method (MEAM). The results show that the interface energies corresponding to Ag(111)/Si(111), Ag(001)/Si(111) and Ag(011)/Si(111) increase successively and the lowest energies 365, 717.7 and 996.1 mJ m−2 corresponding to each interface appear at twist angles θ of 30, 0 and 25.24°, respectively. Considering minimization of interface energy, we can conclude that the Ag films deposited on Si(111) substrate will result in a (111) preferred orientation, especially at a twist angle of θ = 30°. Copyright © 2005 John Wiley & Sons, Ltd. read less NOT USED (low confidence) L. Zhang and J. Feng, “Molecular-dynamics simulation of germanium film growth by cluster deposition,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2005. link Times cited: 4 NOT USED (low confidence) J. Cai, X. Hu, and N. Chen, “Multiple lattice inversion approach to interatomic potentials for compound semiconductors,” Journal of Physics and Chemistry of Solids. 2005. link Times cited: 25 NOT USED (low confidence) J. Delaye and D. Ghaleb, “Combining two types of molecular dynamics for rapid computation of high-energy displacement cascades. II. Application of the method to a 70-keV cascade in a simplified nuclear glass,” Physical Review B. 2005. link Times cited: 21 Abstract: A combined molecular dynamics method is proposed to accelera… read moreAbstract: A combined molecular dynamics method is proposed to accelerate the computation of displacement cascades in nuclear glass arising from recoil nuclei in the 70\char21{}100 keV energy range. The method combines two types of molecular dynamics calculations: classical MD with standard empirical potentials and a simplified form with the potentials reduced to their short-range component to estimate the morphology of a displacement cascade. With this method we were able to reconstitute the behavior of a simplified oxide glass impacted by a 70-keV projectile. Compared with the results obtained by classical molecular dynamics, mechanisms observed at lower energies (temporary depolymerization followed by progressive structure recovery) are correctly reproduced at 70 keV; the number of atom displacements and the intermediate depolymerization peak intensity remain linear at energies ranging from 0 to 70 keV. The large volume of the 70-keV cascade allowed us to demonstrate that structure recovery was not homogeneous: the coolest regions were less annealed than the hottest regions. The residual depolymerization was more intense in regions struck by lower-energy projectiles\char22{}i.e., at the end of the cascade. Local thermal agitation in the hottest regions rapidly diminished as it propagated, and the neighboring regions were largely unaffected. Thermal agitation in the hottest regions thus had little effect on the recovery of regions impacted by low-energy projectiles. read less NOT USED (low confidence) M. Posselt, F. Gao, and D. Zwicker, “Atomistic Study of the Migration of Di- and Tri-Interstitials in Silicon,” Physical Review B. 2005. link Times cited: 40 Abstract: A comprehensive study on the migration of di- and tri-inters… read moreAbstract: A comprehensive study on the migration of di- and tri-interstitials in silicon is performed using classical molecular dynamics simulations with a Stillinger-Weber potential. At first the structures and energetics of the di- and the tri-interstitial are investigated, and the accuracy of the interatomic potential is tested by comparing the results with literature data obtained by tight-binding and density-functional-theory calculations. Then the migration is investigated for temperatures between 800 and 1600 K. Very long simulation times, large computational cells and different initial conditions are considered. The defect diffusivity, the self-diffusion coefficient per defect and the corresponding effective migration barriers are calculated. Compared to a mono-interstitial, the di-interstitial migrates faster, whereas the tri-interstitial diffuses slower. The mobility of the di- and the mono-interstitial is higher than the mobility of the lattice atoms during the diffusion of these defects. On the other hand, the tri-interstitial mobility is lower than the corresponding atomic mobility. The migration mechanism of the di-interstitial shows a pronounced dependence on the temperature. At low temperature a high mobility on zigzag-like lines along a axis within a {l_brace}110{r_brace} plane is found, whereas the change between equivalent directions or equivalent {l_brace}110{r_brace} planes occurs seldomly and requires a long simulationmore » time, but the rate of directional change increases with increasing temperature. During the diffusion within {l_brace}110{r_brace} planes the di-interstitial moves like a wave packet so that the atomic mobility is lower than that of the defect. On the other hand, the change between equivalent {l_brace}110{r_brace} migration planes is characterized by frequent atomic rearrangements. The visual analysis of the tri-interstitial diffusion reveals complex migration mechanisms and a high atomic mobility. The diffusivities and effective migration barriers obtained are compared with the few data from the literature. The implications of the present results for the explanation of experimental data on defect evolution and migration are discussed.« less read less NOT USED (low confidence) K. C. Huang, T. Wang, and J. Joannopoulos, “Superheating and induced melting at semiconductor interfaces.,” Physical review letters. 2005. link Times cited: 14 Abstract: We present ab initio density-functional simulations of the s… read moreAbstract: We present ab initio density-functional simulations of the state of several semiconductor surfaces at temperatures near the bulk melting temperatures. We find that the solid-liquid phase-transition temperature at the surface can be altered via a microscopic (single-monolayer) coating with a different lattice-matched semiconducting material. Our results show that a single-monolayer GaAs coating on a Ge(110) surface above the Ge melting temperature can dramatically reduce the diffusion coefficient of the germanium atoms, going so far as to prevent melting of the bulk layers on the 10 ps time scale. In contrast, a single-monolayer coating of Ge on a GaAs(110) surface introduces defects into the bulk and induces melting of the top layer of GaAs atoms 300 K below the GaAs melting point. To our knowledge, these calculations represent the first ab initio investigation of the superheating and induced melting phenomena. read less NOT USED (low confidence) V. Smirnov et al., “Molecular-dynamics model of energetic fluorocarbon-ion bombardment on SiO2 I. Basic model and CF2+-ion etch characterization,” Journal of Applied Physics. 2005. link Times cited: 25 Abstract: A molecular-dynamics-based model has been developed to under… read moreAbstract: A molecular-dynamics-based model has been developed to understand etching of amorphous SiO2, with and without a fluorocarbon reactive layer, by energetic fluorocarbon (CFx+) ions. The model includes a representation of the solid and a set of interatomic potentials required for the SiO2–CFx interaction system. Two- and three-body pseudopotentials have either been obtained from published literature or computed using ab initio techniques. The Stillinger–Weber potential construct is used to represent potentials in our model and particle trajectories are advanced using the velocity-Verlet algorithm. The model is validated by comparing computed bond lengths and energies with published experimental results. Computed yield for Ar+ ion sputtering of SiO2 is also compared with published data. In the computational results described in this article, the model SiO2 test structure (with a thin fluorocarbon reactive layer) is prepared by starting with α-quartz ([001] orientation) and bombarding it with 50-eV CF2+ ions. ... read less NOT USED (low confidence) G. Li, C. S. Liu, and Z.-P. Zhu, “Excess entropy scaling for transport coefficients: diffusion and viscosity in liquid metals,” Journal of Non-crystalline Solids. 2005. link Times cited: 33 NOT USED (low confidence) S. G. Mayr and R. Averback, “Ion-irradiation-induced stresses and swelling in amorphous Ge thin films,” Physical Review B. 2005. link Times cited: 33 Abstract: Mechanical stresses and morphology during growth and ion bom… read moreAbstract: Mechanical stresses and morphology during growth and ion bombardment of amorphous Ge thin films are investigated by a combination of in situ stress measurements and molecular dynamics computer simulations. Strong compressive stresses are generated during irradiation that subsequently lead to severe swelling. The simulations indicate that interstitial-mediated viscous flow in combination with well-localized vacancy defects are the main ingredients responsible for the observed phenomena. read less NOT USED (low confidence) F. Giessibl, “AFM’s path to atomic resolution,” Materials Today. 2005. link Times cited: 106 NOT USED (low confidence) Y. Ma and S. Garofalini, “Application of the Wolf damped Coulomb method to simulations of SiC.,” The Journal of chemical physics. 2005. link Times cited: 14 Abstract: A multibody interatomic potential is developed for bulk SiC … read moreAbstract: A multibody interatomic potential is developed for bulk SiC using a modification of the Wolf et al. summation technique [D. Wolf, P. Keblinski, S. R. Phillpot, and J. Eggebrecht, J. Chem. Phys. 110, 8254 (1999)] for the electrostatic interaction. The technique is modified to account for the short-range nonpoint charge effect. The nonelectrostatic interaction is modeled by a simple Morse-stretch term. This potential is then applied to beta-SiC to calculate various bulk properties using molecular dynamics simulations. The simulated x-ray diffraction pattern, radial distribution functions, lattice constant, elastic constants, and defect energy agree well with experimental data. read less NOT USED (low confidence) T. Hanada and T. Yao, “Formation and evolution of strain-induced self-assembled dot,” Microelectron. J. 2005. link Times cited: 4 NOT USED (low confidence) T. Thonhauser and G. Mahan, “Predicted Raman spectra of Si[111] nanowires,” Physical Review B. 2005. link Times cited: 24 Abstract: We present calculated Raman spectra for freestanding Si[111]… read moreAbstract: We present calculated Raman spectra for freestanding Si[111] nanowires with diameters from $d\ensuremath{\approx}1\phantom{\rule{0.3em}{0ex}}\mathrm{nm}$ up to $5\phantom{\rule{0.3em}{0ex}}\mathrm{nm}$. In the first step, we calculate eigenmodes with a Stillinger-Weber-type model. After this, a bond polarizability model is used to calculate Raman spectra out of the eigenmodes obtained in the first step. In addition to the usual silicon peak at $519\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}1}$, we find for all wires a Raman signal originating in a low-frequency breathing mode with a $1∕d$ frequency dependence. We also give an analytic derivative that generalizes this result to arbitrary nanowires. Our findings can therefore be used for a new and simple way to determine the diameter of nanowires. read less NOT USED (low confidence) W. Moon and H. Hwang, “A modified Stillinger–Weber empirical potential for boron nitride,” Applied Surface Science. 2005. link Times cited: 23 NOT USED (low confidence) S. Sinha, P. Schelling, S. Phillpot, and K. Goodson, “Scattering of g-process longitudinal optical phonons at hotspots in silicon,” Journal of Applied Physics. 2005. link Times cited: 49 Abstract: Transistors with gate lengths below 100 nm generate phonon h… read moreAbstract: Transistors with gate lengths below 100 nm generate phonon hotspots with dimensions on the order of 10 nm and peak power densities of about 50W∕μm3. This work employs molecular dynamics to investigate the impact of lattice energy density on phonon scattering at the hotspot. The hotspot studied in this work consists of longitudinal optical phonons involved in the g-type intervalley scattering of conduction electrons in silicon. A comparison of the decay modes in hotspots with high and moderate energy densities reveals that the decay mechanisms are the same but the relaxation rates differ. Scattering occurs through a three phonon process of the form LO→LA+TA, involving the zone-edge transverse acoustic modes. An increase in the energy density from a moderate value of 5 to 125W∕μm3 changes the relaxation time from 79 to 16 ps, approximately proportional to the the maximum initial amplitude of the phonons. This work improves the accuracy of the scattering rates of optical phonons and helps in advancing the el... read less NOT USED (low confidence) M. H. Saani et al., “Lattice relaxation in many-electron states of the diamond vacancy,” Physical Review B. 2005. link Times cited: 7 NOT USED (low confidence) J. Feldman and N. Bernstein, “Vibrational spectroscopy of an amorphous∕crystalline sandwich structure for silicon: Numerical results,” Physical Review B. 2004. link Times cited: 19 NOT USED (low confidence) N. Mingo and D. Broido, “Lattice thermal conductivity crossovers in semiconductor nanowires.,” Physical review letters. 2004. link Times cited: 71 Abstract: For binary compound semiconductor nanowires, we find a strik… read moreAbstract: For binary compound semiconductor nanowires, we find a striking relationship between the nanowire's thermal conductivity kappa(nwire), the bulk material's thermal conductivity kappa(bulk), and the mass ratio of the material's constituent atoms, r, as kappa(bulk)/kappa(nwire) (alpha) (1+1/r)(-3/2). A significant consequence is the presence of crossovers in which a material with higher bulk thermal conductivity than the rest is no longer the best nanowire thermal conductor. We show that this behavior stems from a change in the dominant phonon scattering mechanism with decreasing nanowire size. The results have important implications for nanoscale heat dissipation, thermoelectricity, and thermal conductivity of nanocomposites. read less NOT USED (low confidence) Y. Mo, M. Bazant, and E. Kaxiras, “Sulfur point defects in crystalline and amorphous silicon,” Physical Review B. 2004. link Times cited: 44 Abstract: We present first-principles calculations for the behavior of… read moreAbstract: We present first-principles calculations for the behavior of sulfur point defects in crystalline and amorphous silicon structures. By introducing the sulfur point defects at various representative positions in the samples, including substitutional and interstitial sites in the crystal and fourfold coordinated or miscoordinated sites (dangling bond and floating bond sites ) in the amorphous, we analyze the energetics in detail and determine the most stable structures. Two important conclusions we draw are: (a) in crystalline Si, the S defects form pairs in which the two S atoms are energetically bound but not covalently bonded; (b) in amorphous Si, they preferentially occupy threefold coordinated sites, even when the starting configuration has higher coordination (four- or fivefold). The implications of these results for the electronic structure of sulfur-doped Si samples are also analyzed in the context of the present calculations. read less NOT USED (low confidence) F. Tavazza, D. Landau, and J. Adler, “Phase diagram and structural properties for a compressible Ising ferromagnet at constant volume,” Physical Review B. 2004. link Times cited: 14 NOT USED (low confidence) N. Martsinovich, A. L. Rosa, M. Heggie, and P. Briddon, “First Principles Calculations of Hydrogen Aggregation in Silicon,” Defect and Diffusion Forum. 2004. link Times cited: 0 Abstract: We use DFT calculations to investigate the problem of hydrog… read moreAbstract: We use DFT calculations to investigate the problem of hydrogen aggregation in silicon. We study atomic structures of finite hydrogen aggregates containing four or more hydrogen atoms. Beyond four hydrogen atoms, complexes consisting of Si-H bonds are likely to form, rather than aggregates of H2 molecules, which are the most stable diatomic hydrogen complex. Our calculations show that the basic structural unit of such complexes is a hydrogenated dislocation loop, which is formed spontaneously by a structural transformation of two H∗2 complexes. Hydrogen-induced formation of dislocation loops may account for the experimental observations of dislocation loops in proton-implanted or hydrogen plasma-treated silicon. We indicate the routes leading from H∗2 aggregates and hydrogenated dislocation loops to twodimensional hydrogen-induced platelets. We discuss the effect of hydrogen-catalysed formation of dislocation loops on the plasticity of silicon. read less NOT USED (low confidence) B. Becker, P. Schelling, and S. Phillpot, “Computational studies of nanoscale phonon transport and interfacial scattering,” Physica Status Solidi (c). 2004. link Times cited: 4 Abstract: We use molecular-dynamics simulation of phonon wave-packets … read moreAbstract: We use molecular-dynamics simulation of phonon wave-packets to study interfacial phonon scattering. Phonon scattering at a simple interface in a diamond-structured material is used to demonstrate the usefulness of the approach. We also present more recent results for interfacial scattering in a silicon nanowire. These preliminary results show that interfacial scattering in a nanoscale system is significantly different than scattering in the corresponding bulk system. Finally, we discuss methodological improvements in wave packet dynamics that will permit for direct comparison with experimental findings, including in the low-temperature regime where quantum effects are important. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) read less NOT USED (low confidence) S. Izumi, S. Hara, T. Kumagai, and S. Sakai, “Classification of amorphous-silicon microstructures by structural parameters: molecular dynamics study,” Computational Materials Science. 2004. link Times cited: 13 NOT USED (low confidence) R. Kobayashi and T. Nakayama, “Theoretical study on generation and atomic structures of stacking-fault tetrahedra in Si film growth,” Thin Solid Films. 2004. link Times cited: 6 NOT USED (low confidence) J. Chen, A. Béré, G. Nouet, and P. Ruterana, “Analysis of faceting of grain boundaries in GaN,” Superlattices and Microstructures. 2004. link Times cited: 2 NOT USED (low confidence) F. Tavazza, L. Nurminen, D. Landau, A. Kuronen, and K. Kaski, “Hybrid Monte Carlo-molecular dynamics algorithm for the study of islands and step edges on semiconductor surfaces: application to Si/Si (001).,” Physical review. E, Statistical, nonlinear, and soft matter physics. 2004. link Times cited: 7 Abstract: A classical, hybrid Monte Carlo-molecular dynamic (MC-MD) al… read moreAbstract: A classical, hybrid Monte Carlo-molecular dynamic (MC-MD) algorithm is introduced for the study of phenomena like two-dimensional (2D) island stability or step-edge evolution on semiconductor surfaces. This method presents the advantages of working off lattice and utilizing bulk-fitted potentials. It is based on the introduction of collective moves, such as dimer jumps, in the MC algorithm. MD-driven local relaxations are considered as trial moves for the MC. The algorithm is applied to the analysis of 2D Si islands on Si(001). Results on early stages of island formation, island stability versus temperature and system size, and step-edge evolution are presented. In all cases good qualitative agreement with experimental results is found. read less NOT USED (low confidence) S. Ogata and R. Belkada, “A hybrid electronic-density-functional/molecular-dynamics simulation scheme for multiscale simulation of materials on parallel computers: applications to silicon and alumina,” Computational Materials Science. 2004. link Times cited: 18 NOT USED (low confidence) F. Mota, M. Caturla, J. Perlado, E. Domínguez, and A. Kubota, “Atomistic simulations of threshold displacement energies in SiO2,” Journal of Nuclear Materials. 2004. link Times cited: 15 NOT USED (low confidence) A. Rykov, K. Nomura, T. Mitsui, and M. Seto, “Low-energy excitations in brownmillerites and related oxides,” Physica B-condensed Matter. 2004. link Times cited: 14 NOT USED (low confidence) T. Watanabe, D. Yamasaki, K. Tatsumura, and I. Ohdomari, “Improved interatomic potential for stressed Si, O mixed systems,” Applied Surface Science. 2004. link Times cited: 52 NOT USED (low confidence) D. Tzou, J. K. Chen, R. Roybal, and J. Beraun, “Cluster potentials for multi-scale interactions,” International Journal of Heat and Mass Transfer. 2004. link Times cited: 2 NOT USED (low confidence) D. Mason, R. Rudd, and A. Sutton, “Stochastic kinetic Monte Carlo algorithms for long-range Hamiltonians,” Comput. Phys. Commun. 2004. link Times cited: 35 NOT USED (low confidence) T. Kirichenko, S. Banerjee, and G. Hwang, “Interaction of neutral vacancies and interstitials with the Si(001) surface,” Physical Review B. 2004. link Times cited: 10 NOT USED (low confidence) A. Murakawa, H. Ishii, and K. Kakimoto, “An investigation of thermal conductivity of silicon as a function of isotope concentration by molecular dynamics,” Journal of Crystal Growth. 2004. link Times cited: 21 NOT USED (low confidence) R. Narulkar, L. Raff, and R. Komanduri, “Monte Carlo-steepest descent (MC-SD) simulations of nanometric cutting,” Proceedings of the Institution of Mechanical Engineers, Part N: Journal of Nanoengineering and Nanosystems. 2004. link Times cited: 3 Abstract: In order to reduce the computational time, Monte Carlo (MC) … read moreAbstract: In order to reduce the computational time, Monte Carlo (MC) simulations of nanometric cutting have been modified to include a combination of steepest descent (SD) and Monte Carlo procedures. This MC-SD combination is found to reduce the required computational times by factors of at least two to three over those achieved using MC methods alone. The MC-SD method is applied to the nanometric cutting of single-crystal aluminium along the (100) plane with different rake angle tools at a cutting speed of 5m/s. The results obtained from the MC-SD calculations are found to be almost identical to those resulting from the MC simulations. read less NOT USED (low confidence) J. Matsuo, C. Okubo, T. Seki, T. Aoki, N. Toyoda, and I. Yamada, “A new secondary ion mass spectrometry (SIMS) system with high-intensity cluster ion source,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2004. link Times cited: 56 NOT USED (low confidence) W. Rowe et al., “Tribology of Abrasive Machining Processes.” 2004. link Times cited: 408 Abstract: This book draws upon the science of tribology to understand,… read moreAbstract: This book draws upon the science of tribology to understand, predict and improve abrasive machining processes. Pulling together information on how abrasives work, the authors, who are renowned experts in abrasive technology, demonstrate how tribology can be applied as a tool to improve abrasive machining processes. Each of the main elements of the abrasive machining system are looked at, and the tribological factors that control the efficiency and quality of the processes are described. Since grinding is by far the most commonly employed abrasive machining process, it is dealt with in particular detail. Solutions are posed to many of the most commonly experienced industrial problems, such as poor accuracy, poor surface quality, rapid wheel wear, vibrations, work-piece burn and high process costs. This practical approach makes this book an essential tool for practicing engineers. Uses the science of tribology to improve understanding and of abrasive machining processes in order to increase performance, productivity and surface quality of final products. A comprehensive reference on how abrasives work, covering kinematics, heat transfer, thermal stresses, molecular dynamics, fluids and the tribology of lubricants. Authoritative and ground-breaking in its first edition, the 2nd edition includes 30 per cent new and updated material, including new topics such as CMP (Chemical Mechanical Polishing) and precision machining for micro-and nano-scale applications. read less NOT USED (low confidence) J. Godet, L. Pizzagalli, S. Brochard, and P. Beauchamp, “Computer study of microtwins forming from surface steps of silicon,” Computational Materials Science. 2004. link Times cited: 23 NOT USED (low confidence) X. Fu, K. Szeto, S. Dyrting, and P. Sheng, “Geometric characterization of metastable states in tetrahedral bonded amorphous semiconductors,” Physica B-condensed Matter. 2004. link Times cited: 0 NOT USED (low confidence) S. Ashwin, U. Waghmare, and S. Sastry, “Metal-to-semimetal transition in supercooled liquid silicon.,” Physical review letters. 2004. link Times cited: 37 Abstract: Computer simulations, using the Stillinger-Weber potential, … read moreAbstract: Computer simulations, using the Stillinger-Weber potential, have previously been employed to demonstrate a liquid-liquid transition in supercooled silicon near 1060 K. From calculations of electronic structure using an empirical psuedopotential, we show that silicon undergoes an associated metal to semimetal transition with a resistivity jump of roughly 1 order of magnitude. We show that the electronic states near the Fermi energy become localized in the low temperature phase, and that changes in electronic structure between the two phases arise from a change in atomic structure, and not from a change in density. read less NOT USED (low confidence) J. K. Chen, J. Beraun, R. Roybal, and D. Tzou, “Nano- to Microscale Modeling by Cluster Potentials,” Journal of Thermophysics and Heat Transfer. 2004. link Times cited: 2 Abstract: Cluster potentials have been derived in this work by integra… read moreAbstract: Cluster potentials have been derived in this work by integrating the Lennard-Jones (LJ) potential over specific physical domains defining the geometrical shapes of the molecular clusters. For microsystems involving loosely compacted cluster arrays, the asymptotic expressions of the cluster potential are derived and compared to the LJ potential. Capabilities in multiscale modeling are demonstrated by introducing physical boundaries as large clusters of a planar geometry. Numerical examples include pressure and heat-flux distributions in nanoarrays subjected to in-depth heating. read less NOT USED (low confidence) N. Voulgarakis, G. Hadjisavvas, P. Kelires, and G. Tsironis, “Computational investigation of intrinsic localization in crystalline Si,” Physical Review B. 2004. link Times cited: 41 Abstract: We investigate numerically existence and dynamical propertie… read moreAbstract: We investigate numerically existence and dynamical properties of intrinsic localization in crystalline silicon through the use of interatomic Tersoff force fields. We find a band of intrinsic localized modes (discrete breathers) each with lifetime of at least 60 ps in the spectral region 548-578 cm - 1 , located just above the zone end phonon frequency calculated at 536 cm - 1 . The localized modes extend to more than second neighbors and involve pair central-atom compressions in the range from 6.1 % to 8.6% of the covalent bond length per atom. Finite temperature simulations show that they remain robust to room temperatures or higher with a typical lifetime equal to 6 ps. read less NOT USED (low confidence) M. Yu et al., “Studying shallow junction technology by atomistic modeling,” The Fourth International Workshop on Junction Technology, 2004. IWJT ’04. 2004. link Times cited: 0 Abstract: Atomistic modeling has been applied in studying and simulati… read moreAbstract: Atomistic modeling has been applied in studying and simulating the advanced junction technologies. We present in this paper the application of molecular dynamics method in simulation of low energy ion implantation and that of kinetic Monte Carlo method in simulation of enhanced diffusion in annealing. The dose dependent ultra-low energy implantation is well simulated. The simulation indicates that energy contamination is not as serious as it looks. The dissipation of Si extended defects are simulated for both 40 keV and 5 keV Si implantation cases. Enhanced diffusion is simulated. read less NOT USED (low confidence) G. Gutiérrez and J. Rogan, “Structure of liquid GeO2 from a computer simulation model.,” Physical review. E, Statistical, nonlinear, and soft matter physics. 2004. link Times cited: 45 Abstract: The structural properties of liquid GeO2 are investigated by… read moreAbstract: The structural properties of liquid GeO2 are investigated by means of molecular dynamics simulation using a pairwise potential. The simulations were performed in the microcanonical ensemble on systems with up to 576 particles prepared at 21 different densities, corresponding to pressures from -2 to 30 GPa, and temperatures of 1500 K and 3000 K. The pair correlation function, coordination number, angular distribution, and both the neutron and x-ray static structure factors are obtained and compared with those of liquid silica. The analysis of these results for the system at zero pressure indicates that in the liquid state the short range order is dominated by the presence of slightly distorted Ge(O(1/2))(4) tetrahedra. These tetrahedra are linked to each other mainly through the corners, with a Ge-O-Ge angle of approximately 130 degrees, similar to the amorphous phase. Beyond the basic tetrahedron some order persists, but to less extent than in liquid silica. Simulation of systems at higher densities shows a volume collapse in the pressure-volume curve in the range of 4-8 GPa, suggesting the possibility that a liquid-liquid phase transition occurs, as the one observed in the amorphous phase. read less NOT USED (low confidence) S. Shen and S. Atluri, “Computational Nano-mechanics and Multi-scale Simulation,” Cmc-computers Materials & Continua. 2004. link Times cited: 39 Abstract: This article provides a review of the computational nanomech… read moreAbstract: This article provides a review of the computational nanomechanics, from the ab initio methods to classical molecular dynamics simulations, and multitemporal and spatial scale simulations. The recent improvements and developments are briefly discussed. Their applications in nanomechanics and nanotubes are also summarized. read less NOT USED (low confidence) C. R. Miranda and A. Antonelli, “Transitions between disordered phases in supercooled liquid silicon.,” The Journal of chemical physics. 2004. link Times cited: 32 Abstract: We have investigated the transitions between disordered phas… read moreAbstract: We have investigated the transitions between disordered phases in supercooled liquid silicon using computer simulations. The thermodynamic properties were directly obtained from the free energy, which was computed using the recently proposed reversible scaling method. The calculated free energies of the crystalline and liquid phases of silicon at zero pressure, obtained using the environment dependent interatomic potential, are in excellent agreement with the available experimental data. The results show that, at zero pressure, a weak first-order liquid-liquid transition occurs at 1135 K and a continuous liquid-amorphous transition takes place at 843 K. These results are consistent with the existence of a second critical point for the liquid-liquid transition at a negative pressure. read less NOT USED (low confidence) P. Gunes, Şi̇mşek S., and S. Erkoç, “a Comparative Study of Empirical Potential Energy Functions,” International Journal of Modern Physics C. 2004. link Times cited: 2 Abstract: A comparative study has been performed for silicon microclus… read moreAbstract: A comparative study has been performed for silicon microclusters, Si3 and Si4, considering fifteen different empirical potential energy functions. It has been found that only two of the empirical potential energy functions give linear structure more stable for Si3, the remaining potential functions give triangular structure as more stable. In the case of Si4 microclusters eight potential functions give open tetrahedral structure as more stable, two functions give perfect tetrahedral as more stable, three functions give square structure as more stable, and two functions give linear structure as more stable. read less NOT USED (low confidence) A. Dalton and E. Seebauer, “Structure and mobility on amorphous silicon surfaces,” Surface Science. 2004. link Times cited: 11 NOT USED (low confidence) T. Aoki and J. Matsuo, “Surface structure dependence of impact processes of gas cluster ions,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2004. link Times cited: 14 NOT USED (low confidence) D. Humbird and D. Graves, “Improved interatomic potentials for silicon-fluorine and silicon-chlorine.,” The Journal of chemical physics. 2004. link Times cited: 51 Abstract: Improved sets of empirical interatomic potentials for silico… read moreAbstract: Improved sets of empirical interatomic potentials for silicon-fluorine and silicon-chlorine are presented. The Tersoff-Brenner potential form has been reparameterized using the density-functional theory (DFT) cluster calculations of Walch. Halogenated silicon cluster energetics computed with DFT are, on average, within several tenths of an eV of the energies of the corresponding clusters with the reparameterized empirical potential for both Si-F and Si-Cl. Using the reparameterized Tersoff-Brenner potentials, molecular-dynamics simulations of F and Cl atom exposure to undoped silicon surfaces are in excellent agreement with published data on etch probability, halogen coverage at steady state, and etch product distributions. read less NOT USED (low confidence) J. Koga, K. Nishio, T. Yamaguchi, and F. Yonezawa, “Order N Non-Orthogonal Tight-Binding Molecular Dynamics and its Application to the Study of Glass Transition in Germanium,” Journal of the Physical Society of Japan. 2004. link Times cited: 3 Abstract: Order N non-orthogonal tight-binding molecular dynamics base… read moreAbstract: Order N non-orthogonal tight-binding molecular dynamics based on the Fermi operator expansion method is implemented and tested, where N is the number of atoms. The method is described in detail, with several notes on the actual implementation. We find that the potential energy and forces consistent with it are calculated in an O ( N ) fashion almost as easily as in the cases of orthogonal tight-binding models. Our method thus implemented is applied to the study of glass transition in germanium (Ge). We quench liquid Ge well above melting temperature by an N V T ensemble molecular dynamics simulation, with N =512. We investigate the pair correlation function, the static structure factor, and the bond-angle distribution function for liquid, super-cooled liquid, and amorphous Ge. From the analyses of these properties, we find that substantial structural changes occur when the temperature of liquid Ge is decreased. In particular, we find that with the decrease of temperature, covalent bonds in liquid Ge becom... read less NOT USED (low confidence) R. Smith, S. Kenny, and D. Ramasawmy, “Molecular-dynamics simulations of sputtering,” Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences. 2004. link Times cited: 15 Abstract: The use of molecular–dynamics simulations to understand the … read moreAbstract: The use of molecular–dynamics simulations to understand the ejection processes of particles from surfaces after energetic ion bombardment is discussed. Substrates considered include metals, covalent and ionic materials, polymers and molecular solids. It is shown how the simulations can be used to aid interpretation of experimental results by providing the underlying mechanisms behind the ejection processes. read less NOT USED (low confidence) S. Volz, R. Carminati, and K. Joulain, “THERMAL RESPONSE OF SILICON CRYSTAL TO PICO-FEMTOSECOND HEAT PULSE BY MOLECULAR DYNAMICS,” Microscale Thermophysical Engineering. 2004. link Times cited: 5 Abstract: We investigate the thermal response of a silicon crystal irr… read moreAbstract: We investigate the thermal response of a silicon crystal irradiated by a pico-femto heat pulse by using molecular dynamics technique and a linear response theory–based statistical analysis. The thermal susceptibility is first defined in terms of computed quantities and then convoluted with time Gaussian temperature pulses. The qualitative difference between the responses to various pulse durations is explained and the results are compared to those of classical Fourier model. Non-Fourier behaviors are emphasized and a mean phonon relaxation time is identified. read less NOT USED (low confidence) Y. Hada, “A molecular dynamics simulation of cluster dissociation process under cluster ion implantation,” Physica B-condensed Matter. 2003. link Times cited: 4 NOT USED (low confidence) M. Terasawa, Z. Insepov, T. Sekioka, A. A. Valuev, and T. Mitamura, “Sputtering due to Coulomb explosion in highly charged ion bombardment,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2003. link Times cited: 12 NOT USED (low confidence) T. A. Frewen, T. Sinno, E. Dornberger, R. Hoelzl, W. Ammon, and H. Bracht, “Global Parameterization of Multiple Point-Defect Dynamics Models in Silicon,” Journal of The Electrochemical Society. 2003. link Times cited: 9 Abstract: The task of determining globally robust estimates for the th… read moreAbstract: The task of determining globally robust estimates for the thermophysical properties of intrinsic point defects in crystalline silicon remains challenging. Previous attempts at point-defect model regression have focused onthe use of a single type of experimental data but as of yet no single parameter set has produced predictive models for a variety of point-defect related phenomena. A stochastic optimization technique known as simulated annealing is used to perform simultaneous regression of multiple models. Specifically, zinc diffusion in Si wafers and the dynamics of the so-called interstitial-vacancy boundary during Czochralski crystal growth are used to systematically probe point-defect properties. A fully transient model for point-defect dynamics during crystal growth is presented which employs a sophisticated adaptive mesh refinement algorithm to minimize the computational expense associated with each optimization. The resulting framework leads to a quantitatively coherent picture for both experimental systems, which are modeled with a single set of point-defect thermophysical properties. The results are shown to be entirely consistent with other recent model-fitting estimates and indicate that as the number of experiments considered simultaneously within this framework increases it should be possible to systematically specify these properties to higher precision. read less NOT USED (low confidence) L. Pelaz, L. Marqués, M. Aboy, and J. Barbolla, “Modeling of Dopant and Defect Interactions in Si Process Simulators,” Defect and Diffusion Forum. 2003. link Times cited: 1 Abstract: A multi-scale modeling, from ab-initio calculations, through… read moreAbstract: A multi-scale modeling, from ab-initio calculations, through Monte Carlo diffusion simulators, to the continuum models, is necessary to describe the complexity of dopant and defect interactions for process simulators. The advantages that make continuum simulators the standard in industrial applications are maintained only on the basis of the simplicity of the physical models. The inclusion of complex interactions in Kinetic Monte Carlo methods is not a problem from the computational point of view, but they demand a large number of parameters. The fabrication of small devices brings up complex physical mechanisms, for which atomistic simulations seem more appropriate than continuum methods. read less NOT USED (low confidence) S. Sastry and C. A. Angell, “Liquid–liquid phase transition in supercooled silicon,” Nature Materials. 2003. link Times cited: 451 NOT USED (low confidence) A. Selezenev, A. Aleynikov, N. S. Gantchuk, P. V. Yermakov, J. Labanowski, and A. Korkin, “SAGE MD: molecular-dynamic software package to study properties of materials with different models for interatomic interactions,” Computational Materials Science. 2003. link Times cited: 12 NOT USED (low confidence) R. Rurali and E. Hernández, “Trocadero: a multiple-algorithm multiple-model atomistic simulation program,” Computational Materials Science. 2003. link Times cited: 61 NOT USED (low confidence) P. Krasnochtchekov, K. Albe, and R. Averback, “Simulations of the inert gas condensation processes,” International Journal of Materials Research. 2003. link Times cited: 14 Abstract: Inert gas condensation of metallic and covalently bonded nan… read moreAbstract: Inert gas condensation of metallic and covalently bonded nanoparticles has been investigated using molecular-dynamics computer simulations. Using Ge as an example, the different phases of particle growth, nucleation, monomeric growth, and cluster aggregation, have been identified and the kinetics of each described. In addition, the evolutions of the morphologies of the different types of nanoparticles have been studied. It is shown that while covalently bonded nanoparticles tend toward a ramified structure, metallic nanoparticles remain compact, owing to deformation in the crystallized state. Finally, the strong influence of surface segregation on the structure of alloy nanoparticles is illustrated using a model system. read less NOT USED (low confidence) H. Tan, “Combined atomistic and continuum simulation for fracture and corrosion.” 2003. link Times cited: 7 NOT USED (low confidence) N. Bernstein and D. Hess, “Lattice trapping barriers to brittle fracture.,” Physical review letters. 2003. link Times cited: 138 Abstract: We present a multiscale simulation of a crack in silicon und… read moreAbstract: We present a multiscale simulation of a crack in silicon under tensile loading that is consistent with experiment; fracture is brittle with a modest lattice-trapping energy barrier to crack propagation. Our multiscale molecular-dynamics simulation has a tight-binding description of bonding near the crack tip embedded in an empirical-potential (EP) region. Forces on atoms in the tight-binding region are computed using a Green's function method. Comparing our multiscale simulation with EP simulations shows that the EP models severely overestimate lattice trapping, explaining the failure of the Griffith criterion and the dramatic differences in crack morphology. A two-length-scale model for the lattice-trapping energy barrier correctly predicts the critical load for brittle fracture. We argue that lattice trapping plays an important role in the brittle-to-ductile transition. read less NOT USED (low confidence) K. Garikipati, “Couple stresses in crystalline solids: origins from plastic slip gradients, dislocation core distortions, and three-body interatomic potentials,” Journal of The Mechanics and Physics of Solids. 2003. link Times cited: 17 NOT USED (low confidence) C. R. S. Silva, “Optimizing Metropolis Monte Carlo simulations of semiconductors,” Computer Physics Communications. 2003. link Times cited: 7 NOT USED (low confidence) J. Matsuo, T. Seki, T. Aoki, and I. Yamada, “Atomistic study of cluster collision on solid surfaces,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2003. link Times cited: 7 NOT USED (low confidence) K. Gärtner and B. Weber, “Molecular dynamics simulations of solid-phase epitaxial growth in silicon,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2003. link Times cited: 19 NOT USED (low confidence) J. Kioseoglou et al., “Microstructure of planar defects and their interactions in wurtzite GaN films,” Solid-state Electronics. 2003. link Times cited: 10 NOT USED (low confidence) J. Kioseoglou, H. Polatoglou, L. Lymperakis, G. Nouet, and P. Komninou, “A modified empirical potential for energetic calculations of planar defects in GaN,” Computational Materials Science. 2003. link Times cited: 37 NOT USED (low confidence) G. Hobler and G. Otto, “Status and open problems in modeling of as-implanted damage in silicon,” Materials Science in Semiconductor Processing. 2003. link Times cited: 64 NOT USED (low confidence) B. Daly, H. Maris, Y. Tanaka, and S. Tamura, “Molecular dynamics calculation of the in-plane thermal conductivity of GaAs/AlAs superlattices,” Physical Review B. 2003. link Times cited: 26 Abstract: We report on molecular dynamics calculations of the thermal … read moreAbstract: We report on molecular dynamics calculations of the thermal conductivity of superlattices in the direction parallel to the layers. We employ a simple, classical, fcc model that is designed to model the GaAs/AlAs system. Both rough and perfect interfaces are considered. The results are compared to experimental data from the literature. read less NOT USED (low confidence) C. Cousins and M. Heggie, “Elasticity of carbon allotropes. III. Hexagonal graphite: Review of data, previous calculations, and a fit to a modified anharmonic Keating model,” Physical Review B. 2003. link Times cited: 28 Abstract: The experimental data relating to the second- and third-orde… read moreAbstract: The experimental data relating to the second- and third-order elasticity and the zone-center optic modes of hexagonal graphite are reviewed and some amendments proposed. A modified Keating model involving three sets of interactions, one planar and two interlayer, has been developed. The harmonic parameters, four planar and seven interlayer, have been fitted by least-squares procedures to five second-order elastic constants, five zone-center optic-mode frequencies and two assumptions relating to internal strain. The anharmonic parameters comprise three planar and three interlayer ones. They have been fitted to the pressure derivatives of the five second-order constants and of three of the optic-mode frequencies. The full spectrum of inner elastic constants and internal strain tensors is given, the composition of the second- and third-order elastic constants is exposed, and the corresponding elastic compliances calculated. A pressure-induced phase transition is correctly predicted at around 16 GPa. read less NOT USED (low confidence) R. Komanduri, N. Chandrasekaran, and L. Raff, “Molecular dynamic simulations of uniaxial tension at nanoscale of semiconductor materials for micro-electro-mechanical systems (MEMS) applications,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2003. link Times cited: 48 NOT USED (low confidence) S. Erkoç, K. Leblebicioğlu, and U. Halici, “Application of Genetic Algorithms to Geometry Optimization of Microclusters: A Comparative Study of Empirical Potential Energy Functions for Silicon,” Materials and Manufacturing Processes. 2003. link Times cited: 14 Abstract: Evolutionary computation techniques (in particular, genetic … read moreAbstract: Evolutionary computation techniques (in particular, genetic algorithms) have been applied to optimize the structure of microclusters. Various empirical potential energy functions have been used to describe the interactions among the atoms in the clusters. A comparative study of silicon microclusters has been performed. read less NOT USED (low confidence) X. Feng, “MOLECULAR DYNAMICS SIMULATION OF THERMAL CONDUCTIVITY OF NANOSCALE THIN SILICON FILMS,” Microscale Thermophysical Engineering. 2003. link Times cited: 45 Abstract: Molecular dynamics simulations are performed to explore the … read moreAbstract: Molecular dynamics simulations are performed to explore the thermal conductivity in the cross-plane direction of single-crystal thin silicon films. The silicon crystal has diamond structure, and the Stillinger-Weber potential is adopted. The inhomogeneous nonequilibrium molecular dynamics (NEMD) scheme is applied to model heat conduction in thin films. At average temperature T = 500 K, which is lower than the Debye temperature ΘD = 645 K, the results show that in a film thickness range of about 2–32 nm, the calculated thermal conductivity decreases almost linearly as the film thickness is reduced, exhibiting a remarkable reduction as compared with the bulk experimental data. The phonon mean free path is estimated and the size effect on thermal conductivity is attributed to the reduction of phonon mean free path according to the kinetic theory. read less NOT USED (low confidence) A. Kubota, M. Caturla, S. Payne, T. D. Rubia, and J. Latkowski, “Modeling defect production in silica glass due to energetic recoils using molecular dynamics simulations,” Journal of Nuclear Materials. 2002. link Times cited: 13 NOT USED (low confidence) Z. J. Wang and E. Seebauer, “Extraordinary temperature amplification in ion-stimulated surface processes at low energies,” Physical Review B. 2002. link Times cited: 6 Abstract: Molecular dynamics simulations of low-energy noble-gas atoms… read moreAbstract: Molecular dynamics simulations of low-energy noble-gas atoms impacting Si and Ge surfaces reveal a new, unexpectedly strong trade-off between the energy threshold for point defect formation and substrate temperature. Nonuniformities in the net surface potential induced by thermal vibrations dramatically affect the locality of momentum transfer to the surface, thereby amplifying the effect of temperature by several orders of magnitude. This amplification may offer a new means for selecting specific elementary rate processes during plasma processing or ion-beam-assisted deposition. read less NOT USED (low confidence) S. Sastry, “Onset of slow dynamics in supercooled liquid silicon,” Physica A-statistical Mechanics and Its Applications. 2002. link Times cited: 5 NOT USED (low confidence) Y. Umeno, T. Kitamura, K. Date, M. Hayashi, and T. Iwasaki, “Optimization of interatomic potential for Si/SiO2 system based on force matching,” Computational Materials Science. 2002. link Times cited: 25 NOT USED (low confidence) W. Goddard, D. Brenner, S. Lyshevski, and G. Iafrate, “Contributions of Molecular Modeling to Nanometer-Scale Science and Technology.” 2002. link Times cited: 2 NOT USED (low confidence) J. Koga, H. Okumura, K. Nishio, T. Yamaguchi, and F. Yonezawa, “Simulational study of liquid germanium under pressure,” Journal of Non-crystalline Solids. 2002. link Times cited: 8 NOT USED (low confidence) A. Fantini, F. Phillipp, C. Kohler, J. Porsche, and F. Scholz, “Investigation of self-assembled InP-GaInP quantum dot stacks by transmission electron microscopy,” Journal of Crystal Growth. 2002. link Times cited: 10 NOT USED (low confidence) J. Feldman, “Calculations of the generalized dynamic structure factor for amorphous silicon,” Journal of Non-crystalline Solids. 2002. link Times cited: 3 NOT USED (low confidence) R. Garcia and R. Pérez, “Dynamic atomic force microscopy methods,” Surface Science Reports. 2002. link Times cited: 1786 NOT USED (low confidence) S. Hamaguchi and H. Ohta, “Surface molecular dynamics of Si/SiO2 reactive ion etching,” Vacuum. 2002. link Times cited: 10 NOT USED (low confidence) S. Dorfman, D. Ellis, K. C. Mundim, V. Liubich, and D. Fuks, “Many‐Body Ab Initio Potentials in Simulations of Grain Boundary Sliding and Decohesion in Metals,” Advanced Engineering Materials. 2002. link Times cited: 1 Abstract: A direct scheme for theoretical study of sliding and decohes… read moreAbstract: A direct scheme for theoretical study of sliding and decohesion properties of the grain boundaries (GB) in metals is presented here. This approach combines ab initio calculations and Monte Carlo (MC) simulations with non-empirical many-body (MB) potentials. The authors studied the propagation of the elastic field in the vicinity of the GB and show how the sliding or decohesion shifts influence the penetration of the elastic field inside the grain. read less NOT USED (low confidence) F. Finkemeier and W. Niessen, “Reply to ‘Comment on ‘Boson peak in amorphous silicon: A numerical study’ ,’” Physical Review B. 2002. link Times cited: 7 Abstract: Nakhmanson, Drabold, and Mousseau [Phys. Rev. B 66, 087201 (… read moreAbstract: Nakhmanson, Drabold, and Mousseau [Phys. Rev. B 66, 087201 (2002)], preceding paper criticized the model of the present authors [F. Finkemeier and W. von Niessen, Phys. Rev. B 63, 235204 (2001)] which was used for an explanation of the Boson peak in $a\ensuremath{-}\mathrm{Si}.$ NDM criticized the generation of the model and the potential used by us. The low-frequency vibrational density of states $g(\ensuremath{\omega})$ of $a\ensuremath{-}\mathrm{Si}$ are reinvestigated with the help of an improved structural model using the modified Stillinger-Weber potential. The previously described deviation from the Debye ${\ensuremath{\omega}}^{2}$ behavior is shown to be an artifact caused by an unrealistic high defect concentration. Nevertheless the improved model, which possesses a strongly decreased number of defects, still shows the existence of additional low-frequency modes compared to the crystal, which could be part of an explanation of the boson peak arising already in the harmonic approximation. read less NOT USED (low confidence) A.-ul Huda, O. Dutta, and A. Mookerjee, “Study of a Pair of Coupled Continuum Equations Modeling Surface Growth,” International Journal of Modern Physics B. 2002. link Times cited: 1 Abstract: In this communication we introduce a pair of coupled continu… read moreAbstract: In this communication we introduce a pair of coupled continuum equations to model overlayer growth with evaporation-accretion due to thermal or mechanical agitations of the substrate. We gain insight into the dynamics of growth via one-loop perturbative techniques. This allows us to analyze our numerical data. We conclude that there is a crossover behaviour from a roughening regime to a very long-time, large length scale smoothening regime. read less NOT USED (low confidence) J. Shen and P. A. Monson, “A molecular model of adsorption in a dilute semiflexible porous network,” Molecular Physics. 2002. link Times cited: 22 Abstract: A Monte Carlo simulation study has been made of adsorption a… read moreAbstract: A Monte Carlo simulation study has been made of adsorption and desorption of a gas in a semiflexible porous network with a porosity of over 95%, which is comparable with that of silica aerogels. Although dilute, the network has substantial effects on the properties of confined fluids. Network flexibility is shown to make a significant difference to both the adsorption/desorption isotherms and the fluid phase coexistence when compared with the case where the network is rigid. For one of the systems studied the solid volume changes by as much as 30% during desorption. This is qualitatively similar to an effect seen in nitrogen adsorption/desorption in some silica aerogels. read less NOT USED (low confidence) P. Keblinski, M. Bazant, R. Dash, and M. Treacy, “Thermodynamic behavior of a model covalent material described by the environment-dependent interatomic potential,” Physical Review B. 2002. link Times cited: 38 Abstract: Using molecular-dynamics simulations we study the thermodyna… read moreAbstract: Using molecular-dynamics simulations we study the thermodynamic behavior of a single-component covalent material described by the recently proposed environment-dependent interatomic potential (EDIP). The parametrization of EDIP for silicon exhibits a range of unusual properties typically found in more complex materials, such as the existence of two structurally distinct disordered phases, a density increase upon melting of the low-temperature amorphous phase, and negative thermal-expansion coefficients for both the crystal (at high temperatures) and the amorphous phase (at all temperatures). Structural differences between the two disordered phases also lead to a first-order transition between them, which suggests the existence of a second critical point, as is believed to exist for amorphous forms of frozen water. For EDIP-Si, however, the unusual behavior is associated not only with the open nature of tetrahedral bonding but also with a competition between fourfold (covalent) and fivefold (metallic) coordination. The unusual behavior of the model and its unique ability to simulate the liquid/amorphous transition on molecular-dynamics time scales make it a suitable prototype for fundamental studies of anomalous thermodynamics in disordered systems. read less NOT USED (low confidence) D. Graves and D. Humbird, “Surface chemistry associated with plasma etching processes,” Applied Surface Science. 2002. link Times cited: 55 NOT USED (low confidence) J. Robertson, “Diamond-like amorphous carbon,” Materials Science & Engineering R-reports. 2002. link Times cited: 5214 NOT USED (low confidence) A. Béré, J. Chen, P. Ruterana, A. Serra, and G. Nouet, “The atomic configurations of the a threading dislocation in GaN,” Computational Materials Science. 2002. link Times cited: 17 NOT USED (low confidence) N. Toyoda et al., “Secondary ion mass spectrometry with gas cluster ion beams,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2002. link Times cited: 62 NOT USED (low confidence) B. Laird, “Interfaces: Liquid–Solid.” 2002. link Times cited: 0 NOT USED (low confidence) N. Chaâbane, H. Vach, and G. H. Peslherbe, “Complex dynamics during the reactive scattering of Si+ (2P) and H2,” Journal of Non-crystalline Solids. 2002. link Times cited: 2 NOT USED (low confidence) U. Kaiser, J. Biskupek, D. Muller, K. Gärtner, and C. Schubert, “Properties of GeSi Nanocrystals Embedded in Hexagonal SiC,” Crystal Research and Technology. 2002. link Times cited: 14 Abstract: In this paper high-resolution electron microscopy investigat… read moreAbstract: In this paper high-resolution electron microscopy investigations and molecular dynamics simulations of GeSi nanocrystals buried in 4H-SiC are performed, showing that the experimentally observed shapes of the GeSi nanocrystals are strongly correlated with their orientational relationships. Measurements of the lattice spacing suggest that the nanocrystals are strained. Quantum confinement in selected nanocrystals has been detected using spatially-resolved electron energy loss spectroscopy performed in conjunction with atomic resolution annular dark-field scanning TEM. read less NOT USED (low confidence) M. Rouhani, H. Kassem, J. D. Torre, G. Landa, and D. Estève, “Kinetic Monte Carlo simulation of intermixing during semiconductor heteroepitaxy,” Applied Surface Science. 2002. link Times cited: 3 NOT USED (low confidence) M. Murty, “Sputtering: the material erosion tool,” Surface Science. 2002. link Times cited: 54 NOT USED (low confidence) N. Marks, “Modelling diamond-like carbon with the environment-dependent interaction potential,” Journal of Physics: Condensed Matter. 2002. link Times cited: 97 Abstract: The environment-dependent interaction potential is a transfe… read moreAbstract: The environment-dependent interaction potential is a transferable empirical potential for carbon which is well suited for studying disordered systems. Ab initio data are used to motivate and parametrize the functional form, which includes environment-dependence in the pair and triple terms, and a generalized aspherical coordination describing dihedral rotation and non-bonded π-repulsion. Simulations of liquid carbon compare very favourably with Car-Parrinello calculations, while amorphous networks generated by liquid quench have properties superior to Tersoff, Brenner and orthogonal tight-binding calculations. The efficiency of the method enables the first simulations of tetrahedral amorphous carbon by deposition, and a new model for the formation of diamond-like bonding is presented. read less NOT USED (low confidence) J. Kioseoglou, G. Dimitrakopulos, H. Polatoglou, L. Lymperakis, G. Nouet, and P. Komninou, “Atomic-scale models of interactions between inversion domain boundaries and intrinsic basal stacking faults in GaN,” Diamond and Related Materials. 2002. link Times cited: 7 NOT USED (low confidence) V. M. Glazov and L. Pavlova, “The structural peculiarities of the CdTe melt based on the results of the molecular dynamics,” Scandinavian Journal of Metallurgy. 2002. link Times cited: 2 Abstract: The characteristics of the structure of molten cadmium tellu… read moreAbstract: The characteristics of the structure of molten cadmium telluride were calculated using the method of molecular dynamics with the use of a Stillinger-Weber-type potential. The potential parameters adopted in Monte Carlo calculations of the structure of cadmium telluride were used. The molecular dynamics calculations were performed for an NVT ensemble at 1373 K. The results were compared with the neutron diffraction data. The Still-inger-Weber potential was shown to give an insufficiently accurate description of interparticle interactions in cadmium telluride melts. Its reparametrization was required to improve agreement with experiment. read less NOT USED (low confidence) H. Vach, N. Chaâbane, and G. H. Peslherbe, “Direct versus complex-mediated processes for Si+(2P)+H2 reactive scattering,” Chemical Physics Letters. 2002. link Times cited: 4 NOT USED (low confidence) M. Koster and H. Urbassek, “Atomistic simulation of stress effects in a-Si due to low-energy Si impact,” Surface Science. 2002. link Times cited: 12 NOT USED (low confidence) N. Mousseau, G. Barkema, and S. Nakhmanson, “Recent developments in the study of continuous random networks,” Philosophical Magazine B. 2002. link Times cited: 11 Abstract: We report on recent progress in the development of new techn… read moreAbstract: We report on recent progress in the development of new techniques to generate high-quality models of continuous random networks, which are used as models for elemental and binary tetrahedral semiconductors such as amorphous Si and amorphous GaAs. The availability of such models has allowed us to look at a number of outstanding issues regarding their electronic properties, the fundamental role of defects and dynamics. We describe briefly our modifications made to the Wooten-Winer-Weaire bond-switching algorithm, allowing us to produce low-strain amorphous and paracrystalline networks of up to 10000 atoms. Then some of the structural and electronic properties of these models are presented. We also discuss briefly some recent results on the recrystallization of amorphous networks. read less NOT USED (low confidence) R. Komanduri and L. Raff, “A review on the molecular dynamics simulation of machining at the atomic scale,” Proceedings of the Institution of Mechanical Engineers, Part B: Journal of Engineering Manufacture. 2001. link Times cited: 138 Abstract: Molecular dynamics (MD) simulation, like other simulation te… read moreAbstract: Molecular dynamics (MD) simulation, like other simulation techniques, such as the finite difference method (FDM), or the finite element method (FEM) can play a significant role in addressing a number of machining problems at the atomic scale. It may be noted that atomic simulations are providing new data and exciting insights into various manufacturing processes and tribological phenomenon that cannot be obtained readily in any other way—theory, or experiment. In this paper, the principles of MD simulation, relative advantages and current limitations, and its application to a range of machining problems are reviewed. Machining problems addressed include: (a) the mechanics of nanometric cutting of non-ferrous materials, such as copper and aluminium; (b) the mechanics of nanometric cutting of semiconductor materials, such as silicon and germanium; (c) the effect of various process parameters, including rake angle, edge radius and depth of cut on cutting and thrust forces, specific force ratio, energy, and subsurface deformation of the machined surface; the objective is the development of a process that is more efficient and effective in minimizing the surface or subsurface damage; (d) modelling of the exit failures in various work materials which cause burr formation in machining; (e) simulation of work materials with known defect structure, such as voids, grain boundaries, second phase particles; shape, size and density of these defects can be varied using MD simulation as well as statistical mechanical or Monte Carlo approaches; (f) nanometric cutting of nanostructures; (g) investigation of the nanometric cutting of work materials of known crystallographic orientation; (h) relative hardness of the tool material with respect to the work material in cutting; a range of hardness values from the tool being softer than the work material to the tool being several times harder than the work material is considered; and (i) the tool wear in nanometric cutting of iron with a diamond tool. The nature of deformation in the work material ahead of the tool, subsurface deformation, nature of variation of the forces and their ratio, and specific energy with cutting conditions are investigated by this method. read less NOT USED (low confidence) A. Lamzatouar, M. E. Kajbaji, A. Charaï, M. Benaissa, O. H. Duparc, and J. Thibault, “The atomic structure of Σ=33144〈011〉 (θ=20.05°) tilt grain boundary in germanium,” Scripta Materialia. 2001. link Times cited: 5 NOT USED (low confidence) G. Smith, E. Tadmor, N. Bernstein, and E. Kaxiras, “Multiscale simulations of silicon nanoindentation,” Acta Materialia. 2001. link Times cited: 106 NOT USED (low confidence) J. Chen, G. Nouet, and P. Ruterana, “Energetic calculation of coincidence grain boundaries with a modified Stillinger-Weber potential,” Physica Status Solidi B-basic Solid State Physics. 2001. link Times cited: 1 Abstract: Potential energy of two coincidence grain boundaries, Σ = 7 … read moreAbstract: Potential energy of two coincidence grain boundaries, Σ = 7 and 19, was calculated with a Stillinger-Weber potential previously adapted to wurtzite GaN in order to take into account the Ga-Ga and N-N wrong bonds. Their atomic structures, determined before by high resolution electron microscopy, are based on 5/7 and 8 atom ring structural units. By using periodical boundary conditions, it is shown that the high angle grain boundary Σ = 7 (Θ = 21°79/[0001]) has always a smaller energy than Σ = 19 (Θ = 13°17/[0001]). read less NOT USED (low confidence) H. Teichler, “Structural dynamics on the μs scale in molecular-dynamics simulated, deeply undercooled, glass-forming Ni0.5Zr0.5,” Journal of Non-crystalline Solids. 2001. link Times cited: 58 NOT USED (low confidence) I. Golovnev, T. Basova, N. Aleksandrova, and I. Igumenov, “Numerical Investigations of the Interaction of Copper Phthalocyanine Molecules with Silicon Surface,” Molecular Crystals and Liquid Crystals Science and Technology. Section A. Molecular Crystals and Liquid Crystals. 2001. link Times cited: 3 Abstract: The theoretical investigation of the scattering of copper ph… read moreAbstract: The theoretical investigation of the scattering of copper phthalocyanine molecules in the surface field taking account of the vibration-rotational interaction was performed by molecular dynamics method, its propagator modification of the second order of accuracy. A software complex was developed to simulate the interaction of gas molecule assembly with a solid surface at a given temperature and gas volume density. Comparative analysis of molecule scattering was performed for the continuous and crystal silicon substrate models. The following elementary processes were investigated: 1) the scattering of a molecule on Si surface; 2) the collision of two molecules in gas phase; 3) the collision of two molecules one of which is bound on the Si surface. read less NOT USED (low confidence) X. P. Xie, M. Liang, Z. M. Choo, and S. Li, “A COMPARATIVE SIMULATION STUDY OF SILICON (001) SURFACE RECONSTRUCTION USING DIFFERENT INTERATOMIC POTENTIALS,” Surface Review and Letters. 2001. link Times cited: 3 Abstract: We have performed a comparative study of Si(001) surface rec… read moreAbstract: We have performed a comparative study of Si(001) surface reconstruction employing molecular dynamics simulation using the interatomic potentials of Stillinger–Weber, Tersoff and Bazant–Kaxiras. Simulations were carried out for temperatures at 300 K and 1000 K using each of these three potentials. At 300 K, the three potentials were found to generate surface features comprising mainly the simple (2 × 1) reconstruction. At 1000 K, more complex reconstruction similar to the p(2 × 2) and c(2 × 2) patterns was observed on the surfaces of Stillinger–Weber and Tersoff crystals while the surface generated on Bazant–Kaxiras crystal is characterized by disorderliness with no identifiable pattern of reconstruction. read less NOT USED (low confidence) J. Chelikowsky, J. Derby, V. Godlevsky, M. Jain, and J. Raty, “Ab initio simulations of liquid semiconductors using the pseudopotential-density functional method,” Journal of Physics: Condensed Matter. 2001. link Times cited: 13 Abstract: One of the most difficult problems in condensed matter physi… read moreAbstract: One of the most difficult problems in condensed matter physics is describing the microscopic nature of the liquid state. Owing to the dynamical nature of the liquid state, it is not possible to discuss a particular microscopic structure; only ensemble averages can be specified. Such averages can be performed via well crafted molecular dynamics simulations: the length of the simulation, the size of the ensemble and the nature of the interatomic forces must all be carefully analysed. Historically, a problematic issue in doing such simulations is that of how to describe the interatomic forces in the liquid state. This matter is especially challenging for the melt of semiconductors, such as silicon or gallium arsenide, where the chemical bond contains a strong covalent component. It is difficult to use pairwise interatomic potentials in such cases. Although many-body potentials can be utilized for simulations of these materials, one must map quantum phenomena such as hybridization onto classical interatomic potentials. This mapping is complex and difficult. In this review, we illustrate how one can avoid this problem by utilizing quantum forces to simulate liquids. Our focus is on the pseudopotential-density functional method. Within the pseudopotential method, only the valence electrons are explicitly treated and within the density functional theory, exchange and correlation terms are mapped onto an effective one-electron potential. These two approximations allow one to extract quantum forces at every time step of the simulation. The pseudopotential-density functional method is highly accurate and well tested for semiconductors in the solid state, but has only recently been applied to liquids. In this review, we illustrate this approach for a number of semiconducting liquids such as liquid Si, Ge, GaAs, CdTe and GeTe. For these liquids, we will present results for the microstructure, the dynamical properties such as the diffusion constants and the electronic properties such as the conductivity. read less NOT USED (low confidence) A. Serra, “Atomic computer simulation: Large scale calculations of defect properties by empirical potentials,” Physica Status Solidi B-basic Solid State Physics. 2001. link Times cited: 2 Abstract: This paper is aimed at introducing computer simulation of ex… read moreAbstract: This paper is aimed at introducing computer simulation of extended defects in crystalline materials by means of empirical potentials. In this context we understand by large scale calculations those related to a number of atoms from 10 3 to 10 6 and/or a time scale of few nanoseconds (10 2 -10 4 ps) for the evolution of the processes studied. read less NOT USED (low confidence) K. Böhm, R. Stracke, P. Muehlig, and E. Unger, “Motor protein-driven unidirectional transport of micrometer-sized cargoes across isopolar microtubule arrays,” Nanotechnology. 2001. link Times cited: 144 Abstract: Conventional kinesin is a motor protein which translocates o… read moreAbstract: Conventional kinesin is a motor protein which translocates organelles from cell centre to cell periphery along specialized filamentous tracks, called microtubules. The direction of translocation is determined by microtubule polarity. This process of biological force generation can be simulated outside cells with kinesin-coated particles actively moving along immobilized microtubules. The in vitro approaches of kinesin-mediated transport described so far had the disadvantage that concerning their polarity the microtubules were randomly distributed resulting in random transport direction. The present paper demonstrates the unidirectional translocation of kinesin-coated cargoes across arrays of microtubules aligned not only in a geometrically parallel but also in an isopolar fashion. As cargo, glass, gold, and polystyrene beads with diameters between 1 and 10 µm were used. Independent of material and size, these beads were observed to move unidirectionally with average velocities of 0.3-1.0 µm s-1 over distances up to 2.2 mm. Moreover, the isopolar microtubule arrays even enabled the transport of large flat glass particles with an area of up to 24 µm×12 µm and 2-5 µm thickness which obviously contacted more than one microtubule. The controlling transport direction is considered to be an essential step for future developments of motor protein-based microdevices working in nanometre steps. read less NOT USED (low confidence) J. Wang, G. Wang, F. Ding, H. Lee, W. Shen, and J. Zhao, “Structural transition of Si clusters and their thermodynamics,” Chemical Physics Letters. 2001. link Times cited: 44 NOT USED (low confidence) R. Chakarova and I. Pázsit, “Evolution of ion induced point defects in silicon,” Radiation Physics and Chemistry. 2001. link Times cited: 0 NOT USED (low confidence) F. Finkemeier and W. Niessen, “Boson peak in amorphous silicon: A numerical study,” Physical Review B. 2001. link Times cited: 13 Abstract: The low-frequency part of the phonon spectrum of a-Si is inv… read moreAbstract: The low-frequency part of the phonon spectrum of a-Si is investigated for a microscopic model of this amorphous solid even for frequencies below 50 cm{minus}1. This requires system sizes up to 64000 atoms. The variation of a model parameter allows us to generate structures with different degrees of disorder. The vibrational properties are calculated in a harmonic approximation to the Stillinger-Weber potential. The less disordered of our models already show an enhancement of the low-frequency vibrational density of states g({omega}) (VDOS) compared to the crystal. For the more disordered structures additionally a peak in g({omega})/{omega}{sup 2} versus {omega} is observed. The deviation from the Debye {omega}{sup 2} behavior is caused by at least two effects: a shift of the crystalline transverse acoustic peak toward lower frequency and a broadening of the same. Consequently the occurrence of the boson peak in the Raman spectrum of a-Si can be explained already in the harmonic approximation (at least in part) by a complex of phenomena of the low-frequency VDOS. read less NOT USED (low confidence) J. Chen, P. Ruterana, and G. Nouet, “Multiple atomic configurations of the a edge threading dislocation in GaN,” Materials Science and Engineering B-advanced Functional Solid-state Materials. 2001. link Times cited: 24 NOT USED (low confidence) M. Mazzarolo, L. Colombo, G. Lulli, and E. Albertazzi, “Low-energy recoils in crystalline silicon: Quantum simulations,” Physical Review B. 2001. link Times cited: 19 NOT USED (low confidence) R. Vink, G. Barkema, W. F. Weg, and N. Mousseau, “Fitting the Stillinger–Weber potential to amorphous silicon,” Journal of Non-crystalline Solids. 2001. link Times cited: 137 NOT USED (low confidence) H. Hug et al., “Subatomic features in atomic force microscopy images.,” Science. 2001. link Times cited: 25 Abstract: Recently, Giessibl et al . ([1][1]) reported a distinct subs… read moreAbstract: Recently, Giessibl et al . ([1][1]) reported a distinct substructure in atomic force microscopy (AFM) images of individual adatoms on the Si(111)-(7×7) surface. A cross section along the fast scanning direction showed two peaks per adatom, which were interpreted as images of two unsaturated read less NOT USED (low confidence) Y. Ma, “Cluster emission and phase transition behaviours in nuclear disassembly,” Journal of Physics G. 2001. link Times cited: 13 Abstract: The features of the emissions of light particles (LP), charg… read moreAbstract: The features of the emissions of light particles (LP), charged particles (CP), intermediate mass fragments (IMF) and the largest fragment (MAX) are investigated for Xe-129 as functions of temperature and 'freeze-out' density in the frameworks of the isospin-dependent lattice gas model and the classical molecular dynamics model. Definite turning points for the slopes of average multiplicity of LP, CP and IMF, and of the mean mass of the largest fragment (A(max)) are shown around a liquid-gas phase transition temperature and while the lar-est variances of the distributions of LP, CP, IMF and MAX appear there, It indicates that the cluster emission rate can be taken as a probe of nuclear liquid-gas phase transition. Furthermore, the largest fluctuation is simultaneously accompanied at the point of the phase transition as can be noted by investigating both the variances of their cluster multiplicity or mass distributions and the Campi scatter plots within the lattice gas model and the molecular dynamics model, which is consistent with the result of the traditional thermodynamical theory when a phase transition occurs. read less NOT USED (low confidence) Y. Limoge, “Numerical simulations studies of glasses,” Comptes Rendus De L Academie Des Sciences Serie Iv Physique Astrophysique. 2001. link Times cited: 6 NOT USED (low confidence) J. Wang, J. Zhao, F. Ding, W. Shen, H. Lee, and G. Wang, “Thermal properties of medium-sized Ge clusters,” Solid State Communications. 2001. link Times cited: 26 NOT USED (low confidence) M. Itoh, “Atomic-scale homoepitaxial growth simulations of reconstructed III–V surfaces,” Progress in Surface Science. 2001. link Times cited: 52 NOT USED (low confidence) A. Natori, H. Harada, N.-J. Wu, and H. Yasunaga, “Strain effect on surface melting of Si(1 1 1),” Applied Surface Science. 2001. link Times cited: 1 NOT USED (low confidence) E. Ziemniak and C. Jung, “A model for monolayer deposition with interacting particles,” Chaos Solitons & Fractals. 2001. link Times cited: 0 NOT USED (low confidence) P. Lorazo, L. J. Lewis, and M. Meunier, “Picosecond pulsed laser ablation of silicon : a molecular-dynamics study,” Applied Surface Science. 2000. link Times cited: 18 NOT USED (low confidence) F. F. Abraham, “MAADLY Spanning the Length Scales in Dynamic Fracture,” Cmes-computer Modeling in Engineering & Sciences. 2000. link Times cited: 10 Abstract: A challenging paradigm in the computational sciences is the … read moreAbstract: A challenging paradigm in the computational sciences is the coupling of the continuum, the atomistic and the quantum descriptions of matter for a unified dynamic treatment of a single physical problem. We described the achievement of such a goal. We have spanned the length scales in a concerted simulation comprising the finite-element method, classical molecular dynamics, quantum tight-binding dynamics and seamless bridges between these different physical descriptions. We illustrate and validate the methodology for crack propagation in silicon. read less NOT USED (low confidence) M. Dornheim and H. Teichler, “Atomistic Modeling of Misfit Dislocation Network Variants for Ge/Si(111) Interfaces,” Physica Status Solidi B-basic Solid State Physics. 2000. link Times cited: 6 Abstract: For Ge layers on Si(111) surfaces the energy of coherent and… read moreAbstract: For Ge layers on Si(111) surfaces the energy of coherent and semicoherent interfaces with misfit dislocations is numerically analyzed by use of the atomistic anharmonic bond charge model and the Stillinger-Weber approach. For the semicoherent interface, three configurations are considered, differing in the dissociation of the misfit dislocations into Shockley partials and in the partial dislocation patterns. The calculations yield a slight energetic preference of the so-called B variant while the literature reports observation of all three configurations. The deduced critical thickness for the coherent interface is in fair accordance with experimental estimates. read less NOT USED (low confidence) L. Brambilla, L. Colombo, V. Rosato, and F. Cleri, “Solid–liquid interface velocity and diffusivity in laser-melt amorphous silicon,” Applied Physics Letters. 2000. link Times cited: 27 Abstract: We studied the microscopic kinetics of the amorphous-liquid … read moreAbstract: We studied the microscopic kinetics of the amorphous-liquid interface in supercooled laser-melt silicon by means of molecular dynamics computer simulations. The interface velocity was obtained as a function of temperature by direct simulation of the interface motion in an amorphous-liquid model system. The temperature dependence of the kinetic prefactor was extracted from the interface velocity function and compared to the values of self-diffusivity obtained from independent molecular dynamics simulations of bulk amorphous Si. The kinetic prefactor for interfacial diffusion shows a distinctly non-Arrhenius behavior which is attributed to Fulcher–Vogel kinetics in the supercooled liquid. read less NOT USED (low confidence) S. Volz, J. Saulnier, G. Chen, and P. Beauchamp, “Computation of thermal conductivity of Si/Ge superlattices by molecular dynamics techniques,” Microelectronics Journal. 2000. link Times cited: 114 NOT USED (low confidence) R. E. Miller and V. Shenoy, “SIZE-DEPENDENT ELASTIC PROPERTIES OF NANOSIZED STRUCTURAL ELEMENTS,” Nanotechnology. 2000. link Times cited: 1762 Abstract: Effective stiffness properties (D) of nanosized structural e… read moreAbstract: Effective stiffness properties (D) of nanosized structural elements such as plates and beams differ from those predicted by standard continuum mechanics (Dc). These differences (D-Dc)/Dc depend on the size of the structural element. A simple model is constructed to predict this size dependence of the effective properties. The important length scale in the problem is identified to be the ratio of the surface elastic modulus to the elastic modulus of the bulk. In general, the non-dimensional difference in the elastic properties from continuum predictions (D-Dc)/Dc is found to scale as αS/Eh, where α is a constant which depends on the geometry of the structural element considered, S is a surface elastic constant, E is a bulk elastic modulus and h a length defining the size of the structural element. Thus, the quantity S/E is identified as a material length scale for elasticity of nanosized structures. The model is compared with direct atomistic simulations of nanoscale structures using the embedded atom method for FCC Al and the Stillinger-Weber model of Si. Excellent agreement between the simulations and the model is found. read less NOT USED (low confidence) K. Nordlund, J. Nord, J. Frantz, and J. Keinonen, “Strain-induced Kirkendall mixing at semiconductor interfaces,” Computational Materials Science. 2000. link Times cited: 48 NOT USED (low confidence) F. F. Abraham, “DYNAMICALLY SPANNING THE LENGTH SCALES FROM THE QUANTUM TO THE CONTINUUM,” International Journal of Modern Physics C. 2000. link Times cited: 20 Abstract: A challenging paradigm in computational sciences is the coup… read moreAbstract: A challenging paradigm in computational sciences is the coupling of the continuum, the atomistic, and the quantum descriptions of matter for a unified dynamic treatment of a single physical problem. We described the recent achievement of such a goal. We have spanned the length scales in a concerted simulation comprising the finite-element method, classical molecular dynamics, quantum tight-binding dynamics and seamless bridges between these different physical descriptions. We illustrate and validate the methodology for rapid crack propagation in silicon. read less NOT USED (low confidence) T. Kawabe and A. Natori, “Ordering dynamics of anisotropic missing dimer clusters on Si(001) surfaces,” Surface Science. 2000. link Times cited: 1 NOT USED (low confidence) C. Angell and C. T. Moyniha, “Ideal and cooperative bond-lattice representations of excitations in glass-forming liquids: Excitation profiles, fragilities, and phase transitions,” Metallurgical and Materials Transactions B. 2000. link Times cited: 35 NOT USED (low confidence) C. Herrero, “Isotopic effect on the lattice constant of silicon a quantum Monte Carlo simulation,” Physica Status Solidi B-basic Solid State Physics. 2000. link Times cited: 8 Abstract: Path-integral Monte Carlo simulations in the isothermal-isob… read moreAbstract: Path-integral Monte Carlo simulations in the isothermal-isobaric ensemble have been carried out to study the dependence of the lattice parameter of silicon upon the isotopic mass. This computational method allows a quantitative and nonperturbative study of such anharmonic effect. Atomic nuclei were treated as quantum particles interacting via a Stillinger-Weber-type potential. At 300 K, the isotopic effect leads to a decrease of 0.8 and 1.6 x 10 -4 A in the lattice parameter of isotopically pure crystals of 29 Si and 30 Si, respectively, as compared to the crystal with natural isotopic composition. At low temperatures (T 50 K), this isotopic effect is 50% larger than at room temperature. Results of the quantum simulations are compared with those derived from classical Monte Carlo simulations (infinite-mass limit) and with results of quasiharmonic approximations. read less NOT USED (low confidence) B. Lebouvier, A. Hairie, G. Nouet, and E. Paumier, “Analysis of Distortions in 110 Tilt Silicon Bicrystals,” Physica Status Solidi B-basic Solid State Physics. 2000. link Times cited: 0 Abstract: The empirical potentials used for defect simulation in silic… read moreAbstract: The empirical potentials used for defect simulation in silicon are fitted on elastic or phonon properties. Usually they are not able to take into account all the distortions present in a defected material. On the basis of the potential proposed by Vanderbilt, Taole and Narasimhan a method is presented to separate the contribution of distortions linked to elastic properties from the contribution of distortions linked to phonon properties. The method is applied to grain boundaries in silicon simulated by potentials in the harmonic approximation. The phonon contribution is found slightly predominant with respect to the elastic one. read less NOT USED (low confidence) F. Giessibl, S. Hembacher, H. Bielefeldt, and J. Mannhart, “Subatomic Features on the Silicon (111)-(7x7) Surface Observed by Atomic Force Microscopy.,” Science. 2000. link Times cited: 316 Abstract: The atomic force microscope images surfaces by sensing the f… read moreAbstract: The atomic force microscope images surfaces by sensing the forces between a sharp tip and a sample. If the tip-sample interaction is dominated by short-range forces due to the formation of covalent bonds, the image of an individual atom should reflect the angular symmetry of the interaction. Here, we report on a distinct substructure in the images of individual adatoms on silicon (111)-(7x7), two crescents with a spherical envelope. The crescents are interpreted as images of two atomic orbitals of the front atom of the tip. Key for the observation of these subatomic features is a force-detection scheme with superior noise performance and enhanced sensitivity to short-range forces. read less NOT USED (low confidence) T. Sinno, E. Dornberger, W. Ammon, R. A. Brown, and F. Dupret, “Defect engineering of Czochralski single-crystal silicon,” Materials Science & Engineering R-reports. 2000. link Times cited: 112 NOT USED (low confidence) C. Herrero, “Path-integral Monte Carlo study of amorphous silicon,” Journal of Non-crystalline Solids. 2000. link Times cited: 8 NOT USED (low confidence) K. Kakimoto, T. Umehara, and H. Ozoe, “Molecular dynamics analysis of point defects in silicon near solid–liquid interface,” Applied Surface Science. 2000. link Times cited: 2 NOT USED (low confidence) Aı̈choune N., V. Potin, P. Ruterana, A. Hairie, G. Nouet, and E. Paumier, “An empirical potential for the calculation of the atomic structure of extended defects in wurtzite GaN,” Computational Materials Science. 2000. link Times cited: 82 NOT USED (low confidence) M. Mäki-Jaskari, K. Kaski, and A. Kuronen, “Simulations of crack initiation in silicon,” Computational Materials Science. 2000. link Times cited: 6 NOT USED (low confidence) C. Tzoumanekas and P. Kelires, “Segregation, clustering, and suppression of phase separation in amorphous silicon–germanium alloys,” Journal of Non-crystalline Solids. 2000. link Times cited: 10 NOT USED (low confidence) C. Mathioudakis and P. Kelires, “Softening of elastic moduli of amorphous semiconductors,” Journal of Non-crystalline Solids. 2000. link Times cited: 17 NOT USED (low confidence) G. Subramanian, K. Jones, M. Law, M. Caturla, S. Theiss, and T. D. Rubia, “Relative Stability of Silicon Self-Interstitial Defects,” MRS Proceedings. 2000. link Times cited: 3 Abstract: {l_brace}311{r_brace} defects and dislocation loops are form… read moreAbstract: {l_brace}311{r_brace} defects and dislocation loops are formed after ion-implantation and annealing of a silicon wafer. Recent Transmission Electron Microscopy studies by Li and Jones have shown that sub-threshold dislocation loops nucleate from {l_brace}311{r_brace} defects. In our study, the conjugate gradient method with the Stillinger Weber potential is used to relax different configurations such as {l_brace}311{r_brace} defects with a maximum of five chains and perfect dislocation loops. From the formation energies thus obtained we find that there is an optimal width for each length of the {l_brace}311{r_brace} defects. Moreover the relative stability of {l_brace}311{r_brace}s and loops is studied as a function of defect size. We observe that at very small sizes the perfect loops are more stable than the {l_brace}311{r_brace}s. This may provide an explanation for the experimental observation by Robertson et al that, in an annealing study of end of range damage of amorphized samples, 45% of the loops had nucleated in the first 10 minutes of anneal. We propose that homogeneous nucleation, as against unfaulting of the {l_brace}311{r_brace}s, could be the source of these loops. read less NOT USED (low confidence) R. Rudd, “Coupling of length scales in MEMS modeling: the atomic limit of finite elements,” Design, Test, Integration, and Packaging of MEMS/MOEMS. 2000. link Times cited: 3 Abstract: We discuss concurrent multiscale simulations of the dynamic … read moreAbstract: We discuss concurrent multiscale simulations of the dynamic and temperature-dependent behavior of sub-micron MEMS, especially micro-resonators. The coupling of length scales methodology we have developed employs an atomistic description of small but key regions of the device, consisting of millions of atoms, coupled concurrently to a finite element model of the periphery. This novel technique accurately models the behavior of the mechanical components of MEMS down to the atomic scales. This paper addresses general issues involved in this kind of multiscale simulation, with a particular emphasis on how finite elements can be extended to ensure a reliable model as the mesh spacing is refined to the atomic scale. We discuss how the coupling of length scales technique has been sued to identify atomistic effects in sub-micron resonators. read less NOT USED (low confidence) Pérez-Martı́n A., J. Domínguez-Vázquez, and Jiménez-Rodrı́guez J. J., “A MD study of low energy boron bombardment on silicon.,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2000. link Times cited: 11 NOT USED (low confidence) H. Fang, X. Fu, S. Dyrting, K. Szeto, and P. Sheng, “Microscopic description of double-well potential in tetrahedrally bonded amorphous semiconductors,” Physica B-condensed Matter. 2000. link Times cited: 1 NOT USED (low confidence) T. Seki, T. Aoki, J. Matsuo, and I. Yamada, “STM observation of surface vacancies created by ion impact,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2000. link Times cited: 12 NOT USED (low confidence) P. Lorazo, L. J. Lewis, and M. Meunier, “Molecular-dynamics simulations of picosecond pulsed laser ablation and desorption of silicon,” Photonics West - Lasers and Applications in Science and Engineering. 2000. link Times cited: 8 Abstract: Molecular-dynamics simulations are used to investigate singl… read moreAbstract: Molecular-dynamics simulations are used to investigate single- shot pulsed laser ablation and desorption of crystalline silicon. The motion of approximately 32000 atoms, contained in a 5 X 5 X 27 nm3 surface rectangular box irradiated by a single 308 nm, 10 ps, Gaussian laser pulse is followed on the picosecond time scale. Because melting and, possibly, ablation or desorption of the target following absorption of the laser pulse are described within the thermal annealing model, care is taken not to exceed carrier densities of approximately 1022 cm-3. More precisely, the interaction of photons with the target is thought to cause the generation of a dense gas of hot electrons and holes which thermalizes, at first, on a time scale of a few tens of femtoseconds through carrier-carrier scattering. These hot photocarriers then transfer their kinetic energy to the lattice by means of carrier-phonon interactions characterized by a very fast initial cooling rate. The result is the creation, above a characteristic threshold energy, of a plume containing single atoms and clusters leaving the target with high axial velocities. Preliminary results about the melting fluence threshold and mechanisms underlying ablation are presented. Carrier diffusion is found to be an essential mechanism for relaxation and is presented as a possible cause of subsurface boiling. read less NOT USED (low confidence) K. Kakimoto, T. Umehara, and H. Ozoe, “Molecular dynamics analysis on diffusion of point defects,” Journal of Crystal Growth. 2000. link Times cited: 7 NOT USED (low confidence) Y. Saito, N. Sasaki, H. Moriya, A. Kagatsume, and S. Noro, “Parameter Optimization of Tersoff Interatomic Potentials Using a Genetic Algorithm,” Jsme International Journal Series A-solid Mechanics and Material Engineering. 2000. link Times cited: 10 Abstract: A method that gives the parameters of advanced Tersoff inter… read moreAbstract: A method that gives the parameters of advanced Tersoff interatomic potentials for describing nonequilibrium atomic structures has been developed. This method uses a genetic algorithm to optimize the Tersoff potential parameters fitted to first-principles-calculated cohesive energies of various carbon systems, including bulk systems with atomic defects and amorphous, surface, or cluster systems under stress. These optimized parameters converge towards a set of Tersoff potential parameters that well describes not only crystals but also amorphous systems. read less NOT USED (low confidence) B. Weber, D. Stock, and K. Gärtner, “Defect-related growth processes at an amorphous/crystalline interface : a molecular dynamics study,” Materials Science and Engineering B-advanced Functional Solid-state Materials. 2000. link Times cited: 12 NOT USED (low confidence) S. Jiang and J. Belak, “Chapter 15 - Molecular Dynamics of Thin Films under Shear,” Theoretical and Computational Chemistry. 1999. link Times cited: 1 NOT USED (low confidence) C. Jo and K. Lee, “Ionization potentials and cohesive energies of silicon clusters from the semi-empirical total energy tight binding method,” Physics Letters A. 1999. link Times cited: 6 NOT USED (low confidence) M. Zachariah and M. Carrier, “Molecular Dynamics Computation of Gas-Phase Nanoparticle Sintering: A Comparison with Phenomenological Models,” Journal of Aerosol Science. 1999. link Times cited: 135 NOT USED (low confidence) M. Sahlaoui, M. Rouhani, D. Estève, and A. Ayadi, “Strained semiconductors structures: simulation of the thin films heteroepitaxial growth,” Applied Surface Science. 1999. link Times cited: 2 NOT USED (low confidence) T. Suzuki, H. Minoda, Y. Tanishiro, and K. Yagi, “TED analysis of the Si(113) surface structure,” Surface Science. 1999. link Times cited: 4 NOT USED (low confidence) A. Natori and H. Harada, “Surface melting of vicinal Si(111) surfaces,” Surface Science. 1999. link Times cited: 5 NOT USED (low confidence) S. Myers and D. Follstaedt, “FORCES BETWEEN CAVITIES AND DISLOCATIONS AND THEIR INFLUENCE ON SEMICONDUCTOR MICROSTRUCTURES,” Journal of Applied Physics. 1999. link Times cited: 16 Abstract: An approximate continuum method for computing the energy of … read moreAbstract: An approximate continuum method for computing the energy of interaction between cavities and strain fields in complex configurations is described and tested by comparison with results for simple, exactly solvable cases. The method is then used to examine semiquantitatively the effective forces between cavities and screw and edge dislocations, taking into account the effects of surface tension and pressurized gas within the cavity. The discussion encompasses not only local interactions involving individual cavities, but also the combined forces acting upon dislocations in the vicinity of multiple cavities and simultaneously within range of external-surface image forces. The results are used to interpret a range of observed microstructures in semiconductors and to assess the possible exploitation of cavity–dislocation binding for dislocation control in Si–Ge heteroepitaxial structures. read less NOT USED (low confidence) A. Natori and T. Kawabe, “Stability of anisotropic missing dimer clusters on Si(001) surfaces,” Surface Science. 1999. link Times cited: 0 NOT USED (low confidence) T. D. Rubia, M. Caturla, E. Alonso, N. Soneda, and M. Johnson, “The primary damage state and its evolution over multiple length and time scales,” Radiation Effects and Defects in Solids. 1999. link Times cited: 12 Abstract: During his long and illustrious career, Professor Kiritani m… read moreAbstract: During his long and illustrious career, Professor Kiritani made many of the most significant and revealing observations regarding the nature of the primary damage state and the fate of the produced defects in irradiated metals and semiconductors. We present a review of recent results of molecular dynamics (MD) and kinetic Monte Carlo (KMC) simulations of defect production and annealing in irradiated metals and semiconductors. The MD simulations describe the primary damage state in two prototypical elemental metals and in one-elemental semiconductor, namely Fe, Au, and Si. These materials were all thoroughly investigated by Prof. Kiritani and his colleagues using neutron irradiation followed by TEM observation, and here we attempt to provide some further understanding of the experimental observations by using atomic-scale computer simulation tools. We describe the production of interstitial and vacancy clusters in the cascades and highlight the differences among the various materials. In particula... read less NOT USED (low confidence) B. W. Roberts, W. Luo, K. A. Johnson, and P. Clancy, “An order(N) tight-binding molecular dynamics study of intrinsic defect diffusion in silicon,” Chemical Engineering Journal. 1999. link Times cited: 8 NOT USED (low confidence) H. Cox, R. Johnston, and J. Murrell, “Empirical Potentials for Modeling Solids, Surfaces, and Clusters,” IEEE Journal of Solid-state Circuits. 1999. link Times cited: 48 Abstract: A review of studies that have been made using the Murrell–Mo… read moreAbstract: A review of studies that have been made using the Murrell–Mottram two-plus-three-body empirical potential is presented. The explicit many-body nature of the potential is described and the fitting of these potentials to experimental data on one or more solid phases is detailed. Comparisons are made between potentials for various nonmetallic and metallic elements, from which trends in the parameters defining the potentials can clearly be seen. Examples of the many applications of these potentials to the study of solids (relative stabilities and phase transitions), surfaces (energies, relaxation and reconstructions), melting (both of the bulk and of the surfaces), and clusters (structures, growth, and dynamics) are given. read less NOT USED (low confidence) A. Dyson and P. Smith, “Improved empirical interatomic potential for C—Si—H systems,” Molecular Physics. 1999. link Times cited: 30 Abstract: The Brenner hydrocarbon potential was extended recently to i… read moreAbstract: The Brenner hydrocarbon potential was extended recently to include interactions with silicon. This extended Brenner potential has now been improved by the fitting of bond order correction terms, and the introduction of an adjustable parameter into the angular function. The new potential gives an excellent description of small Si m H n molecules and radicals. Its treatment of the low index surfaces of silicon and β-SiC is also significantly improved, although the recently proposed non-dimerized structure for the silicon terminated (001) surface of β-SiC is not described properly. Calculations of the chemisorption of C2H2 and CH3 onto the (001) surfaces of silicon and β-SiC using this improved potential are reported. Also presented are some initial results of molecular dynamics simulations of the Si(111) 7 × 7:CH3 and hydrogenated Si(001) 2 × 1:C2H2 chemisorption systems. read less NOT USED (low confidence) C. Herrero, “Dependence of the silicon lattice constant on isotopic mass,” Solid State Communications. 1999. link Times cited: 31 NOT USED (low confidence) T. Watanabe and I. Ohdomari, “Modeling of SiO2/Si(100) interface structure by using extended -Stillinger-Weber potential,” Thin Solid Films. 1999. link Times cited: 29 NOT USED (low confidence) U. Wad, A. V. Limaye, M. Gokhale, and S. Ogale, “Comparative study of adatom induced relaxations and energetics for Si, Ge and carbon adsorption on a (2×1) Si(001) surface,” Bulletin of Materials Science. 1999. link Times cited: 1 NOT USED (low confidence) L. Xu, “A statistical thermodynamic model for oxygen segregation during Czochralski growth of silicon single crystals,” Journal of Crystal Growth. 1999. link Times cited: 5 NOT USED (low confidence) S. Wefing, “Modeling of continuous random networks: a case study for vitreous GeO2. I. Model generation,” Journal of Non-crystalline Solids. 1999. link Times cited: 11 NOT USED (low confidence) K. Kakimoto, S. Kikuchi, and H. Ozoe, “Molecular dynamics simulation of oxygen in silicon melt,” Journal of Crystal Growth. 1999. link Times cited: 3 NOT USED (low confidence) N. Mousseau and G. Barkema, “Exploring high-dimensional energy landscapes,” Comput. Sci. Eng. 1999. link Times cited: 12 Abstract: Maps are not reserved for geography. Chemical reactions, ato… read moreAbstract: Maps are not reserved for geography. Chemical reactions, atomic diffusion and protein folding all involve atomic displacements determined by the topography of a complex energy landscape. These landscapes are largely unexplored, and our first priority is to identify their key features: the energy minima and the connecting paths between them. Such a study represents a formidable task. The effort needed to map a space increases exponentially with its dimensionality and becomes rapidly out of reach for the high-dimensional problems of interest in physics, chemistry and biology. Therefore, we have to satisfy ourselves with only a very crude knowledge of these energy landscapes. Recently, many researchers have been developing algorithms for exploring and mapping the potential energy landscapes of systems as diverse as polypeptides, chemical reactions, Lennard-Jones clusters and silica glass. In this article, we address some of the general issues and present an algorithm, called the activation-relaxation technique (ART), which we developed for mapping high-dimensional landscapes. read less NOT USED (low confidence) S. Volz and G. Chen, “LATTICE DYNAMIC SIMULATION OF SILICON THERMAL CONDUCTIVITY,” Physica B-condensed Matter. 1999. link Times cited: 29 NOT USED (low confidence) K. A. Jackson, “Computer modeling of atomic scale crystal growth processes,” Journal of Crystal Growth. 1999. link Times cited: 29 NOT USED (low confidence) E. Spohr, “Computer Simulations of Electrochemical Interfaces.” 1999. link Times cited: 14 NOT USED (low confidence) D. Timpel, M. Schaible, and K. Scheerschmidt, “Molecular dynamics studies of silica wafer bonding,” Journal of Applied Physics. 1999. link Times cited: 17 Abstract: Molecular dynamics simulations are performed to investigate … read moreAbstract: Molecular dynamics simulations are performed to investigate the atomic processes initiated by the adhesion of two silica surfaces, which are covered with adsorbates of oxygen, hydrogen or water molecules. The calculations describe the mechanism of hydrophilic silicon wafer bonding in terms of empirical potentials assumed. The challenge of the macroscopically relevant computations is to understand and to predict the formation of covalent bonds as a function of initial silica structures, external forces, adsorbates, and annealing temperatures applied. read less NOT USED (low confidence) J. Fritsch and U. Schröder, “DENSITY FUNCTIONAL CALCULATION OF SEMICONDUCTOR SURFACE PHONONS,” Physics Reports. 1999. link Times cited: 42 NOT USED (low confidence) T. Akiyama, A. Oshiyama, and O. Sugino, “Magic Numbers of Multivacancy in Crystalline Si: Tight-Binding Studies for the Stability of the Multivacancy,” Journal of the Physical Society of Japan. 1998. link Times cited: 16 Abstract: We perform microscopic total-energy calculations based on a … read moreAbstract: We perform microscopic total-energy calculations based on a transferable tight-binding model combined with conjugate-gradient minimization technique for various multivacancies V n in Si. We find that stable multivacancies (magic numbers of negative Si clusters) are V 6 , V 10 , V 14 , V 17 , V 22 , V 26 and V 35 . We also find that both topological networks of vacant sites and relaxation of surrounding atoms are crucial to determine energetics of the multivacancies. read less NOT USED (low confidence) B. R. A. Neves, J. M. C. Vilela, and M. S. Andrade, “Scanning probe microscopy: an introduction,” Cerâmica. 1998. link Times cited: 12 Abstract: During the last few years, the structural analysis of materi… read moreAbstract: During the last few years, the structural analysis of materials has gone through a great advancement which is related to the development of Scanning Probe Microscopy techniques. Originated in the last decade, these techniques were strengthened and spread worldwide during the 90s. They constitute a new methodology of analysis, involving both knowledge and technology from a multitude of different areas. Their large application spectrum is due, mainly, to: large nanometric-scale resolution; capability of operation in air, liquid or in vacuum environments; and the great quantitative magnification in the z direction. In this paper, the basic ideas concerning the most utilized techniques are described. Applications of each technique, evidencing its potentialities in nanostructural analysis, are also illustrated by some examples of works carried out at the Laboratorio de Nanoscopia of the Fundacao Centro Tecnologico de Minas Gerais - CETEC. read less NOT USED (low confidence) B. Pailthorpe, D. R. G. Mitchell, and N. Bordes, “Thermal diffusion in molecular dynamics simulations of thin film diamond deposition,” Thin Solid Films. 1998. link Times cited: 7 NOT USED (low confidence) F. F. Abraham, J. Broughton, N. Bernstein, and E. Kaxiras, “Spanning the length scales in dynamic simulation,” Computers in Physics. 1998. link Times cited: 288 Abstract: couple different length and time scales in serial fashion. B… read moreAbstract: couple different length and time scales in serial fashion. By this we mean that one set of calculations at a fundamental level, and of high computational complexity, is used to evaluate constants for use in a more approximate or phenomenological computational methodology at longer length or time scales. In pioneering work of this sort in the 1980s, Clementi and coworkers1 used high-quality quantum-mechanical methods to evaluate the interaction of several water molecules. From this database they parameterized an empirical potential for use in molecular-dynamics atomistic simulations. Such a simulation was then used to evaluate the viscosity of water from the atomic autocorrelation function. Finally, the computed viscosity was used in a computational-fluid-dynamics calculation to predict tidal circulation in Buzzards Bay, MA. This tour de force of computational physics is a powerful example of the sequential coupling of length and time scales: one series of calculations is used as input to the next up the length and time hierarchy. There are many other examples in the literature. But what underlies all these schemes is that an appropriate computational methodology is used for a given scale or task, whether it be the accuracy of quantum mechanics at the shortest scales or fluid dynamics at the longest scales. In contrast, there has been comparatively little effort devoted to the parallel coupling of different computational schemes for a simultaneous attack on a given problem; in our case, our interest dictates specific attention toward issues in materials or solid-state physics. We will focus specifically on the coupling of length scales for the three mechanics describing materials phenomena: quantum mechanics, atomistic mechanics, and continuum mechanics. read less NOT USED (low confidence) G. Gilmer, H.-C. Huang, and C. Roland, “Thin film deposition: fundamentals and modeling,” Computational Materials Science. 1998. link Times cited: 111 NOT USED (low confidence) C. Chui and M. Boyce, “A control volume technique for computing continuum deformation measures in discrete polymeric systems,” Journal of Non-crystalline Solids. 1998. link Times cited: 0 NOT USED (low confidence) P. Klein and H. Gao, “Crack nucleation and growth as strain localization in a virtual-bond continuum,” Engineering Fracture Mechanics. 1998. link Times cited: 185 NOT USED (low confidence) J. Q. Xie and J. Feng, “Molecular-dynamics simulation of silicon film growth from cluster beams,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1998. link Times cited: 8 NOT USED (low confidence) A. Mazzone, “AN EXTENSION OF THE LCAO METHOD ISOTHERMAL DYNAMICS,” International Journal of Modern Physics C. 1998. link Times cited: 0 Abstract: This work presents a dynamical version of the LCAO method wh… read moreAbstract: This work presents a dynamical version of the LCAO method which includes extension variables, such as temperature and pressure. As an illustrative example, the method is applied to the temperature response of small silicon clusters. A comparison is made with molecular dynamics calculations using standard interatomic potentials. read less NOT USED (low confidence) X. Liu, Z. Zhen, and J.-cheng Zhang, “New Potential Energy Functions for Diamond and α-Tin Crystals,” Chinese Physics Letters. 1998. link Times cited: 1 Abstract: A new model of potential energy functions for atomic solids … read moreAbstract: A new model of potential energy functions for atomic solids is given and applied to diamond and α-tin crystals. In the new model, a factor expressing the characters of covalent bonds has been included. Therefore it is suitable for covalent crystals. New potentials of C and α-Sn crystals accurately reproduce experimental elastic constants and phonon dispersion curves and so on. The set of new potentials is accurate enough for computer simulations. read less NOT USED (low confidence) M. H. Shapiro, “Using molecular dynamics simulations to investigate surface modification processes,” Surface & Coatings Technology. 1998. link Times cited: 3 NOT USED (low confidence) C. R. Zacharias, M. R. Lemes, and A. D. Pino, “Combining genetic algorithm and simulated annealing: A molecular geometry optimization study,” Journal of Molecular Structure-theochem. 1998. link Times cited: 42 NOT USED (low confidence) G. Greenwood and Y.-P. Liu, “Finding Low Energy Conformations of Atomic Clusters Using Evolution Strategies,” Evolutionary Programming. 1998. link Times cited: 6 NOT USED (low confidence) S. Nomura, T. Iitaka, X. Zhao, T. Sugano, and Y. Aoyagi, “Electronic structure of nanocrystalline/amorphous silicon: a novel quantum size effect,” Materials Science and Engineering B-advanced Functional Solid-state Materials. 1998. link Times cited: 4 NOT USED (low confidence) V. M. Glazov and L. Pavlova, “Liquation phenomena in CMT melts and structural features in cadmium and mercury tellurides in a liquid phase,” Journal of Crystal Growth. 1998. link Times cited: 7 NOT USED (low confidence) J. Feldman, S. Bickham, G. Engel, and D. Bn, “Modes in amorphous silicon,” Philosophical Magazine Part B. 1998. link Times cited: 2 Abstract: We discuss how the vibrational modes in an amorphous materia… read moreAbstract: We discuss how the vibrational modes in an amorphous material can be characterized by various correlation functions. The spectrum of modes can be expected to contain both extended and localized states separated by mobility edges. The inverse participation ratio can be used as a measure of localization. To examine the vibrational modes in more detail, we propose to study moduli of Fourier transforms of powers of the eigenvector components. We have applied the analysis to vibrational modes of amorphous silicon. The structural and potential models that we use are based on the Wooten—Winer—Weaire bond-switching algorithm and Stillinger—Weber classical potential. The structural models are cubic supercells, periodically repeated. Whereas models ranging in size from 216 to 4096 atoms have been studied, only the 4096-atom model results are included here. In the analysis, we employ only q vectors that are consistent with the boundary conditions used to obtain the modes. Upon averaging over q-vector direct... read less NOT USED (low confidence) C. Goringe, D. Bowler, and E. Hernández, “Tight-binding modelling of materials,” Reports on Progress in Physics. 1997. link Times cited: 453 Abstract: The tight-binding method of modelling materials lies between… read moreAbstract: The tight-binding method of modelling materials lies between the very accurate, very expensive, ab initio methods and the fast but limited empirical methods. When compared with ab initio methods, tight-binding is typically two to three orders of magnitude faster, but suffers from a reduction in transferability due to the approximations made; when compared with empirical methods, tight-binding is two to three orders of magnitude slower, but the quantum mechanical nature of bonding is retained, ensuring that the angular nature of bonding is correctly described far from equilibrium structures. Tight-binding is therefore useful for the large number of situations in which quantum mechanical effects are significant, but the system size makes ab initio calculations impractical. In this paper we review the theoretical basis of the tight-binding method, and the range of approaches used to exactly or approximately solve the tight-binding equations. We then consider a representative selection of the huge number of systems which have been studied using tight-binding, identifying the physical characteristics that favour a particular tight-binding method, with examples drawn from metallic, semiconducting and ionic systems. Looking beyond standard tight-binding methods we then review the work which has been done to improve the accuracy and transferability of tight-binding, and moving in the opposite direction we consider the relationship between tight-binding and empirical models. read less NOT USED (low confidence) C. Wang and K. Ho, “Material simulations with tight-binding molecular dynamics,” Journal of Phase Equilibria. 1997. link Times cited: 15 NOT USED (low confidence) L. Porter, J. F. Justo, and S. Yip, “The importance of Grüneisen parameters in developing interatomic potentials,” Journal of Applied Physics. 1997. link Times cited: 54 Abstract: We show that three representative interatomic potential func… read moreAbstract: We show that three representative interatomic potential functions for Si fail to describe properly the Gruneisen parameters γn, although one model is able to give a satisfactory account of the thermal expansion coefficient, α, by virtue of a fortuitous cancellation of errors in γn for the acoustic and optic modes. This suggests that in developing robust interatomic potentials intended to predict the thermomechanical behavior of crystals, the database used in parameter adjustment should include the fundamental quantities, γn, rather than the composite quantity α. read less NOT USED (low confidence) R. Averback and T. D. Rubia, “Displacement damage in irradiated metals and semiconductors,” Journal of Physics C: Solid State Physics. 1997. link Times cited: 310 NOT USED (low confidence) I. Suni, “Effect of three-body dispersion interactions on the surface dynamics of Ar(111),” Surface Science. 1997. link Times cited: 1 NOT USED (low confidence) J. Perlado, “Behavior and computer simulation of SiC under irradiation with energetic particles,” Journal of Nuclear Materials. 1997. link Times cited: 26 NOT USED (low confidence) T. D. Rubia, N. Soneda, M. Caturla, and E. Alonso, “Defect production and annealing kinetics in elemental metals and semiconductors,” Journal of Nuclear Materials. 1997. link Times cited: 39 NOT USED (low confidence) L. Marqués, M. Jaraíz, J. Rubio, J. Vicente, L. Bailón, and J. Barbolla, “Molecular dynamics simulations of ion bombardment processes,” Materials Science and Technology. 1997. link Times cited: 3 Abstract: AbstractAn improved molecular dynamics technique that allows… read moreAbstract: AbstractAn improved molecular dynamics technique that allows reduction of the computation time required in ion bombardment simulations is presented. This technique has been used to study the influence of the target temperature and structure on the argon sputtering of silicon. Molecular dynamics simulations of l keV Ar+ ion bombardment of silicon were carried out for several types of sample: (100) crystalline at 0 K, (100) crystalline at 300 K, and amorphous at 300 K. The yield of the sputtering process and the energy distribution of the sputtered atoms have been obtained. These results show that the sputtering process depends on the target surface binding energy which, in turn, is very sensitive to the structure of the sample surface. read less NOT USED (low confidence) C. Grein, “First principles calculations of Si(2 1 1) surface reconstructions,” Journal of Crystal Growth. 1997. link Times cited: 20 NOT USED (low confidence) J. Oh and C. Grein, “Modeling of CdTe(1 1 1)B/Si(0 0 1) interfaces,” Journal of Crystal Growth. 1997. link Times cited: 4 NOT USED (low confidence) Z. Zhang, F. Wu, and M. Lagally, “AN ATOMISTIC VIEW OF Si(001) HOMOEPITAXY1,” Annual Review of Materials Science. 1997. link Times cited: 25 Abstract: ▪ Abstract Growth of thin films from atoms deposited from th… read moreAbstract: ▪ Abstract Growth of thin films from atoms deposited from the gas phase is intrinsically a non-equilibrium phenomenon dictated by a competition between kinetics and thermodynamics. Precise control of the growth becomes possible only after achieving an understanding of this competition. In this review, we present an atomistic view of the various kinetic aspects in a model system, the epitaxy of Si on Si(001), as revealed by scanning tunneling microscopy and total-energy calculations. Fundamentally important issues investigated include adsorption dynamics and energetics, adatom diffusion, nucleation, sticking, and detachment. We also briefly discuss the inverse process of growth, removal by sputtering or etching. We aim our discussions to an understanding at a quantitative level whenever possible. read less NOT USED (low confidence) C. Grein, J. Faurie, V. Bousquet, É. Tournié, R. Benedek, and T. D. Rubia, “Simulations of ZnSe/GaAs heteroepitaxial growth,” Journal of Crystal Growth. 1997. link Times cited: 24 NOT USED (low confidence) M. Muhlhoff and H. Urbassek, “Ion beam mixing of a-MoSi2,” Radiation Effects and Defects in Solids. 1997. link Times cited: 1 Abstract: Using molecular dynamics simulation, we study the mixing of … read moreAbstract: Using molecular dynamics simulation, we study the mixing of an α-MoSi2 crystal by 1 keV Ar ions. The observed order of magnitude of the mixing is compatible with a spike model of ion beam mixing. The influence of the target surface and of chemical effects are discussed. read less NOT USED (low confidence) B. Weber, D. Stock, K. Gärtner, and C. Wende, “MD simulation of ion beam induced crystallization and amorphization in silicon,” Radiation Effects and Defects in Solids. 1997. link Times cited: 2 Abstract: The processes of IBIEC and IBIIA in Si are investigated by m… read moreAbstract: The processes of IBIEC and IBIIA in Si are investigated by molecular dynamics simulations using the Stillinger-Weber potential. For this purpose two amorphous Si/crystalline Si systems of 5120 and 1440 Si atoms are prepared. The ion beam irradiation is simulated by recoils started near the a/c interface. The investigations are performed for different temperatures (10K, RT, 600K), different energies of the recoils (15 eV, 20 eV, 50 eV) and different densities of the recoils represented by different numbers (1, 10, 50) of simultaneously started recoils. For IBIEC and IBIIA the energy and the density of the recoils, respectively, proved to be the important quantities. The microscopic structure near the interface is analyzed and the processes responsible for the IBIEC and the IBIIA are discussed. read less NOT USED (low confidence) C. Denton, V. Konoplev, A. Gras-marti, and J. Jiménez-Rodríguez, “Annealing of radiation damage in Si. A molecular dynamics study,” Radiation Effects and Defects in Solids. 1997. link Times cited: 0 Abstract: We investigate the annealing of damage produced by a dense c… read moreAbstract: We investigate the annealing of damage produced by a dense collision cascade in the bulk of a silicon target. The evolution of the damage with time (up to 50ps) and its dependence with the annealing temperature (up to 1700 K) are studied. We find that the damage present at the end of the relaxation stage is larger for high temperatures, but when the thermal equilibrium is reached throughout the target, the annealing is more pronounced at higher temperatures. We also model non-linear effects in the annealing of the damage due to two interacting cascades and find qualitative agreement with experimental reports. read less NOT USED (low confidence) I. Jenčič, J. Peternelj, and I. Robertson, “Randomization-and-relaxation model revisited,” Radiation Effects and Defects in Solids. 1997. link Times cited: 0 Abstract: The interatomic potentials of Stillinger-Weber and Tersoff w… read moreAbstract: The interatomic potentials of Stillinger-Weber and Tersoff were incorporated into the randomization-and-relaxation model, which was originally developed for modelling amorphous silicon by using the Keating interatomic potential. The inclusion of more recent and more complicated interatomic potentials resulted in a more sophisticated set of bond switching rules which form the basis for the randomization-and-relaxation algorithm. This improved model was then used to model small isolated amorphous zones which are produced by individual heavy ions during ion implantation in silicon. The temperature evolution during zone creation was calculated by using idealized thermal spike model. The structure and stability of these amorphous zones was examined with respect to the energy of incoming ion and with respect to the interatomic potential employed. It was established that significantly lower spike energy is required to create a stable amorphous region than in the simulation where the Keating potential wa... read less NOT USED (low confidence) M. Shapiro, “Using molecular dynamics simulations to investigate sputtering processes,” Radiation Effects and Defects in Solids. 1997. link Times cited: 8 Abstract: The popularity of molecular dynamics (MD) techniques for the… read moreAbstract: The popularity of molecular dynamics (MD) techniques for the investigation of sputtering processes continues to grow, driven in large measure by the rapid increase in the performance-to-price ratio for modern workstations and high-end personal computers. The ready availability of these inexpensive, powerful computing platforms has encouraged researchers to use MD methods to better understand a variety of problems in sputtering. These include studies of: (1) sputtering induced by complex projectiles: (2) the ejection of small clusters during sputtering: (3) the role of inelastic effects during sputtering: (4) sputtering from complex target materials; and (5) chemical effects during sputtering. Increases in computing power also have made it possible to use more realistic many-body potentials in these simulations. This paper reviews some of the recent literature in these areas, and provides an overview of the progress made in the past few years. read less NOT USED (low confidence) W. Möller, “Computer simulation of ion-assisted thin film deposition,” Radiation Effects and Defects in Solids. 1997. link Times cited: 4 Abstract: Ion assistance has been very successful in modern processes … read moreAbstract: Ion assistance has been very successful in modern processes of physical or chemical vapour deposition, as it promotes the production of high-quality films and, in particular, the formation of new thin film materials with extreme properties [1–5]. In contrast to a broad range of experimental experience, the basic understanding of the effects of ion bombardment during thin film deposition is still in the state of a beginning. Therefore, the field is still mostly relying on broad empirical investigations rather than focused studies of optimization, which would be based on the basic understanding of the underlying mechanisms. Such studies require both well-directed experiments and a reliable modelling. The slow progress in this area is related to the large degree of complexity associated with the interplay of surface mechanisms, and both energetic and thermal processes in the near-surface bulk, which may be of physical and chemical nature. Consequently, the ability of analytical models is rather limi... read less NOT USED (low confidence) R. Chatterjee and B. Garrison, “Pushing the limits of classical modeling of bombardment events in solids,” Radiation Effects and Defects in Solids. 1997. link Times cited: 5 Abstract: Bombardment of solids with keV atoms leads to violent collis… read moreAbstract: Bombardment of solids with keV atoms leads to violent collisions with subsequent ejection of target particles. This review discusses how classical molecular dynamics simulations designed to describe the bombardment events can give insight into microscopic processes where not only classical but also quantum effects such as electronic excitation and organic reactions play an important role. By incorporating a simple excitation/de-excitation model into the simulation, we have shown that collisional events are important to describe the distribution of excited state atoms measured experimentally. Molecular dynamics simulations employing a reactive many-body potential of small hydrocarbon molecules adsorbed on a metal surface predict the occurrence of various collision induced organic reactions prior to ejection. Lateral motion of particles in the region right above the surface plays an important role in signal enhancement. The calculations predict several processes such as direct molecular ejection, d... read less NOT USED (low confidence) B. Weber, K. Gärtner, and D. Stock, “MD-SIMULATION OF ION INDUCED CRYSTALLIZATION AND AMORPHIZATION PROCESSES IN SILICON,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1997. link Times cited: 15 NOT USED (low confidence) J. F. Justo, V. Bulatov, and S. Yip, “Core effects in dislocation intersection,” Scripta Materialia. 1997. link Times cited: 6 NOT USED (low confidence) P. Keblinski, S. Phillpot, D. Wolf, and H. Gleiter, “Thermodynamically stable amorphous intergranular films in nanocrystalline silicon,” Physics Letters A. 1997. link Times cited: 17 NOT USED (low confidence) R. Herrmann, J. Gerlach, and E. Campbell, “Molecular dynamics simulation of laser ablation of silicon,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1997. link Times cited: 27 NOT USED (low confidence) H. Urbassek, “Molecular-dynamics simulation of sputtering,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1997. link Times cited: 101 NOT USED (low confidence) M. Rouhani, R. Malek, A. Gué, G. Bouyssou, and D. Estève, “Monte Carlo simulation of the effect of interstitial atoms interaction on the heteroepitaxial growth of compound semiconductors,” Materials Science and Engineering B-advanced Functional Solid-state Materials. 1997. link Times cited: 5 NOT USED (low confidence) V. Bulatov, M. Nastar, J. F. Justo, and S. Yip, “Atomistic modeling of crystal-defect mobility and interactions,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1997. link Times cited: 3 NOT USED (low confidence) T. D. Rubia, “Defect production mechanisms in metals and covalent semiconductors,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1996. link Times cited: 14 NOT USED (low confidence) Yu, Wang, and Stroud, “Empirical molecular-dynamics study of diffusion in liquid semiconductors.,” Physical review. B, Condensed matter. 1996. link Times cited: 46 Abstract: We report the results of an extensive molecular-dynamics stu… read moreAbstract: We report the results of an extensive molecular-dynamics study of diffusion in liquid Si and Ge (l-Si and l-Ge) and of impurities in l-Ge, using empirical Stillinger-Weber (SW) potentials with several choices of parameters. We use a numerical algorithm in which the three-body part of the SW potential is decomposed into products of two-body potentials, thereby permitting the study of large systems. One choice of SW parameters agrees very well with the observed l-Ge structure factors. The diffusion coefficients D(T) at melting are found to be approximately 6.4\ifmmode\times\else\texttimes\fi{}${10}^{\mathrm{\ensuremath{-}}5}$ ${\mathrm{cm}}^{2}$/s for l-Si, in good agreement with previous calculations, and about 4.2\ifmmode\times\else\texttimes\fi{}${10}^{\mathrm{\ensuremath{-}}5}$ and 4.6\ifmmode\times\else\texttimes\fi{}${10}^{\mathrm{\ensuremath{-}}5}$ ${\mathrm{cm}}^{2}$/s for two models of l-Ge. In all cases, D(T) can be fitted to an activated temperature dependence, with activation energies ${\mathit{E}}_{\mathit{d}}$ of about 0.42 eV for l-Si, and 0.32 or 0.26 eV for two models of l-Ge, as calculated from either the Einstein relation or from a Green-Kubo-type integration of the velocity autocorrelation function. D(T) for Si impurities in l-Ge is found to be very similar to the self-diffusion coefficient of l-Ge. We briefly discuss possible reasons why the SW potentials give D(T)'s substantially lower than ab initio predictions. \textcopyright{} 1996 The American Physical Society. read less NOT USED (low confidence) P. Stephenson, M. Radny, and P. V. Smith, “A modified Stillinger-Weber potential for modelling silicon surfaces,” Surface Science. 1996. link Times cited: 19 NOT USED (low confidence) A. Darcy, A. Galijatovic, R. Barth, T. Kenny, K. D. Krantzman, and T. A. Schoolcraft, “Molecular dynamics simulations of silicon-fluorine etching.,” Journal of molecular graphics. 1996. link Times cited: 11 NOT USED (low confidence) T. D. Rubia, J. Perlado, and M. Tobin, “Radiation effects in silicon carbide: high energy cascades and damage accumulation at high temperature,” Journal of Nuclear Materials. 1996. link Times cited: 16 NOT USED (low confidence) B. Hartke, “Global geometry optimization of clusters guided by N-dependent model potentials,” Chemical Physics Letters. 1996. link Times cited: 48 NOT USED (low confidence) M. Kotrla, “Numerical simulations in the theory of crystal growth,” Computer Physics Communications. 1996. link Times cited: 86 NOT USED (low confidence) V. Luchnikov, N. N. Medvedev, A. Appelhagen, and A. Geiger, “Medium-range structure of amorphous silicon studied by the Voronoi—Delaunay method,” Molecular Physics. 1996. link Times cited: 17 Abstract: Structural inhomogeneities and their effect on the dynamics … read moreAbstract: Structural inhomogeneities and their effect on the dynamics are investigated for a molecular dynamics model of quenched amorphous silicon. The structure of the model is analysed with the help of the Voronoi—Delaunay approach, which is a convenient tool for this purpose. The silicon structure is found to be rather homogeneous. Only localized defects are found, and no medium-range regions of ‘imperfect’ structure as were observed in a Lennard-Jones glass by V. A. Luchnikov, N. N. Medvedev, Yu. I. Naberukhin and V. N. Novikov (1995, Phys. Rev. B, 51, 15 569). It is assumed that the inhomogeneity in glasses is the result of competition between the tendency of atoms to pack locally into the most favourable arrangements and the necessity to realize space filling structures. For spherical atoms a regular tetrahedron of four atoms is the densest local configuration; however, such units cannot cover the whole space. As a result, Lennard-Jones glasses have regions of structural inhomogeneity with an extension of 3–... read less NOT USED (low confidence) E. Kaxiras, “Review of atomistic simulations of surface diffusion and growth on semiconductors,” Computational Materials Science. 1996. link Times cited: 17 NOT USED (low confidence) L. E. Carter and E. Carter, “Simulated reaction dynamics of F atoms on partially fluorinated Si(100) surfaces,” Surface Science. 1996. link Times cited: 11 NOT USED (low confidence) M. Jentschel, K. Heinig, H. Börner, J. Jolie, and E. Kessler, “Atomic collision cascades studied with the Crystal-GRID method,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1996. link Times cited: 12 NOT USED (low confidence) W. Pickett, J. Feldman, and J. Deppe, “Thermal transport across boundaries in diamond structure materials,” Modelling and Simulation in Materials Science and Engineering. 1996. link Times cited: 20 Abstract: Previous measurements of the thermal conductivity of chemica… read moreAbstract: Previous measurements of the thermal conductivity of chemical vapour deposition diamond films show values of near, or even exceeding, that of natural diamond in spite of the polycrystalline nature of the films. These data have led us to consider whether there can be a `resonant' transfer of energy between identical crystallites separated by a material with different vibrational properties. We consider here a model of energy transfer between diamond-structure crystallites (Stillinger - Weber silicon) separated by a barrier region in which the mass is altered. We find that, for a pulse of energy deposited in one crystallite, there can be an efficient transfer of energy through the barrier region and subsequent build-up in a neighbouring crystallite if the vibrational spectrum of the barrier region is harder than that of the crystallites. If the vibrational spectrum of the barrier material is softer, the energy accumulation in the barrier region is at least as rapid as in the neighbouring crystallite and energy is retained longer in the region where it was deposited. The microscopic reasons behind this behaviour are discussed, and we conclude that the transmission probability between neighbouring crystallites leads to a more physical interpretation than a resonant transfer between next-neighbour crystallites. read less NOT USED (low confidence) S. Kato and H. Hu, “Molecular dynamics simulation of the thin film fabrication process,” Surface Science. 1996. link Times cited: 1 NOT USED (low confidence) T. Yamaguchi and S. Miyoshi, “Electronic states of fullerenes adsorbed on Si surface,” Surface Science. 1996. link Times cited: 3 NOT USED (low confidence) A. Dyson and P. V. Smith, “Extension of the Brenner empirical interatomic potential to CSiH systems,” Surface Science. 1996. link Times cited: 70 NOT USED (low confidence) J. R. Patel and E. Fontes, “X Ray Standing Waves: Thermal Vibration Amplitudes at Surfaces.” 1996. link Times cited: 0 NOT USED (low confidence) E. V. Blagov, G. L. Klimchitskaya, A. A. Lobashov, and V. Mostepanenko, “How to describe AFM constant force surfaces in repulsive mode,” Surface Science. 1996. link Times cited: 12 NOT USED (low confidence) C. Roland, “Effects of Stress on Step Energies and Surface Roughness,” MRS Bulletin. 1996. link Times cited: 16 NOT USED (low confidence) A.-Q. Chen and L. Corrales, “Semiempirical methodology for simulating covalently bonded materials: Application to silicon,” Journal of Chemical Physics. 1996. link Times cited: 4 Abstract: A recently introduced semiempirical methodology is used to m… read moreAbstract: A recently introduced semiempirical methodology is used to model and simulate silicon via molecular dynamics. This approach is capable of grasping essential qualitative and quantitative features of the coupling between the electronic coordinates and the geometric structure. Properties of the bulk diamond crystal, the melt and amorphous solid states are obtained using optimization techniques and molecular dynamics simulations. The pair distribution function of the amorphous state is in excellent agreement with experimental and other molecular dynamics simulation results. read less NOT USED (low confidence) M. Ichimura, “Stillinger-Weber potentials for III-V compound semiconductors and their application to the critical thickness calculation for InAs/GaAs,” Physica Status Solidi (a). 1996. link Times cited: 52 Abstract: Parameters in the Stillinger-Weber interatomic potentials ar… read moreAbstract: Parameters in the Stillinger-Weber interatomic potentials are obtained for III–V compounds from the cohesive energy, the lattice constant, and the elastic properties. The obtained potentials coincide with the Keating potentials for small distortion (<1%) but are more accurate for larger distortion. Using the SW potentials, the critical thickness of misfit dislocation nucleation is calculated for InAs/(001)GaAs. The critical thickness is 5 ML for a 60° dislocation and 2 ML for an edge dislocation. These thicknesses are smaller than those calculated using the Keating potentials. Results obtained by the classical elastic theory do not agree with the present results. read less NOT USED (low confidence) G. Gilmer, C. Roland, D. Stock, M. Jaraíz, and T. D. Rubia, “Simulations of thin film deposition from atomic and cluster beams,” Materials Science and Engineering B-advanced Functional Solid-state Materials. 1996. link Times cited: 27 NOT USED (low confidence) D. Timpel, K. Scheerschmidt, and S. Ruvimov, “HREM simulations of particles and interfaces refined by molecular dynamics relaxations,” Materials Science and Engineering B-advanced Functional Solid-state Materials. 1996. link Times cited: 2 NOT USED (low confidence) C. Herrero and R. Ramírez, “Low-temperature delocalization of hydrogen in crystalline silicon,” Solid State Communications. 1996. link Times cited: 3 NOT USED (low confidence) M. Rouhani, A. Gué, R. Malek, G. Bouyssou, and D. Estève, “Surface morphology due to enhanced migration in heteroepitaxial growth of compound semiconductors,” Materials Science and Engineering B-advanced Functional Solid-state Materials. 1996. link Times cited: 7 NOT USED (low confidence) A. Horsfield, “A computationally efficient differentiable Tight-Binding energy functional,” Materials Science and Engineering B-advanced Functional Solid-state Materials. 1996. link Times cited: 16 NOT USED (low confidence) I. Suni and E. Seebauer, “Surface self diffusion at high temperatures: new simulational insights,” Thin Solid Films. 1996. link Times cited: 5 NOT USED (low confidence) D. McCulloch, N. Marks, D. Mckenzie, and S. Prawer, “Molecular dynamics and experimental studies of preferred orientation induced by compressive stress,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1995. link Times cited: 17 NOT USED (low confidence) Z. Rycerz, “A New Efficient Method for Molecular Dynamics Simulation of Three-Body Potential Systems,” Molecular Simulation. 1995. link Times cited: 1 Abstract: An efficient order of N molecular dynamics method for the si… read moreAbstract: An efficient order of N molecular dynamics method for the simulation of two-body and three-body systems is presented. Due to its high speed it enables one to simulate large MD systems on a mainframe and investigate some complex processes in terms which are closer to experimental conditions (e.g. crystal growth or ion implantation on relatively large-by MD standards-substrates). read less NOT USED (low confidence) D. Wolf, S. Phillpot, and P. Keblinski, “Atomistic simulation of nanocrystalline materials,” MRS Proceedings. 1995. link Times cited: 2 Abstract: Atomistic simulations show that high-energy grain boundaries… read moreAbstract: Atomistic simulations show that high-energy grain boundaries in nanocrystalline copper and nanocrystalline silicon are highly disordered. In the case of silicon the structures of the grain boundaries are essentially indistinguishable from that of bulk amorphous silicon. Based on a free-energy argument, we suggest that below a critical grain size nanocrystalline materials should be unstable with respect to the amorphous phase. read less NOT USED (low confidence) D. A. Drabold, P. Ordejón, J. Dong, and R. Martin, “Spectral properties of large fullerenes : from cluster to crystal,” Solid State Communications. 1995. link Times cited: 73 NOT USED (low confidence) C. Angell, “Simulation of glasses and glass-forming liquids after two decades : some perspectives,” Computational Materials Science. 1995. link Times cited: 6 NOT USED (low confidence) X. Liu, “New model of potential energy functions for atomic solids. Part 2. New potentials of silicon and germanium crystals,” Journal of Molecular Structure-theochem. 1995. link Times cited: 1 NOT USED (low confidence) L. Xin-hou, “New Model of Potential Energy Functions for Atomic Solids and Application to Silicon Crystal,” Chinese Physics Letters. 1995. link Times cited: 1 Abstract: A new theoretical model of potential energy functions for at… read moreAbstract: A new theoretical model of potential energy functions for atomic solids is developed. An angular factor is included in this model and its effect is discussed. Using this new model, a new preliminary potential for silicon crystal is derived. Calculated phonon dispersion curves, using this new potential, is given. A good agreement has been found. read less NOT USED (low confidence) H.-C. Huang, N. Ghoniem, J. Wong, and M. Baskes, “Molecular dynamics determination of defect energetics in beta -SiC using three representative empirical potentials,” Modelling and Simulation in Materials Science and Engineering. 1995. link Times cited: 102 Abstract: The determination of formation and migration energies of poi… read moreAbstract: The determination of formation and migration energies of point and clustered defects in SiC is of critical importance to a proper understanding of atomic phenomena in a wide range of applications. We present here calculations of formation and migration energies of a number of point and clustered defect configurations. A newly developed set of parameters for the modified embedded-atom method (MEAM) is presented. Detailed molecular dynamics calculations of defect energetics using three representative potentials, namely the Pearson potential, the Tersoff potential and the MEAM, have been performed. Results of the calculations are compared to first-principles calculations and to available experimental data. The results are analysed in terms of developing a consistent empirical interatomic potential and are used to discuss various atomic migration processes. read less NOT USED (low confidence) K. Maekawa and A. Itoh, “Friction and tool wear in nano-scale machining—a molecular dynamics approach,” Wear. 1995. link Times cited: 218 NOT USED (low confidence) P. Weakliem, Z. Zhang, and H. Metiu, “Missing dimer vacancies ordering on the Si(100) surface,” Surface Science. 1995. link Times cited: 23 NOT USED (low confidence) R. Smith, K. Beardmore, A. Gras-marti, R. Kirchner, and R. Webb, “A molecular dynamics study of energetic particle impacts on carbon and silicon,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1995. link Times cited: 20 NOT USED (low confidence) L. Marqués, J. Rubio, M. Jaraíz, L. Enríquez, and J. Barbolla, “An improved molecular dynamics scheme for ion bombardment simulations,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1995. link Times cited: 22 NOT USED (low confidence) V. Bulatov, S. Yip, and A. Argon, “Atomic modes of dislocation mobility in silicon,” Philosophical Magazine. 1995. link Times cited: 128 Abstract: Mechanisms of partial dislocation mobility in the {111} glid… read moreAbstract: Mechanisms of partial dislocation mobility in the {111} glide system of silicon have been studied in full atomistic detail by applying novel effective relaxation and sampling algorithms in conjunction with the Stillinger-Weber empirical interatomic potential and simulation models of up to 90000 atoms. Low-energy pathways are determined for the generation, annihilation and motion of in-core defects of the 30°-partial dislocation, specifically, the individual left and right components of a double-kink, an antiphase defect (APD), and various kink-APD complexes. It is shown that the underlying mechanisms in these defect reactions fall into three distinct categories, characterized by the processes of bond-breaking, bond switching, and bond exchange, respectively. The quantitative results reveal a strong left-right asymmetry in the kinetics of kink propagation and a strong APD-kink binding; these have not been recognized previously and therefore hold implications for further experiments. The present wo... read less NOT USED (low confidence) M. Ichimura and J. Narayan, “NEGATIVE SURFACE ENERGY CHANGE ASSOCIATED WITH STEP FORMATION CAUSED BY MISFIT DISLOCATION NUCLEATION IN SEMICONDUCTOR HETEROSTRUCTURES,” Philosophical Magazine. 1995. link Times cited: 12 Abstract: We have calculated the surface energy change due to step for… read moreAbstract: We have calculated the surface energy change due to step formation caused by misfit dislocation nucleation in thin-film semiconductor heterostructures. It is found that the surface energy change is negative for compressive misfit stress in the heteroepitaxial film, while it is positive for tensile misfit stress. This conclusion is in contrast to the classical model where the step formation energy is always positive and independent of the sign of the misfit. The calculated energy change is qualitatively explained by counting the number of dangling bonds on the surface. Using atomistic simulations, we have calculated the critical thickness of dislocation nucleation taking into account the surface energy change, and found that it varied from 4 nm for Ge films on Si(001) substrates to 6 nm for Si films on Ge(001) substrates having the same misfit. read less NOT USED (low confidence) K. Gärtner et al., “Round robin computer simulation of ion transmission through crystalline layers,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1995. link Times cited: 65 NOT USED (low confidence) M. Posselt and K. Heinig, “Comparison of BC and MD simulations of low-energy ion implantation,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1995. link Times cited: 8 NOT USED (low confidence) J. Rubio, L. Marqués, M. Jaraíz, L. Bailón, and J. Barbolla, “Molecular dynamics simulation of amorphous silicon sputtering by Ar+ ions,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1995. link Times cited: 14 NOT USED (low confidence) S. Itoh, P. Ordejón, and R. Martin, “Order-N tight-binding molecular dynamics on parallel computers,” Computer Physics Communications. 1995. link Times cited: 32 NOT USED (low confidence) J. Crain, G. Ackland, and S. Clark, “Exotic structures of tetrahedral semiconductors,” Reports on Progress in Physics. 1995. link Times cited: 29 Abstract: Recent experimental and theoretical studies of exotic forms … read moreAbstract: Recent experimental and theoretical studies of exotic forms of tetrahedrally coordinated semiconductors are reviewed. These unusual phases are synthesized as long-lived metastable forms of the elemental semiconductors silicon and germanium by the application and subsequent removal of high pressure. Rather than being simply crystallographic oddities, the bonding arrangements in these phases show many similarities to those found in amorphous semiconductors. As a result, these dense structures have been used as so-called 'complex crystal' models for the amorphous state. Advances in experimental and computational techniques have recently allowed for detailed study of the structural, electronic and vibrational properties of these phases to be made under variable temperature and pressure conditions. In view of the considerable difficulties associated with performing theoretical studies of non-crystalline solids, the BC8 and ST12 structures are useful in that an understanding of their properties provides insight into the essential physics of amorphous tetrahedral semiconductors. read less NOT USED (low confidence) V. Konoplev and A. Gras-marti, “Molecular dynamics simulation of low-energy collision cascades and atomic mixing in silicon,” Philosophical Magazine. 1995. link Times cited: 4 Abstract: We investigate atomic relocation processes in silicon at OK,… read moreAbstract: We investigate atomic relocation processes in silicon at OK, initiated by an internal 100eV silicon recoil. The molecular dynamics code MODYSEM is used, based on a Tersoff potential for silicon. A fitting procedure was used for the generation of 8 potential valid over the whole energy range of interest. The contribution of the collisional, spontaneous relaxation and thermalization stages to the atomic relocation process are discussed. A threshold distance for the definition of relocated atoms is determined, which separates atomic displacements into stable and unstable (or transient) groups. The atomic mixing process is quantified in terms of the first and second spatial moments over the relocation cross-section. These moments depend on the criterion used to define a relocated Si atom, with short-distance thermal-like atomic displacements, which appear during the thermalization stage, dominating the values of the spatial moments. However, the moments of the relocation cross-section calculated by c... read less NOT USED (low confidence) C. Meli, J. Broughton, P. Vashishta, and R. Kalia, “Direct simulation of next generation devices by atomistic simulation,” Proceedings of the 1995 IEEE International Frequency Control Symposium (49th Annual Symposium). 1995. link Times cited: 0 Abstract: The case in point is afforded by quartz crystal oscillators … read moreAbstract: The case in point is afforded by quartz crystal oscillators (QCOs). These devices rely upon very simple mechanical principles for their operation. Present QCOs can be manufactured in the 100 micron length scale regime; they involve megahertz frequencies. Next generation oscillators will hit the sub-micron regime where they will afford gigahertz frequencies and much higher sensitivities (e.g., force, mass, etc.). It is this size regime that may be directly accessed by modern atomistic simulation; that is the multi million atom system size. read less NOT USED (low confidence) T. Ito, “RECENT PROGRESS IN COMPUTER-AIDED MATERIALS DESIGN FOR COMPOUND SEMICONDUCTORS,” Journal of Applied Physics. 1995. link Times cited: 50 Abstract: Recent progress in computational materials science in the ar… read moreAbstract: Recent progress in computational materials science in the area of semiconductor materials is reviewed. Reliable predictions can now be made for a wide range of problems, such as band structure and structural and thermodynamic properties of various compound semiconductors, using electronic theories such as the pseudopotential method. Further applications are examined by investigating the behavior of various atomic species in semiconductors, including the stability and band structure of heterostructures, superlattices, lattice defects, alloy systems, and surface‐related properties such as surface reconstruction, surface passivation, and adatom migration during thin film growth. The empirical interatomic potentials, pseudopotential, and stochastic Monte Carlo methods are used. An overview of these issues is provided and the latest achievements are presented to illustrate the capability of the theoretical‐computational approach by comparing experimental results. The constituents of the semiconductors that are... read less NOT USED (low confidence) M. Ichimura and J. Narayan, “Role of surface step on misfit dislocation nucleation and critical thickness in semiconductor heterostructures,” Materials Science and Engineering B-advanced Functional Solid-state Materials. 1995. link Times cited: 24 NOT USED (low confidence) K. Kakimoto, “Molecular dynamics simulation of mass transfer in molten silicon,” Journal of Applied Physics. 1995. link Times cited: 12 Abstract: The diffusion constant in a silicon melt is calculated using… read moreAbstract: The diffusion constant in a silicon melt is calculated using molecular dynamics simulation based on the modified Stillinger–Weber [Phys. Rev. B 31, 5262 (1985)] interatomic potential in the temperature range 1550 Kread less NOT USED (low confidence) J. Feldman and M. Kluge, “Realistic model calculations based on the Kubo theory for the thermal conductivity of amorphous insulators,” Philosophical Magazine Part B. 1995. link Times cited: 10 Abstract: The thermal conductivity of models of amorphous silicon and … read moreAbstract: The thermal conductivity of models of amorphous silicon and vitreous silica are discussed. In previous work on amorphous silicon, 216-and 1000-atom models were studied within the Kubo theory and the harmonic approximation using the Stillinger-Weber potential and good agreement with the experimental high-temperature apparent saturation value was obtained. In order to test the model dependence of such results we performed calculations for models based on the Keating potential. The Keating model apparently gives much less force-constant disorder than does the Stillinger-Weber model, as evident from the N dependence and the frequency range of localized states. We also present results of calculations for vitreous silica based on the Feuston-Garofalini model that we relaxed, using their potential, to zero pressure. The results for vitreous silica are in fair agreement with experiment at temperatures above 100K which corresponds to the lowest normal-mode frequency contained within the model. read less NOT USED (low confidence) M. Greuter et al., “KR INCORPORATION IN SPUTTERED AMORPHOUS SI LAYERS,” Journal of Applied Physics. 1995. link Times cited: 5 Abstract: Amorphous Si layers were grown by krypton plasma sputter dep… read moreAbstract: Amorphous Si layers were grown by krypton plasma sputter deposition at 310 °C. By pulsation of the substrate potential between 0 and 50 eV, the Kr concentration in the layers could be varied to a maximum of 5.5 at. %. A model which describes trapping of inert gas atoms in the sputtered layer in terms of implantation and trapping, diffusion, growth, resputtering, and gas sputtering is presented. High‐resolution electron microscopy, electrode‐probe (x‐ray) microanalysis, positron annihilation, Raman spectroscopy, Mossbauer spectroscopy, and bending and hardness measurements were performed on the deposited layers. It turns out that the ion assisted growth leads to a strong reduction of open volume defects. The experiments point to the presence of very small Kr agglomerates. From the Mossbauer experiments a lower limit of 250 K for the Debye temperature of the Kr agglomerates is derived. Molecular‐dynamic simulations from which the Debye temperatures of Kr mono‐, di‐, and trimers in amorphous Si can be derive... read less NOT USED (low confidence) R. M. MV and Atwater, “Empirical interatomic potential for Si-H interactions.,” Physical review. B, Condensed matter. 1995. link Times cited: 99 Abstract: An empirical TersofF-type interatomic potential has been dev… read moreAbstract: An empirical TersofF-type interatomic potential has been developed for describing Si-H interactions. The potential gives a reasonable fit to bond lengths, angles and energetics of silicon hydride molecules and hydrogen-terminated silicon surfaces. The frequencies of most vibrational modes are within 15% of the experimental and ab initio theory values. The potential is computationally efficient and suitable for molecular dynamics investigations of various processing treatments of hydrogen-terminated silicon surfaces. read less NOT USED (low confidence) M. Caturla, T. D. Rubia, and M. Jaraíz, “Atomic scale simulations of arsenic ion implantation and annealing in silicon,” MRS Proceedings. 1995. link Times cited: 4 Abstract: We present results of multiple-time-scale simulations of 5, … read moreAbstract: We present results of multiple-time-scale simulations of 5, 10 and 15 keV low temperature ion implantation of arsenic on silicon (100), followed by high temperature anneals. The simulations start with a molecular dynamics (MD) calculation of the primary state of damage after 10ps. The results are then coupled to a kinetic Monte Carlo (MC) simulation of bulk defect diffusion and clustering. Dose accumulation is achieved considering that at low temperatures the damage produced in the lattice is stable. After the desired dose is accumulated, the system is annealed at 800{degrees}C for several seconds. The results provide information on the evolution for the damage microstructure over macroscopic length and time scales and affords direct comparison to experimental results. We discuss the database of inputs to the MC model and how it affects the diffusion process. read less NOT USED (low confidence) C. Kui-ying, L. Hongbo, and H. Zhuangqi, “LOCAL ORIENTATIONAL ORDER IN BINARY-LIQUID LI-IN ALLOYS,” Journal of Physics: Condensed Matter. 1995. link Times cited: 8 Abstract: The local orientational order in binary liquid Li-In alloys … read moreAbstract: The local orientational order in binary liquid Li-In alloys at a constant temperature has been systematically studied using molecular dynamics simulations combined with potential mapping techniques. The generalized non-local model pseudopotential theory has been chosen as the fundamental theory for our calculation. Both the orientational order parameters and pair analysis approach have been adopted to examine the characterization of structures in binary liquid Li-In alloys. It demonstrates that the mapping procedure produces a significant image enhancement of the short-range order, and the third-order invariant of the spherical harmonics is much more sensitive to the icosahedral symmetry than is the quadratic invariant. In addition, the bonded pairs with various symmetries, icosahedra, defective icosahedra, etc, formed in liquid Li-In alloys are also examined and the relationship between these quantities and compositions are investigated. The results further show that distributions of the attractive part of the potentials play an important role in characterizing liquid structures. Finally, a detailed discussion of the results has been given. read less NOT USED (low confidence) L. E. Carter and E. Carter, “F2 reaction dynamics with defective Si(100): defect-insensitive surface chemistry,” Surface Science. 1995. link Times cited: 21 NOT USED (low confidence) F. Streitz and J. Mintmire, “Electrostatic-based model for alumina surfaces,” Thin Solid Films. 1994. link Times cited: 12 NOT USED (low confidence) Y. Xia, C. Tan, Y. Xing, H. Yang, X. Sun, and B. Gong, “Molecular-Dynamics Simulation of Surface Relaxation for Tersoff-Dodson Type (100) Si,” Chinese Physics Letters. 1994. link Times cited: 1 Abstract: Surface relaxation and lattice dynamics of (100) Si have bee… read moreAbstract: Surface relaxation and lattice dynamics of (100) Si have been studied using Tersoff-Dodson type Si potential. The average temperature of the lattice is studied as well. The temperature fluctuates with a frequency of 9.5 × 1012 Hz, that is about the average frequency of the optical phonons in Si. The (100) Si surface relaxes inward by 0.86 Å, and a reduction of 19% in the first interlayer spacing is found. read less NOT USED (low confidence) F. Streitz and J. Mintmire, “Electrostatic potentials for metal-oxide surfaces and interfaces.,” Physical review. B, Condensed matter. 1994. link Times cited: 288 Abstract: As most technologically important metals will form oxides re… read moreAbstract: As most technologically important metals will form oxides readily, any complete study of adhesion at real metal surfaces must include the metal-oxide interface. The role of this ubiquitous oxide layer cannot be overlooked, as the adhesive properties of the oxide or oxide-metal system can be expected to differ profoundly from the adhesive properties of a bare metal surface. We report on the development of a computational method for molecular-dynamics simulations, which explicitly includes variable charge transfer between anions and cations. This method is found to be capable of describing the elastic properties, surface energies, and surface relaxation of crystalline metal oxides accurately. We discuss in detail results using this method for \ensuremath{\alpha}-alumina and several of its low-index faces. read less NOT USED (low confidence) J. B. Adams et al., “Atomic-level computer simulation,” Journal of Nuclear Materials. 1994. link Times cited: 17 NOT USED (low confidence) M. Schreiber and B. Lamberts, “Determination of parameter-free model potentials for the molecular dynamics simulation of amorphous semiconductors — application to silicon,” Journal of Molecular Structure-theochem. 1994. link Times cited: 0 NOT USED (low confidence) Z. Jiang and R. A. Brown, “Modelling oxygen defects in silicon crystals using an empirical interatomic potential,” Chemical Engineering Science. 1994. link Times cited: 14 NOT USED (low confidence) D. Maroudas and S. Pantelides, “Point defects in crystalline silicon, their migration and their relation to the amorphous phase,” Chemical Engineering Science. 1994. link Times cited: 11 NOT USED (low confidence) M. D. Souza and G. Amaratunga, “A study of the configurations of boron in silicon using an empirical approach,” Computational Materials Science. 1994. link Times cited: 1 NOT USED (low confidence) J. Wong et al., “The threshold energy for defect production in SiC : a molecular dynamics study,” Journal of Nuclear Materials. 1994. link Times cited: 26 NOT USED (low confidence) G. Gilmer and C. Roland, “Simulations of crystal growth: Effects of atomic beam energy,” Applied Physics Letters. 1994. link Times cited: 56 Abstract: We have simulated silicon molecular beam epitaxy on (100) an… read moreAbstract: We have simulated silicon molecular beam epitaxy on (100) and (111) substrates using molecular dynamics methods. We find that the kinetic energy of the atomic beam has a dramatic effect on the crystalline ordering in the deposit. Energetic beams form a crystalline film at less than half the absolute temperature required for a thermal beam. Our simulations show that crystallization is facilitated by the transient atomic motion just after the impact of an atom from the beam. read less NOT USED (low confidence) P. T. Dinda, G. Vlastou-Tsinganos, N. Flytzanis, and A. Mistriotis, “The melting behaviour of small silicon clusters,” Physics Letters A. 1994. link Times cited: 6 NOT USED (low confidence) C. Toh and C. K. Ong, “Effects of an anomalous strain accommodating behavior of Si ad-dimers on the nucleation of regular and defect islands,” Surface Science. 1994. link Times cited: 0 NOT USED (low confidence) K. Ishibashi, K. Tsumuraya, and S. Nakata, “Local vibrational densities of states in glasses: Numerical study of a model of amorphous silicon,” Journal of Chemical Physics. 1994. link Times cited: 3 Abstract: We analyze for the first time the relation between the shape… read moreAbstract: We analyze for the first time the relation between the shape of the local vibrational densities of states (LDOSs) and the local environments of atoms in glasses. We calculated the LDOSs in model silicon glasses by use of a recursion method. The glasses are produced by a constant pressure molecular dynamics method with a three‐body potential by Stillinger and Weber. The transverse optic (TO) peaks reduce in height with an increase of the number of the coordinated atoms. The heights of the TO peaks also decrease with the increase of the number of the coordinated atoms that have (2,3,0) Voronoi signature. The heights of the transverse acoustic peak are insensitive to the number of bonds. The origin of the decrease of the TO peak is discussed. The slopes of the low frequency side of the LDOSs are insensitive to the local structure of the glasses. The long‐range force field in the present glass is the same as that in the crystal state. read less NOT USED (low confidence) K. M. Nelson, C. Cornwell, and L. Wille, “Massively parallel computer simulations of fullerenes and Si-clusters,” Computational Materials Science. 1994. link Times cited: 7 NOT USED (low confidence) G. Gilmer and C. Roland, “Applications of molecular dynamics methods to low energy ion beams and film deposition processes,” Radiation Effects and Defects in Solids. 1994. link Times cited: 12 Abstract: Molecular dynamics methods are used to model the impingement… read moreAbstract: Molecular dynamics methods are used to model the impingement of low energy ions onto crystalline targets, and the effects of these beams on thin film deposition. Simulations of the deposition of silicon films show that the structure of deposits can often be improved by the use of low energy ion beams instead of the conventional thermal beam. We examine the influence of beam energy on the formation of amorphous or crystalline deposits. The influence of ion beams on surface diffusion rates and the interdiffusion between atomic layers near the surface are also considered. Cluster deposition is treated, and the results suggest that cluster beams would be effective for depositing smooth films of materials that do not wet the substrate. We discuss the use of special purpose computers and signal processing boards to extend the time scales of molecular dynamics simulations. Rapid advances in computer hardware, algorithms, and the development of accurate interatomic potentials are dramatically increasing ... read less NOT USED (low confidence) M. Tosi, “Structure of covalent liquids,” Journal of Physics: Condensed Matter. 1994. link Times cited: 28 Abstract: Bond directionality and network formation from local structu… read moreAbstract: Bond directionality and network formation from local structural units are the signature of covalent bonding. On melting a 3D network of covalent bonds tends to break into a metallic liquid (e.g. in Si, Ge and GaAs), unless a sufficiently large electronegativity difference between the components stabilizes the electronic structure through chemical short-range order. The melt may then be a semimetal (e.g. Li4Pb and KPb), an ionic semiconductor (e.g. CsAu) or an insulator (e.g. ZnCl2). Bonding appears to be more stable in networks of lower dimensionality (D=2 as in GeSe2 and YCl3, D=1 as in Se and BeCl2, and D=0 as in P, SbCl3 and AlBr3). Melting from D=2 to D=0 occurs in AlCl3. Intermediate-range order may be preserved in the melt through interatomic correlations over distances of order 5-10 AA. The experimental evidence on illustrative examples of these various trends is reviewed, with emphasis on the interconnection between stable local coordination and intermediate-range order. Parallel illustrations are given of results from simulations based on empirical potentials or fully quantal methods, from data analysis based on the Reverse Monte Carlo method and from primitive models amenable to integral-equations techniques. read less NOT USED (low confidence) G. Myakenkaya, G. L. Gutsev, N. Gerasimenko, V. Frolov, M. A. Chubisov, and J. Corbett, “Self-interstitial complexes in silicon,” Radiation Effects and Defects in Solids. 1994. link Times cited: 2 Abstract: Calculations of space geometry and electron structure of sel… read moreAbstract: Calculations of space geometry and electron structure of self-interstitial atoms (IAs) in Si have been made in cluster approximation by using self-consistent discrete variational Xα-method (DV-Xα), semiempirical MINDO/3 method and molecular dynamic method (MD). The results of DV-Xαcalculation show that a high state density in the band gap and various spin states are observed for interstitial complexes. As follows from the analysis of the data obtained, the methods resulting from neglecting the differential overlapping, can not be used for satisfactory description of IAs properties. MD calculations prove the existence of a new stable configuration, oriented in one of the plane equivalent to (110) and containing a pair of IAs in tetrahedral cavity. The results of theoretical analysis are compared with those available in literature on the properties of IAs in Si. read less NOT USED (low confidence) L. Miller, D. Brice, A. Prinja, and S. T. Picraux, “Molecular dynamics simulations of bulk displacement threshold energies in Si,” Radiation Effects and Defects in Solids. 1994. link Times cited: 19 Abstract: Molecular dynamics (MD) calculations of the bulk threshold d… read moreAbstract: Molecular dynamics (MD) calculations of the bulk threshold displacement energies in single crystal silicon are carried out using the Tersoff potential. The threshold values are angularly dependent and typically vary from 10 to 20 eV for initial primary recoil momentum vectors near open directions in the lattice. An analytic representation of the angular dependence of the threshold values about the and is developed to facilitate comparison with experiment read less NOT USED (low confidence) M. V. Ramakrishna and J.-W. Pan, “Chemical reactions of silicon clusters,” Journal of Chemical Physics. 1994. link Times cited: 27 Abstract: Smalley and co‐workers discovered that chemisorption reactiv… read moreAbstract: Smalley and co‐workers discovered that chemisorption reactivities of silicon clusters vary over three orders of magnitude as a function of cluster size. In particular, they found that Si33, Si39, and Si45 clusters are least reactive towards various reagents compared to their immediate neighbors in size. We explain these observations based on our stuffed fullerene model. This structural model consists of bulk‐like core of five atoms surrounded by fullerene‐like surface. Reconstruction of the ideal fullerene geometry gives rise to fourfold coordinated crown atoms and π‐bonded dimer pairs. This model yields unique structures for Si33, Si39, and Si45 clusters without any dangling bonds and thus explains their lowest reactivity towards chemisorption of closed shell reagents. This model is also consistent with the experimental finding of Jarrold and Constant that silicon clusters undergo a transition from prolate to spherical shapes at Si27. We justify our model based on an in depth analysis of the differences ... read less NOT USED (low confidence) K. Gärtner, D. Stock, C. Wende, and M. Nitschke, “Low energy B-channeling in Si,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1994. link Times cited: 9 NOT USED (low confidence) W. Möller, “Computer simulation of ion-beam assisted film growth,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1994. link Times cited: 1 NOT USED (low confidence) S. B. Zhu and M. R. Philpott, “Interaction of water with metal surfaces,” Journal of Chemical Physics. 1994. link Times cited: 85 Abstract: A new class of potential suitable for modeling the adsorptio… read moreAbstract: A new class of potential suitable for modeling the adsorption of water on different metal sites is described. The new potentials are simple in form and convenient for use in computer simulations. In their real space form they comprise three parts: A pairwise sum of spatially anisotropic 12‐6 potentials, a pairwise sum of isotropic short range potentials, and an image potential. Two modifications of the potential are developed. In the first, the anisotropic potential acts only on the oxygen atom and not on the protons. In the second, the potential acts on all the atoms of the water molecule. In practical calculations it is convenient to transform the potential to a reciprocal space form in the manner described by Steele [Surf. Sci. 36, 317 (1973)]. Adsorption of water at top, bridge, and hollow sites on (100), (110), and (111) surfaces of Pt, Ni, Cu, and Al were studied using two fitting parameters and the results compared with previous theoretical calculations. read less NOT USED (low confidence) P. Alinaghian, S. R. Nlshltani, and D. Pettifor, “Shear constants using angularly dependent bond order potentials,” Philosophical Magazine Part B. 1994. link Times cited: 19 Abstract: Analytic expressions for the shear constants of sp-valent zi… read moreAbstract: Analytic expressions for the shear constants of sp-valent zincblende and f.c.c. structure types are obtained using a first-nearest-neighbour bond order potential. Novel expressions for the tetragonal and trigonal zincblende shear constant C' and C 44 are derived. ImportantlyC' is found to vary as the cube of the bond order. The angular character of the bond order potential is shown to remove the anisotropy constraint of C 44/C' = 2 for f.c.c. lattices within a nearest-neighbour model. read less NOT USED (low confidence) J. Hafner, “Structural, electronic and magnetic properties of liquid, amorphous and quasicrystalline metals,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 1994. link Times cited: 5 NOT USED (low confidence) R. A. Brown, D. Maroudas, and T. Sinno, “Modelling point defect dynamics in the crystal growth of silicon,” Journal of Crystal Growth. 1994. link Times cited: 81 NOT USED (low confidence) D. N. Bernardo, R. Bhatia, and B. Garrison, “keV particle bombardment of solids: molecular dynamics simulations and beyond,” Computer Physics Communications. 1994. link Times cited: 16 NOT USED (low confidence) L. E. Carter, S. Khodabandeh, P. Weakliem, and E. Carter, “First‐principles‐derived dynamics of F2 reactive scattering on Si(100)‐2×1,” Journal of Chemical Physics. 1994. link Times cited: 41 Abstract: We have simulated via molecular dynamics the interaction of … read moreAbstract: We have simulated via molecular dynamics the interaction of F2 with the clean Si(100)‐2×1 reconstructed surface. Using a Stillinger–Weber‐type many‐body potential with the Si–F interactions refit to ab initio data, we find that both vibrational and translational excitation of the incident F2 can lead to increased reactivity, but they do so in different ways. The dominant reaction channels are (a) F‐atom abstraction, leading to the formation of one Si–F bond while the remaining fluorine atom is ejected away from the surface, and (b) dissociative chemisorption, where both fluorine atoms in the incident F2 molecule form Si–F bonds on the surface. Nonreactive scattering is almost never observed. As a result, enhanced reactivity is mainly characterized by an increase in dissociative chemisorption at the expense of F‐atom abstraction and by a corresponding increase in the initial reaction probability S0. We find S0 ranges from 0.57±0.04 for the lowest excitation energies to 0.78±0.04 for the largest translation... read less NOT USED (low confidence) J. P. Shih, S. Sheu, and C. Mou, “A Voronoi polyhedra analysis of structures of liquid water,” Journal of Chemical Physics. 1994. link Times cited: 50 Abstract: Molecular dynamics simulations have been carried out for sin… read moreAbstract: Molecular dynamics simulations have been carried out for sinple point charge (SPC) water, in normal, compressed, and stretched states. A detailed analysis of local structures using both pair correlation and Voronoi polyhedra distribution, which describes the information about the multiparticle distribution, was reported. We examine the oxygen–oxygen pair correlation function and the distributions of Voronoi polyhedra in response to the variation of density and temperature. The asphericity distributions of Voronoi polyhedra reveals the anisotropicity of local arrangements of water molecules. It is found local pair distributions depend on the asphericities of center molecules. A high value of the asphericity parameter η corresponds to an icelike local structure of tetrahedrally bonded network patch. Loosely bonded structures, with low value of asphericity, have much less hydrogen bonding, and they are more susceptible to density fluctuation. Partition of local structures according to the asphericity of Voro... read less NOT USED (low confidence) P. Šandera and J. Pokluda, “Improvement of the Mackenzie theory on ideal shear strength,” Scripta Metallurgica Et Materialia. 1993. link Times cited: 12 NOT USED (low confidence) T. Kaplan, M. Chisholm, and M. Mostoller, “Simulations of the dislocation array at Ge/Si interfaces,” MRS Proceedings. 1993. link Times cited: 0 Abstract: When Ge is grown epitaxially on Si(001), the 4% mismatch bet… read moreAbstract: When Ge is grown epitaxially on Si(001), the 4% mismatch between the lattice parameters of Ge and Si can produce a regular two-dimensional grid of (a/2) [1,{plus_minus}1,0] edge dislocations at the interface, a checkerboard with a spacing of {approximately} 100 {Angstrom}. We have performed classical molecular dynamical simulations of this checkboard in large microcrystals. Results show the expected 5-fold plus 7-fold ring structure at the cores of the individual dislocations, and a new closed symmetric structure of 18 atoms at their intersections. Tetrahedral coordination is everywhere retained, with relatively small changes in the bond lengths of less than 10 and in the bond angles of less than 25%. The energetics and dislocation offset of the system are explored for the Stillinger-Weber and Tersoff potentials. read less NOT USED (low confidence) J. Chelikowsky and N. Binggeli, “First principles simulation of liquid silicon,” Solid State Communications. 1993. link Times cited: 11 NOT USED (low confidence) M. J. Uttormark, M. Thompson, L. A. Báez, and P. Clancy, “Solid/Liquid Cluster Recognition in Heterogeneous Systems,” Molecular Simulation. 1993. link Times cited: 13 Abstract: Criteria are presented which enable the differentiation betw… read moreAbstract: Criteria are presented which enable the differentiation between the extent of solid-like and liquid-like character in a heterogeneous system on a per atom basis. Such criteria are developed for two different interatomic potentials, the Stillinger-Weber model for group IV semiconductors and the Lennard-Jones model for insulators. For the Stillinger-Weber potential model, three criteria are presented: one based on the coordination number of nearest neighbors, one based on the three-body energy, and one based on the angular positions (spatial arrangements) of neighbors. For the Lennard-Jones model an angular criterion is used. The difficulties associated with the assignation of interfacial atoms (those with partial solid and partial liquid character) are discussed. The effectiveness of these criteria for both models is tested by application to the identification of solid-like nuclei in the melt. read less NOT USED (low confidence) D. Vvedensky, N. Haider, T. Shitara, S̆milauer P., and J. L. Beeby, “Evolution of surface morphology during epitaxial growth,” Philosophical Transactions of the Royal Society of London. Series A: Physical and Engineering Sciences. 1993. link Times cited: 11 Abstract: We examine the type of information that can be obtained from… read moreAbstract: We examine the type of information that can be obtained from Monte Carlo simulations of epitaxial growth. A basic model will be first introduced and some of the features that make it suitable for describing both atomic-scale processes and large-scale morphologies will be pointed out. The ability of this model to reproduce experimental data will then be addressed. The first example discussed will be growth on GaAs(OO1) vicinal surfaces, where the density of surface steps on the simulated surfaces reproduces quantitatively the evolution of the reflection high-energy electron diffraction (RHEED) intensity oscillations for appropriately chosen growth and diffraction conditions. This work will then be used as a basis for examining the predictions of the simulated surface morphologies on patterned substrates, based on comparisons with micro-RHEED measurements. Extensions of the basic model to more complex growth scenarios where the atomic constituents are delivered in the form of heteroatomic molecules will also be discussed. read less NOT USED (low confidence) X. Gong, Q. Zheng, and Y.-zhen He, “Structural properties of silicon clusters: an empirical potential study,” Journal of Physics: Condensed Matter. 1993. link Times cited: 14 Abstract: By using our newly proposed empirical interatomic potential … read moreAbstract: By using our newly proposed empirical interatomic potential for silicon, the structure and some dynamical properties of the silicon cluster Sin (10read less NOT USED (low confidence) A. Mistriotis, A. Zdetsis, G. Froudakis, and M. Menon, “Reproduction of quantum tight-binding effects in silicon clusters by a four-body classical model,” Journal of Physics: Condensed Matter. 1993. link Times cited: 0 Abstract: The results obtained by a recently proposed empirical potent… read moreAbstract: The results obtained by a recently proposed empirical potential for silicon which includes four-body terms are compared with the results of quantum-mechanical tight-binding calculations. In particular, the ground-state energy and structure of the Si33 cluster were computed by both methods. By performing an equivalent calculation using only up to three-body interactions the authors demonstrate that the four-body term is absolutely necessary in order to achieve good agreement with the quantum method. read less NOT USED (low confidence) P. Alinaghian, P. Gumbsch, A. Skinner, and D. Pettifor, “Bond order potentials: a study of s- and sp-valent systems,” Journal of Physics: Condensed Matter. 1993. link Times cited: 20 Abstract: The relative structural stability of s- and sp-valent system… read moreAbstract: The relative structural stability of s- and sp-valent systems is examined within the fourth-moment approximation to the recently derived tight binding bond order potentials. At this low level of approximation the authors find that the application of a sum rule constraint to the choice of terminator is necessary to get good results. In particular, the competition between graphite, diamond and simple cubic sp-valent lattices is modelled well by the new angularly dependent bond order potentials. read less NOT USED (low confidence) S. J. Cook and P. Clancy, “Impurity segregation in Lennard‐Jones A/AB heterostructures. I. The effect of lattice strain,” Journal of Chemical Physics. 1993. link Times cited: 35 Abstract: The solidification kinetics of Lennard‐Jones heterostructure… read moreAbstract: The solidification kinetics of Lennard‐Jones heterostructures are investigated using nonequilibrium molecular dynamics computer simulation techniques. The heterostructures are of the form A/A1−xBx. In this paper, the nature of the A and B atoms comprising the alloy differ only in size, the B atoms being 10% larger than the A atoms. The segregation of the solute B atoms from the solid into both a surface‐melted thin film (wetting the solid–vapor interface) and into a bulk‐liquid phase following energy input from a simulated laser pulse is studied. The segregation of the (impurity) B atoms into the liquid is found to be enhanced at the (111) orientation when the AB alloy is under strain, but enhanced on the (100) orientation when the alloy is strain free. Comparison to the solute redistribution theories of Aziz (the continuous growth model) and of Jackson, Gilmer, and Leamy shows good agreement with the simulation‐derived segregation coefficients in most cases. The periodic stepwise growth model of Aziz is ... read less NOT USED (low confidence) C. S. Carmer, B. Weiner, and M. Frenklach, “Molecular dynamics with combined quantum and empirical potentials: C2H2 adsorption on Si(100),” Journal of Chemical Physics. 1993. link Times cited: 71 Abstract: Classical trajectory calculations were employed to study the… read moreAbstract: Classical trajectory calculations were employed to study the reaction of acetylene with dimer sites on the Si(100) surface at 105 K. Two types of potential energy functions were combined to describe interactions for different regions of the model surface. A quantum mechanical potential based on the semiempirical AM1 Hamiltonian was used to describe interactions between C2H2 and a portion of the silicon surface, while an empirically parametrized potential was developed to extend the size of the surface and simulate the dynamics of the surrounding silicon atoms. Reactions of acetylene approaching different sites were investigated, directly above a surface dimer, and between atoms from separate dimers. In all cases, the outcome of C2H2 surface collisions was controlled by the amount of translational energy possessed by the incoming molecule. Acetylene molecules with high translational energy reacted with silicon dimers to form surface species with either one or two Si–C bonds. Those molecules with low transl... read less NOT USED (low confidence) R. Gallego and M. Ortiz, “A harmonic/anharmonic energy partition method for lattice statics computations,” Modelling and Simulation in Materials Science and Engineering. 1993. link Times cited: 21 Abstract: A method of lattice statics analysis is developed. Considera… read moreAbstract: A method of lattice statics analysis is developed. Consideration of anharmonic effects is restricted to finite regions surrounding lattice defects. All displacements of the crystal are expressed as the effect of unknown forces applied to a perfect harmonic lattice of infinite extent. Displacements are related to the unknown applied forces by means of the Green function of the perfect harmonic lattice, so that equilibrating forces need only be applied to the anharmonic region. The unknown forces are determined so as to maximize the complementary energy of the crystal, which yields a lower bound to the potential energy. The method does not require the explicit enforcement of equilibrium or compatibility conditions across the boundary between the harmonic and anharmonic regions. The performance of the method is assessed on the basis of selected numerical examples. The rate of convergence of the method with increasing domain size is found to be cubic. This is one or two orders of magnitude faster than rigid boundary methods based on the harmonic and continuum solutions, respectively. read less NOT USED (low confidence) U. Landman, R. Barnett, C. L. Cleveland, and W. Luedtke, “Materials by numbers,” Physica D: Nonlinear Phenomena. 1993. link Times cited: 2 NOT USED (low confidence) D. Anderson, J. Kieffer, and S. Klarsfeld, “Molecular dynamic simulations of the infrared dielectric response of silica structures,” Journal of Chemical Physics. 1993. link Times cited: 22 Abstract: The molecular dynamic simulation technique was used to model… read moreAbstract: The molecular dynamic simulation technique was used to model the vibrational behavior of crystalline (α and β cristobalite) and amorphous silica structures. To this end a refined potential function was developed, which allows one to reproduce the correct structural geometries, the corresponding infrared spectra, and to observe a reversible phase transformation between α and β cristobalite. The complex dielectric constants in the infrared frequency range were calculated from the dipole moment time correlation functions. While idealized cristobalite exhibits the simplest spectrum with only two narrow bands, the increase of structural complexity and reduction of symmetry characteristic for the real cristobalites and amorphous silica, creates additional features in the infrared spectra. These structural changes predominantly affect the coordination of oxygen, and generate a broader spread in the normal modes characterizing the vibrations of this species. A unique method for the identification of atomic trajec... read less NOT USED (low confidence) W. Jian, Z. Jian, Z. Kaiming, and X. Xide, “STRUCTURES OF Si AND Ge CLUSTERS UNDER MODIFIED STILLINGER-WEBER POTENTIAL,” Acta Physica Sinica (overseas Edition). 1993. link Times cited: 0 Abstract: Structural behaviors of silicon and germanium clusters under… read moreAbstract: Structural behaviors of silicon and germanium clusters under the recently proposed modified Stillinger-Weber (SW) potential have been studied by molecular dynamics method along with the conjugate-gradient optimization. Since the SW potentials have been derived from the properties of bulk materials, it gives relatively large discrepancy when the cluster number is small, e. g. n=3 and 4. When n>4, the ground-state structures under the modified SW potential are close to that from the first-principle calculation. The binding energies are also improved under the modified SW potential. These results may be attributed to the relative enhancement of the two-body term over the three-body term in the modified SW potential, which leads to structures with a preferential coordination number 4. Structural behaviors of germanium clusters are similar to those of silicon. read less NOT USED (low confidence) Tsumuraya, Ishibashi, and Kusunoki, “Statistics of Voronoi polyhedra in a model silicon glass.,” Physical review. B, Condensed matter. 1993. link Times cited: 14 Abstract: We clarify the local structure in a model silicon glass by u… read moreAbstract: We clarify the local structure in a model silicon glass by use of Voronoi-polyhedron analysis. The glass is produced by molecular dynamics with a Stillinger-Weber potential. The atoms in the glass are nearly distinguishable: there are about 200 types in the system with 216 atoms. The analysis clarifies that the polyhedra are formed by a small number of large-area polygons or by a large number of small-area polygons. This feature is different from those in Lennard-Jones glasses or metallic glasses and is attributed to the loose-packed structure even in the glass state, in which the atoms still have directional bonding read less NOT USED (low confidence) R. Kalia, S. W. Leeuw, A. Nakano, and P. Vashishta, “Molecular dynamics simu-lations of Coulombic systems on ditributed-memory MIMD machines,” Computer Physics Communications. 1993. link Times cited: 33 NOT USED (low confidence) J. Kew, M. Wilby, and D. Vvedensky, “Continuous-space Monte Carlo simulations of epitaxial growth,” Journal of Crystal Growth. 1993. link Times cited: 13 NOT USED (low confidence) C. Toh and C. K. Ong, “Diffusion and interconversion of ’defect’ ad-dimers on the Si(001) 2*1 surface: a molecular statics study,” Journal of Physics: Condensed Matter. 1993. link Times cited: 7 Abstract: The authors use a modified form of the Stillinger-Weber pote… read moreAbstract: The authors use a modified form of the Stillinger-Weber potential to obtain the binding energy and geometry of a number of Si ad-dimer structures on the fully relaxed Si(001) 2*1 surface by canonical Monte Carlo simulation. At low temperatures they show the possible existence of two kinds of 'defect' ad-dimers which may hinder normal 1*2 growth. The mechanisms for both diffusion and interconversion of such dimers are then elucidated by examining their associated minimum-energy paths. read less NOT USED (low confidence) D. Maroudas and R. A. Brown, “Atomistic calculation of the self‐interstitial diffusivity in silicon,” Applied Physics Letters. 1993. link Times cited: 34 Abstract: Formation and migration properties of self‐interstitial atom… read moreAbstract: Formation and migration properties of self‐interstitial atoms in silicon are calculated using systematic atomistic simulations based on the Stillinger–Weber interatomic potential [F. H. Stillinger and T. A. Weber, Phys. Rev. B 31, 5262 (1985)]. The lowest energy configuration of an interstitial atom is calculated to be an extended configuration with a formation energy that is 1.2 eV lower than the formation energy of the higher symmetry configuration with lowest energy. A mechanism for the interpretation of dopant diffusion data is proposed based on this result. The calculated lower bound for the diffusion coefficient of self‐interstitials described by a simple migration path is in good agreement with experimental data over the temperature range 733 K read less NOT USED (low confidence) W. G. Hoover, “Nonequilibrium molecular dynamics at Livermore and Los Alamos.” 1993. link Times cited: 2 NOT USED (low confidence) S. M. Lee, C. G. Hoover, J. Kallman, W. G. Hoover, A. J. D. Groot, and F. Wooten, “Computational diagnostics for detecting phase transitions during nanoindentation,” MRS Proceedings. 1992. link Times cited: 0 Abstract: We study nanoindenmtion of silicon using nonequilibrium mole… read moreAbstract: We study nanoindenmtion of silicon using nonequilibrium molecular dynamics simulations. with up to a million particles. Both crystalline and amorphous silicon samples are considered. We use compumtional diffraction pattems as a diagnostic tool for detecting phase transitions resulting from structural changes. Simulations of crystalline samples show a transition to the amorphous phase in a region a few atomic layers thick surrounding the lateral faces of the indenter, as has been suggested by experimental results. Our simulation results provide estimates for the yield strength (nanohardness) of silicon for a range of temperatures. read less NOT USED (low confidence) J. Siepmann and M. Sprik, “Ordering of fractional monolayers of H2O on Ni(110),” Surface Science. 1992. link Times cited: 17 NOT USED (low confidence) W. Luedtke and U. Landman, “Solid and liquid junctions,” Computational Materials Science. 1992. link Times cited: 33 NOT USED (low confidence) E. Kaxiras and L. L. Boyer, “Exploring the structure of solids through magic strains: prediction of a new metallic phase of Si,” Modelling and Simulation in Materials Science and Engineering. 1992. link Times cited: 8 Abstract: A new approach that allows thorough exploration of low-energ… read moreAbstract: A new approach that allows thorough exploration of low-energy structures with arbitrary symmetry for any material is presented, along with an application to silicon. This approach, coupled with first-principles total-energy calculations, has led the authors to discover a previously unknown metastable structure of Si. The physical properties of this structure and the insight they afford to metallic versus covalent bonding and the nature of the amorphous and liquid phases are discussed. read less NOT USED (low confidence) M. Rouhani, A. Gué, M. Sahlaoui, and D. Estève, “Strained semiconductor structures: simulation of the first stages of the growth,” Surface Science. 1992. link Times cited: 16 NOT USED (low confidence) R. Fournier, S. Sinnott, and A. Depristo, “Density functional study of the bonding in small silicon clusters,” Journal of Chemical Physics. 1992. link Times cited: 90 Abstract: We report the ground electronic state, equilibrium geometry,… read moreAbstract: We report the ground electronic state, equilibrium geometry, vibrational frequencies, and binding energy for various isomers of Sin(n = 2–8) obtained with the linear combination of atomic orbitals‐density functional method. We used both a local density approximation approach and one with gradient corrections. Our local density approximation results concerning the relative stability of electronic states and isomers are in agreement with Hartree–Fock and Mo/ller–Plesset (MP2) calculations [K. Raghavachari and C. M. Rohlfing, J. Chem. Phys. 89, 2219 (1988)]. The binding energies calculated with the gradient corrected functional are in good agreement with experiment (Si2 and Si3) and with the best theoretical estimates. Our analysis of the bonding reveals two limiting modes of bonding and classes of silicon clusters. One class of clusters is characterized by relatively large s atomic populations and a large number of weak bonds, while the other class of clusters is characterized by relatively small s atomic p... read less NOT USED (low confidence) D. Athanasopoulos and S. Garofalini, “Molecular dynamics simulations of the effect of adsorption on SiO2 surfaces,” Journal of Chemical Physics. 1992. link Times cited: 36 Abstract: Molecular dynamics computer simulations were used to study t… read moreAbstract: Molecular dynamics computer simulations were used to study the adsorption of model Pt on silica and the effect of this adsorption on the structure of the silica surface. Silica glass and amorphized crystalline surfaces were used as the silica substrates. Results showed a 5–6 A thick adsorbate/substrate interface and an approximately 1 A compression of the substrate surface caused by the presence of the adsorbate film. A significant decrease in the Si–O–Si bond‐angle distribution was observed as a result of the adsorption. The shift to smaller bond angles was caused by a distortion of the siloxane bonds in five‐ and six‐membered rings rather than the formation of small sized rings. The smaller bond angles indicate that more reactive sites may exist in the surface. read less NOT USED (low confidence) W. Niessen and V. G. Zakrzewski, “Complex Electron Affinity Processes in Clusters of S and Si.” 1992. link Times cited: 2 Abstract: Vertical and in some cases adiabatic electron affinities are… read moreAbstract: Vertical and in some cases adiabatic electron affinities are calculated for the clusters S4 and Sin, n = 3 – 7 with large basis sets. The effects of electron correlation are taken into account by CI and Green function techniques. The clusters show a complex behaviour upon electron attachment. The isomers of 84 show normal electron capture processes as well as electron attachment with shake-up. The Si clusters show multiple affinity states resulting from capture of an electron into different orbitals: Si3 C2v has at least three, Si4 D2h four, Si5 D3h two, Si6 D4v one, Si6 C2v three and Si7 D5h two affinity states (vertical processes: Sin + e− ± Sin + hν). For the Sin clusters in some cases shake-up affinities are calculated which are positive. The effects of electron correlation on the electron affinities are extremely large for the Si clusters in particular. In several cases the differences between the adiabatic and vertical electron affinities are very large amounting up to 1.5 eV. read less NOT USED (low confidence) W. G. Hoover and W. G. Hoover, “Nonequilibrium molecular dynamics,” Nuclear Physics. 1992. link Times cited: 2 NOT USED (low confidence) R. Rao and D. Debnath, “Evaluation of the potential function of liquid germanium from experimental structure factors and computation of elastic constants and phonon frequencies,” Physica Status Solidi B-basic Solid State Physics. 1992. link Times cited: 2 Abstract: Rao-Joarder's equation for the determination of potenti… read moreAbstract: Rao-Joarder's equation for the determination of potential function is used to derive the latter. The computed potential function of liquid Ge shows an inflection in the positive region and a negative minimum. The inflection is attributed to the first nearest-neighbour distance and the negative minimum to the second nearest-neighbour distance. The present computed potential function is found to be similar to that obtained by different methods. The derived potential function along with the measured values of g(r) is used in the evaluation of longitudinal and transverse phonon frequencies through Takeno and Goda's equations. The low-k values of phonon frequencies are found to be nearly linear with k. From the slope of these frequencies the elastic constants are calculated. Schofield's equations are also used in the calculation of elastic constants. The values obtained by different methods are found to be interconsistent. The potential function is utilised in the evaluation of the characteristic frequency of the atoms in the liquid. The computed value is compared with that obtained from low temperature heat capacities and average frequencies obtained by different methods. They are found to be fairly interconsistent.
Zur Bestimung der Potentialfunktion wird die Gleichung von Rao und Joarder benutzt. Fur flussiges Ge zeigt die berechnete Potentialfunktion einen Knick im positiven Bereich und ein negatives Minimum. Der Knick wird dem Abstand zum nachsten, das Minimum dem zum ubernachsten Nachbarn zugeschrieben. Die hier durchgefuhrten Berechnungen der Potentialfunktion liefern ahnliche Ergebnisse wie andere Methoden. Zusammen mit gemessenen g(r)-Werten wird die Potentialfunktion zur Berechnung der longitudinalen und transversalen Phononenfrequenzen nach der Gleichung von Takeno und Goda benutzt. Fur kleine k-Werte variieren die Phononenfrequenzen annahernd linear mit k. Aus der Steigerung dieser Abhangigkeit und aus Schofield's Gleichung werden die elastischen Konstanten berechnet, die Ergebnisse sind miteinander konsistent. Die Potentialfunktion wird auserdem benutzt, um die charakteristischen Frequenzen der Atome in der Flussigkeit zu berechnen. Die erhaltenen Werte stimmen leidlich mit den aus den Tieftemperaturwarmekapazitaten ermittelten Frequenzen und den nach verschiedenen Methoden erhaltenen Durchschnittsfrequenzen uberein. read less NOT USED (low confidence) J. H. Wilson, D. A. Mcinnes, J. Knall, A. Sutton, and J. Pethica, “Quantitative voltage-dependent STM image simulations for semiconductors,” Ultramicroscopy. 1992. link Times cited: 7 NOT USED (low confidence) R. Overney, L. Howald, J. Frommer, E. Meyer, D. Brodbeck, and H. Güntherodt, “Molecular surface structure of organic crystals observed by atomic force microscopy,” Ultramicroscopy. 1992. link Times cited: 8 NOT USED (low confidence) S. Erkoç, “A New Class of Empirical Many‐Body Potential Energy Functions for Bulk and Cluster Properties,” Physica Status Solidi B-basic Solid State Physics. 1992. link Times cited: 17 Abstract: A new empirical many-body potential energy function (PEF) is… read moreAbstract: A new empirical many-body potential energy function (PEF) is proposed, which comprices two- and three-body atomic interactions. The two-body potential is a kind of hybrid function and the three-body potential is formed by additive and nonadditive functions. The additive part is expressed in terms of two-body interactions, and the nonadditive part is expressed as triple-dipole function. The PEF satisfies bulk cohesive energy, bulk stability condition, and bulk modulus. The PEF is parameterized for gold, silver, and copper elements in f.c.c. crystal structure. The elastic constants of the elements are calculated, and the structural stability and energetics of microclusters containing 3 to 7 atoms of the same elements are investigated. The calculated elastic constants are in good agreement with experimental values, and the most stable microcluster geometries are qualitatively in agreement with the available literature data.
Eine neue empirische Vielteilchen-Potential-Energie-Funktion (PEF) wird vorgeschlagen, die atomare Zwei- und Drei-Korperwechselwirkungen enthalt. Das Zweikorperpotential ist eine Art von Hybrid- funktion und das Dreikorperpotential wird durch additive und nichtadditive Funktionen gebildet. Der additive Teil wird mit Zweikorperwechselwirkungen ausgedrockt, und der nichtadditive Teil als Tripel-Dipolfunktion. Die PEF genugt der Volumenkohasionsenergie, der Volumenstabilitatsbedin- gung und dem Elastizitatsmodul. Die PEF wird fur Gold, Silber und Kupfer in k.f.z. Kristallstruktur parametrisiert. Die elastischen Konstanten der Elemente werden berechnet und die Strukturstabilitat und -energie der 3 bis 7 Atome enthaltenen Mikrocluster derselben Elemente untersucht. Die berechneten elastischen Konstanten sind in guter Ubereinstimmung mit experimentellen Werten und die stabilsten Mikroclustergeometrien sind mit Literaturdaten qualitativ in Ubereinstimmung. read less NOT USED (low confidence) Trần, Thevuthasan, Kim, Herman, Friedman, and Fadley, “Photoelectron-diffraction and photoelectron-holography study of a Ge(111) high-temperature surface phase transition.,” Physical review. B, Condensed matter. 1992. link Times cited: 28 NOT USED (low confidence) J. Holender and G. J. Morgan, “The electronic structure and conductivity of large models of amorphous silicon,” Journal of Physics: Condensed Matter. 1992. link Times cited: 19 Abstract: Calculations of the electronic properties of very large mode… read moreAbstract: Calculations of the electronic properties of very large models of amorphous silicon are presented using Chadi's tight-binding model and the equation-motion method. The electronic density of states and the conductivity are calculated for structures containing up to 13824 atoms generated using molecular dynamics techniques. The structures contain defects, but the importance of this work is that one can make comparisons with earlier calculations using pseudopotentials, work with larger structures, use longer run times and lay the basis for calculations on hydrogenated a-Si and calculations of more complex properties, such as the Hall coefficient which is a longstanding problem. read less NOT USED (low confidence) B. Sumpter, C. Getino, and D. W. Noid, “Computational studies of submicron probing of polymer surfaces. I,” Journal of Chemical Physics. 1992. link Times cited: 7 Abstract: The atomistic details of the interaction of an atomic force … read moreAbstract: The atomistic details of the interaction of an atomic force microscopic (AFM) probe with a polymer surface are examined by using the molecular‐dynamics method. It is found that the perturbation of the AFM probe can produce a deformation of the local structure of the polymer surface. The dynamics study reveals how the structural changes evolve during the surface probing experiment, and whether the deformations result in permanent or reversible structural damage upon removing the probe. The effects of probe features (radius of curvature) and load force on the surface deformation(s) and image resolution are investigated in both a constant‐force and constant‐height AFM mode. Load forces between 10−8 and 10−11 N were determined to be an optimum working range for nondestructive AFM probing of polymer surfaces, and consequently for well‐resolved surface image production. read less NOT USED (low confidence) J. Holender and G. J. Morgan, “The double-sign anomaly of the Hall coefficient in amorphous silicon : verification by computer simulations,” Philosophical Magazine Letters. 1992. link Times cited: 10 Abstract: We present the first computer simulations of the Hall effect… read moreAbstract: We present the first computer simulations of the Hall effect for a realistic model of a solid, namely amorphous silicon, and succeed in verifying the anomalous change in sign of the Hall coefficient as the Fermi energy is moved from the valence band to the conduction band in accordance with the observations of LeComber, Jones and Spear in 1977. A model for this behaviour is proposed based on previous computations of the spectral function and a theory of gap formation. read less NOT USED (low confidence) R. Smith, “A semi-empirical many-body interatomic potential for modelling dynamical processes in gallium arsenide,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1992. link Times cited: 55 NOT USED (low confidence) U. Landman, W. Luedtke, and E. Ringer, “Atomistic mechanisms of adhesive contact formation and interfacial processes,” Wear. 1992. link Times cited: 114 NOT USED (low confidence) F. Trouw, “Molecular dynamics simulation and inelastic neutron scattering,” Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 1992. link Times cited: 12 NOT USED (low confidence) J. A. Lupo and M. J. Sabochick, “Structure and elastic properties of nanophase silicon,” Nanostructured Materials. 1992. link Times cited: 12 NOT USED (low confidence) H. Metiu, Y. Lu, and Z. Zhang, “Epitaxial Growth and the Art of Computer Simulations,” Science. 1992. link Times cited: 102 Abstract: The results of kinetic simulations of the aggregates formed … read moreAbstract: The results of kinetic simulations of the aggregates formed during the deposition of atoms on a semiconductor surface are reviewed. Because the kinetic parameters are poorly known and the accuracy of the existing interatomic potentials has not been sufficiently tested, the goal has been to reach a qualitative understanding of the formation of unusual patterns during growth, such as the segregation of aluminum during the growth of aluminum-gallium-arsenide (AlGaAs) coherent tilted superlattices and the formation of thin, long, and parallel islands during the deposition of Si on an Si(100) surface. Kinetic mechanisms for these phenomena are proposed. read less NOT USED (low confidence) J. Narayan and S. Sharan, “Mechanism of formation of 60° and 90° misfit dislocations in semiconductor heterostructures,” Materials Science and Engineering B-advanced Functional Solid-state Materials. 1991. link Times cited: 49 NOT USED (low confidence) P. Clancy, “Computer Simulation of Crystal Growth and Dissolution in Metals and Semiconductors,” International Journal of High Performance Computing Applications. 1991. link Times cited: 0 Abstract: understanding of the underlying atomic-scale mechanisms resp… read moreAbstract: understanding of the underlying atomic-scale mechanisms responsible for a variety of phenomena concerned with materials processing (for a nontechnical introduction to the subject, see Phillpot, Yip, and Wolf, 1989). For example, atomic-scale simulations using both Monte Carlo and molecular dynamics techniques have been used to emulate processes such as crystal growth of semiconductors (Landman et al., 1988; Broughton and Abraham, 1986; Grabow, Gilmer, and Bakker, 1990), molecular beam epitaxy (Das Sarma, 1990; Srivastava, Garrison, and Brenner, 1989), amorphization (Hsieh and Yip, 1989), and chemical vapor deposition (Brenner, 1990). Molecular Dynamics simulation techniques are a statistical mechanical formulation of appropriate equations of motion for a system of atoms. A semi-empirical model is used to describe the interatomic or intermolecular potential energy function, allowing the forces between particles to be established. For the microcanonical ensemble (constant number of particles, volume, and total energy), Newton’s second law of motion can then be solved, knowing the forces between particles and hence obtaining the accelerations for a system of particles. From these accelerations, the particle velocities and positions as a function of time can thus be established using one of many algorithms developed for the purpose of projecting forward (or backward) in time (Allen and Tildesley, 1987; Heerman, 1986). The solution of these differential equations is repeated for as long as is necessary to capture the event of interest (or as long as one’s computing budget will allow!). A number of &dquo;tricks&dquo; to speed the computation have been devised, such as the use of so-called neighbor lists, or the optimization of the coding for the subroutine which calculates the forces, as well as vectorization read less NOT USED (low confidence) K. Masuda-Jindo, V. Tewary, and R. Thomson, “Theoretical study of the fracture of brittle materials: atomistic calculations,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 1991. link Times cited: 7 NOT USED (low confidence) J. Hafner, “Effective interatomic forces and atomic and electronic structure of liquid and amorphous metals,” Journal of Physics: Condensed Matter. 1991. link Times cited: 5 Abstract: The state of the art in the calculation of interatomic force… read moreAbstract: The state of the art in the calculation of interatomic forces in s, p and d-bonded metals and alloys, and their application in the atomistic simulation of the structural and electronic properties of liquid and amorphous phases are reviewed. read less NOT USED (low confidence) R. Virkkunen, K. Laasonen, and R. Nieminen, “Molecular dynamics using the tight-binding approximation: application to liquid silicon,” Journal of Physics: Condensed Matter. 1991. link Times cited: 32 Abstract: The authors present molecular dynamical simulations of liqui… read moreAbstract: The authors present molecular dynamical simulations of liquid silicon using the tight-binding approximation for electron-mediated interactions. Several structural and dynamical properties of liquid silicon are calculated and compared with the results of ab initio and classical molecular dynamics. The tight-binding model with parameters fitted to bulk crystalline properties is found to be very successful in characterizing the liquid state, which facilitates large-scale dynamical simulations. read less NOT USED (low confidence) W. Morgan and D. B. Boercker, “Simulating growth of Mo/Si multilayers,” Applied Physics Letters. 1991. link Times cited: 27 Abstract: Multilayer structures of alternating thin layers of molybden… read moreAbstract: Multilayer structures of alternating thin layers of molybdenum and silicon are of great interest as x‐ray optics components and a considerable amount of effort has been expended in their development. The efficiencies of these structures depend upon both the accurate control of the layer thicknesses and the sharpness in the interface between layers. High‐ resolution electron microscopy reveals that the interface created by deposition of Mo on Si is much more diffuse than that produced by depositing Si on Mo. We have used molecular dynamics to simulate the deposition processes and observe significant penetration of the Si substrates by the incident Mo atoms, while incident Si atoms remain on the surface of the Mo substrate. read less NOT USED (low confidence) H. Melman and S. Garofalini, “Microstructural evaluation of simulated sodium silicate glasses,” Journal of Non-crystalline Solids. 1991. link Times cited: 54 NOT USED (low confidence) S. Clarke, M. Wilby, and D. Vvedensky, “Theory of homoepitaxy on Si(001): I. Kinetics during growth,” Surface Science. 1991. link Times cited: 85 NOT USED (low confidence) Z. Badirkhan, M. Rovere, and M. Tosi, “Liquid-solid transition in the bond-particle model for elemental semiconductors,” Philosophical Magazine Part B. 1991. link Times cited: 1 Abstract: Solidification of silicon and germanium involves a reconstru… read moreAbstract: Solidification of silicon and germanium involves a reconstruction of covalent tetrahedral bonds from a metallic liquid having a higher density and coordination than the solid. We first contrast the metallic liquid structure of germanium with that of its semiconducting amorphous state, in order to emphasize the changes in the atomic structure factor that arise from reconstruction of the interatomic bonds. We then use the density wave theory of freezing to discuss the liquid-solid transition within a pseudo-classical model, which describes the liquid structure by means of partial structure factors giving the pair correlations between atoms and bond particles. The phase transition is viewed as a freezing of the bonds, driven by tetrahedrally constrained attractions between ionic cores and valence electrons and accompanied by an opening of the structure to allow long-range connectivity of tetrahedral atomic units. Quantitative calculations on the bond-particle model illustrate the relationship betwee... read less NOT USED (low confidence) K. Masuda-Jindo, V. Tewary, and R. Thomson, “Atomic theory of fracture of brittle materials: Application to covalent semiconductors,” Journal of Materials Research. 1991. link Times cited: 14 Abstract: Using the lattice Green’s function approach and LCAO (linear… read moreAbstract: Using the lattice Green’s function approach and LCAO (linear combination of atomic orbitals) electron theory, we investigate the atomistic configuration and lattice trapping of cracks in Si. The LCAO electron theory coupled to second order perturbation theory (SOP) has been used to derive explicit expressions for the bond breaking nonlinear forces between Si atoms. We calculate the cracked lattice Green’s functions for a crack on the (111) plane and lying in the (110) direction. With the nonlinear forces acting in a cohesive region near the crack tips, the crack structure is then calculated. The calculated structure possesses a crack opening at the Griffith load which should allow penetration of typical external molecules to the crack tip at the Griffith loading. Other consequences for chemical reactions at the crack tip are discussed in the light of these results. The lattice trapping is low, only a few percent of the Griffith load. read less NOT USED (low confidence) B. Dodson, “Chemical effects in sub-keV ion-solid interactions,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1991. link Times cited: 8 NOT USED (low confidence) P. Mahon, B. Pailthorpe, and G. Bacskay, “A quantum mechanical calculation of interatomic interactions in diamond,” Philosophical Magazine Part B. 1991. link Times cited: 14 Abstract: Ab initio Hartree–Fock self-consistent-field-theory calculat… read moreAbstract: Ab initio Hartree–Fock self-consistent-field-theory calculations have been performed on neopentane, a C5 cluster, subjected to bond stretching and bending distortions. The potential energy surface was fitted by a Stillinger-Weber potential reparametrized for carbon in the diamond form. This potential provides a good description of the C–C interaction and should be useful in molecular dynamics, simulations of diamond. read less NOT USED (low confidence) W. Tiller, “The role of ledges in stress tensor-mediated surface processes for Si and GaAs,” Metallurgical Transactions A. 1991. link Times cited: 0 NOT USED (low confidence) M. Heggie, “Semiclassical interatomic potential for carbon and its application to the self-interstitial in graphite,” Journal of Physics: Condensed Matter. 1991. link Times cited: 33 Abstract: A semiclassical interatomic potential for carbon is discusse… read moreAbstract: A semiclassical interatomic potential for carbon is discussed which is based on the proximity cell (the Wigner-Seitz cell) around each atom. It introduces three internal degrees of freedom per atom, representing the magnitude and direction of the p orbital that is not involved in sp hybridization. Its direct interpolation between sp2 and sp3 configurations combined with good elastic properties allows its use on problematic defects, such as the interplanar interstitial in graphite, which is given as an example. read less NOT USED (low confidence) M. Kohyama, “On the transferable SETB method for Si,” Journal of Physics: Condensed Matter. 1991. link Times cited: 21 Abstract: The two types of transferable semi-empirical tight-binding (… read moreAbstract: The two types of transferable semi-empirical tight-binding (SETB) method for Si recently proposed by Goodwin et al. (1989) and by Sawada, which are intended to reproduce the binding energies and equilibrium volumes of variously coordinated structures of Si, have been examined and compared with each other. It has been found that there are some drawbacks in the method proposed by Goodwin et al, and that the method proposed by Sawada is much superior. The parameters in the Sawada method have been readjusted in order to apply this method to lattice defects or disordered systems of Si. The present results indicate the importance of incorporating the dependence on the local environment into the repulsive energy in the transferable SETB method. This can be explained by the origin of the repulsive energy. read less NOT USED (low confidence) L. J. Álvarez, A. Alavi, and J. Siepmann, “A vectorisable algorithm for calculating three-body interactions,” Computer Physics Communications. 1991. link Times cited: 4 NOT USED (low confidence) Z. Q. Wang and D. Stroud, “Bond-orientational order in liquid Si,” Journal of Chemical Physics. 1991. link Times cited: 19 Abstract: We study bond‐orientational order in liquid Si via Monte Car… read moreAbstract: We study bond‐orientational order in liquid Si via Monte Carlo simulation in conjunction with empirical two‐ and three‐body potentials of the form proposed by Stillinger and Weber. Bond‐orientational order (BOO) is described in terms of combinations of spherical harmonic functions. Liquid Si is found to have pronounced short‐range BOO corresponding to l=3, as expected for a structure with local tetrahedral order. No long‐range BOO is found either in the equilibrium or the supercooled liquid. When the three‐body potential is artificially removed, the tetrahedral bond‐orientation order disappears and the liquid assumes a close‐packed structure. read less NOT USED (low confidence) J. H. Wilson, J. Todd, and A. Sutton, “Modelling of silicon surfaces: a comparative study,” Journal of Physics: Condensed Matter. 1990. link Times cited: 25 Abstract: A theoretical study of the Si(110)-1*1, Si(100)-2*1, Si(111)… read moreAbstract: A theoretical study of the Si(110)-1*1, Si(100)-2*1, Si(111)-2*1 and Si(113)-1*1 surfaces is presented. The authors use both the semi-empirical tight-binding bond model and the classical potential of Stillinger and Weber to describe interatomic forces. Energy minimization calculations are carried out in order to deduce the stable atomic configurations. The authors show that the semi-empirical tight-binding approach can produce results in reasonable agreement with other experimental and theoretical work and they demonstrate that charge transfer is not an important factor governing the stability of these surfaces. In a comparative study, involving not only static energy minimization but also Monte Carlo simulated annealing, the authors show why the classical potential does not perform well in describing surface atomic structure. read less NOT USED (low confidence) A. Silverman, J. Adler, and R. Weil, “Computer modelling of the diffusion mechanisms of fluorine in amorphous silicon,” Thin Solid Films. 1990. link Times cited: 9 NOT USED (low confidence) J. Hafner and W. Jank, “The electronic structure of liquid metals,” Journal of Physics: Condensed Matter. 1990. link Times cited: 1 Abstract: The authors present first-principles calculations of the ele… read moreAbstract: The authors present first-principles calculations of the electronic structure of molten simple and transition metals. read less NOT USED (low confidence) D. Sanders, D. B. Boercker, and S. Falabella, “Coating technology based on the vacuum arc-a review,” IEEE Transactions on Plasma Science. 1990. link Times cited: 125 Abstract: An overview of the current state of vacuum-arc-based coating… read moreAbstract: An overview of the current state of vacuum-arc-based coating technology is presented, with particular emphasis on defining those areas where further investigation would reap the greatest benefits. Particular attention is given to the 'continuous' cathodic arc, which is currently the best understood approach and which has been most successfully adapted for large-scale commercial coating in the United States. It is noted that the greatest promise of ion-based coating technology based on the vacuum arc is the potential for increased control over the coating process. Unlike the case for neutral coating atoms, the presence of a charge on coating ions gives a 'handle' to exert forces on them using electrostatic fields. One can in theory control the trajectory of these ions between the coating source and part to be coated. One can also control the energy with which they impact the substrate. It may even be possible to control the extent of their reactivity. > read less NOT USED (low confidence) T. D. de la Rubia and M. Guinan, “Progress in the development of a molecular dynamics code for high-energy cascade studies,” Journal of Nuclear Materials. 1990. link Times cited: 146 NOT USED (low confidence) B. Feuston and S. Garofalini, “Water‐induced relaxation of the vitreous silica surface,” Journal of Applied Physics. 1990. link Times cited: 107 Abstract: The formation of a vitreous silica surface in the presence o… read moreAbstract: The formation of a vitreous silica surface in the presence of water vapor is investigated through the molecular dynamics simulation technique. Three‐body potentials are employed to describe the interatomic interactions. The structure of the reconstructed surface is analyzed with respect to the concentration and type of defects. Comparison between surfaces created in the presence of water and those created in a vacuum indicate that H2O‐surface reactions substantially reduce the number of topological (two‐ , three‐ , and four‐membered rings) and bonding defects (under‐ and overcoordinated species) incurred during the relaxation process. Due to the dissociation of water molecules, the wet surface contains excess oxygen with a concentration of 3.1±0.6 silanols per 100 A2, involving approximately 13% geminal sites. read less NOT USED (low confidence) D. M. Zirl and S. Garofalini, “Structure of Sodium Aluminosilicate Glasses,” Journal of the American Ceramic Society. 1990. link Times cited: 119 Abstract: A series of sodium aluminosilicate glasses composed of varyi… read moreAbstract: A series of sodium aluminosilicate glasses composed of varying ratios (R) of Al2O3/Na2O (0.25 R 2.0) has been simulated with the molecular dynamics technique using a tetrahedral form of a three-body interaction potential. Extrema in the activation energies for sodium diffusion and in the diffusion constants for all of the atomic species were observed for glasses with equal concentrations of Al2O3 and Na2O (R= 1.0). These changes corresponded to the minimum observed experimentally in the activation energy for electrical conductivity and to the maximum observed in the viscosity for glasses with compositions of R= 1.0. The coordination of aluminum remained 4 over the entire compositional range, negating the need to invoke a coordination change of aluminum to explain the changes in the physical properties. The changes to the simulated physical properties as R passed through the equivalence point were attributed to the elimination of nonbridging oxygen, to the introduction of oxygen triclusters, and to changes in the distribution of ring structures within the glass networks. read less NOT USED (low confidence) S. Phillpot, D. Wolf, and S. Yip, “Effects of Atomic-Level Disorder at Solid Interfaces,” MRS Bulletin. 1990. link Times cited: 21 Abstract: The importance of interface materials is based largely on th… read moreAbstract: The importance of interface materials is based largely on their inherent inhomogeneity, i.e., that the chemical composition and physical properties at or near an interface can differ dramatically from those of the nearby bulk material. For example, the propagation of a crack along an interface — rather than through the surrounding bulk material — indicates a different mechanical strength near the interface. Also, the elastic response and thermal behavior near an interface can be highly anisotropic in an otherwise isotropic material, and can differ by orders of magnitude from those of the adjacent bulk regions. Typically, these gradients extend over only a few atomic distances. Because relatively few atoms control the properties in the interfacial region, the inherent difficulty in the experimental investigation of buried interfaces is actually an advantage in the atomic-level study of solid interfaces by means of computer-simulation techniques. While the limitations of such simulations are well known, this article will attempt to demonstrate the unique insights they can provide on some aspects of the mechanical behavior of both buried and thin-film interfaces. While to date, relatively little simulation work has focused directly on the observation of crack extension, we will discuss two types of phenomena with particular relevance in the fracture behavior of interface materials, namely their elastic and high-temperature properties. We will conclude with an outlook, too optimistic perhaps, on how the complementary capabilities of continuum-elastic theory, atomic-level computer simulation, and experiment could (and probably should) be combined in a new strategy for tackling the difficult problem of interface fracture to elucidate the underlying complex interplay between elasticity, plasticity, and temperature. read less NOT USED (low confidence) J. Bass and C. Matthai, “Electronic structure of [111] Si/Ge superlattices,” Journal of Physics: Condensed Matter. 1990. link Times cited: 6 Abstract: Using ab initio pseudopotentials the authors have performed … read moreAbstract: Using ab initio pseudopotentials the authors have performed self-consistent calculations on Sin/Gen strained layer superlattices grown on a (111) silicon substrate for n=1, 2, 3 and n=6. They look at the electronic structure and find that, despite strain and folding effects, none of these superlattices have a direct gap. From charge density contours a complete localization of the upper valence band states at the Gamma point is found on the germanium sublattice for the n=6 case. Such localization does not occur for superlattices grown on (001) substrates with the same repeat distance. read less NOT USED (low confidence) R. Kalia, P. Vashishta, L. H. Yang, F. W. Dech, and J. Rowlan, “Quantum Molecular Dynamics: a New Algorithm for Linear and Nonlinear Electron Transport in Disordered Materials,” International Journal of High Performance Computing Applications. 1990. link Times cited: 10 Abstract: Quantum molecular dynamics (QMD) simulations pro vide the re… read moreAbstract: Quantum molecular dynamics (QMD) simulations pro vide the real-time dynamics of electrons and ions through numerical solutions of the time-dependent Schrödinger and Newton equations, respectively. With this technique it is possible to go beyond the structural aspects to study electron dynamics, including linear and nonlinear electron transport, in materials at finite tem peratures. The solution of the time-dependent Schrö dinger equation for the electron wave function is ob tained by a spectral method, which for bulk systems is implemented with discrete fast Fourier (FFT) transforms. For systems with broken symmetry due to surfaces or interfaces, the spectral method combines the solution of a tridiagonal set of equations with FFT. Using QMD simulations we have investigated the localization be havior and the mobility of excess electrons at finite tem peratures in highly disordered systems such as a dense helium gas and amorphous silicon. Future QMD simula tions for many electrons within the framework of time- dependent density functional theory and implementation of molecular dynamics on massively parallel architec tures are discussed. read less NOT USED (low confidence) A. F. Bakker, G. Gilmer, M. Grabow, and K. Thompson, “A special purpose computer for molecular dynamics calculations,” Journal of Computational Physics. 1990. link Times cited: 27 NOT USED (low confidence) S. Erkoç, “Structural stability and energetics of F.C.C. metal microclusters : empirical Many-Body potential energy function calculation,” Physica Status Solidi B-basic Solid State Physics. 1990. link Times cited: 21 Abstract: The structural stability and energetics of microclusters con… read moreAbstract: The structural stability and energetics of microclusters containing 3 to 7 atoms of f.c.c. metal elements are investigated. A recently developed empirical many-body potential function (PEF) is used in the calculations, which comprises two- and threebody atomic interactions. The PEF satisfies both, bulk cohesive energy and stability condition. It is found that the energetically most stable structures of microclusters are in compact form.
Die strukturelle Stabilitat und Energie von Mikroclustern mit 3 bis 7 Atomen von k.f.z.-Metallelementen werden untersucht. Fur die Berechnungen wird eine kurzlich entwickelte empirische Vielkorper-Potentialfunktion (PEF) benutzt, die Zwei- und Drei-Korper-Atomwechselwirkungen einschliest. Die PEF genugt sowohl der Volumenkohasionsenergie als auch der Stabilitatsbedingung. Es wird gefunden, das die energetisch stabilsten Strukturen der Mikrocluster von kompakter Form sind. read less NOT USED (low confidence) E. Blaisten-Barojas and M. Nyden, “Molecular dynamics study of the depolymerization reaction in simple polymers,” Chemical Physics Letters. 1990. link Times cited: 12 NOT USED (low confidence) T. Soules, “Computer simulation of glass structures,” Journal of Non-crystalline Solids. 1990. link Times cited: 41 NOT USED (low confidence) J. MacElroy and K. Raghavan, “Adsorption and diffusion of a Lennard‐Jones vapor in microporous silica,” Journal of Chemical Physics. 1990. link Times cited: 79 Abstract: The properties of a dilute Lennard‐Jones vapor in contact wi… read moreAbstract: The properties of a dilute Lennard‐Jones vapor in contact with an adsorbing microporous medium are investigated using grand canonical ensemble Monte Carlo and molecular dynamics techniques. The bulk structure of the microporous system is modeled as an assembly of randomly distributed interconnected solid spheres, and vapor/surface interactions are treated in two ways: (i) using a smooth continuous interaction potential and (ii) using a molecular model for the surface structure of the solid. The microporous solid representation employed in these simulations is chosen to conform in realistic manner with the bulk and surface properties of silica gel. The results obtained from the simulations include equilibrium partition coefficients, diffusivities, and related microscopic properties. By comparing these results with available experimental data it is shown that the properties of simple nonpolar gases in microporous silica may be predicted with reasonable accuracy. This is particularly true when the molecular ... read less NOT USED (low confidence) J. Gardeniers, L. Giling, F. D. Jong, and J. P. Eerden, “A theoretical study of adsorption equilibria in silicon CVD,” Journal of Crystal Growth. 1990. link Times cited: 15 NOT USED (low confidence) K. Raghavachari, “Theoretical studies on silicon clusters,” Phase Transitions. 1990. link Times cited: 48 Abstract: This is a brief review of the theoretical studies which have… read moreAbstract: This is a brief review of the theoretical studies which have been carried out to understand the nature of the structures, stabilities and fragmentation behavior of silicon clusters. For the small clusters Si2-Si10, accurate quantum chemical or local density functional calculations have been carried out. These studies have shown that the small clusters are more compact and considerably different from any structures which may be inferred from microcrystalline models based on the diamond lattice for silicon. Clusters containing 4, 6, 7 and 10 atoms have been identified as “magic numbers” for small silicon clusters and the ground state energetics of these clusters are consistent with the observations from recent photofragmentation and photoelectron experiments. Recent attempts to study larger silicon clusters including the efforts to derive accurate silicon-silicon interaction potentials are also described. read less NOT USED (low confidence) J. Gardeniers, F. D. Jong, and L. Giling, “Equilibrium structure of Si(001) in relation to adsorption processes during silicon CVD,” Surface Science. 1990. link Times cited: 3 NOT USED (low confidence) D. Brenner and B. Garrison, “Gas‐Surface Reactions: Molecular Dynamics Simulations of Real Systems,” Advances in Chemical Physics. 1990. link Times cited: 8 NOT USED (low confidence) S. Phillpot, D. Wolf, and J. Lutsko, “Anomalous elastic behavior in superlattices of twist grain boundaries in silicon,” Journal of Applied Physics. 1990. link Times cited: 6 Abstract: The elastic constants and moduli of superlattices of high‐an… read moreAbstract: The elastic constants and moduli of superlattices of high‐angle twist grain boundaries on the two densest crystallographic planes of silicon are calculated using Stillinger and Weber’s three‐body potential. While in both cases the Young’s and shear moduli are found to be softened, the Poisson ratios and some elastic constants, in particular C33 (in the direction of the interface‐plane normal), are found to be hardened. It is shown that the elastic behavior is determined by the structural disorder at the interfaces, and that it cannot be understood in terms of the dimensional changes of the system alone. A comparison with similar calculations for metallic superlattices elucidates the role of the covalent nature of bonding of silicon on its elastic behavior. read less NOT USED (low confidence) G. Gilmer, M. Grabow, and A. F. Bakker, “Modeling of epitaxial growth,” Materials Science and Engineering B-advanced Functional Solid-state Materials. 1990. link Times cited: 49 NOT USED (low confidence) C. Carson, J. Bernholc, D. Faux, and C. Hall, “Efficient techniques for computer simulations of heteroepitaxial growth,” Applied Physics Letters. 1990. link Times cited: 7 Abstract: A new discrete Monte Carlo technique suitable for simulation… read moreAbstract: A new discrete Monte Carlo technique suitable for simulations of the kinetics of heteroepitaxial crystal growth has been developed and tested on a 103 atom system. The technique offers sizable speed advantages over previous simulation methods and allows for realistic three‐dimensional studies of the kinetics of both pseudomorphic and misfit growth modes and of the transformation between them. Elements of the method are of general utility and can also be used to substantially improve the efficiency of continuous‐space Monte Carlo and molecular dynamics simulations of growth and other atomic transformations. read less NOT USED (low confidence) F. X. Kelly and L. Ungar, “A molecular dynamics investigation of solute trapping during rapid solidification of silicon,” Journal of Crystal Growth. 1990. link Times cited: 10 NOT USED (low confidence) D. Faux, C. Hall, and J. Bernholc, “A New Monte Carlo Simulation Technique for the Study of Epitaxial Crystal Growth,” Molecular Simulation. 1990. link Times cited: 2 Abstract: A new type of Monte Carlo simulation is described which mode… read moreAbstract: A new type of Monte Carlo simulation is described which models epitaxial crystal growth on non-lattice-matched substrates. The model allows adatoms to immediately occupy positions of local potential minima which are defined by the particle-particle interactions. Adatoms make discrete hops from one minimum to another. This model therefore combines some of the flexibility of continuous-space Monte Carlo with the speed associated with lattice-like simulations. Details of the Monte Carlo procedure are presented for a two-dimensional system where the particle-particle interactions are assumed to be of the Lennard-Jones type. Some results are presented for the case where the adsorbate crystal lattice is larger than the substrate lattice by 2% and 8%. read less NOT USED (low confidence) E. Bauer et al., “Fundamental issues in heteroepitaxy—A Department of Energy, Council on Materials Science Panel Report,” Journal of Materials Research. 1990. link Times cited: 127 Abstract: During the past decade, nonequilibrium techniques have been … read moreAbstract: During the past decade, nonequilibrium techniques have been developed for the growth of epitaxial semiconductors, insulators, and metals which have led to new classes of artificially structured materials. Structures can now be grown which present the materials scientist with systems that exhibit new properties and demonstrate new physical concepts. For example, quantum-well structures with molecular dimensions give rise to new phenomena resulting from quantum mechanical effects. Layered structures with periodicity of a few atomic layers result in coherent behavior for long-range interactions such as magnetism in metallic systems. Metastable structures can be generated which possess important properties not present in equilibrium systems. Studies of these materials are leading to significant advances in our basic understanding of the physics of materials as well as to important new technologies. Despite the rate of progress and the large number of laboratories throughout the world with active programs in various aspects of epitaxial growth, our current understanding of the processes which control growth at a fundamental, atomic level is remarkably primitive. Much of the work to date has been driven by the motivation to produce high quality materials for high performance electronic devices. As a result, most of the effort in epitaxial materials hasmore » concentrated on semiconductors, particularly GaAs and related compounds.« less read less NOT USED (low confidence) S. Garofalini, “Molecular dynamics computer simulations of silica surface structure and adsorption of water molecules,” Journal of Non-crystalline Solids. 1990. link Times cited: 148 NOT USED (low confidence) G. Schoeck and W. Pichl, “Bond trapping of cracks,” Physica Status Solidi (a). 1990. link Times cited: 17 Abstract: A model is presented for stabilization of cracks in an atomi… read moreAbstract: A model is presented for stabilization of cracks in an atomistic solid by “bond trapping”. In contrast to the normal “lattice trapping” which results from the periodicity of the atomic lattice, “bond trapping” depends on special features of the interatomic potentials and will lead to energy dissipation by phonons. It is expected to occur mainly in structures with open lattices with covalent binding, in glass, or in amorphous materials where lattice trapping is not to be expected.
Ein Modell wird vorgestellt fur die Stabilisierung von Rissen in atomaren Festkorpem durch “bond trapping”. Im Gegensatz zum normalen “lattice trapping” das auf der Periodizitat des Atomgitters beruht, hangt “bond trapping” von den speziellen Eigenschaften des interatomaren Potentials ab und gibt Anlas zu Energiedissipation durch Phononen. Es tritt hauptsachlich in offenen Gittern mit homoopolarer Bindung, in Glas oder in amorphen Materialien auf, in denen “lattice trapping” nicht erwartet wird. read less NOT USED (low confidence) M. Tegze and J. Hafner, “Structural and electronic properties of CaZn glasses,” Journal of Non-crystalline Solids. 1990. link Times cited: 1 NOT USED (low confidence) L. Aleksandrov, A. Kogan, and N. P. Tikhonova, “A Monte Carlo study of the silicon film growth from molecular beams,” Thin Solid Films. 1989. link Times cited: 0 NOT USED (low confidence) A. Kobayashi and S. Sarma, “Surface kinetics driven annealing and phase segregation in non-equilibrium crystal growth,” Surface Science. 1989. link Times cited: 0 NOT USED (low confidence) D. J. Oh and R. Johnson, “Relationship between ratio and point defect properties in HCP metals,” Journal of Nuclear Materials. 1989. link Times cited: 38 NOT USED (low confidence) S. Phillpot and D. Wolf, “Structure-energy correlation for grain boundaries in silicon,” Philosophical Magazine. 1989. link Times cited: 24 Abstract: The zero-temperature energies and equilibrium volume expansi… read moreAbstract: The zero-temperature energies and equilibrium volume expansions of point-defect-free grain boundaries (GBs) on the three densest planes of cubic-diamond silicon have been determined using the Stillinger-Weber potential. It is found that the energy of GBs on the second-densest plane are two to three times higher than the energy of those on the first-densest plane, and GBs on the third-densest planes have even higher energies. By examining the radial and angular distribution functions of a GB on each plane, it is shown that the energy of a GB is determined by the disorder in both bond lengths and bond angles. read less NOT USED (low confidence) N. Mousseau and L. J. Lewis, “Computer-simulated model structures for hydrogenated amorphous semiconductors,” Journal of Non-crystalline Solids. 1989. link Times cited: 0 NOT USED (low confidence) T. Halicioǧlu, W. Tiller, H. Pamuk, and S. Erkoç, “The effect of a potential function range on surface properties,” Physica Status Solidi B-basic Solid State Physics. 1989. link Times cited: 1 Abstract: On analyse le role joue par la distance d'une fonction … read moreAbstract: On analyse le role joue par la distance d'une fonction de potentiel sur plusieurs proprietes de surface. On montre qu'elle est un facteur important dans sa transferabilite read less NOT USED (low confidence) J. Rustad, D. Yuen, and F. Spera, “Nonequilibrium molecular dynamics of liquid sulfur in Couette flow,” Journal of Chemical Physics. 1989. link Times cited: 3 Abstract: Previous work in nonequilibrium molecular dynamics (NEMD) ha… read moreAbstract: Previous work in nonequilibrium molecular dynamics (NEMD) has been restricted to systems subject only to pair interactions. We use methods of homogenous NEMD to investigate the nature of liquid sulfur under extreme shear using the potential model developed by Stillinger and Weber which involves explicitly three‐body interaction. Simulations with up to 2048 particles have been carried out at a temperature of 1583 K and a density of 1.805 g cm−3 for shear rates between 0.005 and 1.75 in reduced units. We find that the fluid separates in sheets alternating from high to low density in planes perpendicular to the velocity gradient. No evidence is seen for the transition to the ‘‘string’’ phase as exhibited by two‐body systems. The molecules show a tendency to align in the direction of shear. Data are presented describing the magnitude of this effect. read less NOT USED (low confidence) B. Feuston and S. Garofalini, “Topological and bonding defects in vitreous silica surfaces,” Journal of Chemical Physics. 1989. link Times cited: 122 Abstract: A model structure for an annealed silica surface was obtaine… read moreAbstract: A model structure for an annealed silica surface was obtained through the molecular dynamics simulation technique employing three‐body interaction potentials. Nonbridging oxygen and edge‐sharing tetrahedra were found to form on the oxygen‐terminated surface with three‐coordinated silicon, three‐coordinated oxygen, and three‐membered rings just below the outermost atoms. Four‐membered rings were also created in relatively large concentrations during the surface relaxation. When considering the effect of removing periodic boundary conditions along the z direction, the concentration of larger rings, relative to the bulk, remained unchanged throughout the ∼11 A simulated surface region. A strong physical association between three‐membered rings and three‐coordinated oxygen was found which may account for the D2 defect peak observed in Raman scattering. read less NOT USED (low confidence) A. Paxton and A. Sutton, “A tight-binding study of grain boundaries in silicon,” Acta Metallurgica. 1989. link Times cited: 48 NOT USED (low confidence) Smith, Harrison, and Garrison, “keV particle bombardment of semiconductors: A molecular-dynamics simulation.,” Physical review. B, Condensed matter. 1989. link Times cited: 126 Abstract: Molecular-dynamics simulations have been performed for the k… read moreAbstract: Molecular-dynamics simulations have been performed for the keV particlebombardment of Si/l brace/110/r brace/ and Si/l brace/100/r brace/ using a many-body potential developed byTersoff. Energy and angle distributions are presented along with an analysis ofthe important ejection mechanisms. We have developed a computer logic that onlyintegrates the equations of motion of the atoms that are struck, thusdecreasing the computer time by a factor of 3 from a completemolecular-dynamics simulation. read less NOT USED (low confidence) C. Matthai, “Molecular Dynamics Simulation of Transition Metals as Silicon Substrates,” Molecular Simulation. 1989. link Times cited: 0 Abstract: In recent years the growth of epitaxial layers and strained … read moreAbstract: In recent years the growth of epitaxial layers and strained layer superlattices have been simulated by using the method of molecular dynamics. We have used this method to study the formation of transition metal silicides as the metal is deposited on a silicon substrate. We propose effective empirical potentials to describe the interaction between the metal and silicon and use the Dodson and Stillinger-Weber potentials to model the silicon-silicon interaction. We report on the evolution of nickel layers on the substrate as a function of temperature. read less NOT USED (low confidence) S. Phillpot, D. Wolf, and J. Lutsko, “Elastic softening in nanocrystalline silicon,” MRS Proceedings. 1989. link Times cited: 1 Abstract: It is pointed out that some of the generic physical properti… read moreAbstract: It is pointed out that some of the generic physical properties of a nanocrystalline material are similar to those of a grain-boundary superlattice. The structure and elastic properties of a superlattice of twist boundaries on the (110) plane of silicon are calculated as a function of modulation wavelength using a three-body potential. All elastic moduli are found to be softened. This softening is attributed to the relatively small amount of structural disorder at the interfaces. 8 refs., 4 figs. read less NOT USED (low confidence) J. Lutsko, “Generalized expressions for the calculation of elastic constants by computer simulation,” Journal of Applied Physics. 1989. link Times cited: 203 Abstract: The general expressions, valid for any potential, for the ca… read moreAbstract: The general expressions, valid for any potential, for the calculation of elastic constants through computer simulation are given. At zero temperature, the elastic constants are found to be the sum of a generalization of the Born term and a term accounting for internal relaxations that arise when a system with more than one atom in the primitive unit cell is strained. The fluctuation formulae used in finite temperature simulations are found to be straightforward generalizations of those used for pair potentials. The connection between the finite‐temperature and zero‐temperature methods is also made. read less NOT USED (low confidence) U. Landman, W. Luedtke, and A. Nitzan, “Dynamics of tip-substrate interactions in atomic force microscopy☆,” Surface Science. 1989. link Times cited: 46 NOT USED (low confidence) A. Arnold, N. Mauser, and J. Hafner, “A molecular dynamics study of the structure of liquid germanium,” Journal of Physics: Condensed Matter. 1989. link Times cited: 54 Abstract: The structure of liquid Ge as a function of temperature and … read moreAbstract: The structure of liquid Ge as a function of temperature and density was investigated using molecular dynamics and interatomic forces derived from the pseudopotential theory. The authors present results for the pair correlation function, the static structure factor and the bond-angle distribution function as a function of temperature and density. Our results are in good agreement with diffraction experiments. The density derivative of the structure factor deviates from the prediction of the uniform-fluid model due to the density dependence of the interatomic potential. The bond-angle distribution shows that the local order in liquid Ge is different from that of both the semiconducting and the metallic crystalline phases. With progressive undercooling the structure of the liquid does not tend towards the structure of amorphous Ge, because solidification is associated with a metal-semiconductor transition resulting in state-dependent interatomic potentials. read less NOT USED (low confidence) F. F. Abraham and I. P. Batra, “Theoretical interpretation of atomic-force- microscope images of graphite,” Surface Science. 1989. link Times cited: 28 NOT USED (low confidence) C. Engler, “Potential Surfaces for Chemisorption on Semiconductor Surfaces from Pair Potential Considerations,” Physica Status Solidi B-basic Solid State Physics. 1989. link Times cited: 1 Abstract: A pair potential method, recently proposed by Tersoff, is ex… read moreAbstract: A pair potential method, recently proposed by Tersoff, is extended in order to treat chemisorption problems on semiconductor surfaces. The modified version is tested for chemisorption of atomic hydrogen and oxygen on Si(100)-surface. The calculated data are compared with experiments and ab-initio results.
Eine kurzlich von Tersoff vorgeschlagene Paar-Potential-Methode wird erweitert, um Chemi-sorptionsprobleme an Halbleiteroberflachen behandeln zu konnen. Die modifizierte Version wird fur die Chemisorption von atomarem Wasserstoff und Sauerstoff an der Si(100)-Oberflache getestet. Die berechneten Daten werden mit Experimenten und ab-initio-Ergebnissen verglichen. read less NOT USED (low confidence) S. Paik and S. Sarma, “Adsorbate dynamics on: (I) A lattice-matched substrate,” Surface Science. 1989. link Times cited: 7 NOT USED (low confidence) J. Hafner, M. Tegze, and W. Jank, “Interplay of the atomic and electronic structure in liquid and amorphous metals and alloys,” Journal of The Less Common Metals. 1988. link Times cited: 2 NOT USED (low confidence) S. Phillpot and D. Wolf, “Grain boundaries in silicon from zero temperature through melting,” Journal of the American Ceramic Society. 1988. link Times cited: 11 Abstract: The results of atomistic simulations of twist grain boundari… read moreAbstract: The results of atomistic simulations of twist grain boundaries in covalent silicon are presented and compared with similar studies in metals. Three aspects are discussed in detail: (i) the zero-temperature structure-energy correlation, (ii) the elastic anomalies near a twist boundary at zero temperature, and (iii) the high-temperature stability of a boundary and its role in thermodynamic melting. In each case striking similarities with studies on metals are found, which are attributed to the important role played by atoms in close proximity. By contrast the covalent nature of bonding in silicon appears to play only a minor role. read less NOT USED (low confidence) J. Hafner, M. Tegze, and S. Jaswal, “Ab-initio calculations of the atomic and electronic structure of metallic glasses,” Journal of Non-crystalline Solids. 1988. link Times cited: 2 NOT USED (low confidence) J. Hafner et al., “The atomic and electronic structure of metallic glasses: search for a structure-induced minimum in the density of states,” Journal of Physics F: Metal Physics. 1988. link Times cited: 46 Abstract: The atomic and electronic structures of amorphous and crysta… read moreAbstract: The atomic and electronic structures of amorphous and crystalline Mg-Zn alloys are studied by computer simulation, electronic band-structure calculations and photoemission measurements. The spectra for the metallic glasses and for pure crystalline zinc show a narrow band of Zn 3d states centred at a binding energy EB of about -9.7 eV, overlapping the bottom of a broad sp band. There are indications of a minimum in the electronic density of states at the Fermi level for the glasses and for the pure metals. Molecular dynamics and potential-energy mapping calculations based on pseudopotential-derived interatomic forces are used to construct models for the atomic structure, with no other input than the composition and the atomic numbers and atomic weights of the components. The analysis of these models-which are in reasonable agreement with X-ray and neutron diffraction data-shows that the local topology of the glassy structure is very similar to that of the stable crystalline intermetallic compounds. The glassy structure is best described as a disordered tetrahedral close packing with a weak tendency to chemical short-range order whose precise degree remains to be detailed. The linearised muffin-tin orbital method in the atomic sphere approximation is used to perform self-consistent calculations of the electronic DOS of crystalline Mg and Zn, of the hexagonal Laves phase MgZn2 and of 'amorphous' supercells (each containing 60 atoms) representing glassy MgZn2 and Mg7Zn3 alloys. In each case the authors find a minimum in the DOS at EF, and d bands centred at EB approximately=-7.5 eV. A transition-state calculation shows that the d-band position in the photoemission spectra is shifted relative to the electronic eigenvalue due to self-energy corrections. Photoemission and X-ray emission intensities are calculated from the partial local DOS and the self-consistent potentials in a single-scatterer final-state approximation. The comparison with experimental confirms the validity of the electronic structure calculations. The work represents one of the first ab initio calculations of the atomic and the electronic structure of a metallic glass, and the first confirmation of the existence of a minimum in the electronic DOS at EF. The relevance of the DOS minimum to the structure-potential relationship and to the stability of the glassy phase is discussed. read less NOT USED (low confidence) I. Schuller, “Molecular Dynamics Simulation of Epitaxial Growth,” MRS Bulletin. 1988. link Times cited: 3 Abstract: Molecular dynamics simulation has been used to study the gro… read moreAbstract: Molecular dynamics simulation has been used to study the growth of crystalline or amorphous, metal, and semiconductor films. These simulations show that the general form of the potential is critical in determining the morphology of vapor-phase grown films, with temperature playing a less important role. The high mobility of particles on the growing front implies that thermodynamics, together with kinetics, is important for thin film growth. read less NOT USED (low confidence) B. Feuston and S. Garofalini, “Empirical three‐body potential for vitreous silica,” Journal of Chemical Physics. 1988. link Times cited: 361 Abstract: A three‐body potential suitable for molecular dynamics (MD) … read moreAbstract: A three‐body potential suitable for molecular dynamics (MD) simulations has been developed for vitreous silica by adding three‐body interactions to the Born–Mayer–Huggins (BMH) pair potential. Previous MD simulations with the BMH potential have formed glassy SiO2 through the melt‐quench method with some success. Though bond lengths were found to be in fair agreement with experiment, the distribution of tetrahedral angles was too broad and the model glass contained 6%–8% bond defects. This is indicative of a lack of the local order that is present in the laboratory glass. The nature of the short range order is expected to play an important role when investigating defect formation, surface reconstruction, or surface reactivities. An attempt has been made to increase the local order in the simulated glass by including a directional dependent term in the effective potential to model the partial covalency of the Si–O bond. The vitreous state obtained through MD simulation with this modified BMH potential shows an increase in the short range order with a narrow O–Si–O angle distribution peaked about the tetrahedral angle and a low concentration of bond defects, typically ∼1%–2%. The static structure factor S(q) is calculated and found to be in good agreement with neutron scattering results. Intermediate range order is also discussed in reference to the distribution of ring sizes. read less NOT USED (low confidence) B. Rao and E. Blaisten-Barojas, “New potentials for Si2,” Chemical Physics Letters. 1988. link Times cited: 4 NOT USED (low confidence) T. Haliciogli, H. Pamuk, and S. Erkoç, “Interatomic Potentials with Multi‐Body Interactions,” Physica Status Solidi B-basic Solid State Physics. 1988. link Times cited: 23 Abstract: Various model potentials comprising two- and three-body inte… read moreAbstract: Various model potentials comprising two- and three-body interactions are analyzed comparatively. In this study Tersoff (T), Tersoff-Dodson (TD), Stillinger-Weber (SW), and Pearson-Takai-Halicioglu-Tiller (PTHT) potentials are included and their capabilities in reproducing various bulk, surface, and small cluster properties of silicon are investigated. For a proper comparison properties of small Si clusters are also calculated in this work using the PTHT function. Applicability and limitations of each potential are delineated and discussed. In general, structural properties calculated by these functions are found to be in better agreement with experiments than corresponding energy-related properties.
Verschiedene Modellpotentiale fur Zwei- und Drei-Korperwechselwirkungen werden im Vergleich analysiert. Eingeschlossen sind Tersoff (T)-, Tersoff-Dodson (TD)-, Stillinger-Weber (SW)- und Pearson-Takai-Halicioglu-Tiller (PTHT)-Potentiale und ihre Fahigkeit, verschiedene Volumen-, Oberflachen- und Clustereigenschaften von Silizium zu reproduzieren, werden untersucht. Fur einen exakten Vergleich werden die Eigenschaften von kleinen Silizium-Clustern mit der PTHT-Funktion berechnet. Anwendbarkeit und Grenzen jeden Potentials werden aufgezeichnet und diskutiert. Im allgemeinen wird gefunden, das die mit diesen Funktionen berechneten Struktureigenschaften mit den Experimenten besser ubereinstimmen als entsprechende energieverknupfte Eigenschaften. read less NOT USED (low confidence) J. Narayan, S. Sharan, A. Srivatsa, and A. Nandedkar, “Defects and interfaces in heterostructures,” Materials Science and Engineering B-advanced Functional Solid-state Materials. 1988. link Times cited: 18 NOT USED (low confidence) J. R. Ray, “Elastic constants and statistical ensembles in molecular dynamics,” Computer Physics Reports. 1988. link Times cited: 154 NOT USED (low confidence) M. Heggie, “Self-diffusion, deformation and melting in silicon—microscopic link,” Philosophical Magazine Letters. 1988. link Times cited: 8 Abstract: The possible role of Pandey's concerted exchange mechan… read moreAbstract: The possible role of Pandey's concerted exchange mechanism in silicon diffusion and deformation is discussed with reference to atomistic computer calculations using a form of interatomic total energy potential devised and modified by Tersoff. Our conclusion is that, if concerted exchange is viable for self-diffusion, then a similar mechanism should exist for the creation of edge dipoles in high-temperature-deformed silicon and in silicon near its melting point. We show that a metastable state created during concerted exchange is in fact the smallest conceivable faulted edge dipole. read less NOT USED (low confidence) A. Stoneham, V. Torres, P. Masri, and H. Schober, “Interatomic potentials in semiconductors and their validity for defect calculations,” Philosophical Magazine. 1988. link Times cited: 20 Abstract: We discuss the validation of interatomic forces for defect c… read moreAbstract: We discuss the validation of interatomic forces for defect calculations in semiconductors like silicon. Our tests include estimates of lattice response functions, defect steric energies, and relaxed atomic positions near defects. We find the variation from one potential to another to be substantial, notably because of the dominance of the bond-angle terms in the energy. Differences are less serious in the predicted geometries than in the predicted energies; which indicates preferred strategies for finding relaxed geometries. read less NOT USED (low confidence) G. A. Antonio, B. Feuston, R. Kalia, and P. Vashishta, “Ground‐state and finite‐temperature energetics and topologies of germanium microclusters,” Journal of Chemical Physics. 1988. link Times cited: 16 Abstract: We have investigated the ground‐state and finite‐temperature… read moreAbstract: We have investigated the ground‐state and finite‐temperature properties of Ge microclusters (N=2 to 14) using molecular dynamics (MD) simulation along with the method of steepest‐descent quench (SDQ). The interaction potential adopted is the three‐body Stillinger–Weber potential as modified by Ding and Andersen for amorphous Ge. Our results indicate that the experimentally observed greater stability of certain cluster sizes can be explained by the topology and energetics of the clusters at finite temperature rather than by the binding energies of the ground‐state structures. read less NOT USED (low confidence) T. Matsumiya, “Current Movements in Molecular Dynamics Study with Regard to Its Application to Materials Science and Engineering,” Tetsu To Hagane-journal of The Iron and Steel Institute of Japan. 1988. link Times cited: 3 NOT USED (low confidence) S. Phillpot and D. Wolf, “Atomistic Simulation of Silicon Grain Boundaries,” MRS Proceedings. 1988. link Times cited: 2 Abstract: The bond-bending and bond-stretching three-body potential of… read moreAbstract: The bond-bending and bond-stretching three-body potential of Stillinger and Weber is used to study the energy and structure of grain boundaries in silicon. 10 refs., 3 figs. read less NOT USED (low confidence) T. Beck and R. Berry, “The interplay of structure and dynamics in the melting of small clusters,” Journal of Chemical Physics. 1988. link Times cited: 160 Abstract: Extensive classical simulations of the melting–freezing tran… read moreAbstract: Extensive classical simulations of the melting–freezing transition of small clusters (N=7–33) of rare gas atoms have been performed in which quenching by steepest descent has been coupled to isoergic molecular dynamics. A mechanistic description of the phase change is given in terms of the local potential minima accessed in the transition region and the isomerization pathways for and the frequencies of interwell passages. All of the small clusters, at energies low in the transition range of energy, exhibit some separation (by factors of approximately 5 to 60) of the short time scale for motions about the various potential minima and the longer time scale separating interwell passages. The onset of diffusion is marked by passages over saddles linking the minima. Fully liquid‐like behavior is observed for all the clusters when the time scale separation for the motions no longer exists. The coexistence and magic number phenomena observed in previous simulations are explained in terms of the kinds of potentia... read less NOT USED (low confidence) J. Hafner, “Inherent structure theory of local order in liquid and amorphous alloys. I. The nearly-free-electron case,” Journal of Physics F: Metal Physics. 1988. link Times cited: 31 Abstract: The local order in liquid and amorphous alloys of free-elect… read moreAbstract: The local order in liquid and amorphous alloys of free-electron-like metals has been systematically studied using a molecular dynamics computer simulation linked to a steepest-descent mapping of the instantaneous configurations of the liquid onto local potential energy minima. Atomic interactions are expressed in terms of volume forces and pair forces derived from linear response theory and optimised first-principles pseudopotentials. A detailed study of the pair correlation functions, bond-angle distributions and structure factors after the mapping confirms the existence of an inherent structure of the liquid independent of temperature and density but sensitive to the details of the interatomic forces. The removal of the thermally induced distortions through the mapping produces a significant image enhancement of the short-range order. Comparison with X-ray and neutron diffraction data and with EXAFS measurements shows that the combination of the molecular dynamics simulation with the steepest-descent projection is a very successful technique for modelling the structure of metallic glasses. The author studies the inherent structure of both glass-forming alloys and those that form stable crystalline compounds and find characteristic similarities and differences. The inherent structure of the compound-forming alloy resembles a highly defective version of the tetrahedrally close-packed crystal. In the glass the local order is again of a tetrahedrally close-packed type but contains a substantially larger number of topological defects. read less NOT USED (low confidence) M. Baskes, M. Daw, B. Dodson, and S. Foiles, “Atomic-Scale Simulation in Materials Science,” MRS Bulletin. 1988. link Times cited: 26 Abstract: The potential of applying atomistic simulations in applied m… read moreAbstract: The potential of applying atomistic simulations in applied material science has been established by recent efforts such as those outlined above. Continued development of interatomic potentials suitable for wider classes of materials should result in a tool capable of strong interaction with experiment and of guiding future technological advances. read less NOT USED (low confidence) D. Choi, T. Takai, S. Erkoç, T. Halicioǧlu, and W. Tiller, “Free surfaces and multilayer interfaces in the GaAs/AlAs system,” Journal of Crystal Growth. 1987. link Times cited: 48 NOT USED (low confidence) Pantelides, “Temperature effects in atomic diffusion in silicon.,” Physical review. B, Condensed matter. 1987. link Times cited: 2 NOT USED (low confidence) M. Kluge, J. R. Ray, and A. Rahman, “Pulsed laser melting of silicon: A molecular dynamics study,” Journal of Chemical Physics. 1987. link Times cited: 22 Abstract: We present the results of a molecular dynamics study of the … read moreAbstract: We present the results of a molecular dynamics study of the pulsed laser melting of crystalline silicon. The Stillinger–Weber potential is employed for the atomic interaction. A 23 ps laser pulse of 0.2 J/cm2 is assumed to deliver 9×1013 W/g to the crystal. The energy is delivered at a constant rate over the 23 ps time interval. For the first 14 ps the temperature increases in a linear manner as functions of time. At 14 ps the crystal reaches the limit of superheating and melts over the next 4 ps interval of time. We discuss various quantities as functions of time: temperature, density, energies, and structure factors. An upper limit of 1750 K is determined for melting temperature and a value of 932 J/g for the latent heat, compared to the experimental values 1683 K and 1800 J/g, respectively. read less NOT USED (low confidence) G. Gilmer and M. Grabow, “Models of Thin Film Growth Modes,” JOM. 1987. link Times cited: 19 NOT USED (low confidence) H. Hongxing, “Computer-generated vitreous silica networks,” Journal of Non-crystalline Solids. 1987. link Times cited: 12 NOT USED (low confidence) F. Stillinger, T. Weber, and R. LaViolette, “Chemical reactions in liquids: Molecular dynamics simulation for sulfur,” Journal of Chemical Physics. 1986. link Times cited: 86 Abstract: A combination of two‐atom and three‐atom interactions has be… read moreAbstract: A combination of two‐atom and three‐atom interactions has been selected to represent the structural chemistry of sulfur. This model potential exhibits divalency (bond saturation) and leads to the known preference for Sn molecules to form puckered ring structures. Using this representation of the interactions, molecular dynamics calculations have been performed for 1000 sulfur atoms at the experimental liquid density. Short‐range order has been calculated for the low‐temperature liquid consisting of S8 cyclic molecules, and agrees qualitatively with the (imprecise) available measurements. At elevated temperatures the cyclic S8 molecules in the simulation begin to break open, and their subsequent chemical reactions yield primarily linear polymeric species. A metastable reaction intermediate in the polymerization process has been identified, a ‘‘tadpole’’ consisting of a diradical chain attached weakly to an S8 ring. read less NOT USED (low confidence) M. Kluge, J. R. Ray, and A. Rahman, “Molecular dynamic calculation of elastic constants of silicon,” Journal of Chemical Physics. 1986. link Times cited: 54 Abstract: Stillinger and Weber have introduced a model potential to st… read moreAbstract: Stillinger and Weber have introduced a model potential to study the solid and liquid forms of silicon. This potential has been used in a number of computer simulation studies of silicon. We have calculated the elastic constants of silicon using the Stillinger–Weber potential at three different temperatures T=888, 1164, and 1477 K. The adiabatic elastic constants are calculated using fluctuation formula appropriate for the microcanonical ensemble. We find that the calculated shear modulus C44 is smaller than the experimental values by ∼30% at T=888 K, ∼40% at the two higher temperatures, and the modulus C12 is larger than the experimental value by 25%–30%. Simulations with N=216 and 1728 particles were carried out to check on the number dependence of the results. These two particle numbers give equivalent results for the elastic constants. The calculated elastic constants show the same softening with rising temperature as shown by the experimental values. read less NOT USED (low confidence) W. G. Hoover, “molecular dynamics,” Catalysis from A to Z. 1986. link Times cited: 552 NOT USED (low confidence) B. Dodson and P. Taylor, “Atomistic Monte Carlo calculation of critical layer thickness for coherently strained siliconlike structures,” Applied Physics Letters. 1986. link Times cited: 80 Abstract: Monte Carlo based techniques were used to study the stabilit… read moreAbstract: Monte Carlo based techniques were used to study the stability of thin, coherently strained layers of mismatched siliconlike semiconductor material. The atomic interaction used for this study is the Stillinger–Weber potential [Phys. Rev. B 31, 5262 (1985)], modified to allow modeling of mismatched materials. Layers from 3 to 80 A thickness were considered. For layers greater than about 20 A thickness, the critical layer thickness is accurately described by the continuum theory of Matthews and Blakeslee [J. Cryst. Growth 27, 118 (1974)]. For thinner layers, however, the strain energy associated with misfit dislocations varies from the continuum value, resulting in smaller critical layer thickness, to the extent that critical mismatch as a function of layer thickness becomes nonmonotonic for the thinnest films considered. read less NOT USED (low confidence) D. E. Harrison and M. Jakas, “Simulation of the atomic collision cascade,” Radiation Effects and Defects in Solids. 1986. link Times cited: 15 Abstract: Molecular dynamics computer simulations can be used to evalu… read moreAbstract: Molecular dynamics computer simulations can be used to evaluate pre-existing theorttical concepts, or used directly as a research tool, simulations can directly investigate natural phenomena. The TRIM program, a binary-collision simulation of atomic collision cascades, is a well-known example of the first usage. This paper compares and contrasts TRIM results with computations from a multiple-interaction cascade simulation program, QDYN. QDYN is described in detail; then some issues of potential function development for simulation use are introduced, followed by some examples of QDYN based research. Two current simulation based research topics are presented in greater detail. One is a study of very low energy cascades, where directed bonds and chemical effects are important. The other is the influence of electronic processes on cascade development. Characteristics of atoms ejected from the surface are emphasised. Both topics have potential applications in the simulation of atomic collision cascade... read less NOT USED (low confidence) D. Brenner and B. Garrison, “Dissociative valence force field potential for silicon.,” Physical review. B, Condensed matter. 1986. link Times cited: 42 NOT USED (low confidence) S. Nosé and F. Yonezawa, “Isothermal-isobaric computer simulations of melting and crystallization of a Lennard-Jones system,” Solid State Communications. 1985. link Times cited: 14 NOT USED (low confidence) F. Stillinger and T. Weber, “Inherent structure theory of liquids in the hard‐sphere limit,” Journal of Chemical Physics. 1985. link Times cited: 63 Abstract: Atomic pair correlation functions for liquids provide an ima… read moreAbstract: Atomic pair correlation functions for liquids provide an image of temperature‐dependent short‐range order. If the thermal ensemble of atomic configurations is mapped (by steepest descent on the potential hypersurface) onto potential energy minima, the pair correlation function from the resulting transformed configurations exhibits substantial image enhancement, revealing short‐range order in a much more vivid fashion. Previous studies of model atomic liquids have demonstrated that at fixed density, mapped short‐range order is virtually independent of the initial temperature, and thereby amounts to an ‘‘inherent structure’’ for the liquid. The present paper investigates steepest‐descent mapping and inherent structure for hard spheres, construed as the infinite‐n limit for pair potentials (a/r)n. Methods used are both analytical and simulational, the latter involving molecular dynamics for n=12 and 24. Results show that inherent structures in the hard‐sphere limit are randomly packed configurations, where p... read less NOT USED (low confidence) R. LaViolette and F. Stillinger, “Multidimensional geometric aspects of the solid–liquid transition in simple substances,” Journal of Chemical Physics. 1985. link Times cited: 99 Abstract: Any molecular system explores significantly different region… read moreAbstract: Any molecular system explores significantly different regions of the potential‐energy hypersurface as the system is found, respectively, in the solid and liquid phases. We study in detail the multidimensional geometry of these different regions with molecular‐dynamics calculations for 256 simple atoms in a fixed volume. The atomic interactions are chosen to represent the noble gases. The stable crystal for this model displays a face‐centered cubic structure. We evaluate the local gradient and curvatures of the regions of the hypersurface sampled by the system for a wide range of temperatures. We observe that a significant fraction of the curvatures become negative in the region sampled by the system at temperatures even as low as one‐fourth the melting temperature. Further, the curvature distribution changes dramatically with respect to temperature at the melting point. We also construct and evaluate a new distribution for the distance between the atoms in their instantaneous dynamical configurations and ... read less NOT USED (low confidence) F. Wooten, G. A. Fuller, K. Winer, and D. Weaire, “Computer generation of structural models of amorphous Si: Studies of nucleation of crystallization,” Journal of Non-crystalline Solids. 1985. link Times cited: 6 NOT USED (low confidence) W. G. Hoover, “Nonequilibrium Molecular Dynamics,” Annual Review of Physical Chemistry. 1983. link Times cited: 268 Abstract: The development of nonequilibrium molecular dynamics is desc… read moreAbstract: The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. field. Nonequilibrium molecular dynamicsl - 3 began around 1970 when Bill Ashurst set out to simulate flows of momentum and energy in nonequilibrium liquids by using boundary heat and momentum reservoirs made up of particles. A typical fluid geometry is illustrated in Figure 1. The methods that Ashurst developed were successfully formalized and generalized about ten years later, in work that is still rapidly developing. He achieved his goal, reproducing the experimental situations leading to nonequilibrium transport. It has turned out that the transport coefficients so deternlined depend only very slightly on the amount of deviation from equilibrium. Thus the necessarily large gradients in the computer simulations are perfectly acceptable for quantitative work. By 1980, following pioneering work of Klimenko and Dremin in Russia4 , a joint effort at Los Alamos and Livermore resulted in the simulation and characterization of a strong dense-fluid shockwave5 using 4800 atoms. The measured structure of that shockwave is compared, in Figure 2, to the predictions of the Navier-Stokes equations, and indicates shear viscosity and heat conductivity coefficients only 30% larger than the small-gradient limits of Newtonian viscosity and Fourier heat con duction. The shockwave transport coefficients are a bit bigger because the relatively rigid and disordered shockwave structure is a more efficient medium for transporting momentum and energy. read less NOT USED (low confidence) W. Li, W. Zhang, X. Huang, X. Mu, and Y. Ni, “Regulating phonon transport in silicon nanofilms by resonant nanopillars,” International Journal of Heat and Mass Transfer. 2024. link Times cited: 0 NOT USED (low confidence) L. Feng, X. Zhang, W. Li, M. Liu, and X. Yao, “Multiple structural phase transitions in single crystal silicon subjected to dynamic loading,” Scripta Materialia. 2024. link Times cited: 0 NOT USED (low confidence) H. Liu, W. Li, Z.-L. Cao, X. Huang, and Y. Ni, “Enhanced phonon resonance by non-uniform surface nanopillars in Si nanowires,” International Journal of Heat and Mass Transfer. 2023. link Times cited: 1 NOT USED (low confidence) R. Rabani, S. Merabia, and A. Pishevar, “Conductive heat transfer through nanoconfined argon gas: From continuum to free-molecular regime,” International Journal of Thermal Sciences. 2023. link Times cited: 1 NOT USED (low confidence) NguyenTruongLong et al., “Molecular dynamics simulation of pressure effect on silicene nanoribbons,” Science & Technology Development Journal. 2023. link Times cited: 0 Abstract: Introduction: In 2D materials, the boundary of silicene form… read moreAbstract: Introduction: In 2D materials, the boundary of silicene formed as nanoribbons plays an essential role in synthesis and can be controlled to achieve different characteristics. Our study aims to investigate the structural preference depending on the pressure tolerance and boundary dependency. Methods: The main methodology used in our study is molecular dynamics simulation with Stillinger Weber potentials. Our simulation was carried out on 2D models of honeycomb silicene obtained through high and low pressurized cooling from the liquid state and then heat annealing for a decent time. The final configuration of silicene will be investigated in terms of structures and thermodynamic properties. Results: We found that the effect of the cooling process under high pressure formed a 4-fold ring structure, while at low pressure, 2D honeycomb networks were recovered but with different degrees of defects depending on the boundary condition. The main difference between several transitions of 2D silicene is discussed via the evolution of total energy and the change in coordination number and bond-ring distribution. Conclusions: This study provides insights into the dependency of the structure of silicene on the pressure and boundary, repre-sentedby the first-order transition at lowpressure and a congregationof disorderedlow-numbered rings into the ordered tetragonal formation at high pressure. Notably, our results have shown that silicene nanoribbon materials can be controlled by pressure to obtain unfamiliar structures such as pentagonal and tetragonal networks. read less NOT USED (low confidence) M. Steinhauser, “Computational Multiscale Modeling of Fluids and Solids,” Graduate Texts in Physics. 2022. link Times cited: 30 NOT USED (low confidence) T. Miao, M. Xiang, D. Chen, M. An, and W. Ma, “Thermal transport characteristics of two-dimensional t-PdTe2 and its Janus structures,” International Journal of Heat and Mass Transfer. 2022. link Times cited: 4 NOT USED (low confidence) K. Zhou and B. Liu, “Potential energy functions,” Molecular Dynamics Simulation. 2022. link Times cited: 0 NOT USED (low confidence) O. Kaya and N. Donmezer, “Investigation of the Thermal Transport Properties Across Van der Waals Interfaces of 2D Materials,” IEEE Transactions on Nanotechnology. 2022. link Times cited: 0 Abstract: Two-dimensional (2D) materials have attracted extensive rese… read moreAbstract: Two-dimensional (2D) materials have attracted extensive research interest in various applications in recent years due to their superior thermal, electrical, and optical properties, making them preferable for potential electronic and optoelectronic applications. These 2D materials form Van der Waals interfaces with common substrate materials due to fabrication and/or device requirements. Since the generated heat during the operation of the devices cause degradation and reliability concerns, interface thermal boundary conductance (TBCs) and in-plane thermal conductivities of the interfaces should be well understood for proper thermal management. Herein, we investigate the TBC and in-plane thermal conductivities of the Van der Waals interfaces of 2D materials by approach to-equilibrium molecular dynamics (AEMD) and non-equilibrium molecular dynamics (NEMD) simulations. Our results show that the TBC is higher for the interfaces with stronger phonon DOS and lattice match. Also, the increasing number of 2D material layers increases the TBC of the interface. The results also showed that the thermal conductivity of the materials forming the interface could affect each other's in-plane thermal conductivity. Changes in thermal conductivities of individual in-plane thermal conductivities can be as high as 70%. Change in thermal conductivity depends on the difference in thermal conductivities of materials in contact and only visible in the vicinity of the interface. Thermal management strategies should pay attention to the trade-off between the changes in individual thermal conductivities and TBC of the interfaces. read less NOT USED (low confidence) R. L. Dai, W. Liao, C.-T. Lin, K. Chiang, and S. Lee, “Nano-scale and Atomistic-Scale Modeling of Advanced Materials,” Nano-Bio- Electronic, Photonic and MEMS Packaging. 2021. link Times cited: 0 NOT USED (low confidence) J. Zhang, “Small-scale effects on the piezopotential properties of tapered gallium nitride nanowires: The synergy between surface and flexoelectric effects,” Nano Energy. 2021. link Times cited: 10 NOT USED (low confidence) X. Zhou and D. Tian, “A novel linear elastic constitutive model for continuum-kinematics-inspired peridynamics,” Computer Methods in Applied Mechanics and Engineering. 2021. link Times cited: 16 NOT USED (low confidence) L. Marqués, M. Aboy, P. López, I. Santos, L. Pelaz, and G. Fisicaro, “Atomistic modeling of laser-related phenomena,” Laser Annealing Processes in Semiconductor Technology. 2021. link Times cited: 0 NOT USED (low confidence) S. Chowdhury et al., “Mechanical Properties and Strain Transfer Behavior of Molybdenum Ditelluride (MoTe2) Thin Films,” Journal of Engineering Materials and Technology. 2021. link Times cited: 16 Abstract:
Transition metal dichalcogenides (TMDs) offer superior pro… read moreAbstract:
Transition metal dichalcogenides (TMDs) offer superior properties over conventional materials in many areas such as in electronic devices. In recent years, TMDs have been shown to display a phase switching mechanism under the application of external mechanical strain, making them exciting candidates for phase change transistors. Molybdenum ditelluride (MoTe2) is one such material that has been engineered as a strain-based phase change transistor. In this work, we explore various aspects of the mechanical properties of this material by a suite of computational and experimental approaches. First, we present parameterization of an interatomic potential for modeling monolayer as well as multilayered MoTe2 films. For generating the empirical potential parameter set, we fit results from density functional theory calculations using a random search algorithm known as particle swarm optimization. The potential closely predicts structural properties, elastic constants, and vibrational frequencies of MoTe2 indicating a reliable fit. Our simulated mechanical response matches earlier larger scale experimental nanoindentation results with excellent prediction of fracture points. Simulation of uniaxial tensile deformation by molecular dynamics shows the complete non-linear stress-strain response up to failure. Mechanical behavior, including failure properties, exhibits directional anisotropy due to the variation of bond alignments with crystal orientation. Furthermore, we show the deterioration of mechanical properties with increasing temperature. Finally, we present computational and experimental evidence of an extended c-axis strain transfer length in MoTe2 compared to TMDs with smaller chalcogen atoms. read less NOT USED (low confidence) A. Kabanov, Y. A. Morkhova, I. A. Bezuglov, and V. Blatov, “Computational design of materials for metal-ion batteries,” Reference Module in Chemistry, Molecular Sciences and Chemical Engineering. 2021. link Times cited: 1 NOT USED (low confidence) A. Genoese, A. Genoese, N. Rizzi, and G. Salerno, “On the Role of Interatomic Potentials for Carbon Nanostructures.” 2020. link Times cited: 0 NOT USED (low confidence) K. Nordlund and F. Djurabekova, “Molecular Dynamics Simulations of Non-equilibrium Systems,” Handbook of Materials Modeling. 2020. link Times cited: 3 NOT USED (low confidence) Y. Chalopin, “A Statistical Approach of Thermal Transport at Nanoscales: From Solid-State to Biological Applications,” Handbook of Materials Modeling. 2020. link Times cited: 0 NOT USED (low confidence) M. Hussein and H. Honarvar, “Resonant Thermal Transport in Nanophononic Metamaterials,” Handbook of Materials Modeling. 2020. link Times cited: 3 NOT USED (low confidence) R. Devanathan, “Interatomic Potentials for Nuclear Materials,” Handbook of Materials Modeling. 2020. link Times cited: 1 NOT USED (low confidence) T. Motooka and T. Uda, “Multiscale modeling methods,” Handbook of Silicon Based MEMS Materials and Technologies. 2020. link Times cited: 2 NOT USED (low confidence) Y. A. Kosevich and I. Strelnikov, “Extraordinary phonon transmission through hidden lattice-wave nanochannels as resonance quantum phonon tunneling.” 2020. link Times cited: 2 NOT USED (low confidence) S. Suresh, M. J. Echeverría, and A. Dongare, “Atomistic study of silicon alloying in the spallation behavior of nanocrystalline aluminum systems.” 2020. link Times cited: 1 NOT USED (low confidence) Y. Wang, J. Cao, J. Chai, and J. Shi, “Geometric effects on self-assemble of a BP ribbon on a CNT,” Computational Materials Science. 2020. link Times cited: 0 NOT USED (low confidence) S. Chakraborty and H. Kumar, “Molecular dynamics simulations of two-dimensional materials.” 2020. link Times cited: 1 NOT USED (low confidence) I. Espinosa and R. Mohan, “Molecular modeling of nanoscale features of cement paste and their correlation to engineering mechanical behavior.” 2020. link Times cited: 0 NOT USED (low confidence) G. Ackland and G. Bonny, “Interatomic Potential Development,” Comprehensive Nuclear Materials. 2020. link Times cited: 4 NOT USED (low confidence) W. Cai, J. Li, B. Uberuaga, and S. Yip, “Molecular Dynamics,” Comprehensive Nuclear Materials. 2020. link Times cited: 0 NOT USED (low confidence) J. Yu, Q. Li, and W. Ye, “Investigation of wave interference effect in Si/Ge superlattices with interfering Monte Carlo method,” International Journal of Heat and Mass Transfer. 2019. link Times cited: 4 NOT USED (low confidence) L. P. Wang, “Force Field Development and Nanoreactor Chemistry,” Computational Approaches for Chemistry Under Extreme Conditions. 2019. link Times cited: 1 NOT USED (low confidence) S. Porowski et al., “Melting of tetrahedrally bonded semiconductors: ‘anomaly’ of the phase diagram of GaN?,” Journal of Crystal Growth. 2019. link Times cited: 7 NOT USED (low confidence) “References,” Basic Physics of Nanoscience. 2019. link Times cited: 0 NOT USED (low confidence) T. Zohdi, “Modeling and Simulation of Functionalized Materials for Additive Manufacturing and 3D Printing: Continuous and Discrete Media.” 2018. link Times cited: 11 NOT USED (low confidence) S. Winczewski, M. Y. Shaheen, and J. Rybicki, “Interatomic potential suitable for the modeling of penta-graphene: Molecular statics/molecular dynamics studies,” Carbon. 2018. link Times cited: 34 NOT USED (low confidence) J. Al-Ghalith and T. Dumitricǎ, “Screw-dislocated nanostructures.” 2018. link Times cited: 1 NOT USED (low confidence) S. Brochard et al., “Atomic scale mechanisms and brittle to ductile transition at low size in silicon,” Materials Today: Proceedings. 2018. link Times cited: 1 NOT USED (low confidence) M. Z. Hossain et al., “Anisotropic toughness and strength in graphene and its atomistic origin,” Journal of The Mechanics and Physics of Solids. 2018. link Times cited: 43 NOT USED (low confidence) W. Xiao, Y. Li, and P. Wang, “Uncertainty Quantification of Atomistic Materials Simulation with Machine Learning Potentials.” 2018. link Times cited: 4 NOT USED (low confidence) B. Schultrich, “Structure of Amorphous Carbon.” 2018. link Times cited: 2 NOT USED (low confidence) H. Li and R. Q. Zhang, “Theoretical and Experimental Methods for Determining the Thermal Conductivity of Nanostructures.” 2018. link Times cited: 0 NOT USED (low confidence) T. Zohdi, “PART II—Discrete Element Method (DEM) Approaches: Dynamic Powder Deposition.” 2018. link Times cited: 1 NOT USED (low confidence) A. Shkrebtii and M. Rohlfing, “Determination of the total energy of a many-particle system.” 2018. link Times cited: 0 NOT USED (low confidence) O. Koroleva and A. Mazhukin, “Atomistic modeling of the thermophysical characteristics of silicon in the region of the semiconductor-metal phase transition,” Keldysh Institute Preprints. 2018. link Times cited: 0 NOT USED (low confidence) J. D. Lee, J. Li, Z. Zhang, and L. Wang, “Sequential and Concurrent Multiscale Modeling of Multiphysics: From Atoms to Continuum.” 2018. link Times cited: 8 NOT USED (low confidence) A. Kiselev, “Molecular dynamics simulations of laser ablation in covalent materials.” 2017. link Times cited: 1 Abstract: 15 Deutsche Zusammenfassung 18 I. Theoretical background 27… read moreAbstract: 15 Deutsche Zusammenfassung 18 I. Theoretical background 27 read less NOT USED (low confidence) A. Vakhrushev, A. Fedotov, A. V. Severjuhin, and R. Valeev, “Effect of Pore Size Parameters for Mechanisms of Nanofilm Coatings on Substrates of Porous Alumina,” Bulletin of the South Ural State University. Series "Mathematical Modelling, Programming and Computer Software. 2017. link Times cited: 1 NOT USED (low confidence) Y. Tang, B. Yang, H. Yang, P. Yang, J. Yang, and Y. Hu, “Numerical investigation on mechanical properties of graphene covering silicon nanofilms,” Computational Materials Science. 2017. link Times cited: 5 NOT USED (low confidence) R. Kohli, “Metallic Contaminants on Surfaces and Their Impact.” 2017. link Times cited: 5 NOT USED (low confidence) M. Verdier, K. Termentzidis, and D. Lacroix, “Modeling Thermal Transport in Nano-Porous Semiconductors.” 2017. link Times cited: 2 NOT USED (low confidence) A. Vakhrushev, A. V. Severyukhin, A. Fedotov, and R. Valeev, “Investigation of deposition of nanofilms on a porous aluminium oxide substrate by mathematical modeling techniques.” 2016. link Times cited: 5 Abstract: В работе приведена постановка задачи и описание методики изу… read moreAbstract: В работе приведена постановка задачи и описание методики изучения процессов осаждения нанопленок на подложку из пористого алюминия. Рассмотрены уравнения, составляющие основу многочастичного потенциала, отвечающего модифицированному методу погруженного атома. В качестве осаждаемых материалов брались золото, серебро, железо, галлий, германий и палладий. Расчеты показали, что существуют разные механизмы заращивания пористой подложки из оксида алюминия данными материалами. Для каждого из типов осаждаемых атомов были зафиксированы свои процессы взаимодействия наноструктур и механизмы заращивания подложек и пор. Так, атомы серебра и золота равномерно закрывали поры нанопленкой без проникновения внутрь их, имело место лишь незначительное проседание нанопленки в поры. Атомы железа генерировали наноструктуры в безвоздушной среде над подложкой; заращивание подложки происходило по островному принципу; мелкие наноструктуры железа на подложке постепенно укрупнялись и группировались в бóльшие по размеру; наблюдалось образование наноструктуры железа внутри поры. При осаждении атомов галлия пора также полностью не зарастала, а нанопленка на поверхности подложки формировалась в виде отдельных областей; были заметны небольшие наночастицы галлия на поверхности подложки. Палладий порождал равномерную пленку с небольшим проседанием в области поры; при осаждении атомов палладия непосредственно над порой на протяжении всего этапа конденсации сохранялось отверстие, которое так и не заросло. У всех типов осаждаемых атомов имелись единичные экземпляры, которые достигали дна поры. Наиболее полное и плотное заращивание поры зафиксировано при эпитаксии галлия. Установлено, что пора, заполненная атомами, может рассматриваться как квантовая точка и использоваться для получения оптических и электрических эффектов. Сформулированы практические рекомендации для производства нанопленочных материалов различной структуры. Методики осаждения наноразмерных пленок могут применяться для контроля в конкретных технологических процессах, а также для прогнозирования и проектирования нанопленочных материалов. read less NOT USED (low confidence) S. A. Zielke, “Molecular dynamics simulations of heterogeneous ice nucleation by atmospheric aerosols.” 2016. link Times cited: 1 Abstract: Water droplets in the atmosphere do not freeze homogeneously… read moreAbstract: Water droplets in the atmosphere do not freeze homogeneously until -38◦C. Freezing at warmer temperatures requires heterogeneous ice nuclei (IN). Despite the importance of ice in the atmosphere, little is known about the microscopic mechanisms of heterogeneous ice nucleation. This thesis employs molecular dynamics simulations to investigate ice nucleation by silver iodide, kaolinite, potassium feldspar, gibbsite, and a protein. Silver iodide is one of the best known ice nucleating agents. We examined seven surfaces of silver iodide and observed ice nucleation on three surfaces. The surfaces that nucleated ice organized the first layer of water molecules into a configuration resembling ice, such as chair conformed hexagonal rings. Surfaces that do not nucleate ice do not organize water into icelike configurations, such as planar rings. Results suggest lattice mismatch is insufficient in predicting ice nucleation, and a finer atomistic match is required. Finite silver iodide disks and plates were used to probe the relationship between the size of a nucleating surface and maximum temperature of ice nucleation. Larger disks nucleated ice at warmer temperatures than smaller disks by read less NOT USED (low confidence) A. Markopoulos, P. Koralli, G. Kyriakakis, M. Kompitsas, and D. Manolakos, “Molecular dynamics simulation of material removal with the use of laser beam.” 2016. link Times cited: 3 NOT USED (low confidence) R. Jones, C. Weinberger, S. Coleman, and G. Tucker, “Introduction to Atomistic Simulation Methods.” 2016. link Times cited: 1 NOT USED (low confidence) S. N. Gondakar, S. Vasan, and M. Singh, “Computational Intelligence-Based Parametrization on Force-Field Modeling for Silicon Cluster Using ASBO.” 2016. link Times cited: 0 NOT USED (low confidence) J. Houška, “Force field for realistic molecular dynamics simulations of ZrO2 growth,” Computational Materials Science. 2016. link Times cited: 12 NOT USED (low confidence) Y. Wang, K. Zhang, and G. Xie, “Remarkable suppression of thermal conductivity by point defects in MoS2 nanoribbons,” Applied Surface Science. 2016. link Times cited: 18 NOT USED (low confidence) J. Zhang and S. Meguid, “Piezoelectric Response at Nanoscale.” 2016. link Times cited: 1 NOT USED (low confidence) S. Goel, X. Luo, A. Agrawal, and R. Reuben, “Diamond machining of silicon: A review of advances in molecular dynamics simulation,” International Journal of Machine Tools & Manufacture. 2015. link Times cited: 314 NOT USED (low confidence) A. Chatzopoulos, “Numerical Simulations of Metal-Oxides.” 2015. link Times cited: 0 Abstract: Oxides like silicates, alumina or periclase, are materials w… read moreAbstract: Oxides like silicates, alumina or periclase, are materials with significant properties and are therefore investigated extensively in experiment and in theory. The aim of this PhD thesis was to propose and further to develop methods, which make molecular dynamic simulations of oxides with large particle numbers and for long simulation times possible.
The work consists of three parts. In the first one the already existing methods for simulating oxides will be discussed, while in the second one their methodological progress will be presented. The third chapter is solely reserved for the phenomenon of flexoelectricity, which has been discovered during the visualization of the crack propagation in alumina.
Oxide, wie z.B. Silikate, Korund oder Periklas, sind bedeutende Funktionswerkstoffe und werden daher experimentell wie theoretisch intensiv untersucht. Ziel dieser Dissertation war es, Verfahren vorzustellen und derart zu optimieren, dass sie Molekulardynamiksimulationen von Oxiden mit grosen Teilchenzahlen und uber lange Zeiten ermoglichen.
Die Arbeit gliedert sich dabei in drei Bereiche. Im ersten Teil wird auf die einzelnen bereits vorhandenen Methoden zur Simulation von Oxiden eingegangen, im zweiten Kapitel deren Verbesserung vorgestellt. Der dritte Bereich widmet sich ausschlieslich dem Phanomen der Flexoelektrizitat, welche durch die geschickte Visualisierung der Rissausbreitung in Korund entdeckt wurde. read less NOT USED (low confidence) M. Schmidt, A. Ismail, and R. Sauer, “A CONTINUUM MECHANICAL SURROGATE MODEL FOR ATOMIC BEAM STRUCTURES,” International Journal for Multiscale Computational Engineering. 2015. link Times cited: 14 Abstract: Starting from a fully atomistic system, we outline a general… read moreAbstract: Starting from a fully atomistic system, we outline a general approach to obtain an approximate continuum surrogate model incorporating specific kinematic state variables. The continuum mechanical system is furnished with a hyperelastic material model. We then adapt the procedure to slender structures with beam-like character, such as Silicon nanowires or carbon nanotubes. The surrogate model can be described as a geometrically exact beam, which can be treated numerically using finite elements. Based on molecular dynamics simulations, we show how to obtain for a given atomistic beam system both a set of suitable deformed states as well as generalized stress and strain measures. Finally, we benchmark the obtained continuum model by assessing its accuracy for a beam coming into contact with an infinite Lennard-Jones wall. read less NOT USED (low confidence) D. Alfé, “The Ab Initio Treatment of High-Pressure and High-Temperature Mineral Properties and Behavior.” 2015. link Times cited: 1 NOT USED (low confidence) R. Evarestov, “Group IV Semiconductors.” 2015. link Times cited: 2 NOT USED (low confidence) E. Lampin, “Recrystallization of Silicon by Classical Molecular Dynamics.” 2015. link Times cited: 0 NOT USED (low confidence) B. Johnson, J. McCallum, and M. Aziz, “Solid-Phase Epitaxy.” 2015. link Times cited: 11 NOT USED (low confidence) H. Detz and G. Strasser, “Metropolis Monte Carlo based Relaxation of Atomistic III-V Semiconductor Models,” IFAC-PapersOnLine. 2015. link Times cited: 0 NOT USED (low confidence) A. Evteev, L. Momenzadeh, E. Levchenko, I. Belova, and G. Murch, “Vibrational contribution to thermal transport in liquid cooper: Equilibrium molecular dynamics study,” Computational Materials Science. 2015. link Times cited: 5 NOT USED (low confidence) M. Ganchenkova and R. Nieminen, “Mechanical Properties of Silicon Microstructures.” 2015. link Times cited: 4 NOT USED (low confidence) T. Sinno, “Atomistic Calculation of Defect Thermodynamics in Crystalline Silicon.” 2015. link Times cited: 0 NOT USED (low confidence) Y. Wang and K. Chang, “Continuum shape sensitivity analysis and what-if study for two-dimensional multi-scale crack propagation problems using bridging scale decomposition,” Structural and Multidisciplinary Optimization. 2015. link Times cited: 3 NOT USED (low confidence) K. Gordiz and A. Henry, “Calculation of Modal Contributions to Heat Transfer across Si/Ge Interfaces,” MRS Proceedings. 2015. link Times cited: 1 NOT USED (low confidence) Y. Kosevich, H. Han, L. G. Potyomina, A. Darinskii, and S. Volz, “Phonon Interference and Energy Transport in Nonlinear Lattices with Resonance Defects.” 2015. link Times cited: 3 NOT USED (low confidence) Toffoli̇ H., S. Erkoç, and D. Toffoli, “Modeling of Nanostructures.” 2015. link Times cited: 1 NOT USED (low confidence) K. N. Clayton, J. Khor, and S. Wereley, “Rapid Electrokinetic Patterning and Its Applications.” 2015. link Times cited: 1 NOT USED (low confidence) V. Venkatesh, “Computer simulation studies of carbon nanotube and its interactions with water.” 2014. link Times cited: 1 Abstract: ii addition to defect concentration, the location of defects… read moreAbstract: ii addition to defect concentration, the location of defects in SWCNT will also affect the mechanical properties of water submerged SWCNT. For the case of capped SWCNTs, it was found that the concentration of water molecule encapsulated inside the SWCNT strongly affects the elastic properties of the SWCNT. Another study involved the transport characteristics of water molecules in CNTs using MD simulation. The transport properties of water molecules in a nano-scale channel such as CNTs is critical for its key role in designing the next generation CNT based nanofluidic devices. The effect of channel diameter, defects and the inter-layer spacing on the transport of water molecules is studied by subjecting the flow of water molecules through CNTs under pressure. The findings show that the efficiency of water transport can be improved by deploying bigger SWCNTs that have wide channel diameter. It was however found that defects in the nano-fluidic system will reduce the transport efficiency of water molecules. The results also show that the inter-layer spacing in a double-walled CNTs (DWCNTs) has a significant influence on the transport efficiency of water molecules. The investigations and conclusions obtained from this thesis is expected to further compliment the potential applications of CNTs in nano-fluidics and NEMS devices. read less NOT USED (low confidence) J. Yeo, “Modeling and simulation of the structural evolution and thermal properties of ultralight aerogel and 2D materials.” 2014. link Times cited: 1 NOT USED (low confidence) R. Khanna and V. Sahajwalla, “Atomistic Simulations of Properties and Phenomena at High Temperatures.” 2014. link Times cited: 3 NOT USED (low confidence) Y. Xu and G. Li, “Modeling and Analysis of Strain Effects on Thermoelectric Figure of Merit in Si/Ge Nanocomposites.” 2014. link Times cited: 1 NOT USED (low confidence) N. Zuckerman and J. Lukes, “Combined Kinetic Monte Carlo—Molecular Dynamics Approach for Modeling Phonon Transport in Quantum Dot Superlattices,” Journal of Heat Transfer-transactions of The Asme. 2014. link Times cited: 1 Abstract: A new kinetic Monte Carlo method for modeling phonon transpo… read moreAbstract: A new kinetic Monte Carlo method for modeling phonon transport in quantum dot superlattices is presented. The method uses phonon scattering phase functions and cross sections to describe collisions between phonons and quantum dots. The phase functions and cross sections are generated using molecular dynamics simulation, which is capable of including atomistic effects otherwise unavailable in Monte Carlo approaches. The method is demonstrated for a test case featuring a Si-Ge quantum dot superlattice, and the model is compared against published experiments. It is found that molecular dynamics-derived cross sections must be weighted by diffuse mismatch model-type weighting factors in order to satisfy detailed balance considerations. Additionally, it is found that thin alloy “base layer” films strongly reduce thermal conductivity in these systems and must be included in the modeling to obtain agreement with published experimental data. read less NOT USED (low confidence) Y. Lee and G. Hwang, “Fundamental insight into control of thermal conductivity in silicon-germanium alloy nanowires,” MRS Proceedings. 2014. link Times cited: 0 NOT USED (low confidence) P. Sigmund, “Interatomic Potentials, Scattering and Nuclear Stopping.” 2014. link Times cited: 0 NOT USED (low confidence) C. Liu, “A THEORETICAL STUDY OF INTERACTION OF NANOPARTICLES WITH BIOMOLECULE.” 2014. link Times cited: 0 NOT USED (low confidence) A. Ovrutsky, A. Prokhoda, and M. Rasshchupkyna, “Computer Modeling of Physical Phenomena and Processes.” 2014. link Times cited: 1 NOT USED (low confidence) R. Stoller and E. Zarkadoula, “Primary Radiation Damage Formation in Solids.” 2014. link Times cited: 11 NOT USED (low confidence) S. Hug, “Classical molecular dynamics in a nutshell.,” Methods in molecular biology. 2013. link Times cited: 20 NOT USED (low confidence) J. Li et al., “Complete Realization of the EMMS Paradigm.” 2013. link Times cited: 1 NOT USED (low confidence) J. Li et al., “Many-Core Programming.” 2013. link Times cited: 0 NOT USED (low confidence) V. Astapenko, “Bremsstrahlung of Fast Charged Particles in a Solid Body.” 2013. link Times cited: 0 NOT USED (low confidence) F. Baletto, “Modelling Janus Nanoparticles.” 2013. link Times cited: 2 NOT USED (low confidence) S. Gopalakrishnan and S. Narendar, “Various Modeling Techniques for Nanostructures.” 2013. link Times cited: 1 NOT USED (low confidence) P. Gamallo, L. Martin-Gondre, R. Sayós, C. Crespos, and P. Larrégaray, “Potential Energy Surfaces for the Dynamics of Elementary Gas-Surface Processes.” 2013. link Times cited: 8 NOT USED (low confidence) W. Cai, “1.09 – Molecular Dynamics.” 2012. link Times cited: 29 NOT USED (low confidence) I. Belabbas, J. Chen, and G. Nouet, “A new atomistic model for the threading screw dislocation core in wurtzite GaN,” Computational Materials Science. 2012. link Times cited: 26 NOT USED (low confidence) V. Eyert et al., “Atomistic Simulations of Microelectronic Materials: Prediction of Mechanical, Thermal, and Electrical Properties.” 2012. link Times cited: 0 NOT USED (low confidence) G. Ackland, “1.10 – Interatomic Potential Development.” 2012. link Times cited: 10 NOT USED (low confidence) T. Zohdi, “Introduction: Dynamics of an Individual Charged Particle.” 2012. link Times cited: 0 NOT USED (low confidence) T. Zohdi, “Dynamics of Rigid Clusters of Charged Particles.” 2012. link Times cited: 0 NOT USED (low confidence) A. Chroneos, “Appendix – Atomic-scale computer simulation of functional materials: methodologies and applications.” 2012. link Times cited: 0 NOT USED (low confidence) S. W. Cranford and M. Buehler, “Computational Approaches and Simulation.” 2012. link Times cited: 0 NOT USED (low confidence) M. Hu, X. Zhang, K. Giapis, and D. Poulikakos, “Atomistic Mechanisms of Enhancing Energy Conversion Efficiency of Nanostructured Thermoelectrics.” 2011. link Times cited: 0 NOT USED (low confidence) K. Nordlund, S. Hoilijoki, and E. Holmstrom, “Ion irradiation effects in silicon nanowires,” MRS Proceedings. 2011. link Times cited: 0 NOT USED (low confidence) J. Fang and L. Pilon, “Thermal Conductivity of Crystalline Nanoporous Silicon Using Molecular Dynamics Simulations.” 2011. link Times cited: 0 Abstract: This study establishes that the effective thermal conductivi… read moreAbstract: This study establishes that the effective thermal conductivity keff of crystalline nanoporous silicon is strongly affected not only by the porosity fv and the system’s length Lz but also by the pore interfacial area concentration Ai . The thermal conductivity of crystalline nanoporous silicon was predicted using non-equilibrium molecular dynamics (NEMD) simulations. The Stillinger-Weber potential for silicon was used to simulate the interatomic interactions. Spherical pores organized in a simple cubic lattice were introduced in a crystalline silicon matrix by removing atoms within selected regions of the simulation cell. Effects of the (i) system length ranging from 13 to 130 nm, (ii) pore diameter varying between 1.74 and 5.86 nm, and (iii) porosity ranging from 8% to 38%, on thermal conductivity were investigated. A physics-based model was also developed by combining kinetic theory and the coherent potential approximation. The effective thermal conductivity was proportional to (1 –1.5 fv ) and inversely proportional to the sum (Ai /4 +1 /Lz ). This model was in excellent agreement with the thermal conductivity of nanoporous silicon predicted by MD simulations for spherical pores (present study) as well as for cylindrical pores and vacancy defects reported in the literature. These results will be useful in designing nanostructured materials with desired thermal conductivity by tuning their morphology.Copyright © 2011 by ASME read less NOT USED (low confidence) C. Lorenz and N. Doltsinis, “Molecular Dynamics Simulation: From ‘Ab Initio’ to ‘Coarse Grained.’” 2011. link Times cited: 12 NOT USED (low confidence) J. E. Witman, “The T-shaped anisotropic molecule model: a unique perspective of the glass transition and gelation in low valence, directional, network forming liquids.” 2010. link Times cited: 0 Abstract: Glass and gel formers exhibit unusual mechanical characteris… read moreAbstract: Glass and gel formers exhibit unusual mechanical characteristics and amorphous phases which are highly dependent on their thermal history. We introduce a lattice model with T-shaped molecules that exhibits glassy and gel-like states without introducing artificial frustration. This system has a large number of degenerate energy minima separated by small barriers leading to a broad, kinetically-explored landscape. It particularly replicates valence-limited materials, which can form self-assembled materials with highly controlled physical properties. Despite its remarkable simplicity, this model reveals some of the fundamental kinetic and thermodynamic properties of the glass transition and of gel formation. A dearth of low temperature experimental and simulation measurements has inhibited investigation in this field. We overcome this difficulty by using a modified Metropolis Monte Carlo method to quickly provide equilibrium samples. Then kinetic Monte Carlo techniques are used to explore the properties of the equilibrium system, providing a touchstone for the non-equilibrium glassy states. Fully-dense simulation samples reveal a fragile-to-strong crossover (FSC) near the mean-field (MF) spinodal. At the FSC, the relaxation time returns to Arrhenius behavior with cooling. There is an inflection point in the configurational entropy. This behavior resolves the Kauzmann Paradox which is a result of extrapolation from above the inflection point. In contrast, we find that the configurational entropy remains finite as the temperature goes to zero. We also observe different kinetics as the system is quenched below the FSC, resulting in non-equilibrium, amorphous states with high potential energy persisting for long periods of time. Simulation samples remain at non-equilibrium conditions for observation times exceeding those permitting complete equilibration slightly above the FSC. This suggests the FSC would often be identified as the glass transition without indication that there is true arrest or a diverging length scale. Indeed, our simulations show these samples do equilibrate if sufficient time is allowed. To elucidate the complex, interdependent relation time and length scales at the FSC will require careful consideration of the spatial-dynamic heterogeneity. Dynamic mean-field simulations at high density and in the solvated regime reveal a rich range of morphological features. They are consistent with simulated and experimental results in colloidal systems. Stability limits of decreasing length scales beneath the phase separation bimodal coincide into a single curve, which terminates at the fully-dense MF spinodal, suggesting that gelation and vitrification are the same phenomena. Our work indicates that gelation is, therefore, a result of phase separation arrested by a glass transition. read less NOT USED (low confidence) B. C. Barnes, “Development of Atomistic Potentials for Silicate Materials and Coarse-Grained Simulation of Self-Assembly at Surfaces.” 2010. link Times cited: 0 NOT USED (low confidence) T. Motooka, “Chapter Nine – Multiscale Modeling Methods.” 2010. link Times cited: 0 NOT USED (low confidence) R. W. Nunes and J. F. Justo, “Silicon Nanowires: From Empirical to First Principles Modeling.” 2010. link Times cited: 0 NOT USED (low confidence) H. Lai, S. M. Sea, H. Kennel, and S. Dunham, “Molecular Dynamics Modeling of Stress and Orientation Dependence of Solid Phase Epitaxial Regrowth,” MRS Proceedings. 2010. link Times cited: 2 NOT USED (low confidence) M. Ganchenkova and R. Nieminen, “Chapter Eleven – Mechanical Properties of Silicon Microstructures.” 2010. link Times cited: 3 NOT USED (low confidence) L. J. Lewis and D. Perez, “Theory and Simulation of Laser Ablation – from Basic Mechanisms to Applications.” 2010. link Times cited: 14 NOT USED (low confidence) J. Goicochea, M. Madrid, and C. Amon, “Thermal Properties for Bulk Silicon Based on the Determination of Relaxation Times Using Molecular Dynamics,” Journal of Heat Transfer-transactions of The Asme. 2010. link Times cited: 46 Abstract: Molecular dynamics simulations are performed to estimate aco… read moreAbstract: Molecular dynamics simulations are performed to estimate acoustical and optical phonon relaxation times, dispersion relations, group velocities, and specific heat of silicon needed to solve the Boltzmann transport equation (BTE) at 300 K and 1000 K. The relaxation times are calculated from the temporal decay of the autocorrelation function of the fluctuation of total energy of each normal mode in the ⟨100⟩ family of directions, where the total energy of each mode is obtained from the normal mode decomposition of the motion of the silicon atoms over a period of time. Additionally, silicon dispersion relations are directly determined from the equipartition theorem obtained from the normal mode decomposition. The impact of the anharmonic nature of the potential energy function on the thermal expansion of the crystal is determined by computing the lattice parameter at the cited temperatures using a NPT (i.e., constant number of atoms, pressure, and temperature) ensemble, and are compared with experimental values reported in the literature and with those computed analytically using the quasiharmonic approximation. The dependence of the relaxation times with respect to the frequency is identified with two functions that follow the functional form of the relaxation time expressions reported in the literature. From these functions a simplified version of relaxation times for each normal mode is extracted. Properties, such as group and phase velocities, thermal conductivity, and mean free path, needed to further develop a methodology for the thermal analysis of electronic devices (i.e., from nano- to macroscales) are determined once the relaxation times and dispersion relations are obtained. The thermal properties are validated by comparing the BTE-based thermal conductivity against the predictions obtained from the Green–Kubo method. It is found that the relaxation times closely resemble the ones obtained from perturbation theory at high temperatures; the contribution to the thermal conductivity of the transverse acoustic, longitudinal acoustic, and longitudinal optical modes being approximately 30%, 60%, and 10%, respectively, and the contribution of the transverse optical mode negligible. read less NOT USED (low confidence) S. Sinnott, S. Heo, D. Brenner, J. Harrison, and D. Irving, “Computer Simulations of Nanometer-Scale Indentation and Friction.” 2010. link Times cited: 18 NOT USED (low confidence) B. Jeong and S. Sinnott, “Atomic-Scale Simulations of the Mechanical Behavior of Carbon Nanotube Systems.” 2010. link Times cited: 5 NOT USED (low confidence) N. Mingo, “Green’s Function Methods for Phonon Transport Through Nano-Contacts.” 2009. link Times cited: 30 NOT USED (low confidence) F. Giessibl, “Principles and Applications of the qPlus Sensor.” 2009. link Times cited: 14 NOT USED (low confidence) H. Magoariec and A. Danescu, “Macroscopic Elasticity of Nanoporous Silicon: Bulk and Surface Effects.” 2009. link Times cited: 1 NOT USED (low confidence) C. Li and Q. Meng, “Computer simulation of the vacancy defects interaction with shuffle dislocation in silicon,” Superlattices and Microstructures. 2009. link Times cited: 8 NOT USED (low confidence) M. Luo, “Surface-induced size-dependent Young’s modulus in nanomaterials.” 2008. link Times cited: 0 Abstract: Nanowires and ultra-thin films have wide applications in the… read moreAbstract: Nanowires and ultra-thin films have wide applications in the quickly developed nanotechnology and nanoscience. However, their Young’s modulus varies with the size, which is seemingly contradictory to the conventional continuum elasticity. Investigating and understanding the underlying mechanism of the size-dependent elastic properties in nanomaterials is of both academic and practical significance. In this work, both theoretical modeling and virtual experiments have been made on this issue. A nanoelement, from the traction free bulk lattice, undergoes an initial relaxation, during which its morphology changes and energy reduces, which is an emphasis in this developed methodology and is a distinction from almost other existing models. With different definitions of surfaces and edges, two models for a nanomaterial – a nanowire or an ultra-thin film – are derived based on the same thermodynamics framework. Comparing with most of others’ treatment, Model I has an advantage to mathematically treat a surface phase to be two-dimensional and an edge phase to be one-dimensional. Under external loadings, the initial relaxed state is taken as the reference. Experimentally, relaxation and tension/compression tests in different loading directions have been conducted on SiC, Si and Cu crystalline nanowires with different cross-sectional sizes and ultra-thin films with different thicknesses by Molecular Dynamics (MD) simulations. This systematic study successfully illustrates the intrinsic mechanism of the size-dependent Young’s modulus in nanomaterials and the proposed methodology facilitate characterizing mechanical properties of nanomaterials to some extent when continuum concepts, such as, surface energy and surface elastic constants, are used. read less NOT USED (low confidence) J. Li, X. Dai, S. Liang, K. Tai, Y. Kong, and B. Liu, “Interatomic potentials of the binary transition metal systems and some applications in materials physics,” Physics Reports. 2008. link Times cited: 110 NOT USED (low confidence) R. Sahara, H. Mizuseki, K. Ohno, and Y. Kawazoe, “Thermodynamic Properties of Materials Using Lattice-Gas Models with Renormalized Potentials.” 2008. link Times cited: 2 NOT USED (low confidence) G. Vastola, R. Gatti, A. Marzegalli, F. Montalenti, and L. Miglio, “Detailed Analysis of the Shape-dependent Deformation Field in 3D Ge Islands.” 2008. link Times cited: 12 NOT USED (low confidence) D. Patrick, “Simulation in Force Spectroscopy.” 2008. link Times cited: 0 NOT USED (low confidence) K. Adu, H. Gutiérrez, and P. Eklund, “PHONONS IN SILICON NANOWIRES.” 2008. link Times cited: 2 NOT USED (low confidence) S. Wang, X.-gang Liang, and X. Xu, “Thermal Rectification in Silicon Nanowires With Mass Gradients.” 2008. link Times cited: 1 Abstract: Thermal rectification as a new phenomenon is attracting grea… read moreAbstract: Thermal rectification as a new phenomenon is attracting great attention. Thermal rectification in silicon nanowires with axial mass gradient is investigated by molecular dynamics simulation. The results of the simulations show that the thermal conductivities are different for the heat flux with opposite directions. The rectification efficiency becomes larger when the mass gradient increases. The effect of temperature gradient on the thermal rectification is also considered. The phonon density of states is calculated to explain the phenomenon. It is found that the interface is responsible to the thermal rectification.Copyright © 2008 by ASME read less NOT USED (low confidence) T. Delph, “Near-surface stresses in silicon(001),” Surface Science. 2008. link Times cited: 6 NOT USED (low confidence) O. Sluis, C. Yuan, W. Driel, and G. Zhang, “Advances in Delamination Modeling.” 2008. link Times cited: 12 NOT USED (low confidence) H. Johnson, “Effects of stress on formation and properties of semiconductor nanostructures.” 2007. link Times cited: 1 NOT USED (low confidence) J. Vanhellemont, E. Simoen, I. Romandic, and A. Theuwis, “Grown-in defects in germanium.” 2007. link Times cited: 4 NOT USED (low confidence) W. Eckstein and H. Urbassek, “Computer Simulation of the Sputtering Process.” 2007. link Times cited: 24 NOT USED (low confidence) E. Machlin, “Thermodynamics of Phases having Constant Composition.” 2007. link Times cited: 0 NOT USED (low confidence) A. Bagaturyants, M. A. Deminskii, A. Knizhnik, B. Potapkin, and S. Umanskii, “Chapter 9 Integrated Approach to Dielectric Film Growth Modeling: Growth Mechanisms and Kinetics.” 2007. link Times cited: 2 NOT USED (low confidence) T. Kawamura, Y. Kangawa, and K. Kakimoto, “An investigation of thermal conductivity of nitride-semiconductor nanostructures by molecular dynamics simulation,” Journal of Crystal Growth. 2007. link Times cited: 7 NOT USED (low confidence) G. Hadjisavvas and P. Kelires, “Advances in Monte Carlo Simulations of Nanostructured Materials.” 2007. link Times cited: 0 NOT USED (low confidence) D. Brenner, “Computer Modeling of Nanostructured Materials.” 2007. link Times cited: 5 NOT USED (low confidence) H. Urbassek, “Results of Molecular Dynamics Calculations.” 2007. link Times cited: 20 NOT USED (low confidence) J. Schall, P. Mikulski, G. M. Chateauneuf, G. Gao, and J. Harrison, “Molecular Dynamics Simulations of Tribology.” 2007. link Times cited: 8 NOT USED (low confidence) P. Śpiewak, K. Kurzydłowski, J. Vanhellemont, P. Wabiński, K. Młynarczyk, and I. Romandic, “Simulation of Vacancy Cluster Formation and Binding Energies in Single Crystal Germanium,” MRS Proceedings. 2007. link Times cited: 2 Abstract: Results are presented of the simulation of the properties of… read moreAbstract: Results are presented of the simulation of the properties of vacancy clusters in single crystal germanium. Classical molecular dynamics calculations based on a Stillinger and Weber potential were used in a theoretical investigation of different growth patterns of vacancy clusters Vi. The formation and binding energies of vacancy clusters have been studied in the range 1 i 35. The energetically favourable growth mode and an estimate of the effective surface energy was determined for a vacancy clusters containing up to 35 vacancies read less NOT USED (low confidence) T. Kumagai, S. Hara, S. Izumi, and S. Sakai, “Development of a Bond-Order Potential that can Reproduce the Elastic Constants and Melting Point of Silicon,” Journal of The Society of Materials Science, Japan. 2006. link Times cited: 1 Abstract: The Tersoff potential is one of the most widely used interat… read moreAbstract: The Tersoff potential is one of the most widely used interatomic potentials for silicon. However, its poor descrip-tion of the elastic constants and melting point of diamond silicon is well known. In this research, a new bond-order type interatomic potential has been developed that can reproduce the elastic constants and melting point of diamond silicon as well as the cohesive energies and equilibrium bond lengths of polytypes of silicon. We improved the original Tersoff potential function through the introduction of a flexible angular dependent term. In order to increase the robustness of the potential, systems that include a wide range of local atomic environments are employed for fitting. Optimized potential parameters were found using a genetic algorithm. The elastic constants and melting point of diamond silicon calculated using the developed potential turned out to be C 11 = 166.4GPa, C 12 = 65.3GPa, C 44 = 77.1GPa and T m = 1681K. It was also found that only elastic constants can be reproduced using the original Tersoff potential function, and that our proposed angular dependent term is a key to reproducing the melting point. read less NOT USED (low confidence) J. A. Pascual-Gutiérrez, J. Murthy, and R. Viskanta, “Physical Properties of Confined Silicon Structures Using EDIP.” 2006. link Times cited: 0 Abstract: Physically confined structures such as thin films and nanowi… read moreAbstract: Physically confined structures such as thin films and nanowires are becoming increasingly important in the energy and electronics sectors. This has resulted from the ability to tailor nanostructures to yield physical properties that are significantly different from bulk. The main focus of this work is to examine how physical confinement in one and two dimensions affects the phonon wave vector spectrum within the first Brillouin zone of silicon thin films and silicon nanowires. Dispersion curves as well as density of states (DOS) are obtained using the dynamical matrix approach and a harmonic approximation to the three-body environmentally-dependent interatomic potential (EDIP). It is also shown how these changes in the phonon spectrum for both films and wires affect the volumetric specific heat with respect to bulk. The simulations are carried out assuming ideal free-standing boundary conditions. It is shown that confinement effects on the phonon specific heat are only important below 5 mm for both silicon films and wires.Copyright © 2006 by ASME read less NOT USED (low confidence) J. Helfenstein, “Constitutive law for single crystal silicon (SCSi) based on molecular dynamic potentials.” 2006. link Times cited: 0 Abstract: Using the Modified Embedded Atom Method (MEAM) a new materia… read moreAbstract: Using the Modified Embedded Atom Method (MEAM) a new material model was made accessible to FEM computations. This new model takes into account the molecular dynamics of diamond cubic crystals. It owns a degree of freedom that is not yet used in other potentials that are utilized: the internal displacement of the two sub-lattices in the crystal. This enables the model to reproduce the microscopic relaxation in such crystals as well as the Raman-frequencies in phonon dispersion diagrams that can be measured experimentally. For the case of single crystal silicon (SCSi) all three stiffness moduli were reproduced. Comparisons with experiments for the determination of the ultimative strength of SCSi showed that it behaves softer than real single crystal silicon. Acknowledgements To Ondrej Papes for all the patience and time he found to support me. To my sister Iren for the time she lost helping me with my poor English. To my co-students Reto Somaini and Andreas Schifferle for all the worthwhile discussions, but also for times of fun. read less NOT USED (low confidence) Z. Insepov, J. Allain, A. Hassanein, and M. Terasawa, “Surface erosion by highly-charged ions,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2006. link Times cited: 10 NOT USED (low confidence) V. Ignatova, D. Karpuzov, I. Chakarov, and I. Katardjiev, “Computer simulations of surface analysis using ion beams,” Progress in Surface Science. 2006. link Times cited: 15 NOT USED (low confidence) R. Car, “Chapter 3 Ab initio Molecular Dynamics: Dynamics and Thermodynamic Properties.” 2006. link Times cited: 2 NOT USED (low confidence) G. Zhang, “Challenges and Future Perspectives.” 2006. link Times cited: 46 NOT USED (low confidence) A. Mlayah and J. Groenen, “Resonant Raman Scattering by Acoustic Phonons in Quantum Dots.” 2006. link Times cited: 9 NOT USED (low confidence) H. Tang, J.-M. Rye, M. Buehler, A. Duin, and W. Goddard, “Quantization of crack speeds in dynamic fracture of silicon: Multiparadigm ReaxFF modeling,” MRS Proceedings. 2006. link Times cited: 0 Abstract: We report a study of dynamic cracking in a silicon single cr… read moreAbstract: We report a study of dynamic cracking in a silicon single crystal in which the ReaxFF reactive force field is used for about 3,000 atoms near the crack tip while the other 100,000 atoms of the model system are described with a simple nonreactive force field. The ReaxFF is completely derived from quantum mechanical calculations of simple silicon systems without any empirical parameters. This model has been successfully used to study crack dynamics in silicon, capable of reproducing key experimental results such as orientation dependence of crack dynamics (Buehler et al., Phys. Rev. Lett. 2006). In this article, we focus on crack speeds as a function of loading and crack propagation mechanisms. We find that the steady state crack
speed does not increase continuously with applied load, but instead jumps to a finite value immediately after the critical load, followed by a regime of slow increase. Our results quantitatively reproduce experimental observations of crack speeds during fracture in silicon along the (111) planes, confirming the existence of lattice trapping effects. We observe similar effects in the (110) crack direction. read less NOT USED (low confidence) N. Kalyanasundaram, M. C. Moore, J. Freund, and H. Johnson, “Stress evolution due to medium-energy ion bombardment of silicon,” Acta Materialia. 2006. link Times cited: 54 NOT USED (low confidence) S. Furukawa, N. Aoyama, T. Nishiumi, T. Nitta, H. Takahashi, and M. Nakano, “Molecular Simulation Study on Adsorption of Methanol/Water Mixed Gases in Mesoporous Silicas with Surface Modification,” Kagaku Kogaku Ronbunshu. 2006. link Times cited: 0 Abstract: 1次元細孔をもつメソポーラスシリカへのメタノール/水混合ガスの吸着に対する表面修飾の効果を調べるために,(1)融解/冷却… read moreAbstract: 1次元細孔をもつメソポーラスシリカへのメタノール/水混合ガスの吸着に対する表面修飾の効果を調べるために,(1)融解/冷却アルゴリズムを導入した分子動力学法を用いて,親水性表面(OH表面)およびトリメチルシリル基で置換した疎水性表面(FS表面)をもつメソポーラスシリカをモデル化し,(2)µVTアンサンブル配向バイアス・モンテカルロ法を用いて吸着平衡を計算した.OH表面をもつメソポーラスシリカモデルでは,298 Kにおける純ガスの吸着等温線が,メタノールはステップ状吸着,水は凝縮性吸着の特徴を示し,それぞれの実験値を良好に再現した.FS表面細孔では,水は圧力を上げても吸着しなかったが,メタノールは凝縮性吸着の特徴を示した.すなわち,トリメチルシル基による表面修飾は,水だけでなくメタノールとの親和性も低下させる.温度333 Kにおける等相対圧(各成分の相対圧が等しい)混合ガスの吸着等温線を計算したところ,純ガスでは水を全く吸着しなかったFS表面細孔が混合ガスでは凝縮性吸着機構でアルコールと水を同時に吸着した.また,この系の細孔内局所密度分布から,疎水性のCH3基が疎水表面に多く存在するが,細孔内部ではメタノールと水がほぼ均一な組成で存在することがわかった. read less NOT USED (low confidence) A. Greenstein, Y. Hudiono, S. Nair, and S. Graham, “Modeling Lattice Dynamics and Heat Capacities of Zeolites.” 2006. link Times cited: 0 NOT USED (low confidence) B. Puchala, M. Falk, and K. Garikipati, “Using Elasticity to Correct for Boundary Effects in Calculations of Stress-Diffusion Coupling Parameters.” 2006. link Times cited: 0 NOT USED (low confidence) E. Tadmor and R. Miller, “The Theory and Implementation of the Quasicontinuum Method.” 2005. link Times cited: 26 NOT USED (low confidence) T. Zohdi, “Modeling and direct simulation of near-field granular flows,” International Journal of Solids and Structures. 2005. link Times cited: 50 NOT USED (low confidence) M. Demkowicz and A. Argon, “Unit Shearing Events in Plasticity of Amorphous Silicon,” MRS Proceedings. 2005. link Times cited: 0 NOT USED (low confidence) S. Heo, S. Sinnott, D. Brenner, and J. Harrison, “Computational Modeling of Nanometer-Scale Tribology.” 2005. link Times cited: 19 NOT USED (low confidence) J. Tarus, M. Tantarimäki, and K. Nordlund, “Segregation in SiGe clusters,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2005. link Times cited: 12 NOT USED (low confidence) M. Buehler, A. Duin, and W. Goddard, “Multi-paradigm multi-scale modeling of dynamical crack propagation in silicon using the ReaxFF reactive force field,” MRS Proceedings. 2005. link Times cited: 7 Abstract: We report a study of dynamic cracking in a silicon single cr… read moreAbstract: We report a study of dynamic cracking in a silicon single crystal in which the ReaxFF reactive force field is used for ∼3,000 atoms near the crack tip while the other 100,000 atoms of the model system are described with a simple nonreactive force field. The ReaxFF is completely derived from quantum mechanical calculations of simple silicon systems without any empirical parameters. Our results reproduce experimental observations of fracture in silicon including details of crack dynamics for loading in the [110] orientations, such as dynamical instabilities with increasing crack velocity. We also observe formation of secondary microcracks ahead of the moving mother crack. We conclude with a study of Si(bulk)-O2 systems, showing that Si becomes more brittle in oxygen environments, as known from experiment. read less NOT USED (low confidence) P. Vashishta, R. Kalia, and A. Nakano, “Multimillion Atom Molecular-Dynamics Simulations of Nanostructured Materials and Processes on Parallel Computers.” 2005. link Times cited: 1 NOT USED (low confidence) J. F. Justo, “Modeling Covalent Bond with Interatomic Potentials.” 2005. link Times cited: 1 NOT USED (low confidence) Y. Mishin, “Atomistic Computer Simulation of Diffusion.” 2005. link Times cited: 7 NOT USED (low confidence) T. Akabane and Y. Sasajima, “Computer Experiments on Silicon Nano Indentation,” Journal of The Japan Institute of Metals. 2005. link Times cited: 2 NOT USED (low confidence) B. Thijsse, “Silicon potentials under (ion) attack: towards a new MEAM model,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2005. link Times cited: 24 NOT USED (low confidence) E. Kaxiras and S. Yip, “Introduction: Atomistic Nature of Materials.” 2005. link Times cited: 2 NOT USED (low confidence) A. Haymet, T. Bryk, and E. Smith, “Solute Ions at Ice/Water Interface.” 2005. link Times cited: 3 NOT USED (low confidence) M. Posselt, F. Gao, and D. Zwicker, “Migration of Di- and Tri-Interstitials in Silicon,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2005. link Times cited: 5 NOT USED (low confidence) C. Moura and L. Amaral, “Molecular dynamics simulation of silicon nanostructures,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2005. link Times cited: 31 NOT USED (low confidence) S. Yip, S. Phillpot, and D. Wolf, “Crystal Disordering in Melting and Amorphization.” 2005. link Times cited: 2 NOT USED (low confidence) C. Amon, S. Narumanchi, M. Madrid, C. Gomes, and J. Goicochea, “Hierarchical Modeling of Thermal Transport from Nano-to-Macroscales.” 2005. link Times cited: 4 NOT USED (low confidence) T. Kakinaga, O. Tabata, N. Baba, Y. Isono, J. Korvink, and K. H. Ehrmann, “Simulation of Anisotropic Chemical Etching of Single Crystalline Silicon using Cellular-Automata,” Ieej Transactions on Sensors and Micromachines. 2004. link Times cited: 11 Abstract: We propose a new concept for anisotropic single crystalline … read moreAbstract: We propose a new concept for anisotropic single crystalline silicon (Si) etching simulation. Our approach combines three calculation modules, a molecular dynamics calculation module to define chemical reaction probability, a Cellular-Automaton module to calculate etching rate, and a Wulff-Jaccodine graphical method module to predict an etched shape. This configuration allows mm scale process simulation based on atomic scale physical chemistry of anisotropic Si etching. In this paper, the performance of a newly developed Cellular-Automata module, called CAES (Cellular-Automata Etching simulator), is presented as a first step towards the realization of our simulation concept. read less NOT USED (low confidence) M. Caturla, A. G. Martí, J. Jiménez-Rodríguez, J.-C. J. Saez, and Pérez-Martı́n M., “Molecular Dynamics Simulations of Energy Deposition in Solids,” Advances in Quantum Chemistry. 2004. link Times cited: 4 NOT USED (low confidence) C. Anderson and K. Tamma, “An overview of advances in heat conduction models and approaches for prediction of thermal conductivity in thin dielectric films,” International Journal of Numerical Methods for Heat & Fluid Flow. 2004. link Times cited: 29 Abstract: We first provide an overview of some predominant theoretical… read moreAbstract: We first provide an overview of some predominant theoretical methods currently used for predicting thermal conductivity of thin dielectric films: the equation of radiative transfer, the temperature‐dependent thermal conductivity theories based on the Callaway model, and the molecular dynamics simulation. This overview also highlights temporal and spatial scale issues by looking at a unified theory that bridges physical issues presented in the Fourier and Cattaneo models. This newly developed unified theory is the so‐called C‐ and F‐processes constitutive model. This model introduces the notion of a new dimensionless heat conduction model number, which is the ratio of the thermal conductivity of the fast heat carrier F‐processes to the total thermal conductivity comprised of both the fast heat carriers F‐processes and the slow heat carriers C‐processes. Illustrative numerical examples for prediction of thermal conductivity in thin films are primarily presented. read less NOT USED (low confidence) H. Wilson, N. Marks, D. Mckenzie, and K. Lee, “Molecular dynamics simulations of ion implantation for the fabrication of a solid-state quantum computer,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2004. link Times cited: 7 NOT USED (low confidence) I. Marinescu, W. Rowe, B. Dimitrov, and I. Inasaki, “7 – Molecular Dynamics for Abrasive Process Simulation.” 2004. link Times cited: 0 NOT USED (low confidence) S. Brochard, J. Godet, L. Pizzagalli, and P. Beauchamp, “Atomistic Simulation of Dislocation Generation at Surface Steps in Metals and Silicon.” 2004. link Times cited: 0 NOT USED (low confidence) P. Kratzer, “Atomistic Simulations of Processes at Surfaces.” 2004. link Times cited: 1 NOT USED (low confidence) S. Ogata, “Development of Hybrid Electronic-Density-Functional/Molecular-Dynamics Simulation Schemes for Ceramics and Semiconductors.” 2004. link Times cited: 0 NOT USED (low confidence) K. A. Jackson, “Actual Concepts of Interface Kinetics.” 2004. link Times cited: 5 NOT USED (low confidence) S. Izumi, S. Hara, T. Kumagai, and S. Sakai, “Elastic Properties of the Surfaces and Interfaces of Crystal and Amorphous Silicon.” 2004. link Times cited: 0 NOT USED (low confidence) S. Sinha and K. Goodson, “Nanoscale hotspots due to nonequilibrium thermal transport.” 2004. link Times cited: 0 Abstract: Recent experimental and modeling efforts have been directed … read moreAbstract: Recent experimental and modeling efforts have been directed towards the issue of temperature localization and hotspot formation in the vicinity of nanoscale heat generating devices. The nonequilibrium transport conditions which develop around these nanoscale devices results in elevated temperatures near the heat source which can not be predicted by continuum diffusion theory. Efforts to determine the severity of this temperature localization phenomena in silicon devices near and above room temperature are of technological importance to the development of microelectronics and other nanotechnologies. In this work, we have developed a new modeling tool in order to explore the magnitude of the additional thermal resistance which forms around nanoscale hotspots from temperatures of 100-1000K. The models are based on a two fluid approximation in which thermal energy is transferred between ''stationary'' optical phonons and fast propagating acoustic phonon modes. The results of the model have shown excellent agreement with experimental results of localized hotspots in silicon at lower temperatures. The model predicts that the effect of added thermal resistance due to the nonequilibrium phonon distribution is greatest at lower temperatures, but is maintained out to temperatures of 1000K. The resistance predicted by the numerical code can be easily integrated with continuum modelsmore » in order to predict the temperature distribution around nanoscale heat sources with improved accuracy. Additional research efforts also focused on the measurements of the thermal resistance of silicon thin films at higher temperatures, with a focus on polycrystalline silicon. This work was intended to provide much needed experimental data on the thermal transport properties for micro and nanoscale devices built with this material. Initial experiments have shown that the exposure of polycrystalline silicon to high temperatures may induce recrystallization and radically increase the thermal transport properties at room temperature. In addition, the defect density was observed to play a major role in the rate of change in thermal resistivity as a function of temperature.« less read less NOT USED (low confidence) P. Brommer, “Entwicklung und Test von Wechselwirkungspotenzialen in Quasikristallen.” 2003. link Times cited: 4 Abstract: Im dekagonalen Aluminium-Nickel-Kobalt-Quasikristall (d-AlNi… read moreAbstract: Im dekagonalen Aluminium-Nickel-Kobalt-Quasikristall (d-AlNiCo) zeigt das Aluminium einige besondere Eigenheiten in seiner Beweglichkeit. Bei 80 % der Schmelztemperatur konnen sich einige Aluminiumatome fast frei durch den Kristall bewegen, wahrend andere unbeweglich in ihrer Ruhelage verharren. Molekulardynamische Simulationen konnen Einblicke in die Dynamik dieses Systems verschaffen. Dazu berechnet man aus den interatomaren Kraften die Beschleunigung, die jedes einzelne Atom erfahrt und bewegt dieses dann entsprechend. Im Idealfall gewinnt man diese Krafte mit Ab-Initio-Methoden aus dem quantenmechanischen Vielteilchenproblem. Leider sind diese Methoden aber auf wenige hundert Atome beschrankt - deutlich zu wenig fur einen Quasikristall. Die Verwendung von effektiven Potenzialen erlaubt die Untersuchung wesentlich groserer Systeme. Dazu benotigt man allerdings geeignete Potenziale - und diese existieren nicht fur komplexe Systeme wie Quasikristalle.
Mit dem so genannten Force Matching oder Kraftanpassung kann man nun effektive Potenziale aus mit Ab-Initio-Methoden bestimmten Kraften gewinnen. Dazu wird ein durch eine beschrankte Anzahl von Parametern festgelegtes Potenzial so angepasst, dass die quantenmechanisch berechneten Krafte bestmoglich reproduziert werden. Diesem Verfahren liegt zu Grunde, dass ein Potenzial, das die interatomaren Krafte richtig wiedergeben kann, auch die richtige Dynamik erzeugt.
Im Rahmen dieser Diplomarbeit wurde mit Force Matching ein EAM-Potenzial fur die dekagonale Phase von AlNiCo generiert und verschiedenen Tests unterzogen. Dabei zeigte sich, dass das so erzeugte Potenzial zwar einige dynamische Eigenschaften wie die Aluminium-Diffusion korrekt wiedergeben kann, in anderen Bereichen durch die Hinzunahme von weiteren Referenzstrukturen weiterer Verbesserung bedarf.
Aluminum mobility in decagonal AlNiCo displays interesting peculiarities. At 80 % of the melting temperature some aluminum atoms can move around the quasicrystal, while others remain firmly locked in place. Molecular dynamics simulations can offer insights into the dynamics of this system. Ideally one would use ab-initio methods to evaluate the many-body quantum mechanical equations, but those methods are limited to a few hundred atoms. On the other hand, the application of effective potentials allows much larger systems. Then the problem is to find suitable potentials, which are not available for complex systems like quasicrystals. Force Matching is a way to derive effective potentials from quantum-mechanical input data, thereby combining the advantages of the two methods. The idea is that a potential that reproduces the forces correctly also yields the correct dynamics. The application of this method to the decagonal AlNiCo quasicrystalline phase is described and test simulations with the derived potentials are presented. read less NOT USED (low confidence) F. Mota, M. Caturla, J. Perlado, E. Domínguez, and A. Kubota, “Atomistic simulations of threshold displacement energies in SiO 2,” MRS Proceedings. 2003. link Times cited: 3 Abstract: Silica is one of the candidate materials for final focusing … read moreAbstract: Silica is one of the candidate materials for final focusing mirrors in inertial fusion reactors. This material will be exposed to high neutron irradiation fluxes during operation. Radiation damage results in point defects that can lead to obscuration of this material; that is, degradation of the optical properties of silica. In this paper we present molecular dynamic simulations of defect production in silica glass. Results on the threshold displacement energies due to oxygen Primary Knock-on Atoms (PKA) are reported concluding that a range of energies (20–40 eV) exists in which the defects have a probability to be created. In addition, we determine a range of distances for a PKA to become a stable defect out of its original position. Our present analysis is focused on the formation of Oxygen Deficient Centers (ODC). read less NOT USED (low confidence) G. Voyiadjis, E. Aifantis, and G. Weber, “Constitutive Modeling of Plasticity in Nanostructured Materials.” 2003. link Times cited: 4 NOT USED (low confidence) G. Otto and G. Hobler, “Coupled Kinetic Monte Carlo and Molecular Dynamics Simulations of Implant Damage Accumulation in Silicon,” MRS Proceedings. 2003. link Times cited: 0 NOT USED (low confidence) M. Demkowicz and A. Argon, “High-density liquid-like component facilitates plastic flow in a model amorphous silicon system,” MRS Proceedings. 2003. link Times cited: 6 Abstract: Molecular dynamics simulations show that plastic deformation… read moreAbstract: Molecular dynamics simulations show that plastic deformation behavior of model Stillinger-Weber amorphous Si is very sensitive to the density of the initial unstressed state. Low-density systems exhibit a pronounced yield phenomenon, strain softening, and a dramatic drop in pressure during deformation at constant volume. This behavior is explained by the interplay in every system of the prevailing solid-like and liquid-like components, with the latter being denser and more amenable to plastic flow. read less NOT USED (low confidence) E. J. Albenze, L. A. Matejik, N. F. Fynan, and P. Clancy, “Prediction of the Interface Response Functions for Amorphous and Crystalline Phases of Silicon and Germanium.” 2003. link Times cited: 1 NOT USED (low confidence) A. Abbas, J. Delaye, D. Ghaleb, and G. Calas, “Molecular dynamics study of the structure and dynamic behavior at the surface of a silicate glass,” Journal of Non-crystalline Solids. 2003. link Times cited: 35 NOT USED (low confidence) S. Hosokawa, J. Greif, F. Demmel, and W. Pilgrim, “Phonon dynamics of liquid Si - inelastic X-ray scattering studies,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2003. link Times cited: 8 NOT USED (low confidence) R. Černý and P. Přikryl, “Chapter 3 Modeling Laser-Induced Phase-Change Processes: Theory and Computation,” Semiconductors and Semimetals. 2003. link Times cited: 3 NOT USED (low confidence) E. Blank, “Chapter 2 Structural imperfections in CVD diamond films,” Semiconductors and Semimetals. 2003. link Times cited: 8 NOT USED (low confidence) L. Nurminen, F. Tavazza, D. Landau, A. Kuronen, and K. Kaski, “Monte Carlo Simulation of the Surface Structure of Ge on Si(00l).” 2003. link Times cited: 1 NOT USED (low confidence) C. M. Gilmore and J. Sprague, “Molecular Dynamics Simulation of Thin Film Growth with Energetic Atoms.” 2002. link Times cited: 2 NOT USED (low confidence) C. Angell and S. Borick, “Cooperative Disordering Phase Transitions.” 2002. link Times cited: 0 NOT USED (low confidence) F. Giessibl, “Principle of NC-AFM.” 2002. link Times cited: 16 NOT USED (low confidence) S. Silva, J. D. Carey, R. Khan, E. Gerstner, and J. Anguita, “Amorphous carbon thin films.” 2002. link Times cited: 32 NOT USED (low confidence) J. Chen, P. Ruterana, and G. Nouet, “Theoretical analysis of tilt grain boundaries in GaN at the atomic scale,” MRS Proceedings. 2002. link Times cited: 0 NOT USED (low confidence) P. Ustinov, “CHAPTER 5 – THEORETICAL STUDIES.” 2002. link Times cited: 0 NOT USED (low confidence) T. Watanabe, K. Tatsumura, and I. Ohdomari, “Recent Progress in Theoretical Study of Formation of Semiconductor Surfaces and Interfaces Based on Microscopic Processes. Large-scale Modeling of Silicon-dioxide Films by Means of Molecular Dynamics.,” Hyomen Kagaku. 2002. link Times cited: 0 Abstract: Large-scale modeling of ultra-thin SiO2 films on Si(001) sur… read moreAbstract: Large-scale modeling of ultra-thin SiO2 films on Si(001) surfaces has been performed by means of molecular dynamics utilizing our original inter-atomic potential energy function for Si, O mixed systems. The SiO2 film is formed by layer-by-layer insertion of O atoms into Si-Si bonds in a Si wafer from the surface. The obtained models reproduce quantitatively the structural transition layers near the interface. Through a modeling of vicinal SiO2/Si(001) model including atomic steps, it has been found that oxide film near the step-edge is preferentially amorphized. For a more advanced modeling method, we propose a new simulation procedure where O atoms are introduced into the substrate in one-by-one manner. In the calculation, the oxidation is started from the surface and abrupt change in composition at the SiO2/Si interface is reproduced. Thus, the classical molecular dynamics is a powerful method together with a simplified inter-atomic potential function applicable to mixed systems. read less NOT USED (low confidence) P. Vashishta, “Applications: Physical and Electronic Materials.” 2002. link Times cited: 0 NOT USED (low confidence) J. Bording, J. E. Tibballs, and J. Taftø, “From Liquid to Amorphous Germanium by Molecular Dynamics.” 2002. link Times cited: 0 NOT USED (low confidence) S. Ogata, R. Belkada, F. Shimojo, and A. Nakano, “Moisture effects of crack initiation in nanocrystalline silicon: a hybrid density-functional/molecular-dynamics study,” MRS Proceedings. 2002. link Times cited: 0 NOT USED (low confidence) S. Elliott, “Amorphous Materials: Medium-range Order.” 2001. link Times cited: 2 NOT USED (low confidence) D. Wolf, V. Yamakov, P. Keblinski, S. Phillpot, and H. Gleiter, “High-temperature structure and properties of grain boundaries by molecular-dynamics simulation.” 2001. link Times cited: 2 NOT USED (low confidence) K. Shintani, H. Sugii, M. Nishimura, and T. Nakajima, “Atomistic Simulations of Deposition Processes of Epitaxial Layers,” MRS Proceedings. 2001. link Times cited: 0 NOT USED (low confidence) G. Ackland, “Theory of High Pressure Phases of Group-IV and III–V Semiconductors,” Physica Status Solidi B-basic Solid State Physics. 2001. link Times cited: 12 Abstract: Under high pressure the open, covalent structure of group-IV… read moreAbstract: Under high pressure the open, covalent structure of group-IV and III-V semiconductors collapses to a denser metallic crystal structure. On further pressure increase a range of behaviours is seen. There has been an enormous amout of theoretical and experimental work recently on these phases, and this paper draws together the underlying themes and trends to give the theoretical interpretations of the system, from generic ball and stick thermodynamics, which explains the collapse from diamond to the β-tin and Imma phases, through free electron theory which explains some of the trends in c/a ratios of the various structures, on to accurate electronic structure calculations of specific systems which can determine which of closely related structures have lowest free energy. Also, the observation and causes of disorder and metastability are discussed, and the prospects for high-pressure synthesis in making new materials. read less NOT USED (low confidence) B. Park, W. J. Weber, and L. Corrales, “Molecular Dynamics Simulation Study of Threshold Displacements and Defect Formation in Zircon,” Physical Review B. 2001. link Times cited: 37 NOT USED (low confidence) A. Mazzone, “VERLET METHODS WITH STEPSIZE CONTROL FOR MOLECULAR DYNAMICS CALCULATIONS,” International Journal of Modern Physics C. 2001. link Times cited: 3 Abstract: This study presents a stepsize control method for the numeri… read moreAbstract: This study presents a stepsize control method for the numerical integration of ordinary differential equations. The method is based on the difference between a Verlet coordinates evaluation and an Adams–Bashforth coordinates predictor and can be easily implemented in existing Molecular Dynamics simulations. Numerical tests are made on the equilibrium configuration of crystalline silicon at low temperature. read less NOT USED (low confidence) R. Wagner and E. Gulari, “Simulation of Mechanisms in Strained Silicon Germanium Epitaxy,” MRS Proceedings. 2001. link Times cited: 0 Abstract: Growth of strained semiconductors can lead to self-assembly … read moreAbstract: Growth of strained semiconductors can lead to self-assembly of interesting structures such as quantum dots. Simulation of this growth requires an accurate and efficient model for the interactions of lattice mismatched materials. We present a potential for calculating the bond energies in a diamond-like crystal of silicon and germanium. With this potential we predict the strain profiles in an embedded quantum dot and discuss the mechanisms of island formation. read less NOT USED (low confidence) D. Maroudas, “Modeling of radical-surface interactions in the plasma-enhanced chemical vapor deposition of silicon thin films,” Advances in Chemical Engineering. 2001. link Times cited: 33 NOT USED (low confidence) S. Elliott, “Amorphous Materials, Computer Simulation of.” 2001. link Times cited: 0 NOT USED (low confidence) S. Hamaguchi and H. Ohta, “Modeling of Reactive Ion Etching for Si/Si0 2 Systems.” 2001. link Times cited: 0 NOT USED (low confidence) S. Somasi, B. Khomami, and R. Lovett, “An Integrated Molecular Dynamics and Monte Carlo Approach to Study Epitaxial Deposition of Silicon,” MRS Proceedings. 2001. link Times cited: 0 Abstract: The length and time scales of an atomistic simulation are of… read moreAbstract: The length and time scales of an atomistic simulation are often too small for any direct comparison with experimental observations. In order to study the coverage of pits (COPs) found on the Si (100) surface by epitaxial deposition, we first calculate rate of individual steps using molecular dynamics and then define a sequence of Monte-Carlo steps to study the effect of various factors on effective coverage of COPs. read less NOT USED (low confidence) T. Ito, “Atomistic simulation of epitaxial growth processes.” 2001. link Times cited: 0 NOT USED (low confidence) S. Ogata, F. Shimojo, A. Nakano, P. Vashishta, and R. Kalia, “Hybrid Electronic-density-functional/molecular-dynamics Simulation on Parallel Computers: Oxidation of Si Surface,” MRS Proceedings. 2000. link Times cited: 0 NOT USED (low confidence) S. Phillpot, “AN INTRODUCTION TO THE MOLECULAR-DYNAMICS SIMULATION OF MATERIALS*.” 2000. link Times cited: 1 NOT USED (low confidence) L. Brambilla et al., “Identification of tetrahedrally coordinated atoms in supercooled liquid silicon,” MRS Proceedings. 2000. link Times cited: 0 Abstract: An atomic-scale model of liquid silicon has been cooled from… read moreAbstract: An atomic-scale model of liquid silicon has been cooled from high temperatures down in the temperature range between the amorphous and the crystalline melting temperatures by nanosecond scale molecular dynamics simulations with the Stillinger-Weber potential. Tetrahedrally coordinated sites have been identified, in the supercooled liquids, by using a few structural order parameters. The local structure and the stability of these crystalline-like regions (c-type sites and clusters) have been characterized. These have been regarded as candidates for crystalline embryos. read less NOT USED (low confidence) J. Perlado, L. Malerba, A. Sánchez-Rubio, and T. D. Rubia, “Analysis of displacement cascades and threshold displacement energies in β-sic,” Journal of Nuclear Materials. 2000. link Times cited: 48 NOT USED (low confidence) H. Jónsson, “Theoretical studies of atomic-scale processes relevant to crystal growth.,” Annual review of physical chemistry. 2000. link Times cited: 102 Abstract: The study of adsorption, diffusion, island formation, and in… read moreAbstract: The study of adsorption, diffusion, island formation, and interlayer transport of atoms on a growing surface has been an active field in the past decade, because of both experimental and theoretical advances. Experiments can give detailed images of patterns formed on growing surfaces. An important challenge to the theoretical studies is the identification of dynamical processes controlling the pattern formation and overall surface morphology. This can be achieved by accurate modeling of the atomic interactions, a thorough search for active atomic-scale processes, and simulation of the growth on the experimental timescale to allow for detailed comparison with the experimental measurements. An overview of some of the theoretical methodology used in these studies and results obtained for one of the most extensively studied systems, Pt(111), is given here. A remarkable richness of phenomena has emerged from these studies, where apparently small effects can shift the balance between competing molecular processes and thereby change the morphology of a growing surface. The article concludes with a discussion of possible future directions in this research area. read less NOT USED (low confidence) M. Posselt, “Improving the Understanding of Ion-Beam-Induced Defect Formation and Evolution by Atomistic Computer Simulations,” MRS Proceedings. 2000. link Times cited: 2 NOT USED (low confidence) A. Mazzone, “A molecular dynamics study of ion-induced defects on a silicon stepped surface,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2000. link Times cited: 3 NOT USED (low confidence) K. Shintani, H. Sugii, Y. Kikuchi, and M. Kobayashi, “Atomistic Study of Strain Profiles in Semiconductor Quantum Dot Structures,” MRS Proceedings. 2000. link Times cited: 0 NOT USED (low confidence) E. Lidorikis, M. Bachlechner, R. Kalia, G. Voyiadjis, A. Nakano, and P. Vashishta, “Coupling of Length Scales: Hybrid Molecular Dynamics and Finite Element Approach for Multiscale Nanodevice Simulations,” MRS Proceedings. 2000. link Times cited: 9 Abstract: A hybrid molecular-dynamics/finite-element simulation scheme… read moreAbstract: A hybrid molecular-dynamics/finite-element simulation scheme is applied to describe multiscale phenomena in nanodevices. The quality of both static and dynamic coupling between atomistic and continuum regions is studied. The hybrid scheme is used for the Si/Si 3 N 4 interface problem (static coupling), and for the projectile impact on Si problem (dynamic coupling). Excellent agreement is found between hybrid and full molecular dynamics simulation results in the static case, and no wave reflections are found at the atomistic/continuum hand-shake in the dynamic case. The hybrid scheme is thus validated a powerful and cost effective method for performing multiscale simulations of nanodevices. read less NOT USED (low confidence) K. Nordlund and R. Averback, “Collision cascades in metals and semiconductors: defect creation and interface behavior,” Journal of Nuclear Materials. 2000. link Times cited: 30 NOT USED (low confidence) R. E. Miller and V. B. Shenoy, “Size-dependent elastic properties of nanosized structural elements,” Nanotechnology. 2000. link Times cited: 16 Abstract: Effective stiffness properties (D) of nanosized structural e… read moreAbstract: Effective stiffness properties (D) of nanosized structural elements such as plates and beams differ from those predicted by standard continuum mechanics (Dc). These differences (D-Dc)/Dc depend on the size of the structural element. A simple model is constructed to predict this size dependence of the effective properties. The important length scale in the problem is identified to be the ratio of the surface elastic modulus to the elastic modulus of the bulk. In general, the non-dimensional difference in the elastic properties from continuum predictions (D-Dc)/Dc is found to scale as αS/Eh, where α is a constant which depends on the geometry of the structural element considered, S is a surface elastic constant, E is a bulk elastic modulus and h a length defining the size of the structural element. Thus, the quantity S/E is identified as a material length scale for elasticity of nanosized structures. The model is compared with direct atomistic simulations of nanoscale structures using the embedded atom method for FCC Al and the Stillinger-Weber model of Si. Excellent agreement between the simulations and the model is found. read less NOT USED (low confidence) N. Barriquand, V. Paillard, P. Cabarrocas, G. Landa, and M. Dijafari-Rouhani, “Vibrational Properties of a-Si:H Films Containing Voids: Experiment and Modeling,” MRS Proceedings. 1999. link Times cited: 0 Abstract: In this paper, the authors present results about the vibrati… read moreAbstract: In this paper, the authors present results about the vibrational properties of hydrogenated amorphous silicon films. They expect to explain the slight differences observed in the Raman spectra using atomic-scale modeling. In particular, they focus on the correlation of the results to the density of samples. This should give quantitative structural information which could be correlated to both macroscopic properties and elaboration conditions. read less NOT USED (low confidence) K. Nordlund, P. Partyka, Y. Zhong, I. Robinson, R. Averback, and P. Ehrhart, “Glancing incidence diffuse X-ray scattering studies of implantation damage in Si,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1999. link Times cited: 6 NOT USED (low confidence) W. Rudd and A. Voter, “Bias Potentials for Ttyperdynamics Simulations,” MRS Proceedings. 1998. link Times cited: 2 Abstract: The authors describe their studies of two methods for genera… read moreAbstract: The authors describe their studies of two methods for generating bias potentials for use in hyperdynamics simulations. In the first method, first reported by Steiner, et al, the bias potential is the additional energy needed to keep the total potential energy above a fixed level. This potential exerts a negligible computational load and is very easy to code. The second technique involves computing the iterative Hessian-based bias potential as usual, but including in those calculations only the atoms in a small active region that surrounds the area in which a state transition is expected to occur. This subspace hyperdynamics method is less costly than full HD. The extra computational effort required for HD scales at the size of the active region(s), instead of with the size of the entire simulation domain. The authors have carried out extensive tests of both methods on two problems, the diffusion of adatoms on silver surfaces and the migration of vacancies in bulk silver. Using the first method, to obtain large boosts the bias potential must e so high that many transitions are prevented from occurring. Their results for subspace hyperdynamics are promising; the authors obtain the same results as with full hyperdynamics, but withmore » considerably less computational effort.« less read less NOT USED (low confidence) J. Matsuo, T. Aoki, K. Goto, T. Sugii, and I. Yamada, “Ultra Shallow Junction Formation by Cluster Ion Implantation,” MRS Proceedings. 1998. link Times cited: 7 Abstract: Implantation of B cluster ions into Si using decaborane (B 1… read moreAbstract: Implantation of B cluster ions into Si using decaborane (B 10 H 14 ) has been demonstrated. SIMS measurements show that the depth distribution of boron atoms implanted with a monomer ion is exactly matched by that of boron atoms implanted from decaborane ions, if the cluster ion has an order of magnitude larger acceleration energy. According to the Langmuir-Child equation, two orders of magnitude larger space-charge limited ion beam current is possible when decaborane ions are used. Implanted boron atoms from decaborane ions are electrically activated after annealing. Junction depth of the implanted layer with 3 keV decaborane ions is approximately 20nm after annealing at 900°C. Molecular dynamic caluculations show that implantation efficency of boron monomer ions and decaborane ions are the same. However, the number of displaced silicon atoms per implanted boron atom from a decaborane ion impact is 4 times larger than that by boron monomer impact so that a heavily damaged region is created near the impact zone by decaborane ion penetration. read less NOT USED (low confidence) D. Savage, F. Liu, V. Zielasek, and M. Lagally, “Chapter 2 Fundamental Mechanisms of Film Growth,” Semiconductors and Semimetals. 1998. link Times cited: 9 NOT USED (low confidence) M. Ortiz and R. Phillips, “Nanomechanics of Defects in Solids,” Advances in Applied Mechanics. 1998. link Times cited: 143 NOT USED (low confidence) M. Wooldridge, “Gas-phase combustion synthesis of particles,” Progress in Energy and Combustion Science. 1998. link Times cited: 205 NOT USED (low confidence) P. Alippi and L. Colombo, “Understanding Structure and Electronic Properties of Extended Self-Interstitial Defects in Silicon,” MRS Proceedings. 1998. link Times cited: 0 NOT USED (low confidence) N. Bernstein, M. Aziz, and E. Kaxiras, “Atomistic features of the amorphous–crystal interface in silicon,” Journal of Computer-Aided Materials Design. 1998. link Times cited: 0 NOT USED (low confidence) A. Omeltchenko, A. Nakano, K. Tsuruta, R. Kalia, and P. Vashishta, “Structure and mechanical failure in nanophase silicon nitride.” 1998. link Times cited: 4 NOT USED (low confidence) B. Vessal, “12 – Amorphous Solids.” 1997. link Times cited: 1 NOT USED (low confidence) Z. Wang, W. Yu, and D. Stroud, “Monte Carlo and Molecular Dynamics Simulations of Liquid Semiconductor Surfaces,” MRS Proceedings. 1997. link Times cited: 0 Abstract: We have numerically studied the surface tension and surface … read moreAbstract: We have numerically studied the surface tension and surface profiles of several liquid semiconductors, including Si, Ge, GaAs, CdTe, and their alloys, as a function of temperature and concentration. Two kinds of simulations have been carried out: direct free-energy calculations using Monte Carlo methods, and force summations using molecular dynamics. We use empirical two- and three-body interatomic interactions based on the form originally proposed by Stillinger and Weber for Si, in conjunction with simulation cell sizes ranging from 216 to as large as 8000 atoms and several novel numerical techniques including a direct calculation of the surface entropy. In the case of alloys, we find a striking segregation of the low-surface-tension component to the surface even when the alloy components are miscible at all concentrations. read less NOT USED (low confidence) F. Liu and M. Lagally, “Chapter 7 Epitaxial growth of Si on Si(001),” The Chemical Physics of Solid Surfaces. 1997. link Times cited: 2 NOT USED (low confidence) J. F. Justo, M. Bazant, E. Kaxiras, V. Bulatov, and S. Yip, “Interatomic Potential for Condensed Phases and Bulk Defects in Silicon,” MRS Proceedings. 1997. link Times cited: 5 NOT USED (low confidence) V. M. Glazov, L. Pavlova, and K. V. Rezontov, “Estimation of the Self and Mutual Diffusion Coefficients in Molten CdTe by a Molecular Dynamics Technique.” 1997. link Times cited: 0 NOT USED (low confidence) M. Kohyama, N. Arai, and S. Takeda, “Tight-Binding Calculations of Complex Defects in Semiconductors: Comparison with AB Initio Results,” MRS Proceedings. 1997. link Times cited: 1 NOT USED (low confidence) L. Colombo, A. Bongiorno, and T. D. Rubia, “Formation and Binding Energies of Vacancy Clusters in Silicon,” MRS Proceedings. 1997. link Times cited: 3 Abstract: We critically readdress the problem of vacancy clustering in… read moreAbstract: We critically readdress the problem of vacancy clustering in silicon by perform large-scale tight-binding molecular dynamics simulations. We also compare the results of this quantum-mechanical approach to the widely used model-potential molecular dynamics scheme based on the Tersoff and Stillinger-Weber interatomic potentials. read less NOT USED (low confidence) N. Mousseau, “Computer Modelling of Glasses and Glassy Alloys.” 1997. link Times cited: 0 NOT USED (low confidence) M. Thorpe, B. Djordjević, and D. Jacobs, “The Structure and Mechanical Properties of Networks.” 1997. link Times cited: 7 NOT USED (low confidence) C. Angell, “Strong and Fragile Liquids; Glass Transitions and Polyamorphic Transitions in Covalently Bonded Glassformers.” 1997. link Times cited: 5 NOT USED (low confidence) C. M. Gilmore and J. Sprague, “Computer modeling the deposition of nanoscale thin films,” Nanostructured Materials. 1997. link Times cited: 3 NOT USED (low confidence) R. Car, “Modeling Materials by Ab-Initio Molecular Dynamics.” 1996. link Times cited: 4 NOT USED (low confidence) M. Bachlechner, I. Ebbsjö, R. Kalia, and P. Vashishta, “Molecular Dynamics Study Of Si/Si 3 N 4 Interface,” MRS Proceedings. 1996. link Times cited: 2 NOT USED (low confidence) V. Bakaev and W. Steele, “Chapter 2.1 Computer simulation of adsorption on amorphous oxide surfaces,” Studies in Surface Science and Catalysis. 1996. link Times cited: 2 NOT USED (low confidence) A. Horsfield, “Bond order potentials for the atomistic simulation of covalent systems,” Philosophical Magazine Part B. 1996. link Times cited: 1 Abstract: An angularly dependent many-atom expansion has recently been… read moreAbstract: An angularly dependent many-atom expansion has recently been derived for the bond energy within the tight-binding model for electronic structure. It accounts properly for directional bonding in covalent materials. The application of the method to sp-valent systems is presented here. In particular, for silicon, structural energy differences, surface reconstruction, the Jahn-Teller distortion at a vacancy, and the structure of the liquid have all been modelled successfully. read less NOT USED (low confidence) V. Vítek, “Atomistic Studies Of The Structure Of Grain Boundaries and Dislocations.” 1996. link Times cited: 12 NOT USED (low confidence) L. Xin-hou, “New Potentials of Silicon and Germanium Crystals,” Chinese Physics Letters. 1996. link Times cited: 2 Abstract: In this paper, a new model of potential energy functions for… read moreAbstract: In this paper, a new model of potential energy functions for atomic solids is given and applied to silicon and germanium crystals. Obtained potentials of Si and Ge crystals accurately reproduce experimental elastic constants and phonon dispersion curves. read less NOT USED (low confidence) T. Frauenheim, D. Porezag, T. Köhler, and F. Weich, “Molecular-Dynamic Simulations of Structure Formation in Complex Materials.” 1996. link Times cited: 1 NOT USED (low confidence) K. Gärtner, M. Nitschke, and D. Stock, “Computer simulation study of low energy boron channeling in silicon,” Radiation Effects and Defects in Solids. 1996. link Times cited: 0 Abstract: The channeling of B ions in (001) Si in the energy range of … read moreAbstract: The channeling of B ions in (001) Si in the energy range of 0.2 keV to 5 keV is investigated by computer simulation using binary collision and molecular dynamics computer codes and different interatomic interaction potentials. The B channeling for energies below 1 keV is proved to be quite different from channeling at higher energies. In contrast to the situation at higher energies, the B profiles hardly depend on the angle of incidence. The reason for this behaviour is discussed by studying typical iron trajectories for different energies. read less NOT USED (low confidence) P. Bedrossian, M. Caturla, and T. D. Rubia, “Defect Diffusion During Annealing of Low-Energy Ion-Implanted Silicon,” MRS Proceedings. 1996. link Times cited: 1 Abstract: We present a new approach for investigating the kinetics of … read moreAbstract: We present a new approach for investigating the kinetics of defect migration during annealing of low-energy, ion-implanted silicon, employing a combination of computer simulations and atomic-resolution tunneling microscopy. Using atomically-clean Si(111)-7x7 as a sink for bulk point defects created by 5 keV Xe and Ar irradiation, we observe distinct, temperature-dependent surface arrival rates for vacancies and interstitials. A combination of simulation tools provides a detailed description of the processes that underly the observed temperature-dependence of defect segregation, and the predictions of the simulations agree closely with the experimental observations. read less NOT USED (low confidence) J. Murrell, “Towards a general strategy for global interatomic potentials for elemental solids, surfaces and clusters,” Philosophical Magazine Part B. 1996. link Times cited: 6 Abstract: A review is given of studies that have been made by the Suss… read moreAbstract: A review is given of studies that have been made by the Sussex research group on two-body plus three-body potentials for elemental solids, surfaces and clusters. Parameters are fitted to properties of the bulk solid (cohesive energy, lattice spacing, phonon frequencies, elastic constants and vacancy formation energy), and the potentials have been shown to give sensible structures for clusters and, in the few cases examined, for surface energies and structures. The same functional form of the potential has been used for simple metals, transition metals and group 4 solids. read less NOT USED (low confidence) D. Conrad, K. Scheerschmidt, and U. Gösele, “Molecular dynamics simulations of silicon wafer bonding,” Applied Physics A. 1996. link Times cited: 34 NOT USED (low confidence) H. Ogawa, H. Sasaki, and Y. Waseda, “Variation of the Atomic Arrangement in Liquid Silicon Near the Melting Point,” High Temperature Materials and Processes. 1996. link Times cited: 0 Abstract: This paper describes a possible structure variation of liqui… read moreAbstract: This paper describes a possible structure variation of liquid silicon near the melting point where a density anomaly has been observed. By using the molecular dynamics simulation, a self-consistent picture for the liquid structure in the anomalous density region is proposed by introducing more ordered atomic arrangement close to the β-tin type with a smaller axis length ratio of a/c ≃ 0.7 compared with the normal liquid. read less NOT USED (low confidence) P. Groenberg, J. Boehm, and R. Nieminen, “Molecular dynamics study of oxygen defects in silicon.” 1996. link Times cited: 0 NOT USED (low confidence) C. T. Chan, K. Ho, and K. Bohnen, “Chapter 3 - Surface Reconstruction: Metal Surfaces and Metal on Semiconductor Surfaces.” 1996. link Times cited: 5 NOT USED (low confidence) R. Averback, M. Ghaly, and H. Zhu, “Surface effects during ion beam processing of materials,” MRS Proceedings. 1995. link Times cited: 2 Abstract: Microstructural changes of surfaces during ion implantation … read moreAbstract: Microstructural changes of surfaces during ion implantation have been investigated on the atomic level by molecular dynamics computer simulations. Unlike past surface studies, which have been focused on the problem of sputtering, the current work examines the effects of collective materials response on surface topography. Collective behavior has been noted for the crystal interior in the context of thermal spikes, but the authors show here that it can lead to far more dramatic consequences at the surface. The investigation includes implantation in several metals, but emphasizing Pt, Si and Ge. In addition, the study includes the first simulations of implantations of a metallic glass, CuTi, and amorphous Si. read less NOT USED (low confidence) K. Raghavachari and L. Curtiss, “Accurate Theoretical Studies of Small Elemental Clusters.” 1995. link Times cited: 5 NOT USED (low confidence) M. Rouhani, R. Malek, A. Gué, and D. Estève, “Simulation of the Growth of Lattice Mismatched Semiconductors,” MRS Proceedings. 1995. link Times cited: 0 Abstract: We have studied the growth of lattice mismatched semiconduct… read moreAbstract: We have studied the growth of lattice mismatched semiconductors through the association of the Monte Carlo technique and the Valence Force Field (VFF) approximation. The Monte Carlo technique monitors the atomic motion in the deposited layer using the Arrhenius law and taking into account the impingment of atoms from the gas phase, intralayer and interlayer migrations of atoms and evaporation from the surface. The VFF approximation is used as an energy model to determine the local strain and stress inside the deposited layer by minimizing the total energy. This is performed after each single atomic motion. The strain is assumed to enhance the atomic motion by lowering the activation energy barrier related to the particular event. Results concerning the case of large lattice mismatches are presented. It is observed that the growing surface becomes rapidly rough, showing grooves with (111) facets. The strain relaxation occurs as a result of this roughening and allows the determination of the critical thickness. At higher lattice mismatches, it is seen that the layer orientation changes from(100) to (111) from the beginning. read less NOT USED (low confidence) M. Bazant and E. Kaxiras, “Derivation of Interatomic Potentials by Inversion of Ab Initio Cohesive Energy Curves,” MRS Proceedings. 1995. link Times cited: 3 NOT USED (low confidence) J. P. Eerden, “Atomic Models for Crystal Growth.” 1995. link Times cited: 2 NOT USED (low confidence) X. Liu, “NEW MODEL OF POTENTIAL-ENERGY FUNCTIONS FOR ATOMIC SOLIDS,” Journal of the Chemical Society, Faraday Transactions. 1995. link Times cited: 2 Abstract: A new theoretical model of potential-energy functions for at… read moreAbstract: A new theoretical model of potential-energy functions for atomic solids has been developed. An angular factor has been included in this model and its effect has been discussed. Using this new model a new preliminary potential for silicon crystal has been derived. The calculated phonon dispersion curve along the [q00] direction, using this new potential, has been given. A good agreement has been found with experiment. read less NOT USED (low confidence) S. Ihara and S. Itoh, “Helically coiled and toroidal cage forms of graphitic carbon,” Carbon. 1995. link Times cited: 74 NOT USED (low confidence) T. Sinno and R. A. Brown, “Computation of the Onset of Point Defect Aggregation in Crystalline Silicon Using an Empirical Interatomic Potential,” MRS Proceedings. 1995. link Times cited: 2 NOT USED (low confidence) E. Kim and Y. H. Lee, “Phase separation of Si1-xGex alloys,” MRS Proceedings. 1995. link Times cited: 1 NOT USED (low confidence) L. Wille, C. Cornwell, and W. C. Morrey, “Massively Parallel Molecular Dynamics and Simulations for Many-Body Potentials,” MRS Proceedings. 1995. link Times cited: 2 NOT USED (low confidence) C. Dharma-wardana and F. Perrot, “Density Functional Methods for Plasmas and Liquid Metals.” 1995. link Times cited: 3 NOT USED (low confidence) P. W. Kung et al., “Melting of Aromatic Compounds: Molecular Dynamics Simulations,” MRS Proceedings. 1995. link Times cited: 0 Abstract: We have used constant pressure molecular dynamics calculatio… read moreAbstract: We have used constant pressure molecular dynamics calculations to explore the behavior at various temperatures of two molecular crystals: benzene and a brominated phenyl compound. We observed a melting transition by heating the crystals from a low temperature. In the case of benzene, we performed one heating run of about 1 ns and obtained agreement with the experimental melting point to within some 8%. We have also simulated the melting of a more complex molecular crystal that contains bromine and phenyl groups. We performed four heating runs, with different rates of heating. For total simulation times of about 100, 220, 770, and 1 I50ps, the heating runs predicted melting temperatures that differed from the experimental melting temperature by 53%, 33%, 25%, and 9% respectively. read less NOT USED (low confidence) F. Wooten and D. Weaire, “Chapter 15 Structural models of tetrahedrally bonded amorphous materials,” Data Handling in Science and Technology. 1995. link Times cited: 0 NOT USED (low confidence) B. A. Helmer, D. Graves, and M. E. Barone, “Parameters for Feature Evolution Models in Plasma Etching from Molecular Dynamics Simulation,” MRS Proceedings. 1995. link Times cited: 1 Abstract: The impact of Si with incident energy E i (0.1, 1, 5, 10, 20… read moreAbstract: The impact of Si with incident energy E i (0.1, 1, 5, 10, 20, and 50 eV) and angle θ i (0° and 60° from the surface normal) into three model Si surfaces with varying degrees of F coverage (0 ML F, ∼ 1 ML F, and ∼2 ML F) was simulated using classical molecular dynamics (MD). From the simulation results, the probabilities for incident Si reflection and removal of surface Si and F were obtained as a function of E i , θ i , and F surface coverage. In general, these probabilities were observed to depend significantly on these parameters. This result implies that feature evolution simulations require surface reaction models with the necessary functionality in order to make quantitative predictions. read less NOT USED (low confidence) K. Nordlund, J. Keinonen, and A. Kuronen, “Effect of the interatomic Si-Si-potential on vacancy production during ion implantation of Si,” Physica Scripta. 1994. link Times cited: 16 Abstract: Collision cascades in crystalline silicon due to impinging 1… read moreAbstract: Collision cascades in crystalline silicon due to impinging 10eV - 1keV Si atoms are simulated using molecular dynamics methods. The simulations are carried out for 30-100 events to obtain representative statistics for production of different types of vacancies. The results are used to examine the dependence of vacancy production on the interatomic Si-Si potential between the colliding atoms. The dependence of the number of vacancies was found to be sensitive to the form of the potential well but not to the repulsive potential. The results suggest that within the heavily damaged volume of the collision cascade an interatomic potential with somewhat narrower well than that of the commonly used Stillinger-Weber potential should be used to simulate the vacancy production in silicon. read less NOT USED (low confidence) J. Chelikowsky and N. Binggeli, “Doing materials science with a supercomputer: on the road to 1000 atom systems,” Computational Materials Science. 1994. link Times cited: 5 NOT USED (low confidence) J. Holender and G. J. Morgan, “Electron localization in models of hydrogenated amorphous silicon and pure amorphous silicon,” Modelling and Simulation in Materials Science and Engineering. 1994. link Times cited: 12 Abstract: Presents the first calculations of the electronic density of… read moreAbstract: Presents the first calculations of the electronic density of states, the electrical conductivity and the inverse participation ratio as a function of energy for a large model of hydrogenated amorphous silicon. The model contains 1555 Si atoms and 400 H atoms and all Si atoms are fourfold coordinated. This model has a clear gap in the density of electronic states. The 'mobility gap' (estimated from the conductivity versus energy curves) is about 0.6 eV wider than the gap in the electronic density of states. The authors also present for comparison the same calculations on a defected model of amorphous Si with 1728 atoms which contains states within the gap arising mainly from departure from tetrahedral geometry. read less NOT USED (low confidence) M. Kohyama and S. Takeda, “Calculation of the structure and properties of the 113 planar interstitial defects in Si.” 1994. link Times cited: 0 NOT USED (low confidence) F. Streitz and J. Mintmire, “Metal/oxide interfaces: an electrostatics-based model,” Composite Interfaces. 1994. link Times cited: 7 Abstract: We report on the development of a novel computational method… read moreAbstract: We report on the development of a novel computational method for molecular dynamics simulations which explicitly includes variable charge transfer between anions and cations. This method is found to be capable of describing the elastic properties, surface energies, and surface relaxation of crystalline metal-oxides accurately. We present results for a simulation of adhesive failure at a model metal/oxide heterophase interface between an aluminum (111) face and an α-alumina (0001) face. Our results indicate that this approach can provide physically realistic empirical potentials for future simulations on mixed metal/metal-oxide systems. read less NOT USED (low confidence) A. Varshneya, “Chapter 5 – Glass Compositions and Structures.” 1994. link Times cited: 12 NOT USED (low confidence) G. Sandre, L. Colombo, and D. Marić, “Computer Simulation of Thermal Annealing Effects on Self Implanted Silicon,” MRS Proceedings. 1994. link Times cited: 0 NOT USED (low confidence) T. D. Rubia, M. Caturla, and M. Tobin, “Molecular dynamics studies of radiation effects in silicon carbide,” MRS Proceedings. 1994. link Times cited: 14 Abstract: We discuss results of molecular dynamics computer simulation… read moreAbstract: We discuss results of molecular dynamics computer simulation studies of 3 keV and 5 keV displacement cascades in {beta}-SIC, and compare them to results of 5 keV cascades in pure silicon. The SiC simulations are performed with the Tersoff potential. For silicon we use the Stillinger-Weber potential. Simulations were carried out for Si recoils in 3 dimensional cubic computational cells With periodic boundary conditions and up to 175,616 atoms. The cascade lifetime in SiC is found to be extremely short. This, combined with the high melting temperature of SiC, precludes direct lattice amorphization during the cascade. Although large disordered regions result, these retain their basic crystalline structure. These results are in contrast with observations in pure silicon where direct-impact amorphization from the cascade is seen to take place. The SiC results also show anisotropy in the number of Si and C recoils as well as in the number of replacements in each sublattice. Details of the damage configurations obtained will be discussed. read less NOT USED (low confidence) R. P. Messmer, “Computational materials science — a personal perspective of an industrial scientist,” Computational Materials Science. 1994. link Times cited: 6 NOT USED (low confidence) A. Veen, H. Schut, R. Hakvoort, A. V. Fedorov, and K. T. Westerduin, “Helium and Hydrogen Induced Growth of Microcavities in Silicon; Application to Gas And Impurity Collection,” MRS Proceedings. 1994. link Times cited: 14 Abstract: Thermal helium desorption spectrometry and positron beam ana… read moreAbstract: Thermal helium desorption spectrometry and positron beam analysis have been used to monitor the growth of helium vacancy clusters during room temperature helium irradiation of silicon and curing subsequent annealing to 1,300 K. Experimental results obtained with hydrogen irradiation show that also hydrogen can be used to create cavities. There is a rather sharp threshold dose for creating cavities that will survive 1,300 K annealing. It appears that positrons from a sensitive probe for the trapping and release of impurities inside the cavities. Results of atomistic calculations are used to discuss thermal stability of helium vacancy complexes. The results are related to recent impurity gettering studies based on impurity trapping at helium induced gettering centers. read less NOT USED (low confidence) R. Smith and R. Webb, “Atomic collisions in semiconductors,” Radiation Effects and Defects in Solids. 1994. link Times cited: 1 Abstract: Energetic particle bombardment of semi-conductors (Si and Ga… read moreAbstract: Energetic particle bombardment of semi-conductors (Si and GaAs) is studied by means of Molecular Dynamics simulations using many-body potentials. The simulations show that the diamond lattice structures can lead to the trajectories of particles within the crystal being channelled even at low energies. Some results concerning damage production, low energy implantation profiles and angular distributions of ejected particles are presented. read less NOT USED (low confidence) H. Rafii-Tabar, H. Kamiyama, Y. Maruyama, K. Ohno, and Y. Kawazoe, “An Application of Classical Molecular Dynamics Simulation and AB Initio Density-Functional Calculation in Surface Physics,” Molecular Simulation. 1994. link Times cited: 8 Abstract: Classical molecular dynamics simulation and ab initio mixed … read moreAbstract: Classical molecular dynamics simulation and ab initio mixed basis Car-Parrinello methods are discussed and applied to the investigation of the results of a recently performed STM-based experiment involving the adsorption of C60 molecules on the dimerized Si surface. We show that these methods are capable of providing the theoretical basis for this experiment and test the validity of the associated conjectures. A mixed-basis all-electron formalism for the Car-Parrinello method is proposed to obtain the detailed understanding of the electronic states and dynamics of surface structure. A band structure calculation using this formalism is performed for the c(4 × 3) structure of C60 adsorbed on Si (100) surface and is compared with the experimental results. read less NOT USED (low confidence) B. R. Eggen, R. Johnston, and J. Murrell, “Carbon cluster structures and stabilities predicted from solid-state potentials,” Journal of the Chemical Society, Faraday Transactions. 1994. link Times cited: 23 Abstract: An empirical potential-energy function comprising two- and t… read moreAbstract: An empirical potential-energy function comprising two- and three-body terms, whose parameters have been determined from the properties of diamond and graphite, is used to study the structures and energies of carbon microclusters.The binding energy per atom of smaller linear clusters increases monotonically with the number of atoms, whereas cyclic clusters display an optimal energy per atom for six-membered rings. The energies of fullerenes are sensitive to nuclearity and shape, with icosahedral C60 and D5h C70 being the most stable clusters. The potential predicts the binding energy of C60 to be 7.25 eV per atom, in good agreement with experimental measurements.For larger clusters, spherical fragments of cubic bulk structures have been investigated; diamond fragments become relatively more stable than other cubic fragments for more than approximately 100 atoms. Open nanotubes are found to be most stable for circumferences containing five hexagons. Vibrational frequencies were calculated and correlated with experimental results for some clusters. read less NOT USED (low confidence) F. Streitz and J. Mintmire, “Atomic Scale Simulations of Tensile Failure in Metal Oxides,” MRS Proceedings. 1994. link Times cited: 1 Abstract: The authors describe atomic-scale simulations of the failure… read moreAbstract: The authors describe atomic-scale simulations of the failure under tensile load of an aluminum-alumina heterostructure, comparing the results with similar simulations of failure in metallic aluminum and the ceramic {alpha}-alumina. The simulations were performed using a novel computational method which explicitly includes variable charge transfer between cations and anions in an empirical potential. From their simulations they estimate the theoretical limit of yield stress for the interface to be approximately 2 GPa, at a strain of only a few percent. The theoretical limit for yield stress in {alpha}-alumina, for comparison, is about 45 GPa. read less NOT USED (low confidence) C. Dharma-wardana, “Density Functional and Non-Equilibrium Methods for Unusual States of Matter Produced Using Short-Pulse Lasers.” 1994. link Times cited: 2 NOT USED (low confidence) M. Zachariah and M. Carrier, “Atomistic Simulation of Vapor-Phase Nanoparticle Formation,” MRS Proceedings. 1994. link Times cited: 3 NOT USED (low confidence) G. Gilmer, “Materials processing: unleashing the power of computer simulations,” Computational Materials Science. 1994. link Times cited: 3 NOT USED (low confidence) J. Hafner, “Quantum Theory of Structure: Crystals and Quasicrystals, Melts and Glasses.” 1994. link Times cited: 0 NOT USED (low confidence) M. Laradji, D. Landau, and B. Dünweg, “A Monte Carlo Simulation of the Stillinger-Weber Model for Si-Ge Alloys,” MRS Proceedings. 1994. link Times cited: 1 Abstract: The bulk phase behavior of silicon-germanium alloys is inves… read moreAbstract: The bulk phase behavior of silicon-germanium alloys is investigated by means of a constant pressure Monte Carlo simulation of the Stillinger-Weber potential in the semi-grand-canonical ensemble. At low temperatures, Si and Ge phase separate into a Si-rich phase and a Ge-rich phase. The two-phase region is terminated by a critical point whose nature is investigated thoroughly by the multihistogram method combined with finite size scaling analysis. These results showed that the critical behavior of the alloy belongs to the mean field universality class, presumably due to the elastic degrees of freedom. We have also studied the structural properties of the mixture and found that the linear thermal expansions of both Si and Ge agree well with experiments. We also verified Vegard's law above the critical point and calculated bond length distributions. read less NOT USED (low confidence) R. Rentsch and I. Inasaki, “Molecular Dynamics Simulation for Abrasive Processes,” CIRP Annals. 1994. link Times cited: 80 NOT USED (low confidence) A. Haymet, “Calculation of entropy,” Computational Materials Science. 1994. link Times cited: 1 NOT USED (low confidence) F. Streitz and J. Mintmire, “Charge transfer and bonding in metallic oxides,” Journal of Adhesion Science and Technology. 1994. link Times cited: 27 Abstract: We discuss the development of interaction potentials which e… read moreAbstract: We discuss the development of interaction potentials which explicitly allow for charge transfer in metallic oxides. The charge transfer is calculated self-consistently using a charge equilibration approach, which allows the amount of charge transferred to respond to the electrostatic environment. We model the metal-metal, metal-oxygen, and oxygen-oxygen interactions with Rydberg function pair potentials. By fitting the Rydberg potential parameters to the elastic and structural constants of the material, we arrive at an efficient model for the simulation of metallic oxides. We demonstrate the applicability of the model by describing some preliminary results on the rutile phase of titanium dioxide. read less NOT USED (low confidence) C. Wang, K. Ho, and C. Chan, “Material research with tight-binding molecular dynamics,” Computational Materials Science. 1994. link Times cited: 14 NOT USED (low confidence) M. Sprik, “Effective Pair Potentials and Beyond.” 1993. link Times cited: 12 NOT USED (low confidence) M. M. Souza and G. Amaratunga, “Self Diffusion in Silicon Using the Ackland Potential.” 1993. link Times cited: 2 NOT USED (low confidence) D. Vvedensky, “Theory of Atomic-Scale Processes during Epitaxial Growth: Current Status.” 1993. link Times cited: 3 NOT USED (low confidence) J. P. Eerden, “CHAPTER 6 – Crystal Growth Mechanisms.” 1993. link Times cited: 58 NOT USED (low confidence) M. Zachariah, M. Carrier, and E. Blaisten-Barojas, “Molecular Dynamics Simulation of Large Cluster Growth,” MRS Proceedings. 1993. link Times cited: 4 NOT USED (low confidence) M. Kluge, J. Feldman, and J. Broughton, “Molecular Dynamics Simulations of Thermal Conductivity in Insulating Glasses.” 1993. link Times cited: 1 NOT USED (low confidence) O. Marti, “CHAPTER 1 – SXM: An Introduction.” 1993. link Times cited: 3 NOT USED (low confidence) H. Inoue, A. Makishima, Y. Akasaka, and I. Yasui, “Structure and Frequency Spectra of Silica Glass Simulated by Molecular Dynamics Method.” 1993. link Times cited: 0 NOT USED (low confidence) G. Gilmer, “CHAPTER 8 – Atomic-scale Models of Crystal Growth.” 1993. link Times cited: 5 NOT USED (low confidence) R. Lucchese and W. Marlow, “Gas-Phase Cluster Dynamics: Clustering and Growth.” 1993. link Times cited: 1 NOT USED (low confidence) B. Pailthorpe, “Molecular Dynamics Simulations of Diamond and Carbon Clusters,” MRS Proceedings. 1993. link Times cited: 0 NOT USED (low confidence) U. Landman and W. Luedtke, “Consequences of Tip—Sample Interactions.” 1993. link Times cited: 11 NOT USED (low confidence) M. Aoki, P. Gumbsch, and D. Pettifor, “Angular-Dependent Many-Atom Bond-Order Potentials.” 1993. link Times cited: 5 NOT USED (low confidence) Hausleitner and Hafner, “Hybridized nearly-free-electron tight-binding-bond approach to interatomic forces in disordered transition-metal alloys. II. Modeling of metallic glasses.,” Physical review. B, Condensed matter. 1992. link Times cited: 71 NOT USED (low confidence) D. Maroudas and R. A. Brown, “Atomistic Simulations of Point Defect Properties in Silicon,” MRS Proceedings. 1992. link Times cited: 0 Abstract: A systematic analysis based on atomistic simulations is pres… read moreAbstract: A systematic analysis based on atomistic simulations is presented for the calculation of energies and equilibrium concentrations of intrinsic point defects in silicon. Calculation of Gibbs free energies is based on the quasi-harmonic approximation for the reference state and the cumulant analysis of the enthalpy distribution function from Monte Carlo simulations in the reference state. Results are presented for the temperature dependence of enthalpies, volumes, and free energies of formation and thermal equilibrium concentrations of vacancies and self-interstitials. read less NOT USED (low confidence) D. Wales and M. C. Waterworth, “Structures and rearrangements of model silicon clusters,” Journal of the Chemical Society, Faraday Transactions. 1992. link Times cited: 12 Abstract: We present a study of small silicon clusters bound by the em… read moreAbstract: We present a study of small silicon clusters bound by the empirical potential-energy function of Li, Johnston and Murrell (LJM). Analytic first and second derivatives of the potential are employed in molecular dynamics simulations and geometry optimisations of both minima and transition states. Frequency analyses of all the resulting stationary points enable us to define the topology of the potential-energy surfaces, and rearrangement mechanisms are characterised for various clusters containing up to 50 atoms. read less NOT USED (low confidence) U. Landman, W. Luedtke, and E. Ringer, “Molecular Dynamics Simulations of Adhesive Contact Formation and Friction.” 1992. link Times cited: 32 NOT USED (low confidence) G. Dereli, “Stillinger-Weber Type Potentials in Monte Carlo Simulation of Amorphous Silicon,” Molecular Simulation. 1992. link Times cited: 16 Abstract: The growth of amorphous silicon on a substrate of a two-laye… read moreAbstract: The growth of amorphous silicon on a substrate of a two-layer slab of crystalline silicon with various surface indices is simulated with Stillinger-Weber type interatomic potentials. The growth is realized by means of a continuum Monte Carlo method and the radial distribution functions are evaluated for various cases. read less NOT USED (low confidence) D. Lévesque and J. Weis, “Recent Progress in the Simulation of Classical Fluids,” Topics in Applied Physics. 1992. link Times cited: 4 NOT USED (low confidence) L. L. Boyer, E. Kaxiras, M. Mehl, J. Feldman, and J. Broughton, “Application of Magic Strains to Predict New Ordered Phases: A Five-Fold Coordinated Crystal Structure for Silicon.” 1992. link Times cited: 1 NOT USED (low confidence) S. Li, R. Johnston, and J. Murrell, “Cluster structures and stabilities from solid-state potentials. Application to silicon clusters,” Journal of the Chemical Society, Faraday Transactions. 1992. link Times cited: 40 Abstract: An empirical potential-energy function comprising two- and t… read moreAbstract: An empirical potential-energy function comprising two- and three-body terms, whose parameters have been determined from the properties of solid silicon, is used to study the structures and energies of silicon microclusters. For small clusters, densely packed (non-diamond) structures are found which are in broad agreement with ab initio calculations. For larger clusters, optimisations starting from fragments of the cubic bulk solids indicate that close-packed structures are favoured initially and that diamond structures become relatively more stable only for clusters of well above 100 atoms. read less NOT USED (low confidence) Y. Mo, J. Kleiner, M. B. Webb, and M. Lagally, “Surface self-diffusion of Si on Si(001),” Surface Science. 1992. link Times cited: 153 NOT USED (low confidence) J. E. Angelo, W. Gerberich, G. Bratina, L. Sorba, and A. Franciosi, “Tem Investigations of CdTe/GaAs(001) Interfaces,” MRS Proceedings. 1992. link Times cited: 0 Abstract: In this study, cross-sectional transmission electron microsc… read moreAbstract: In this study, cross-sectional transmission electron microscopy (XTEM) was used to investigate the defect structure which occurs at the interface between CdTe(001) and GaAs(001). The heterostructures were fabricated by molecular beam epitaxy on chemically etched and thermally deoxidized GaAs(001) substrates as well as GaAs(001) buffer layers grown in-situ by molecular beam epitaxy. This allowed for investigation of the GaAs surface preparation on the subsequent interfacial structure. The as-etched substrate led to a microscopically rough interface with the CdTe depositing in etch pits on the GaAs surface, while growth on the buffer layer led to a macroscopically flat interface. Further, growth was accomplished on different Te-induced surface reconstructions ((6×1) vs (2×1)) in an effort to understand the role of the precursor surface treatment on the subsequent interfacial structure. In this case growth on the (6×1) reconstruction led to the introduction of (111)-oriented inclusions at the interface, while the (2×1) reconstruction led to pure (001)-oriented growth. A mechanism for the formation of planar defects at the CdTe/GaAs(001) interface is described which is based on local misorientations of the CdTe and GaAs. Finally, preliminary results of ex-situ annealing experiments on the interfacial defect structure will be discussed. read less NOT USED (low confidence) J. Mei, B. Cooper, Y. Hao, S. P. Lim, and F. L. Vanscoy, “New Technique for AB Initio Atomistic Potentials and Application to Thermal Expansion of Ni/Cr Alloys,” MRS Proceedings. 1992. link Times cited: 3 NOT USED (low confidence) S. Sharan and J. Narayan, “Semiconductor Heterostructures: Formation of Defects and Their Reduction.” 1992. link Times cited: 3 NOT USED (low confidence) M. Grabow, “How Small a System is Too Small for Studying Liquid Behavior,” MRS Proceedings. 1992. link Times cited: 0 NOT USED (low confidence) S. Sarma and K. E. Khor, “Empirical potential approach to the stability and energetics of thin films and surfaces,” Applied Surface Science. 1992. link Times cited: 1 NOT USED (low confidence) F. Ercolessi and J. B. Adams, “Interatomic Potentials From First-Principles Calculations,” MRS Proceedings. 1992. link Times cited: 22 Abstract: We propose a new scheme to extract “optimal” interatomic pot… read moreAbstract: We propose a new scheme to extract “optimal” interatomic potentials starting from a large number of atomic configurations (and their forces) obtained from first-principles calculations. The method appears to be able to overcome the difficulties encountered by traditional fitting approaches when using rich and complex analytical forms, and constitute a step forward towards large-scale simulations of condensed matter systems with a degree of accuracy comparable to that obtained by ab initio methods. A first exploratory application to aluminum is presented. read less NOT USED (low confidence) E. Blaisten-Barojas, “High Temperature Molecular Dynamics Studies of Cluster Growth and Polymer Degradation.” 1992. link Times cited: 0 NOT USED (low confidence) E. Meyer and H. Heinzelmann, “Scanning Force Microscopy (SFM).” 1992. link Times cited: 38 NOT USED (low confidence) C. Satoko, “Application of the Car-Parrinello Molecular Dynamics to Some Microclusters.” 1992. link Times cited: 0 NOT USED (low confidence) S. Yip, “Simulation Studies of Interfacial Phenomena — Melting, Stress Relaxation and Fracture.” 1992. link Times cited: 0 NOT USED (low confidence) T. Okada, S. Kambayashi, M. Yabuki, Y. Tsunashima, Y. Mirata, and S. Onga, “A new thin film Growth/Regrowth Process Design and Experimental Comparisons with Molecular Dynamic Analyses,” MRS Proceedings. 1992. link Times cited: 0 Abstract: A new concept of thin film growth/regrowth process design ta… read moreAbstract: A new concept of thin film growth/regrowth process design taking atomic motions into account using molecular dynamics is proposed. In the system, a modified many-body Tersoff-type interatomic potential for silicon has been adopted. The mathematical derivation of higher order derivatives was rigorously treated. Among many applications, the solid phase growth process was studied. It has been found from simulation studies that the solid phase growth of crystalline silicon proceeded along the [110] direction layer by layer. Furthermore, it has been obtained that all the atoms are activated in an extremely thin amorphous silicon film. Based on simulated results, an experiment using an extremely thin amorphous silicon film was carried out. It has been found that the perfect spherical silicon crystals with a uniform size and spacing can be grown from a thin amorphous silicon film. read less NOT USED (low confidence) D. Pettifor and M. Aoki, “Analytic Bond Order Potentials within Tight Binding Hückel Theory.” 1992. link Times cited: 1 NOT USED (low confidence) W. Li, R. Kalia, and P. Vashishta, “Structure, Fragmentation, and Phonons in Silicon Microclusters,” MRS Proceedings. 1992. link Times cited: 0 Abstract: Molecular-dynamics simulations are performed to investigate … read moreAbstract: Molecular-dynamics simulations are performed to investigate structures, vibrational spectra, and fragmentation channels of silicon microclusters ranging in size from 32 to 52 atoms. Structural information is derived from pair-distribution functions, bond-angle distributions, and the structure and statistics of rings. Molecular-dynamics simulation results for energetics suggest that 33, 39, 45 and 51 atom clusters are highly stable. These magic-number clusters have predominantly five and six membered rings. With an increase in “temperature”, most clusters tend to fragment by loosing one atom at a time. Vibrational densities of states of 32-52 atom silicon clusters show only minor deviations from the bulk behavior. read less NOT USED (low confidence) U. Landman, W. Luedtke, and E. Ringer, “Paper I (I) Atomic Scale Mechanisms of Adhesion, Friction and Wear,” Tribology and Interface Engineering Series. 1992. link Times cited: 0 NOT USED (low confidence) M. Robinson, “Computer Simulation of Atomic Collision Processes in Solids,” MRS Proceedings. 1992. link Times cited: 2 Abstract: Computer simulation is a major tool for studying the interac… read moreAbstract: Computer simulation is a major tool for studying the interactions of swift ions with solids which underlie processes such as particle backscattering, ion implantation, radiation damage, and sputtering. Numerical models are classed as molecular dynamics or binary collision models, along with some intermediate types. Binary collision models are divided into those for crystalline targets and those for structureless ones. The foundations of such models are reviewed, including interatomic potentials, electron excitations, and relationships among the various types of codes. Some topics of current interest are summarized. read less NOT USED (low confidence) J. Ferrante and G. Bozzolo, “Computational Techniques in Tribology and Material Science at the Atomic Level.” 1992. link Times cited: 2 NOT USED (low confidence) J. Villain, J. Rouviere, and I. Vilfan, “Phenomenology of Surface Reconstruction.” 1991. link Times cited: 0 NOT USED (low confidence) G. Gilmer and A. F. Bakker, “MOLECULAR DYNAMICS SIMULATIONS OF MOLECULAR BEAM EPITAXY,” Computer Aided Innovation of New Materials. 1991. link Times cited: 1 NOT USED (low confidence) M. Duesbery and G. Richardson, “The dislocation core in crystalline materials,” Critical Reviews in Solid State and Materials Sciences. 1991. link Times cited: 134 Abstract: The art of forming materials into technologically useful art… read moreAbstract: The art of forming materials into technologically useful artifacts by manipulation of the dislocation substructure dates back at least 8000 years to the Sumerian coppersmiths.1 Physical understanding of the mechanisms involved, on the other hand, began little more than 50 years ago; modem knowledge suggests that even now this understanding is far from complete. read less NOT USED (low confidence) J. C. Phillips, “Quantum Structural Diagrams.” 1991. link Times cited: 2 NOT USED (low confidence) Y. Xie, G. H. Gilmcr, E. Fitzgerald, and J. Michel, “Columnar Structure Growth by Silicon Molecular Beam Epitaxy,” MRS Proceedings. 1991. link Times cited: 3 Abstract: Si columnar structures were fabricated using Si MBE on Si su… read moreAbstract: Si columnar structures were fabricated using Si MBE on Si substrates with column sizes in the order of ∼ 100 A. The objective is to explore a viable approach to fabricate quantum wire structures. The growth of the structures, which was due to the growth instability, was an excellent example of a self-limiting process. The dependence of column morphology on the critical parameters, e.g., Si molecular beam incident angle, substrate temperature, substrate rotation, speed, etc., were demonstrated. Comparison between the experimental and the computer simulation results demonstrated the importance of the latent heat related atom migration as compared to the normal surface diffusion at low substrate temperatures and several A/s beam fluxes. A substrate temperature window (≈125°C) was observed which allowed the fabrication of crystalline micro-columns on Si (100) substrates. RHEED studies indicated that the crystalline micro- columns were heavily twined. The twinning phenomenon was also observed in the computer simulation results and interpreted as a result of the reduction in twin formation energy due to the extremely small dimension of the columns. Thermal stability of the columnar structures is discussed. Finally, photoluminescence studies and some potential applications are also discussed. read less NOT USED (low confidence) G. Galli and M. Parrinello, “Ab-Initio Molecular Dynamics: Principles and Practical Implementation.” 1991. link Times cited: 105 NOT USED (low confidence) J. Uppenbrink and D. Wales, “Packing schemes for Lennard-Jones clusters of 13 to 150 atoms: minima, transition states and rearrangement mechanisms,” Journal of the Chemical Society, Faraday Transactions. 1991. link Times cited: 49 Abstract: Clusters of 13–150 Lennard-Jones atoms have been investigate… read moreAbstract: Clusters of 13–150 Lennard-Jones atoms have been investigated, with attention given to clusters at both ‘magic’ and intermediate nuclearities. Icosahedral, decahedral and face-centred-cubic structures are compared in terms of their relative energies and the topology of the potential-energy surfaces. In particular, both gradient and second-derivative optimisation schemes are employed, and all structures are characterised in terms of their force constants. We find a number of interesting relationships between the three principal structural morphologies. Different capping routes are also compared to investigate possible growth schemes for the clusters of intermediate size. We find that the presence or absence of particular capping or surface atoms can be crucial in determining structural stability, showing that even this simple model potential can provide insights into the chemistry of small metal particles, as observed from experiment. read less NOT USED (low confidence) J. MacElroy and K. Raghavan, “Transport of an adsorbing vapour in a model silica system,” Journal of the Chemical Society, Faraday Transactions. 1991. link Times cited: 22 Abstract: A simple, though realistic, model of the structure of microp… read moreAbstract: A simple, though realistic, model of the structure of microporous silica is used in simulation studies of the properties of a Lennard-Jones (12–6) vapour adsorbed in a confined space over a wide range of pore filling conditions. The silica medium is composed of randomly distributed interconnected microspheres of SiO2 reminiscent of a gel-like material formed from a colloidal suspension. Each microsphere in the assembly is generated from a molecular model of bulk vitreous SiO2 which in turn is based on a modified Born–Mayer–Huggins pair potential and the Stillinger–Weber three-body potential for the silicon–oxygen system.Vapour sorption within the voids of this microporous medium is investigated via molecular dynamics and Monte Carlo simulations. Of particular interest in these studies is the dynamical behaviour of moderately dense adsorbed phases in the transition region between “monolayer” coverage and complete pore filling. In this intermediate region, adsorbed fluid transport properties are known to undergo a radical change in character, ranging from free-molecule activated diffusion at low pore filling to both diffusive and bulk collective motion at high densities. Detailed microscopic information on the dynamics of such systems is currently unavailable, and in this paper the mechanisms associated with this transition region are examined with the aid of dynamical self-and cross-correlation functions of the adsorbed vapour. The time-dependent properties of the adsorbed phase are also investigated using an inert, nonadsorbing molecular probe. The results from the latter studies provide an interesting insight into the percolation behaviour of porous media in the presence of immobile and mobile adsorbed films. read less NOT USED (low confidence) O. Sankey et al., “First-principles electronic structure calculations with molecular dynamics made easy,” Superlattices and Microstructures. 1991. link Times cited: 3 NOT USED (low confidence) S. Balm, A. Allaf, H. Kroto, and J. Murrell, “Potential-energy function for large carbon clusters,” Journal of the Chemical Society, Faraday Transactions. 1991. link Times cited: 8 Abstract: A potential function consisting of pair and three-body terms… read moreAbstract: A potential function consisting of pair and three-body terms has been devised for large carbon clusters on the basis of qualitative assumptions regarding the structures and stabilities of isolated and fused carbon rings. The potential predicts that the C60 icosahedral structure is stable to radial and tangential displacements of atoms and has a binding energy of 14.10 eV per atom. This is larger than that of a planar coronene-like (11.52 eV per atom) and a non-planar corannulene-like all carbon structure (11.41 eV per atom). read less NOT USED (low confidence) N. Winograd and B. Garrison, “Surface Structure and Reaction Studies by Ion-Solid Collisions,” ChemInform. 1991. link Times cited: 4 NOT USED (low confidence) M. J. Uttormark, M. Thompson, and P. Clancy, “Dissolution and Growth Kinetics of Small Crystals in Liquids,” MRS Proceedings. 1991. link Times cited: 0 NOT USED (low confidence) G. Gilmer, C. Roland, and R. Karunasiri, “Molecular Dynamics Studies of Impurity Segregation and Trapping.,” MRS Proceedings. 1991. link Times cited: 0 Abstract: The ability to make highly doped δ-layers in semiconductors … read moreAbstract: The ability to make highly doped δ-layers in semiconductors depends on the rate of interchange of atoms between layers at the crystal surface. We have simulated molecular beam epitaxy on a silicon (100) surface covered with a monolayer of impurity atoms. The kinetics of impurity segregation to the surface was examined for various growth conditions and segregation energies. We find that segregation is facilitated by appreciable inter-layer diffusion of atoms in the top several layers. The amount of diffusion is much greater during deposition than it is when the beam is off. read less NOT USED (low confidence) J. Chelikowsky and K. M. Glassford, “Classical Potentials for Covalent Solids and Clusters: Application to Silicon and Silicon Dioxide,” MRS Proceedings. 1990. link Times cited: 0 NOT USED (low confidence) J. Feldman and E. Kaxiras, “Vibrational Properties of Si Microclusters and Comparison to the Amorphous Material,” MRS Proceedings. 1990. link Times cited: 0 NOT USED (low confidence) B. Dodson, “Nonadiabatic bonding interactions in sub-keV ion-solid processes,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1990. link Times cited: 4 NOT USED (low confidence) R. Biswas, I. Kwon, and C. Soukoulis, “Molecular Dynamics Simulations of the Structural, Vibrational and Electronic Properties of Amorphous Silicon,” MRS Proceedings. 1990. link Times cited: 1 NOT USED (low confidence) M. Rouhani and D. Estève, “Growth Processes at Surfaces.” 1990. link Times cited: 0 NOT USED (low confidence) J. Broughton, M. Pederson, D. Papaconstantopoulos, and D. J. Singh, “GaAs Total Energy Tight Binding Hamiltonians for use in Molecular Dynamics,” MRS Proceedings. 1990. link Times cited: 0 Abstract: A self-consistent non-orthogonal semi-empirical tight bindin… read moreAbstract: A self-consistent non-orthogonal semi-empirical tight binding Hamiltonian is proposed for GaAs, or any sp system, which is simple, reliable, transferable, accurate and fast to evaluate. Matrix elements are functions of charges, distances between atoms and simple cosines of angles between s and p-electron densities and interatomic vectors which maintain the simplicity of Slater-Koster parameterizations. The tight binding scheme is fit against a large data base of local density functional derived total energies for systems of differing coordination and geometry. The Hamiltonian fulfills the correct Virial constraint, invokes the physically correct relationship between overlap and kinetic energy matrix elements and defines charges via Mulliken or Lowdin schemes. Such Hamiltonians will allow the reliable simulation of statistical mechanically interesting systems of order hundred or more atoms over physically useful periods of time of order tens to hundreds of thousands of time steps within not unreasonable supercomputer budgets. read less NOT USED (low confidence) S. Nagano and S. Ohnishi, “EFFECT OF THE QUANTUM ELECTRONS TO FORMATION OF A CRYSTALLINE ORDER IN ALKALI METALS.” 1990. link Times cited: 0 NOT USED (low confidence) S. J. Cook and P. Clancy, “A Comparison of Semiconductor Models for the Study of Liquid Phase Epitaxy,” MRS Proceedings. 1990. link Times cited: 0 Abstract: The phase behavior of silicon is studied using the Modified … read moreAbstract: The phase behavior of silicon is studied using the Modified Embedded Atom Method (MEAM) proposed by Baskes, Nelson and Wright. We find this model to quantitatively reproduce aspects of both the solid and liquid phases with an accuracy comparable to the widely-used Stillinger-Weber (SW) potential, thus providing an opportunity to examine the consistency of results obtained previously using the SW model. Although the models are very different, they both produce solid-liquid interfaces on both silicon (100) and (111) which have very similar morphologies. We find that the MEAM predicts the melting point of silicon to be 1445K, or 14% lower than the experimental value. The model also predicts the heat of melting to be 34.9 kJ/mol, 45% lower than the experimental value of 50.6 kJ/mol, and a liquid density which is 5.4% larger than that of the solid at the melting point, which is the density ratio found by experiment. The liquid density is found to be too low with respect to experiment. We also suggest a correction which might be applied to the MEAM model to improve its description of the liquid phase. read less NOT USED (low confidence) M. J. Uttormark, S. J. Cook, M. Thompson, and P. Clancy, “Dissolution Dynamics of Sub-Critical Clusters in Liquid Silicon,” MRS Proceedings. 1990. link Times cited: 5 NOT USED (low confidence) P. Dallot and P. Bristowe, “A Morphological Approach to Constructing Interatomic Potentials: An Application to Silicon.,” MRS Proceedings. 1990. link Times cited: 0 NOT USED (low confidence) L. Yang, R. Kalia, and P. Vashishta, “Electron trapping in amorphous silicon: A quantum molecular dynamics study,” MRS Proceedings. 1990. link Times cited: 0 Abstract: Quantum molecular dynamics (QMD) simulations provide the rea… read moreAbstract: Quantum molecular dynamics (QMD) simulations provide the real-time dynamics of electrons and ions through numerical solutions of the time-dependent Schrodinger and Newton equations, respectively. Using the QMD approach we have investigated the localization behavior of an excess electron in amorphous silicon at finite temperatures. For time scales on the order of a few picoseconds, we find the excess electron is localized inside a void of radius {approximately}3 {Angstrom} at finite temperatures. 12 refs. read less NOT USED (low confidence) A. Carlsson, “Derivation of Angular Forces for Semiconductors and Transition Metals.” 1990. link Times cited: 4 NOT USED (low confidence) A. Carlsson, “Beyond Pair Potentials in Elemental Transition Metals and Semiconductors,” Journal of Physics C: Solid State Physics. 1990. link Times cited: 169 NOT USED (low confidence) T. Takai, D. Choi, Y. T. Thathachari, T. Halicioǧlu, and W. Tiller, “A Potential Energy Function for GaAs Systems,” Physica Status Solidi B-basic Solid State Physics. 1990. link Times cited: 5 Abstract: Les calculs indiquent que la fonction potentielle avec les p… read moreAbstract: Les calculs indiquent que la fonction potentielle avec les parametres determines fournissent d'assez bonnes proprietes liees a l'energie et a la structure pour les surfaces et le volume de GaAs. La fonction est capable de reproduire des valeurs acceptables pour Ga cristallin pur read less NOT USED (low confidence) Z. Jian, Z. Kaiming, and X. Xide, “Theoretical prediction of melting temperature for silicon,” Chinese Physics Letters. 1990. link Times cited: 2 Abstract: A dynamical calculation of the state equation is presented t… read moreAbstract: A dynamical calculation of the state equation is presented to give a good prediction of the melting temperature for silicon which is much better than the molecular dynamics simulation result and agrees satisfactorily with the experimental value. read less NOT USED (low confidence) J. Hafner, “The Structural and Electronic Properties of Molten Metals, Semimetals, and Semiconductors.” 1990. link Times cited: 0 NOT USED (low confidence) G. Ackland, “A Pair Potential Model of Covalent Bonding in Silicon.” 1990. link Times cited: 0 NOT USED (low confidence) B. Dodson, “Molecular dynamics modeling of vapor-phase and very-low-energy ion-beam crystal growth processes,” Critical Reviews in Solid State and Materials Sciences. 1990. link Times cited: 26 Abstract: The development of techniques capable of performing atomicsc… read moreAbstract: The development of techniques capable of performing atomicscale computer simulation of realistic materials science problems is a recent phenomenon. Although the initial attempts to utilize such simulation techniques began not long after introduction of the first digital computers, application was mainly limited to highly idealized statistical mechanics problems due to the computational complexity of more realistic problems. Such problems were generally studied in systems consisting of up to several hundred atoms interacting through simple pairwise potentials. These simulations were of great value in fundamental studies of melting and other phase transitions, the structure of simple classical and quantum liquids, and simple diffusion problems. read less NOT USED (low confidence) M. Manninen, R. Nieminen, and M. Puska, “Introduction to Many-Atom Interactions in Solids.” 1990. link Times cited: 0 NOT USED (low confidence) J. P. Eerden, L. Guang-zhao, F. D. Jong, and M. J. Anders, “Monte Carlo simulation of covalent surfaces,” Journal of Crystal Growth. 1990. link Times cited: 13 NOT USED (low confidence) S. Klemm, D. A. Drabold, and O. Sankey, “Ab-Initio Simulations to Study the Configurational Entropy of Column IV Microclusters,” MRS Proceedings. 1990. link Times cited: 0 NOT USED (low confidence) U. Landman and W. Luedtke, “Molecular Dynamics Simulations of Materials: Beyond Pair Interactions.” 1989. link Times cited: 0 NOT USED (low confidence) A. Nandedkar, S. Sharan, and J. Narayan, “Atomic Structure of Dislocations and Interfaces in Semiconductor Heterostructures,” MRS Proceedings. 1989. link Times cited: 1 NOT USED (low confidence) M. Menon and R. Allen, “Simulation of Atomic and Molecular Processes at Solid Surfaces.” 1989. link Times cited: 0 NOT USED (low confidence) A. Carlsson, “Angular Forces in Transition Metals and Diamond Structure Semiconductors.” 1989. link Times cited: 1 NOT USED (low confidence) D. Wolf, J. Lutsko, and M. Kluge, “Physical Properties of Grain-Boundary Materials: Comparison of EAM and Central-Force Potentials.” 1989. link Times cited: 18 NOT USED (low confidence) O. Sankey and D. J. Niklewski, “A Simplified First-Principles Tight-Binding Method for Molecular Dynamics Simulations and Other Applications.” 1989. link Times cited: 0 NOT USED (low confidence) J. Hafner, “Quantum Theory of Structure: sp-Bonded Systems.” 1989. link Times cited: 11 NOT USED (low confidence) P. Peercy, “Fundamental issues in heteroepitaxy (condensed from the DOE panel report),” MRS Proceedings. 1989. link Times cited: 4 NOT USED (low confidence) J. A. Lupo and M. J. Sabochick, “Atomistic Simulation Study of Interfaces in Nanophase Silicon,” MRS Proceedings. 1989. link Times cited: 0 NOT USED (low confidence) M. Duesbery, D. Michel, and B. Joós, “Molecular Dynamics studies of Dislocations in SI,” MRS Proceedings. 1989. link Times cited: 4 NOT USED (low confidence) M. Tosi, “Freezing of Coulomb Liquids.” 1989. link Times cited: 3 NOT USED (low confidence) D. Hamann, “Calculation of Surface Structural Energies.” 1988. link Times cited: 0 NOT USED (low confidence) E. Blaisten-Barojas, “Computer Simulation of Clusters.” 1988. link Times cited: 3 NOT USED (low confidence) U. Landman, W. Luedtke, and M. W. Ribarsky, “Micromechanics and Microdynamics Via Atomistic Simulations,” MRS Proceedings. 1988. link Times cited: 4 NOT USED (low confidence) M. Grabow and G. Gilmer, “Thin film growth modes, wetting and cluster nucleation,” Surface Science. 1988. link Times cited: 135 NOT USED (low confidence) A. Haymet, M. Kramer, and C. H. Marshall, “Spin dependent force model of molecular liquids: Theory and simple applications,” Journal of Chemical Physics. 1988. link Times cited: 7 Abstract: We introduce a spin dependent force model for molecular liqu… read moreAbstract: We introduce a spin dependent force model for molecular liquids, in which the force between two atoms depends both on the interatomic separation distance and internal, quantum degrees of freedom. In this paper we introduce an additional approximation and treat the internal degrees of freedom semiclassically. We explore some simple properties of this model applied to hydrogen atoms and molecules. Using input from quantum chemistry calculations for the electronic potential energy surfaces, we calculate an effective molecule–molecule potential energy and the dynamics of two and three atom systems. We also perform molecular dynamic simulations which propagate both position and internal ‘‘spin’’ degrees of freedom. read less NOT USED (low confidence) A. Sutton, “Modelling of the Atomic and Electronic Structures of Interfaces,” MRS Proceedings. 1988. link Times cited: 6 NOT USED (low confidence) B. Dodson, J. Tsao, and P. Taylor, “Stability and metastability of semiconductor strained-layer structures,” Superlattices and Microstructures. 1988. link Times cited: 3 NOT USED (low confidence) D. J. Oh and R. Johnson, “A Semi-Empirical Potential for Graphite,” MRS Proceedings. 1988. link Times cited: 4 NOT USED (low confidence) U. Landman, “Molecular Dynamics Simulations in Material Science and Condensed Matter Physics.” 1988. link Times cited: 6 NOT USED (low confidence) D. Weaire and F. Wooten, “The Sillium Model.” 1988. link Times cited: 1 NOT USED (low confidence) I. Schuller, “The role of thermodynamic phase diagrams and lattice matching in superlattice growth,” Superlattices and Microstructures. 1988. link Times cited: 2 NOT USED (low confidence) B. Feuston, R. Kalia, and P. Vashishta, “Fragmentation and Structure of Silicon Microclysters.” 1987. link Times cited: 0 NOT USED (low confidence) W. Andreoni and P. Ballone, “Small semiconductor and metal clusters,” Physica Scripta. 1987. link Times cited: 7 Abstract: The purpose of this article is twofold: to define briefly th… read moreAbstract: The purpose of this article is twofold: to define briefly the state of the art of theoretical approaches to electronic, structural and thermal properties of small aggregates of metals and semiconductor elements, and to present new (sometimes preliminary) results of computer simulations on silicon, sodium and gold clusters. In particular, these calculations use the unified-molecular-dynamics-density-functional (Car-Parrinello) method for clusters of very small size (SiN and NaN with N up to 10), and effective many-body potentials for the gold clusters of larger size (N up to 1000). The connection between experiments and theory is discussed critically. read less NOT USED (low confidence) J. R. Ray and A. Rahman, “Calculation of Elastic Constants Using Molecular Dynamics.” 1987. link Times cited: 0 NOT USED (low confidence) S. Ohnishi, S. Saito, C. Satoko, and S. Sugano, “Atomic and Electronic Structures of Semiconductor Clusters.” 1987. link Times cited: 2 NOT USED (low confidence) D. Choi, T. Halicioǧlu, and W. Tiller, “Surface Stress Tensor Mediation of the Ledge Nucleation/Growth Process with the Surface Reconstruction Process in GaAs,” MRS Proceedings. 1987. link Times cited: 3 Abstract: A new GaAs semiempirical potential energy function which uti… read moreAbstract: A new GaAs semiempirical potential energy function which utilizes both two-body and three-body contributions has been used to evaluate the surface energy and surface stress tensor for the (111) and (00 1 )(As-terminated) surfaces as well as for ledges on the (00 1 ) surface. Both surface and ledge reconstruction patterns appear to be driven by stress tensor considerations and a long range ledge-ledge interaction arises via the stress tensor. The impact of this finding on two dimensional cluster formation and nucleation at the growing surface is very substantial. read less NOT USED (low confidence) B. Dodson, “Atomic-Scale Simulation of Silicon Atomic Beam Deposition,” MRS Proceedings. 1987. link Times cited: 0 Abstract: The mechanisms which control low energy (10–100 eV) beam dep… read moreAbstract: The mechanisms which control low energy (10–100 eV) beam deposition of silicon onto a relaxed (111) silicon substrate have been studied using a molecular dynamics technique. A many-body empirical potential was used to describe the covalent Si-Si bonding. 10 eV silicon beams with near-perpendicular incidence were simulated to study capture mechanisms and the local lattice excitation resulting from impact. Grazing angles of incidence (3°–30°) were studied for beam energies of 20–100 eV. For incidence angles less than an energy- and orientation-dependent critical value, the phenomenon of ‘surface channeling’ is predicted, in which the incoming particle is steered parallel to, and roughly 2 A above, the surface of the substrate through inelastic substrate interactions. The phenomena seen in low-energy beam deposition offer new avenues of control over growth of modulated semiconductor structures. read less NOT USED (low confidence) E. Blaisten-Barojas and D. Lévesque, “A Molecular Dynamics Study of Silicon Clusters.” 1987. link Times cited: 7 NOT USED (low confidence) F. Wooten and D. Weaire, “Modeling Tetrahedrally Bonded Random Networks by Computer,” Journal of Physics C: Solid State Physics. 1987. link Times cited: 102 NOT USED (low confidence) R. Nieminen, “Dynamics of atoms in low-symmetry systems,” Physica Scripta. 1987. link Times cited: 3 Abstract: Recent ideas to extend the scope and applicability of large-… read moreAbstract: Recent ideas to extend the scope and applicability of large-scale computer simulation of condensed phases are discussed. These include (i) the use of simulated annealing and related methods in first-principles calculations and (ii) the development "effective-medium" and similar approximate approaches to interatomic interactions in low-symmetry situations. Examples of applications to molecular dynamics simulations are presented. read less NOT USED (low confidence) J. Gunton, “Kinetics of Adatom Ordering on Surfaces.” 1987. link Times cited: 3 NOT USED (low confidence) B. Dodson and P. Taylor, “Atomistic calculation of stability and metastability of coherently strained silicon-like structures,” MRS Proceedings. 1986. link Times cited: 0 Abstract: Monte Carlo based microscopic techniques were used to study … read moreAbstract: Monte Carlo based microscopic techniques were used to study the stability and metastability of thin coherently strained layers of mismatched silicon-like semiconductor material grown on the (111) silicon surface. The structural energy was calculated using three-body empirical potentials. For layers greater than about 20 A thickness, the critical layer thickness associated with thermodynamic stability is accurately described by the continuum theory of Matthews and Blakeslee. For thinner layers, however, the stability properties vary considerably from those predicted by the continuum theory. The test system is found to be metastable against the nucleation of misfit dislocations to a lattice mismatch of about 11% for a strained layer six monolayers thick, compared to the 4% mismatch stability limit. read less NOT USED (low confidence) M. F. Schneider, I. Schuller, and A. Rahman, “MOLECULAR-DYNAMICS SIMULATION OF THIN-FILM GROWTH,” MRS Proceedings. 1986. link Times cited: 1 Abstract: The epitaxial growth of thin films has been studied by molec… read moreAbstract: The epitaxial growth of thin films has been studied by molecular-dynamics computer simulation. In these simulations atoms are projected towards a temperature-controlled substrate, and the equations of motion of all atoms are solved for a given interaction potential. The calculations give insight into the microscopic structure of thin films, the dynamics of the adsorption process, and they help answer the way in which substrate temperature, form of the substrate, flux of impinging atoms, and form of the interaction potential, affect epitaxial growth. Simulations were performed for monatomic and binary systems with spherically symmetric atomic interactions, and for systems in which the atoms are interacting via a three-body potential to simulate the epitaxial growth of silicon. read less NOT USED (low confidence) S. Pantelides, “Defect Reactions and Atomic Diffusion in Silicon,” MRS Proceedings. 1986. link Times cited: 2 NOT USED (low confidence) B. Dodson and P. Taylor, “Monte Carlo stability analysis of two-dimensional Lennard-Jones strained layer superlattice interfaces,” Superlattices and Microstructures. 1986. link Times cited: 2 NOT USED (low confidence) F. F. Abraham, “Computational statistical mechanics methodology, applications and supercomputing,” Advances in Physics. 1986. link Times cited: 221 Abstract: Computer simulation is adding a new dimension to scientific … read moreAbstract: Computer simulation is adding a new dimension to scientific investigation, establishing a role of equal importance with the traditional approaches of experiment and theory. In this paper, we provide a text for understanding the computer simulation methodology of classical statistical mechanics. After developing the theoretical basis of the simulation techniques, the Monte Carlo and Langevin methods and various molecular dynamics methods are described. A very limited discussion is provided on interatomic potential functions, numerical integration schemes, and general simulation procedures for modelling different physical situations and for circumventing excessive computational burdens. The simulation methods are then illustrated using a variety of physical problems studied over the last several years at our laboratory. They include spinodal decomposition of a two-dimensional (2D) fluid, the melting of 2D and quasi-2D films, the structure and energetics of an incommensurate physisorbed film, and th... read less NOT USED (low confidence) J. Broughton and P. B. Allen, “Electronic Properties of Liquid Silicon,” MRS Proceedings. 1985. link Times cited: 0 NOT USED (low confidence) B. Dodson, “Monte Carlo stability analysis of strained layer superlattice interfaces,” MRS Proceedings. 1985. link Times cited: 0 NOT USED (low confidence) U. Landman et al., “Microscopic Phenomena of Macroscopic Conseouences:Interfaces, Glasses, and Small Aggregates,” MRS Proceedings. 1985. link Times cited: 2 NOT USED (low confidence) E. Arnold et al., “Formation of Facets at the Solid-Melt Interface in Silicon,” MRS Proceedings. 1985. link Times cited: 1 Abstract: We have done experimental and theoretical studies of the ori… read moreAbstract: We have done experimental and theoretical studies of the origins of facet formation at the solid-liquid interface in laser-beam-melted silicon films. Two laser beams were used to produce a molten zone with a closely controlled thermal profile in a thin single-crystal film of silicon, and the liquid-solid interface was observed in situ. A transition to a faceted structure was found to occur under conditions of near thermal equilibrium. The solidliquid interface was also studied theoretically by means of molecular dynamics simulations, incorporating pair- and three-body terms in the interaction potential. Similarly to the experimental system, the solid-melt interface in the simulated system breaks up into facets defined by (111) planes. The melt region in the vicinity of the faceted planes exhibits a certain degree of ordering due to the influence of the crystalline potential. read less NOT USED (low confidence) R. Biswas and D. Hamann, “Classical Two and Three-Body Interatomic Potentials for Silicon Simulations,” MRS Proceedings. 1985. link Times cited: 2 Abstract: We develop two and three-body classical interatomic potentia… read moreAbstract: We develop two and three-body classical interatomic potentials that model structural energies for silicon. These potentials provide a global fit to a database of firstprinciples calculations of the energy for bulk and surface silicon structures which spans a wide range of atomic coordinations and bonding geometries. This is accomplished using a new “separable” form for the 3-body potential that reduces the 3-body energy to a product of 2-body sums and leads to computations of the energy and atomic forces in n 2 steps as opposed to n 3 for a general 3-body potential. Simulated annealing is performed to find globally minimum energy states of Si-atom clusters with these potentials using a Langevin molecular dynamics approach. read less NOT USED (low confidence) T. Weber, “Surface Reconstruction of SI(100),” MRS Proceedings. 1985. link Times cited: 4 NOT USED (low confidence) B. Dodson and P. Taylor, “Monte Carlo simulation of growth of crystalline and amorphous silicon,” MRS Proceedings. 1985. link Times cited: 0 NOT USED (high confidence) J. Utterson and R. Erban, “Symmetries of many-body systems imply distance-dependent potentials.,” Physical review. E. 2023. link Times cited: 0 Abstract: Considering an interatomic potential U(q), where q=[q_{1},q_… read moreAbstract: Considering an interatomic potential U(q), where q=[q_{1},q_{2},⋯,q_{N}]∈R^{3N} is a vector describing positions q_{i}∈R^{3}, it is shown that U can be defined as a function of the interatomic distance variables r_{ij}=|q_{i}-q_{j}| provided the potential U satisfies some symmetry assumptions. Moreover, the potential U can be defined as a function of a proper subset of the distance variables r_{ij}, provided N>5, with the number of distance variables used scaling linearly with the number of atoms N. read less NOT USED (high confidence) J.-C. Griesser, L. Frérot, J. A. Oldenstaedt, M. Müser, and L. Pastewka, “Analytic elastic coefficients in molecular calculations: Finite strain, nonaffine displacements, and many-body interatomic potentials,” Physical Review Materials. 2023. link Times cited: 1 Abstract: Elastic constants are among the most fundamental and importa… read moreAbstract: Elastic constants are among the most fundamental and important properties of solid materials, which is why they are routinely characterized in both experiments and simulations. While conceptually simple, the treatment of elastic constants is complicated by two factors not yet having been concurrently discussed: finite-strain and non-affine, internal displacements. Here, we revisit the theory behind zero-temperature, finite-strain elastic constants and extend it to explicitly consider non-affine displacements. We further present analytical expressions for second-order derivatives of the potential energy for two-body and generic many-body interatomic potentials, such as cluster and empirical bond-order potentials. Specifically, we revisit the elastic constants of silicon, silicon carbide and silicon dioxide under hydrostatic compression and dilatation. Based on existing and new results, we outline the effect of multiaxial stress states as opposed to volumetric deformation on the limits of stability of their crystalline lattices. read less NOT USED (high confidence) E. Sanscartier, F. Saint-Denis, K.-’E. Bolduc, and N. Mousseau, “Evaluating approaches for on-the-fly machine learning interatomic potentials for activated mechanisms sampling with the activation-relaxation technique nouveau.,” The Journal of chemical physics. 2023. link Times cited: 1 Abstract: In the last few years, much effort has gone into developing … read moreAbstract: In the last few years, much effort has gone into developing general machine-learning potentials capable of describing interactions for a wide range of structures and phases. Yet, as attention turns to more complex materials, including alloys and disordered and heterogeneous systems, the challenge of providing reliable descriptions for all possible environments becomes ever more costly. In this work, we evaluate the benefits of using specific vs general potentials for the study of activated mechanisms in solid-state materials. More specifically, we test three machine-learning fitting approaches using the moment-tensor potential to reproduce a reference potential when exploring the energy landscape around a vacancy in Stillinger-Weber silicon crystal and silicon-germanium zincblende structures using the activation-relaxation technique nouveau (ARTn). We find that a targeted on-the-fly approach specific to and integrated into ARTn generates the highest precision on the energetics and geometry of activated barriers while remaining cost-effective. This approach expands the types of problems that can be addressed with high-accuracy ML potential. read less NOT USED (high confidence) N. Nguyen, “Fast proper orthogonal descriptors for many-body interatomic potentials,” Physical Review B. 2022. link Times cited: 1 Abstract: The development of differentiable invariant descriptors for … read moreAbstract: The development of differentiable invariant descriptors for accurate representations of atomic environments plays a central role in the success of interatomic potentials for chemistry and materials science. We introduce a method to generate fast proper orthogonal descriptors for the construction of many-body interatomic potentials and discuss its relation to exising empirical and machine learning interatomic potentials. A traditional way of implementing the proper orthogonal descriptors has a computational complexity that scales exponentially with the body order in terms of the number of neighbors. We present an algorithm to compute the proper orthogonal descriptors with a computational complexity that scales linearly with the number of neighbors irrespective of the body order. We show that our method can enable a more efficient implementation for a number of existing potentials and provide a scalable systematic framework to construct new many-body potentials. The new potentials are demonstrated on a data set of density functional theory calculations for Tantalum and compared with other interatomic potentials. read less NOT USED (high confidence) P. Lunkenheimer, A. Loidl, B. Riechers, A. Zaccone, and K. Samwer, “Thermal expansion and the glass transition,” Nature Physics. 2022. link Times cited: 8 NOT USED (high confidence) Y. Singh, M. Santra, and R. S. Singh, “Anomalous Vapor and Ice Nucleation in Water at Negative Pressures: A Classical Density Functional Theory Study.,” The journal of physical chemistry. B. 2022. link Times cited: 1 Abstract: In contrast to the abundance of work on the anomalous behavi… read moreAbstract: In contrast to the abundance of work on the anomalous behavior of water, the relationship between the water's thermodynamic anomalies and kinetics of phase transition from metastable water is relatively unexplored. In this work, we have employed classical density functional theory to provide a unified and coherent picture of nucleation (both vapor and ice) from metastable water at negative pressure conditions. Our results suggest a peculiar nonmonotonic temperature dependence of vapor-liquid surface tension at temperatures where vapor-liquid coexistence is metastable with respect to the ice phase. The vapor nucleation barrier on isochoric cooling also shows a nonmonotonic temperature dependence. We further report that, for low density isochores, the temperature of the minimum vapor nucleation barrier (TΔΩv/min*) does not coincide with the temperature of maximum density (TMD) where metastability is maximum. The difference between the TΔΩv/min* and the TMD, however, decreases with increasing the density of the isochore. The vapor nucleation barrier along isobars shows an interesting crossover behavior in the vicinity of the Widom line on lowering the temperature. Our results on the ice nucleation suggest an anomalous retracing behavior of the nucleation barrier along isotherms at negative pressures and theoretically validate the recent findings that the reentrant ice(Ih)-liquid coexistence line can induce a drastic change in the kinetics of ice nucleation. Thus, this study establishes a direct connection between the metastable water's thermodynamic anomalies and the (vapor and ice) nucleation kinetics. In addition, this study provides deeper insights into the origin of the isothermal compressibility maximum on isochoric cooling. read less NOT USED (high confidence) X. Zhang et al., “Defect-characterized phase transition kinetics,” Applied Physics Reviews. 2022. link Times cited: 7 Abstract: Phase transitions are a common phenomenon in condensed matte… read moreAbstract: Phase transitions are a common phenomenon in condensed matter and act as a critical degree of freedom that can be employed to tailor the mechanical or electronic properties of materials. Understanding the fundamental mechanisms of the thermodynamics and kinetics of phase transitions is, thus, at the core of modern materials design. Conventionally, studies of phase transitions have, to a large extent, focused on pristine bulk phases. However, realistic materials exist in a complex form; their microstructures consist of different point and extended defects. The presence of defects impacts the thermodynamics and kinetics of phase transitions, but has been commonly ignored or treated separately. In recent years, with the significant advances in theoretical and experimental techniques, there has been an increasing research interest in modeling and characterizing how defects impact or even dictate phase transitions. The present review systematically discusses the recent progress in understanding the kinetics of defect-characterized phase transitions, derives the key mechanisms underlying these phase transitions, and envisions the remaining challenges and fruitful research directions. We hope that these discussions and insights will help to inspire future research and development in the field. read less NOT USED (high confidence) H. Wang and S. Torquato, “Equilibrium states corresponding to targeted hyperuniform nonequilibrium pair statistics.,” Soft matter. 2022. link Times cited: 3 Abstract: The Zhang-Torquato conjecture [G. Zhang and S. Torquato, Phy… read moreAbstract: The Zhang-Torquato conjecture [G. Zhang and S. Torquato, Phys. Rev. E, 2020, 101, 032124.] states that any realizable pair correlation function g2(r) or structure factor S(k) of a translationally invariant nonequilibrium system can be attained by an equilibrium ensemble involving only (up to) effective two-body interactions. To further test and study this conjecture, we consider two singular nonequilibrium models of recent interest that also have the exotic hyperuniformity property: a 2D "perfect glass" and a 3D critical absorbing-state model. We find that each nonequilibrium target can be achieved accurately by equilibrium states with effective one- and two-body potentials, lending further support to the conjecture. To characterize the structural degeneracy of such a nonequilibrium-equilibrium correspondence, we compute higher-order statistics for both models, as well as those for a hyperuniform 3D uniformly randomized lattice (URL), whose higher-order statistics can be very precisely ascertained. Interestingly, we find that the differences in the higher-order statistics between nonequilibrium and equilibrium systems with matching pair statistics, as measured by the "hole" probability distribution, provide measures of the degree to which a system is out of equilibrium. We show that all three systems studied possess the bounded-hole property and that holes near the maximum hole size in the URL are much rarer than those in the underlying simple cubic lattice. Remarkably, upon quenching, the effective potentials for all three systems possess local energy minima (i.e., inherent structures) with stronger forms of hyperuniformity compared to their target counterparts. Our methods are expected to facilitate the self-assembly of tunable hyperuniform soft-matter systems. read less NOT USED (high confidence) N. Nguyen and A. Rohskopf, “Proper orthogonal descriptors for efficient and accurate interatomic potentials,” J. Comput. Phys. 2022. link Times cited: 6 NOT USED (high confidence) J. Bulin, J. Hamaekers, M. P. Ariza, and M. Ortiz, “Interatomic-Potential-Free, Data-Driven Molecular Dynamics,” Computer Methods in Applied Mechanics and Engineering. 2022. link Times cited: 2 NOT USED (high confidence) J. Thomas, H. Chen, and C. Ortner, “Body-Ordered Approximations of Atomic Properties,” Archive for Rational Mechanics and Analysis. 2022. link Times cited: 1 NOT USED (high confidence) S. Banik et al., “CEGANN: Crystal Edge Graph Attention Neural Network for multiscale classification of materials environment,” npj Computational Materials. 2022. link Times cited: 10 NOT USED (high confidence) S. Torquato and H. Wang, “Precise determination of pair interactions from pair statistics of many-body systems in and out of equilibrium.,” Physical review. E. 2022. link Times cited: 5 Abstract: The determination of the pair potential v(r) that accurately… read moreAbstract: The determination of the pair potential v(r) that accurately yields an equilibrium state at positive temperature T with a prescribed pair correlation function g_{2}(r) or corresponding structure factor S(k) in d-dimensional Euclidean space R^{d} is an outstanding inverse statistical mechanics problem with far-reaching implications. Recently, Zhang and Torquato [Phys. Rev. E 101, 032124 (2020)2470-004510.1103/PhysRevE.101.032124] conjectured that any realizable g_{2}(r) or S(k) corresponding to a translationally invariant nonequilibrium system can be attained by a classical equilibrium ensemble involving only (up to) effective pair interactions. Testing this conjecture for nonequilibrium systems as well as for nontrivial equilibrium states requires improved inverse methodologies. We have devised an optimization algorithm to precisely determine effective pair potentials that correspond to pair statistics of general translationally invariant disordered many-body equilibrium or nonequilibrium systems at positive temperatures. This methodology utilizes a parameterized family of pointwise basis functions for the potential function whose initial form is informed by small-, intermediate- and large-distance behaviors dictated by statistical-mechanical theory. Subsequently, a nonlinear optimization technique is utilized to minimize an objective function that incorporates both the target pair correlation function g_{2}(r) and structure factor S(k) so that the small intermediate- and large-distance correlations are very accurately captured. To illustrate the versatility and power of our methodology, we accurately determine the effective pair interactions of the following four diverse target systems: (1) Lennard-Jones system in the vicinity of its critical point, (2) liquid under the Dzugutov potential, (3) nonequilibrium random sequential addition packing, and (4) a nonequilibrium hyperuniform "cloaked" uniformly randomized lattice. We found that the optimized pair potentials generate corresponding pair statistics that accurately match their corresponding targets with total L_{2}-norm errors that are an order of magnitude smaller than that of previous methods. The results of our investigation lend further support to the Zhang-Torquato conjecture. Furthermore, our algorithm will enable one to probe systems with identical pair statistics but different higher-body statistics, which will shed light on the well-known degeneracy problem of statistical mechanics. read less NOT USED (high confidence) Y. Wang, Z. Fan, P. Qian, M. A. Caro, and T. Ala‐Nissila, “Quantum-corrected thickness-dependent thermal conductivity in amorphous silicon predicted by machine learning molecular dynamics simulations,” Physical Review B. 2022. link Times cited: 11 Abstract: Amorphous silicon (a-Si) is an important thermal-management … read moreAbstract: Amorphous silicon (a-Si) is an important thermal-management material and also serves as an ideal playground for studying heat transport in strongly disordered materials. Theoretical prediction of the thermal conductivity of a-Si in a wide range of temperatures and sample sizes is still a challenge. Herein we present a systematic investigation of the thermal transport properties of a-Si by employing large-scale molecular dynamics (MD) simulations with an accurate and efficient machine-learned neuroevolution potential (NEP) trained against abundant reference data calculated at the quantum-mechanical density-functional-theory level. The high efficiency of NEP allows us to study the effects of finite size and quenching rate in the formation of a-Si in great detail. We find that it requires a simulation cell up to $64,000$ atoms (a cubic cell with a linear size of 11 nm) and a quenching rate down to $10^{11}$ K s$^{-1}$ for fully convergent thermal conductivity. Structural properties, including short- and medium-range order as characterized by the pair correlation function, angular distribution function, coordination number, ring statistics and structure factor are studied to demonstrate the accuracy of NEP and to further evaluate the role of quenching rate. Using both the heterogeneous and the homogeneous nonequilibrium MD methods and the related spectral decomposition techniques, we calculate the temperature- and thickness-dependent thermal conductivity values of a-Si and show that they agree well with available experimental results from 10 K to room temperature. Our results also highlight the importance of quantum effects in the calculated thermal conductivity and support the quantum correction method based on the spectral thermal conductivity. read less NOT USED (high confidence) B. Burlacu, M. Kommenda, G. Kronberger, S. M. Winkler, and M. Affenzeller, “Symbolic Regression in Materials Science: Discovering Interatomic Potentials from Data,” ArXiv. 2022. link Times cited: 2 NOT USED (high confidence) J. Barrat and L. Berthier, “Computer simulations of the glass transition and glassy materials,” Comptes Rendus. Physique. 2022. link Times cited: 4 Abstract: We provide an overview of the different types of computation… read moreAbstract: We provide an overview of the different types of computational techniques developed over the years to study supercooled liquids, glassy materials and the physics of the glass transition. We organise these numerical strategies into four broad families. For each of them, we describe the general ideas without discussing any technical details. We summarise the type of questions which can be addressed by any given approach and outline the main results which have been obtained. Finally we describe two important directions for future computational studies of glassy systems. read less NOT USED (high confidence) Y. Kurniawan et al., “Extending OpenKIM with an Uncertainty Quantification Toolkit for Molecular Modeling,” 2022 IEEE 18th International Conference on e-Science (e-Science). 2022. link Times cited: 0 Abstract: Atomistic simulations are an important tool in materials mod… read moreAbstract: Atomistic simulations are an important tool in materials modeling. Interatomic potentials (IPs) are at the heart of such molecular models, and the accuracy of a model's predictions depends strongly on the choice of IP. Uncertainty quantification (UQ) is an emerging tool for assessing the reliability of atomistic simulations. The Open Knowledgebase of Interatomic Models (OpenKIM) is a cyberinfrastructure project whose goal is to collect and standardize the study of IPs to enable transparent, reproducible research. Part of the OpenKIM framework is the Python package, KIM-based Learning-Integrated Fitting Framework (KLIFF), that provides tools for fitting parameters in an IP to data. This paper introduces a UQ toolbox extension to KLIFF. We focus on two sources of uncertainty: variations in parameters and inadequacy of the functional form of the IP. Our implementation uses parallel-tempered Markov chain Monte Carlo (PTMCMC), adjusting the sampling temperature to estimate the uncertainty due to the functional form of the IP. We demonstrate on a Stillinger–Weber potential that makes predictions for the atomic energies and forces for silicon in a diamond configuration. Finally, we highlight some potential subtleties in applying and using these tools with recommendations for practitioners and IP developers. read less NOT USED (high confidence) Z. Fan et al., “GPUMD: A package for constructing accurate machine-learned potentials and performing highly efficient atomistic simulations.,” The Journal of chemical physics. 2022. link Times cited: 46 Abstract: We present our latest advancements of machine-learned potent… read moreAbstract: We present our latest advancements of machine-learned potentials (MLPs) based on the neuroevolution potential (NEP) framework introduced in Fan et al. [Phys. Rev. B 104, 104309 (2021)] and their implementation in the open-source package gpumd. We increase the accuracy of NEP models both by improving the radial functions in the atomic-environment descriptor using a linear combination of Chebyshev basis functions and by extending the angular descriptor with some four-body and five-body contributions as in the atomic cluster expansion approach. We also detail our efficient implementation of the NEP approach in graphics processing units as well as our workflow for the construction of NEP models and demonstrate their application in large-scale atomistic simulations. By comparing to state-of-the-art MLPs, we show that the NEP approach not only achieves above-average accuracy but also is far more computationally efficient. These results demonstrate that the gpumd package is a promising tool for solving challenging problems requiring highly accurate, large-scale atomistic simulations. To enable the construction of MLPs using a minimal training set, we propose an active-learning scheme based on the latent space of a pre-trained NEP model. Finally, we introduce three separate Python packages, viz., gpyumd, calorine, and pynep, that enable the integration of gpumd into Python workflows. read less NOT USED (high confidence) A. Giri, C. Dionne, and P. Hopkins, “Atomic coordination dictates vibrational characteristics and thermal conductivity in amorphous carbon,” npj Computational Materials. 2022. link Times cited: 9 NOT USED (high confidence) M. Choi, M. Pasetto, Z.-Q. Shen, E. Tadmor, and D. Kamensky, “Atomistically-informed continuum modeling and isogeometric analysis of 2D materials over holey substrates,” Journal of the Mechanics and Physics of Solids. 2022. link Times cited: 1 NOT USED (high confidence) U. Yadav and S. Ghosh, “An atomistic-based finite deformation continuum membrane model for monolayer Transition Metal Dichalcogenides,” Journal of the Mechanics and Physics of Solids. 2022. link Times cited: 0 NOT USED (high confidence) Q. Xu, N. Salles, J. Chevalier, and J. Amodeo, “Atomistic simulation and interatomic potential comparison in α-Al2O3: lattice, surface and extended-defects properties,” Modelling and Simulation in Materials Science and Engineering. 2022. link Times cited: 3 Abstract: Aluminum oxide (α-Al2O3) is known as one of the major cerami… read moreAbstract: Aluminum oxide (α-Al2O3) is known as one of the major ceramic oxide and is currently used for its advanced mechanical properties. Nowadays, it requires a more in-depth description at small-scales especially for applications in the fields of nanocrystalline ceramic fabrication and nanomechanics. In this study, we investigate the transferability of several types of interatomic potentials including rigid ion, 2/3-body and many-body variable charge models. In particular, a special attention is paid to the material properties that are the most relevant for nanomechanical applications such as lattice properties, surface and stacking fault energies as well as dislocation modeling. Simulation outcomes are compared to reliable DFT simulations and most up-to-date experiments available from the literature. read less NOT USED (high confidence) A. Mittelstädt, A. Schliwa, and P. Klenovský, “Modeling electronic and optical properties of III–V quantum dots—selected recent developments,” Light, Science & Applications. 2022. link Times cited: 16 NOT USED (high confidence) R. Lot, L. Martin-Samos, S. de Gironcoli, and A. Hémeryck, “Developing a Neural Network potential to investigate interface phenomena in solid-phase epitaxy,” 2021 IEEE 16th Nanotechnology Materials and Devices Conference (NMDC). 2021. link Times cited: 0 Abstract: In this work, we develop a new neural network potential for … read moreAbstract: In this work, we develop a new neural network potential for silicon and perform accurate molecular dynamics simulations of the liquid, amorphous and diamond phases. The potential is tested against several physical properties and the solid phase epitaxy process is simulated. read less NOT USED (high confidence) D. Chen, X.-Y. Jiang, D. Wang, J. I. Vidallon, H. Zhuang, and Y. Jiao, “Multihyperuniform long-range order in medium-entropy alloys,” Acta Materialia. 2021. link Times cited: 6 NOT USED (high confidence) J. L. Suter and P. Coveney, “Principles governing control of aggregation and dispersion of aqueous graphene oxide,” Scientific Reports. 2021. link Times cited: 11 NOT USED (high confidence) A. Hosseini et al., “Super-Suppression of Long Phonon Mean-Free-Paths in Nano-Engineered Si due to Heat Current Anticorrelations,” Materials Today Physics. 2021. link Times cited: 3 NOT USED (high confidence) R. Rabani, S. Merabia, and A. Pishevar, “Conductive Heat Transfer Through Nanoconfined Gas: From Continuum to Free-Molecular Regime,” SSRN Electronic Journal. 2021. link Times cited: 0 Abstract: : In the past few decades, great efforts have been devoted t… read moreAbstract: : In the past few decades, great efforts have been devoted to studying heat transfer on the nanoscale due to its importance in multiple technologies such as thermal control and sensing applications. Heat conduction through the nanoconfined gas medium differs from macroscopic predictions due to several reasons. The continuum assumption is broken down; the surface forces which extend deeper through the gas medium become prominent due to the large surface-to-volume ratio, and, finally, the gas molecules are accumulated nonuniformly on the solid surfaces. In this work, to better understand the combination of these phenomena on the heat conduction through the nanoconfined gas medium, we present a series of molecular dynamics simulations of argon gas confined between either metals or silicon walls. The gas density is set so that gas experiences a wide range of Knudsen numbers from continuum to the free molecular regime. It is observed that the intrinsic characteristics of the solid determine the gas density distribution near the walls and consequently in the bulk region, and these distributions control the heat conduction through the gas medium. While the nanochannel walls have their most significant impact on the density and temperature distributions of the rarefied gas, the pressure and the heat flux across the gas domain converge toward a plateau as the gas becomes denser. We propose new analytical formulas for calculating the gas pressure, induced heat flux, and effective thermal conductivity through the strongly nanoconfined gas, which incorporates the wall force field impacts on the gas transport characteristics for the Knudsen number in the range of 0.05 to 20. continuum to rarefied gas conditions. read less NOT USED (high confidence) M. Wen, Y. Afshar, R. Elliott, and E. Tadmor, “KLIFF: A framework to develop physics-based and machine learning interatomic potentials,” Comput. Phys. Commun. 2021. link Times cited: 12 NOT USED (high confidence) M. Friedrich, M. Seitz, and U. Stefanelli, “Tilings with Nonflat Squares: A Characterization,” Milan Journal of Mathematics. 2021. link Times cited: 0 NOT USED (high confidence) T. Jarrin, A. Jay, N. Richard, and A. Hémeryck, “Coping with the stochasticity of collision cascades in Molecular Dynamics simulations,” Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms. 2021. link Times cited: 1 NOT USED (high confidence) F. Berthier, Q. Lullien, and B. Legrand, “Effective site energy and cluster expansion approaches for the study of phase diagrams,” Physical Review B. 2021. link Times cited: 0 Abstract: We apply the cluster expansion (CE) method to determine the … read moreAbstract: We apply the cluster expansion (CE) method to determine the effective cluster interactions (ECIs) from a simple energetic model that depends on both local and global composition. This model is defined by the site energies of random solid solutions of a one-dimensional alloy Co-Pt. We explore how these local and global dependencies are reflected on the cluster interactions. The energies of the structures are not well reproduced with concentration-independent interactions. Moreover, the interactions have a larger range than the energetic model which is limited to the nearest neighbors. By fitting the ECIs on the site energies, we suggest a mean-field-type weighting of the excess variables present in clusters of large size. We show that the site energy formalism controls the size of the clusters required for CE convergence and their concentration dependence. Finally, we take advantage of the site energy formalism to describe the elastic and chemical effects that control the thermodynamics of the alloy as a function of the ECIs. read less NOT USED (high confidence) D. Fijan and M. Wilson, “Thermodynamic anomalies in silicon and the relationship to the phase diagram,” Journal of Physics: Condensed Matter. 2021. link Times cited: 1 Abstract: The evolution of thermodynamic anomalies are investigated in… read moreAbstract: The evolution of thermodynamic anomalies are investigated in the pressure–temperature (pT) plane for silicon using the well-established Stillinger–Weber potential. Anomalies are observed in the density, compressibility and heat capacity. The relationships between them and with the liquid stability limit are investigated and related to the known thermodynamic constraints. The investigations are extended into the deeply supercooled regime using replica exchange techniques. Thermodynamic arguments are presented to justify the extension to low temperature, although a region of phase space is found to remain inaccessible due to unsuppressible crystallisation. The locus corresponding to the temperature of minimum compressibility is shown to display a characteristic ‘S’-shape in the pT projection which appears correlated with the underlying crystalline phase diagram. The progression of the anomalies is compared to the known underlying phase diagrams for both the crystal/liquid and amorphous/liquid states. The locations of the anomalies are also compared to those obtained from previous simulation work and (limited) experimental observations. read less NOT USED (high confidence) X. Zhang, H. Nguyen, J. T. Paci, S. Sankaranarayanan, J. L. Mendoza-Cortes, and H. Espinosa, “Multi-objective parametrization of interatomic potentials for large deformation pathways and fracture of two-dimensional materials,” npj Computational Materials. 2021. link Times cited: 11 NOT USED (high confidence) Z. Fan et al., “Neuroevolution machine learning potentials: Combining high accuracy and low cost in atomistic simulations and application to heat transport,” Physical Review B. 2021. link Times cited: 42 Abstract: We develop a neuroevolution-potential (NEP) framework for ge… read moreAbstract: We develop a neuroevolution-potential (NEP) framework for generating neural network based machine-learning potentials. They are trained using an evolutionary strategy for performing large-scale molecular dynamics (MD) simulations. A descriptor of the atomic environment is constructed based on Chebyshev and Legendre polynomials. The method is implemented in graphic processing units within the open-source GPUMD package, which can attain a computational speed over $10^7$ atom-step per second using one Nvidia Tesla V100. Furthermore, per-atom heat current is available in NEP, which paves the way for efficient and accurate MD simulations of heat transport in materials with strong phonon anharmonicity or spatial disorder, which usually cannot be accurately treated either with traditional empirical potentials or with perturbative methods. read less NOT USED (high confidence) D. Dockar, L. Gibelli, and M. Borg, “Shock-induced collapse of surface nanobubbles.,” Soft matter. 2021. link Times cited: 5 Abstract: The collapse of cavitation bubbles often releases high-speed… read moreAbstract: The collapse of cavitation bubbles often releases high-speed liquid jets capable of surface damage, with applications in drug delivery, cancer treatment, and surface cleaning. Spherical cap-shaped surface nanobubbles have previously been found to exist on immersed substrates. Despite being known nucleation sites for cavitation, their collapsing dynamics are currently unexplored. Here, we use molecular dynamics simulations to model the shock-induced collapse of different surface nanobubble sizes and contact angles. Comparisons are made with additional collapsing spherical nanobubble simulations near a substrate, to investigate the differences in their jet formation and resulting substrate pitting damage. Our main finding is that the pitting damage in the surface nanobubble simulations is greatly reduced, when compared to the spherical nanobubbles, which is primarily caused by the weaker jets formed during their collapse. Furthermore, the pit depths for surface nanobubble collapse do not depend on bubble size, unlike in the spherical nanobubble cases, but instead depend only on their contact angle. We also find a linear scaling relationship for all bubble cases between the final substrate damage and the peak pressure impulse at the impact centre, which can now be exploited to assess the relative damage in other computational studies of collapsing bubbles. We anticipate the more controlled surface-damage features produced by surface nanobubble cavitation jets will open up new applications in advanced manufacturing, medicine, and precision cleaning. read less NOT USED (high confidence) F. Giessibl, “Probing the Nature of Chemical Bonds by Atomic Force Microscopy,” Molecules. 2021. link Times cited: 6 Abstract: The nature of the chemical bond is important in all natural … read moreAbstract: The nature of the chemical bond is important in all natural sciences, ranging from biology to chemistry, physics and materials science. The atomic force microscope (AFM) allows to put a single chemical bond on the test bench, probing its strength and angular dependence. We review experimental AFM data, covering precise studies of van-der-Waals-, covalent-, ionic-, metallic- and hydrogen bonds as well as bonds between artificial and natural atoms. Further, we discuss some of the density functional theory calculations that are related to the experimental studies of the chemical bonds. A description of frequency modulation AFM, the most precise AFM method, discusses some of the experimental challenges in measuring bonding forces. In frequency modulation AFM, forces between the tip of an oscillating cantilever change its frequency. Initially, cantilevers were made mainly from silicon. Most of the high precision measurements of bonding strengths by AFM became possible with a technology transfer from the quartz watch technology to AFM by using quartz-based cantilevers (“qPlus force sensors”), briefly described here. read less NOT USED (high confidence) J. Thomas, H. Chen, and C. Ortner, “Rigorous body-order approximations of an electronic structure potential energy landscape.” 2021. link Times cited: 4 NOT USED (high confidence) S. Zhang et al., “Defect agglomeration induces a reduction in radiation damage resistance of In-rich In x Ga1−x N,” Journal of Physics D: Applied Physics. 2021. link Times cited: 4 Abstract: To investigate the reason for the reduction in damage resist… read moreAbstract: To investigate the reason for the reduction in damage resistance of In x Ga1−x N with increasing indium (In) content, we used molecular dynamics methods to simulate the threshold displacement energies, the individual recoil damage and the overlapping cascade processes in In x Ga1−x N (x = 0.3, 0.5, 0.7) during ion implantation. The average threshold displacement energy of In x Ga1−x N decreases a little (from 41.0 eV to 34.6 eV) as the In content increases (from 0.3 to 0.7) and the number of defects produced by individual cascades increases less than 30% with increasing In content (from 0.3 to 0.7), while the overlapping cascade simulations showed that with In content increasing the dynamic annealing processes in cascades were significantly suppressed. Thus, the suppression of dynamic annealing in the cascades is the main reason for the reduction of damage resistance of In x Ga1−x N by adding In content. The analysis of defect distribution during overlapping cascades showed that defects in In-rich In x Ga1−x N (x = 0.7) agglomerate more rapidly as the irradiation dose increases and are likely to form large clusters, which are harder to anneal during cascade evolution. Therefore, the suppression of dynamic annealing in In-rich In x Ga1−x N can be attributed to the rapid agglomeration of defects with the irradiation dose. read less NOT USED (high confidence) Y. Zhou, “Assessing the quantum effect in classical thermal conductivity of amorphous silicon,” Journal of Applied Physics. 2021. link Times cited: 18 Abstract: While it is well known that the vibrational modes are fully … read moreAbstract: While it is well known that the vibrational modes are fully occupied and the quantum effect can be ignored only if the temperature is high enough, e.g., well above the Debye temperature of the systems, all vibrational modes are assumed to be fully occupied at any temperatures in classical molecular dynamics. Therefore, the thermal conductivity of crystals predicted by classical molecular dynamics at low temperatures, e.g., much lower than the corresponding Debye temperature, is unphysical. Even by applying the quantum corrections on the classical thermal conductivity of crystals, the results are still unreasonable since both the occupation and intrinsic scattering process of the vibrations are determined by the temperatures. However, the scattering picture in amorphous silicon is quite different from that in its corresponding crystal counterpart. How the quantum effect will affect the thermal transport in amorphous silicon is still unclear. Here, by systematically investigating thermal transport of amorphous silicon using equilibrium molecular dynamics, the structure factor method and the Allen–Feldman theory, we directly observe that all the vibrational modes are fully occupied at any temperatures and the quantum effect on the scattering process can be ignored. By assuming all the vibrational modes are fully occupied, the thermal conductivity calculated using the structure factor method and the Allen–Feldman theory agrees quite well with the results computed using Green–Kubo equilibrium molecular dynamics. By correcting the excitation state of the vibrations in amorphous silicon, the thermal conductivity calculated by the structure factor method and the Allen–Feldman theory can fully capture the experimentally measured temperature dependence. Our study proves that the quantum effect on the scattering process caused by the distribution functions for the amorphous materials in molecular dynamics simulations, i.e., Boltzmann distributions in molecular dynamics simulations vs Bose–Einstein distributions for the bosons, can be ignored, while the quantum effect on the excitation states of the vibrations are important and must be considered. read less NOT USED (high confidence) F. Dai, D. Zhao, and L. Zhang, “Atomic Simulations of Packing Structures, Local Stress and Mechanical Properties for One Silicon Lattice with Single Vacancy on Heating,” Materials. 2021. link Times cited: 2 Abstract: The effect of vacancy defects on the structure and mechanica… read moreAbstract: The effect of vacancy defects on the structure and mechanical properties of semiconductor silicon materials is of great significance to the development of novel microelectronic materials and the processes of semiconductor sensors. In this paper, molecular dynamics is used to simulate the atomic packing structure, local stress evolution and mechanical properties of a perfect lattice and silicon crystal with a single vacancy defect on heating. In addition, their influences on the change in Young’s modulus are also analyzed. The atomic simulations show that in the lower temperature range, the existence of vacancy defects reduces the Young’s modulus of the silicon lattice. With the increase in temperature, the local stress distribution of the atoms in the lattice changes due to the migration of the vacancy. At high temperatures, the Young’s modulus of the silicon lattice changes in anisotropic patterns. For the lattice with the vacancy, when the temperature is higher than 1500 K, the number and degree of distortion in the lattice increase significantly, the obvious single vacancy and its adjacent atoms contracting inward structure disappears and the defects in the lattice present complex patterns. By applying uniaxial tensile force, it can be found that the temperature has a significant effect on the elasticity–plasticity behaviors of the Si lattice with the vacancy. read less NOT USED (high confidence) C. W. Park, M. Kornbluth, J. Vandermause, C. Wolverton, B. Kozinsky, and J. Mailoa, “Accurate and scalable graph neural network force field and molecular dynamics with direct force architecture,” npj Computational Materials. 2021. link Times cited: 80 NOT USED (high confidence) M. Zhao, R. Dang, L. Jin, and W. Yu, “Structures and energies of Σ3 asymmetric tilt grain boundaries in silicon,” Journal of Materials Research. 2021. link Times cited: 2 Abstract: We optimize 23 silicon Σ3 asymmetric tilt grain boundaries (… read moreAbstract: We optimize 23 silicon Σ3 asymmetric tilt grain boundaries (ATGBs) using Stillinger Weber (SW), Tersoff and the optimized Modified Embedded Atom Method (MEAM) potentials. It is demonstrated that conventional GB optimization via rigid body translations in combination with atom deletions is totally incapable of driving an as-constructed flat Si grain boundary (GB) to its equilibrated state since it may inevitably cause lattice distortions in GB. But it can be easily achieved by initially introducing some pre-designed steps into as-constructed flat GB model. These steps are composed of coherent twin boundary (CTB) and symmetric incoherent twin boundary (SITB) facets. By doing so, energies of all 23 ATGBs are greatly reduced. Meanwhile, some ATGBs may have degenerate states with different structures but same energies. This work not only facilitates the structural characterization of Si Σ3 ATGBs, but may provide new insights into microstructure design in polycrystalline silicon. read less NOT USED (high confidence) C. Liu et al., “Molecular Dynamics Simulation on Cutting Mechanism in the Hybrid Machining Process of Single-Crystal Silicon,” Nanoscale Research Letters. 2021. link Times cited: 14 NOT USED (high confidence) T. Brink, E. Milanese, and J. Molinari, “Effect of wear particles and roughness on nanoscale friction,” Physical Review Materials. 2021. link Times cited: 9 Abstract: Frictional contacts lead to the formation of a surface layer… read moreAbstract: Frictional contacts lead to the formation of a surface layer called the third body, consisting of wear particles and structures resulting from their agglomerates. Its behavior and properties at the nanoscale control the macroscopic tribological performance. It is known that wear particles and surface topography evolve with time and mutually influence one another. However, the formation of the mature third body is largely uncharted territory and the properties of its early stages are unknown. Here we show how a third body initially consisting of particles acting as roller bearings transitions into a shear-band-like state by forming adhesive bridges between the particles. Using large-scale atomistic simulations on a brittle model material, we find that this transition is controlled by the growth and increasing disorganization of the particles with increasing sliding distance. Sliding resistance and wear rate are at first controlled by the surface roughness, but upon agglomeration wear stagnates and friction becomes solely dependent on the real contact area in accordance with the plasticity theory of contact by Bowden and Tabor. read less NOT USED (high confidence) P. Sun, J. Hastings, D. Ishikawa, A. Baron, and G. Monaco, “Universal Two-Component Dynamics in Supercritical Fluids,” The Journal of Physical Chemistry. B. 2021. link Times cited: 0 Abstract: Despite the technological importance of supercritical fluids… read moreAbstract: Despite the technological importance of supercritical fluids, controversy remains about the details of their microscopic dynamics. In this work, we study four supercritical fluid systems—water, Si, Te, and Lennard-Jones fluid—via classical molecular dynamics simulations. A universal two-component behavior is observed in the intermolecular dynamics of these systems, and the changing ratio between the two components leads to a crossover from liquidlike to gaslike dynamics, most rapidly around the Widom line. We find evidence to connect the liquidlike component dominating at lower temperatures with intermolecular bonding and the component prominent at higher temperatures with free-particle, gaslike dynamics. The ratio between the components can be used to describe important properties of the fluid, such as its self-diffusion coefficient, in the transition region. Our results provide an insight into the fundamental mechanism controlling the dynamics of supercritical fluids and highlight the role of spatiotemporally inhomogeneous dynamics even in thermodynamic states where no large-scale fluctuations exist in the fluid. read less NOT USED (high confidence) S. Yoo, B. Lee, and K. Kang, “Density functional theory study of the mechanical behavior of silicene and development of a Tersoff interatomic potential model tailored for elastic behavior,” Nanotechnology. 2021. link Times cited: 8 Abstract: Silicene, a graphene-like 2D material made from Si atoms, ha… read moreAbstract: Silicene, a graphene-like 2D material made from Si atoms, has been fabricated and studied for its promising applications in micro/nanoelectronics. For the reliable function of silicene devices, it is important to investigate silicene’s mechanical properties. In this study, the authors conducted density functional theory (DFT) simulations of mechanical tests of silicene and investigated the elastic modulus and mechanical response such as structural transformation. In addition, the authors optimized the Tersoff potential parameters using a gradient-based minimization with a grid search method in hyperdimensional parameter space, to match the DFT calculation results in the elastic regime. With the new parameter set, the elastic moduli of silicene in the zigzag (ZZ) and armchair (AC) directions were computed with molecular statics (MS) simulations and compared with those of other Si interatomic potential models and DFT results. In addition, uniaxial tensile tests along the ZZ and AC directions were performed to examine how far the Tersoff model is transferable with our new parameter set to describe the nonlinear mechanical behavior of silicene. The results of uniaxial tensile tests suggest that the angle penalty function in the Tersoff model needs to be modified and that the stress–strain curve predicted with this modification shows improvement compared to the original function. read less NOT USED (high confidence) J. Weinreich, M. Paleico, and J. Behler, “Properties of α-Brass Nanoparticles II: Structure and Composition,” The Journal of Physical Chemistry C. 2021. link Times cited: 4 Abstract: Nanoparticles have become increasingly interesting for a wid… read moreAbstract: Nanoparticles have become increasingly interesting for a wide range of applications, because in principle it is possible to tailor their properties by controlling size, shape and composition. One of these applications is heterogeneous catalysis, and a fundamental understanding of the structural details of the nanoparticles is essential for any knowledge-based improvement of reactivity and selectivity. In this work we investigate the atomic structure of brass nanoparticles containing up to 5000 atoms as a typical example for a binary alloy consisting of Cu and Zn. As systems of this size are too large for electronic structure calculations, in our simulations we use a recently parametrized machine learning potential providing close to density functional theory accuracy. This potential is employed for a structural characterization as a function of chemical composition by various types of simulations like Monte Carlo in the Semi-Grand Canonical Ensemble and simulated annealing molecular dynamics. Our analysis reveals that the distribution of both elements in the nanoparticles is inhomogeneous, and zinc accumulates in the outermost layer, while the first subsurface layer shows an enrichment of copper. Only for high zinc concentrations alloying can be found in the interior of the nanoparticles, and regular patterns corresponding to crystalline bulk phases of $\alpha$-brass can then be observed. The surfaces of the investigated clusters exhibit well-ordered single-crystal facets, which can give rise to grain boundaries inside the clusters. The melting temperature of the nanoparticles is found to decrease with increasing zinc-atom fraction, a trend which is well-known also for the bulk phase diagram of brass. read less NOT USED (high confidence) S. Cajahuaringa and A. Antonelli, “Non-equilibrium free-energy calculation of phase-boundaries using LAMMPS,” Computational Materials Science. 2021. link Times cited: 2 NOT USED (high confidence) Y. Yang, T. Luo, and Y. Xiang, “Convergence from Atomistic Model to Peierls-Nabarro Model for Dislocations in Bilayer System with Complex Lattice,” ArXiv. 2021. link Times cited: 0 Abstract: In this paper, we prove the convergence from the atomistic m… read moreAbstract: In this paper, we prove the convergence from the atomistic model to the Peierls–Nabarro (PN) model of two-dimensional bilayer system with complex lattice. We show that the displacement field of the dislocation solution of the PN model converges to the dislocation solution of the atomistic model with secondorder accuracy. The consistency of PN model and the stability of atomistic model are essential in our proof. The main idea of our approach is to use several low-degree polynomials to approximate the energy due to atomistic interactions of different groups of atoms of the complex lattice. Mathematics Subject Classification: 35Q70, 35Q74, 74A50, 74G10. read less NOT USED (high confidence) H.-S. Jin, P. Song, C.-G. Jon, and J.-C. Kim, “Thermodynamic properties of fcc metals using reparameterized MEAM potentials,” Indian Journal of Physics. 2021. link Times cited: 4 NOT USED (high confidence) S. Naik, M. H. Naik, I. Maity, and M. Jain, “Twister: Construction and structural relaxation of commensurate moiré superlattices,” Comput. Phys. Commun. 2021. link Times cited: 15 NOT USED (high confidence) J. Keith et al., “Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems,” Chemical Reviews. 2021. link Times cited: 224 Abstract: Machine learning models are poised to make a transformative … read moreAbstract: Machine learning models are poised to make a transformative impact on chemical sciences by dramatically accelerating computational algorithms and amplifying insights available from computational chemistry methods. However, achieving this requires a confluence and coaction of expertise in computer science and physical sciences. This Review is written for new and experienced researchers working at the intersection of both fields. We first provide concise tutorials of computational chemistry and machine learning methods, showing how insights involving both can be achieved. We follow with a critical review of noteworthy applications that demonstrate how computational chemistry and machine learning can be used together to provide insightful (and useful) predictions in molecular and materials modeling, retrosyntheses, catalysis, and drug design. read less NOT USED (high confidence) Y. Mishin, “Machine-Learning Interatomic Potentials for Materials Science,” Electrical Engineering eJournal. 2021. link Times cited: 103 NOT USED (high confidence) M. Haro et al., “Nano-vault architecture mitigates stress in silicon-based anodes for lithium-ion batteries,” Communications Materials. 2021. link Times cited: 8 NOT USED (high confidence) S. C. Costa-Prado and J. Rino, “An interaction potential for zinc selenide: A molecular dynamics study,” Journal of Applied Physics. 2021. link Times cited: 2 Abstract: The structural, thermodynamic, and dynamical properties of z… read moreAbstract: The structural, thermodynamic, and dynamical properties of zinc selenide, as well as the structural phase transformation induced by pressure, based on a many-body interatomic potential that considers two- and three-body interactions, were studied using molecular dynamics simulations. The potential was able to describe the energetics of the zinc-blende, wurtzite, and rock-salt structures of ZnSe. The effective interatomic potential was parameterized using experimental values of the bulk modulus and cohesive energy at an experimental density. Other properties, not used in the parameterization of the potential, such as the vibrational density of states, were correctly described. Cooling from the liquid, an amorphous phase or a re-crystallized material could be obtained. Pair distribution function, coordination number, volume change, and bond angle distributions are presented and compared with available experimental data. The structural phase transition from zinc-blend to rock-salt induced by hydrostatic pressure was obtained at ∼21 GPa for monocrystals and ∼16 GPa for polycrystals. read less NOT USED (high confidence) O. Koroleva, M. Demin, A. Mazhukin, and V. Mazhukin, “Modeling of electronic and phonon thermal conductivity of silicon in a wide temperature range,” Journal of Physics: Conference Series. 2021. link Times cited: 7 Abstract: In the present article, using the methods of mathematical mo… read moreAbstract: In the present article, using the methods of mathematical modeling, the thermal conductivity of silicon was obtained in a wide temperature range (0.3 ≼ T ≼ 3 kK), including the region of semiconductor-metal phase transformations. As it is known, there are two mechanisms of heat transfer in a solid: elastic lattice vibrations and free electrons, therefore, in the study of the thermal conductivity of silicon, the lattice and electronic components were taken into account. The lattice (phonon) thermal conductivity in this work was determined within the framework of the atomistic approach. The Stillinger–Weber and Kumagai–Izumi–Hara–Sakai interaction potentials were used for modeling. The results of the comparison of the phonon thermal conductivity obtained from the simulation results with the used interaction potentials are presented. The modeling of the thermal conductivity of the electronic subsystem of silicon with intrinsic conductivity in this work is based on the use of the quantum statistics of the electron gas using the Fermi–Dirac integrals. The total thermal conductivity of silicon, obtained as the sum of the electronic and phonon components, is compared with the experimental data. read less NOT USED (high confidence) W. Nöhring, J.-C. Griesser, P. Dondl, and L. Pastewka, “Surface lattice Green’s functions for high-entropy alloys,” Modelling and Simulation in Materials Science and Engineering. 2021. link Times cited: 0 Abstract: We study the surface elastic response of pure Ni, the random… read moreAbstract: We study the surface elastic response of pure Ni, the random alloy FeNiCr and an average FeNiCr alloy in terms of the surface lattice Green’s function. We propose a scheme for computing per-site Green’s function and study their per-site variations. The average FeNiCr alloys accurately reproduces the mean Green’s function of the full random alloy. Variation around this mean is largest near the edge of the surface Brillouin-zone and decays as q −2 with wavevector q towards the Γ-point. We also present expressions for the continuum surface Green’s function of anisotropic solids of finite and infinite thickness and show that the atomistic Green’s function approaches continuum near the Γ-point. Our results are a first step towards efficient contact calculations and Peierls–Nabarro type models for dislocations in high-entropy alloys. read less NOT USED (high confidence) C. Zhang et al., “Crystallization of the P3Sn4 Phase upon Cooling P2Sn5 Liquid by Molecular Dynamics Simulation Using a Machine Learning Interatomic Potential,” Journal of Physical Chemistry C. 2021. link Times cited: 3 Abstract: We performed molecular dynamics simulations to study the cry… read moreAbstract: We performed molecular dynamics simulations to study the crystallization of the P3Sn4 phase from P2Sn5 liquid using a machine learning (ML) interatomic potential with desirable efficiency and accur... read less NOT USED (high confidence) V. Dufour-Décieux, R. Freitas, and E. Reed, “Atomic-Level Features for Kinetic Monte Carlo Models of Complex Chemistry from Molecular Dynamics Simulations.,” The journal of physical chemistry. A. 2021. link Times cited: 3 Abstract: The high computational cost of evaluating atomic interaction… read moreAbstract: The high computational cost of evaluating atomic interactions recently motivated the development of computationally inexpensive kinetic models, which can be parameterized from molecular dynamics (MD) simulations of the complex chemistry of thousands of species or other processes and accelerate the prediction of the chemical evolution by up to four orders of magnitude. Such models go beyond the commonly employed potential energy surface fitting methods in that they are aimed purely at describing kinetic effects. So far, such kinetic models utilize molecular descriptions of reactions and have been constrained to only reproduce molecules previously observed in MD simulations. Therefore, these descriptions fail to predict the reactivity of unobserved molecules, for example, in the case of large molecules or solids. Here, we propose a new approach for the extraction of reaction mechanisms and reaction rates from MD simulations, namely, the use of atomic-level features. Using the complex chemical network of hydrocarbon pyrolysis as an example, it is demonstrated that kinetic models built using atomic features are able to explore chemical reaction pathways never observed in the MD simulations used to parameterize them, a critical feature to describe rare events. Atomic-level features are shown to construct reaction mechanisms and estimate reaction rates of unknown molecular species from elementary atomic events. Through comparisons of the model ability to extrapolate to longer simulation time scales and different chemical compositions than the ones used for parameterization, it is demonstrated that kinetic models employing atomic features retain the same level of accuracy and transferability as the use of features based on molecular species, while being more compact and parameterized with less data. We also find that atomic features can better describe the formation of large molecules enabling the simultaneous description of small molecules and condensed phases. read less NOT USED (high confidence) R. Kobayashi, “nap: A molecular dynamics package with parameter-optimization programs for classical and machine-learning potentials,” J. Open Source Softw. 2021. link Times cited: 8 Abstract: The nap is a package for molecular dynamics (MD) simulation … read moreAbstract: The nap is a package for molecular dynamics (MD) simulation consisting of an MD program ( pmd ) that can perform large-scale simulation using a spatial-decomposition technique and two parameter-optimization programs: one for classical (CL) potentials ( fp.py ) and another for machine-learning (ML) potentials ( fitpot ). Since the numbers of parameters to be optimized are much different between CL and ML potentials, optimization approaches for them are also different; meta-heuristic global minimum-search algorithms for the CL potentials, in which the numbers of parameters are usually much less than one hundred, and gradient-based methods for the ML potentials. The parameters of CL potentials can be optimized to any target quantity that can be computed using the potentials since meta-heuristic methods do not require the derivatives of the quantity with respect to parameters. On the other hand, ML-potential parameters can be optimized to only energies, forces on atoms and stress components of reference systems, mainly because gradient-based methods require the derivatives of other quantities with respect to parameters, and the analytical derivatives and the coding of them are usually painful and sometimes impossible. Potentials can be used in combination with any other potential, such as pair and angular potentials, short-range and long-range potentials, CL and ML potentials. With using the nap package, users can perform MD simulation of solid-state materials with the choice of different levels of complexity (CL or ML) by creating interatomic potentials optimized to quantum-mechanical calculation data even if no potential is available. read less NOT USED (high confidence) M. Schiebl and I. Romero, “Energy-momentum conserving integration schemes for molecular dynamics,” Computational Mechanics. 2021. link Times cited: 0 NOT USED (high confidence) Y.-S. Lin, G. P. P. Pun, and Y. Mishin, “Development of a physically-informed neural network interatomic potential for tantalum,” Computational Materials Science. 2021. link Times cited: 9 NOT USED (high confidence) D. Richard, G. Kapteijns, J. A. Giannini, M. L. Manning, and E. Lerner, “Simple and Broadly Applicable Definition of Shear Transformation Zones.,” Physical review letters. 2021. link Times cited: 4 Abstract: Plastic deformation in amorphous solids is known to be carri… read moreAbstract: Plastic deformation in amorphous solids is known to be carried by stress-induced localized rearrangements of a few tens of particles, accompanied by the conversion of elastic energy to heat. Despite their central role in determining how glasses yield and break, the search for a simple and generally applicable definition of the precursors of those plastic rearrangements-the so-called shear transformation zones (STZs)-is still ongoing. Here we present a simple definition of STZs-based solely on the harmonic approximation of a glass's energy. We explain why and demonstrate directly that our proposed definition of plasticity carriers in amorphous solids is more broadly applicable compared to anharmonic definitions put forward previously. Finally, we offer an open-source library that analyzes low-lying STZs in computer glasses and in laboratory materials such as dense colloidal suspensions for which the harmonic approximation is accessible. Our results constitute a physically motivated methodological advancement towards characterizing mechanical disorder in glasses, and understanding how they yield. read less NOT USED (high confidence) T. Hao, Z. Zhang, T. Ahmed, J. Xu, S. Brown, and Z. Hossain, “Line-defect orientation- and length-dependent strength and toughness inhBN,” Journal of Applied Physics. 2021. link Times cited: 1 Abstract: Applying classical molecular dynamics simulations, we report… read moreAbstract: Applying classical molecular dynamics simulations, we report the effects of length ( λ) and orientation ( θ) of a line-defect on strength and toughness in defective 2D hexagonal boron nitride. Results reveal the existence of a “transition angle,” θ t = 2.47 °, at which both toughness and strength are insensitive to the finite length of the defect in an infinite domain. For θ θ t, they show the opposite behavior. Examination of the stress-fields shows that θ-dependent variation in stress-localization at the edges of the line-defect and symmetry-breaking of the stress-fields with respect to the defect-axis govern the disparate θ-dependent behavior. For θ θ t, the stress-intensity at the edges is strongly localized at the opposite sides of the line-defect. The stress-intensity increases asymptotically with the increasing defect-length and reduces the strength and toughness of the defective lattice. The stress-localization, however, saturates at a “saturation angle” of around 60 ° for strength and 30 ° for toughness. Additionally, there exists a critical defect-length λ c = 60 A, below which there is a strong θ-dependent variation in elastic interactions between the edges, affecting strength and toughness substantially. For λ > λ c, the elastic interactions saturate and make both strength and toughness insensitive to the change in the length of the defect. read less NOT USED (high confidence) C. Polanco, “Nonequilibrium Green’s functions (NEGF) in vibrational energy transport: a topical review,” Nanoscale and Microscale Thermophysical Engineering. 2021. link Times cited: 9 Abstract: ABSTRACT Recent advances in fabrication techniques have enab… read moreAbstract: ABSTRACT Recent advances in fabrication techniques have enabled the development of materials sculpted at the nanoscale (~10 nm). These “nano-materials” could revolutionize thermal management technologies by providing novel ways to manipulate energy propagation in solids. Atomistic simulations are critical to forging this revolution, given their ability to describe a system’s dynamics on an atom by atom basis. This topical review focuses on nonequilibrium Green’s functions (NEGF) simulations to model vibrational energy propagation at the nanoscale. NEGF is an atomistic and purely quantum mechanical approach well-suited to compute thermal transport in spatially varying systems such as “nano-materials.” This review presents the NEGF methodology from a top-to-bottom perspective, focusing on the concepts behind the mathematical expressions. We start describing the implementation of NEGF that assumes harmonic interatomic potentials (h-NEGF) and some recent advances that distinguish the transport contributions by different polarizations. This review also discusses the less common implementation of NEGF that includes the anharmonic terms of the potentials (a-NEGF), outlining existing approximations and standing challenges. Our success in tackling these challenges will determine whether we will harness the full potential of NEGF to describe thermal transport from a quantum mechanical standpoint. read less NOT USED (high confidence) S. Ringdahl, S. Xiao, J. He, and Z. Zhang, “Machine Learning Based Prediction of Nanoscale Ice Adhesion on Rough Surfaces,” Coatings. 2020. link Times cited: 7 Abstract: It is widely recognized that surface roughness plays an impo… read moreAbstract: It is widely recognized that surface roughness plays an important role in ice adhesion strength, although the correlation between the two is far from understood. In this paper, two approaches, molecular dynamics (MD) simulations and machine learning (ML), were utilized to study the nanoscale intrinsic ice adhesion strength on rough surfaces. A systematic algorithm for making random rough surfaces was developed and the surfaces were tested for their ice adhesion strength, with varying interatomic potentials. Using MD simulations, the intrinsic ice adhesion strength was found to be significantly lower on rougher surfaces, which was attributed to the lubricating effect of a thin quasi-liquid layer. An increase in the substrate–ice interatomic potential increased the thickness of the quasi-liquid layer on rough surfaces. Two different ML algorithms, regression and classification, were trained using the results from the MD simulations, with support vector machines (SVM) emerging as the best for classifying. The ML approach showed an encouraging prediction accuracy, and for the first time shed light on using ML for anti-icing surface design. The findings provide a better understanding of the role of nanoscale roughness in intrinsic ice adhesion and suggest that ML can be a powerful tool in finding materials with a low ice adhesion strength. read less NOT USED (high confidence) P. Hao, D. Zhao, Y. Luan, J. Liu, and Q. Wang, “Critical role of the bending stiffness of the monolayer black phosphorus in its mechanical behaviors: molecular dynamics simulation,” Nanotechnology. 2020. link Times cited: 0 Abstract: Black phosphorus (BP) is a novel two-dimensional nanostructu… read moreAbstract: Black phosphorus (BP) is a novel two-dimensional nanostructure with wide potential applications in such areas as nanoresonators and nanosensors. In this study, we concentrate on the role of the bending stiffness of the BP monolayer in its mechanical performances, including tension, compression, buckling and bending. Firstly, the stress–strain curve and Young’s modulus of the single layer black phosphorus (SLBP) nanoribbon with different chiral structures are obtained in the tension process via the molecular dynamics (MD) simulation. Next, the loading behavior of the SLBP nanoribbon during compression is simulated via MD. It was found that the bending stiffness of the nanoribbon has an essential effect on its postbuckling behaviors, and an empirical formula is proposed which can accurately depict the postbuckling process. Eventually, the bending properties of chiral SLBP nanoribbons are explored via the MD simulation, and the modified expression of the bending stiffness can better predict its large deflection. These findings are beneficial for us to fully understand mechanical responses of BP, which hold implications in engineering new materials and devices at nanoscale. read less NOT USED (high confidence) M. Maździarz, “Transferability of Molecular Potentials for 2D Molybdenum Disulphide,” Materials. 2020. link Times cited: 4 Abstract: An ability of different molecular potentials to reproduce th… read moreAbstract: An ability of different molecular potentials to reproduce the properties of 2D molybdenum disulphide polymorphs is examined. Structural and mechanical properties, as well as phonon dispersion of the 1H, 1T and 1T’ single-layer MoS2 (SL MoS2) phases, were obtained using density functional theory (DFT) and molecular statics calculations (MS) with Stillinger-Weber, REBO, SNAP and ReaxFF interatomic potentials. Quantitative systematic comparison and discussion of the results obtained are reported. read less NOT USED (high confidence) Y. Ouyang, Z. Zhang, C. Yu, J. He, G. Yan, and J. C. hyperlinks, “Accuracy of Machine Learning Potential for Predictions of Multiple-Target Physical Properties,” Chinese Physics Letters. 2020. link Times cited: 9 NOT USED (high confidence) D. Unruh, C. M. Hansen, R. V. Meidanshahi, S. Goodnick, and G. Zimányi, “From Femtoseconds to Gigaseconds: Performance Degradation in Silicon Heterojunction Solar Cells,” 2021 IEEE 48th Photovoltaic Specialists Conference (PVSC). 2020. link Times cited: 2 Abstract: a-Si/c-Si heterojunction solar cells hold the efficiency wor… read moreAbstract: a-Si/c-Si heterojunction solar cells hold the efficiency world record around 27%, yet their market penetration is delayed. One concern is the presence of an amorphous Si layer that some suspect may speed up the degradation of their performance. To address this concern, we developed the SolDeg structural simulation platform that is capable of capturing extremely slow degradation processes in a-Si. SolDeg integrates molecular dynamics methods that optimize the Si structure with femtosecond time steps, with the nudged elastic band method that captures the defect generation on time scales extending to gigaseconds. In this paper we report SolDeg simulations for Si-only heterojunctions. The SolDeg platform enabled us to determine the defect generation rate to be in the 15-20%/year range, translating into a 1-1.5%/year Voc degradation rate. These results establish that SolDeg can be a uniquely useful platform to describe degradation processes with an eye on finding strategies to mitigate the performance degradation of these promising heterojunction cells. read less NOT USED (high confidence) S. Schoenholz and E. D. Cubuk, “JAX, M.D. A framework for differentiable physics,” Journal of Statistical Mechanics: Theory and Experiment. 2020. link Times cited: 96 Abstract: We introduce JAX MD, a software package for performing diffe… read moreAbstract: We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of physics simulation environments, as well as interaction potentials and neural networks that can be integrated into these environments without writing any additional code. Since the simulations themselves are differentiable functions, entire trajectories can be differentiated to perform meta-optimization. These features are built on primitive operations, such as spatial partitioning, that allow simulations to scale to hundreds-of-thousands of particles on a single GPU. These primitives are flexible enough that they can be used to scale up workloads outside of molecular dynamics. We present several examples that highlight the features of JAX MD including: integration of graph neural networks into traditional simulations, meta-optimization through minimization of particle packings, and a multi-agent flocking simulation. JAX MD is available at https://www.github.com/google/jax-md. read less NOT USED (high confidence) T. Jarrin, A. Jay, A. Hémeryck, and N. Richard, “Parametric study of the Two-Temperature Model for Molecular Dynamics simulations of collisions cascades in Si and Ge,” Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms. 2020. link Times cited: 6 NOT USED (high confidence) A. Javili, A. McBride, and P. Steinmann, “A geometrically exact formulation of peridynamics,” Theoretical and Applied Fracture Mechanics. 2020. link Times cited: 14 NOT USED (high confidence) G. Ripani, A. Flachmüller, C. Peter, and A. Palleschi, “Coarse-Grained Simulation of the Adsorption of Water on Au(111) Surfaces Using a Modified Stillinger–Weber Potential,” ACS Omega. 2020. link Times cited: 2 Abstract: For reproducing the behavior of water molecules adsorbed on … read moreAbstract: For reproducing the behavior of water molecules adsorbed on gold surfaces in terms of density of both bulk and interfacial water and in terms of structuring of water on top of gold atoms, the implementation of a multibody potential is necessary, thus the Stillinger–Weber potential was tested. The goal is using a single nonbonded potential for coarse-grained models, without the usage of explicit charges. In order to modify the angular part of the Stillinger–Weber potential from a single cosine to a piecewise function accounting for multiple equilibrium angles, employed for Au–Au–Au and Au–Au–water triplets, it is necessary to create a version of the simulation package LAMMPS that supports the assignment of multiple favored angles. This novel approach is able to reproduce the data obtained using quantum mechanical calculations and density profiles of both bulk and adsorbed water molecules obtained using classical polarizable force fields. read less NOT USED (high confidence) P. Cao, J. Sheng, J. Wu, and F. Ning, “Mechanical creep instability of nanocrystalline methane hydrates.,” Physical chemistry chemical physics : PCCP. 2020. link Times cited: 4 Abstract: Mechanical creep behaviors of natural gas hydrates are of im… read moreAbstract: Mechanical creep behaviors of natural gas hydrates are of importance for understanding the mechanical instability of gas hydrate-bearing sediments on Earth. Limited by the experimental challenges, intrinsic creep mechanisms of nanocrystalline methane hydrates remain largely unknown yet at the molecular scale. Herein, using large-scale molecular dynamics simulations, mechanical creep behaviors of nanocrystalline methane hydrates are investigated. It is revealed that mechanical creep responses are greatly dictated by internal microstructures of crystalline grain size and external conditions of temperature and static stress. Interestingly, a long steady-state creep is observed in nanocrystalline methane hydrates, which can be described by a modified constitutive Bird-Dorn-Mukherjee model. Microstructural analysis shows that deformations of crystalline grains, grain boundary diffusion and grain boundary sliding collectively govern the mechanical creep behaviors of nanocrystalline methane hydrates. Furthermore, structural transformation also appears to be important in their mechanical creep behaviors. This study provides new insights into understanding the mechanical creep scenarios of gas hydrates. read less NOT USED (high confidence) L. de Sousa Oliveira, S. A. Hosseini, A. Greaney, and N. Neophytou, “Heat current anticorrelation effects leading to thermal conductivity reduction in nanoporous Si,” Physical Review B. 2020. link Times cited: 9 Abstract: Prevailing nanostructuring strategies focus on increasing ph… read moreAbstract: Prevailing nanostructuring strategies focus on increasing phonon scattering and reducing the mean-free-path of phonons across the spectrum. In nanoporous Si materials, for example, boundary scattering reduces thermal conductivity drastically. In this work, we identify an unusual anticorrelated specular phonon scattering effect which can result in additional reductions in thermal conductivity of up to ~ 80% for specific nanoporous geometries. We further find evidence that this effect has its origin in heat trapping between large pores with narrow necks. As the heat becomes trapped between the pores, phonons undergo multiple specular reflections such that their contribution to the thermal conductivity is partly undone. We find this effect to be wave-vector dependent at low temperatures. We use large-scale molecular dynamics simulations, wave packet analysis, as well as an analytical model to illustrate the anticorrelation effect, evaluate its impact on thermal conductivity, and detail how it can be controlled to manipulate phonon transport in nanoporous materials. read less NOT USED (high confidence) M. Michlíček, S. Hamaguchi, and L. Zajíčková, “Molecular dynamics simulation of amine groups formation during plasma processing of polystyrene surfaces,” Plasma Sources Science and Technology. 2020. link Times cited: 9 Abstract: Plasma treatment and plasma polymerization processes aiming … read moreAbstract: Plasma treatment and plasma polymerization processes aiming to form amine groups on polystyrene surfaces were studied in-silico with molecular dynamics simulations. The simulations were compared with two experiments, (i) plasma treatment in N2/H2 bipolar pulsed discharge and (ii) plasma polymerization in cyclopropylamine/Ar radio frequency (RF) capacitively coupled discharge. To model favorable conditions for the incorporation of primary amine groups, we assumed the plasma treatment as the flux of NH2 radicals and energetic NH3 ions, and the plasma polymerization as the flux of cyclopropylamine molecules and energetic argon ions. It is shown in both the simulation and the experiment that the polystyrene treatment by the bipolar pulsed N2/H2 plasmas with an applied voltage of about ±1 kV formed a nitrogen-rich layer of a thickness of only a few nm. The simulations also showed that, as the NH3 incident energy increases, the ratio of primary amines to the total number of N atoms on the surface decreases. It is because the energetic ion bombardment brakes up N–H bonds of primary amines, which are mostly brought to the surface by NH2 radical adsorption. Our previous experimental work on the CPA plasma polymerization showed that increased RF power invested in the plasma leads to the deposition of films with lower nitrogen content. The MD simulations showed an increase of the nitrogen content with the Ar energy and a limited impact of the energetic bombardment on the retention of primary amines. Thus, the results highlighted the importance of the gas-phase processes on the nitrogen incorporation and primary amines retention in the plasma polymers. However, the higher energy flux towards the growing film clearly decreases amount of hydrogen and increases the polymer cross-linking. read less NOT USED (high confidence) Z. Li, Y. Yan, J. Wang, and Y. Geng, “Molecular Dynamics Study on Tip-Based Nanomachining: A Review,” Nanoscale Research Letters. 2020. link Times cited: 8 NOT USED (high confidence) K. González-López and E. Lerner, “An energy-landscape-based crossover temperature in glass-forming liquids.,” The Journal of chemical physics. 2020. link Times cited: 4 Abstract: The systematic identification of temperature scales in super… read moreAbstract: The systematic identification of temperature scales in supercooled liquids that are key to understanding those liquids' underlying glass properties, and their formation-history dependence, is a challenging task. Here, we study the statistics of particles' squared displacements δr2 between equilibrium liquid configurations at temperature T and their underlying inherent states, using computer simulations of 11 different computer glass formers. We show that the relative fluctuations of δr2 are nonmonotonic in T, exhibiting a maximum whose location defines the crossover temperature TX. Therefore, TX marks the point of maximal heterogeneity during the process of tumbling down the energy landscape, starting from an equilibrium liquid state at temperature T down to its underlying inherent state. We extract TX for the 11 employed computer glasses, ranging from tetrahedral glasses to packs of soft elastic spheres, and demonstrate its usefulness in putting the elastic properties of different glasses on the same footing. Interestingly, we further show that TX marks the crossover between two distinct regimes of the mean ⟨δr2⟩: a high temperature regime in which ⟨δr2⟩ scales approximately as T0.5 and a deeply supercooled regime in which ⟨δr2⟩ scales approximately as T1.3. Further research directions are discussed. read less NOT USED (high confidence) K. Talaat, B. Cowen, and O. Anderoglu, “Method of information entropy for convergence assessment of molecular dynamics simulations,” Journal of Applied Physics. 2020. link Times cited: 0 Abstract: The lack of a reliable method to evaluate the convergence of… read moreAbstract: The lack of a reliable method to evaluate the convergence of molecular dynamics simulations has contributed to discrepancies in different areas of molecular dynamics. In the present work, the method of information entropy is introduced to molecular dynamics for stationarity assessment. The Shannon information entropy formalism is used to monitor the convergence of the atom motion to a steady state in a continuous spatial domain and is also used to assess the stationarity of calculated multidimensional fields such as the temperature field in a discrete spatial domain. It is demonstrated in this work that monitoring the information entropy of the atom position matrix provides a clear indicator of reaching steady state in radiation damage simulations, non-equilibrium molecular dynamics thermal conductivity computations, and simulations of Poiseuille and Couette flow in nanochannels. A main advantage of the present technique is that it is non-local and relies on fundamental quantities available in all molecular dynamics simulations. Unlike monitoring average temperature, the technique is applicable to simulations that conserve total energy such as reverse non-equilibrium molecular dynamics thermal conductivity computations and to simulations where energy dissipates through a boundary as in radiation damage simulations. The method is applied to simulations of iron using the Tersoff/ZBL splined potential, silicon using the Stillinger–Weber potential, and to Lennard–Jones fluid. Its applicability to both solids and fluids shows that the technique has potential for generalization to other areas in molecular dynamics. read less NOT USED (high confidence) M. Stricker, B. Yin, E. Mak, and W. Curtin, “Machine learning for metallurgy II. A neural-network potential for magnesium,” Physical Review Materials. 2020. link Times cited: 26 Abstract: Interatomic potentials are essential for studying fundamenta… read moreAbstract: Interatomic potentials are essential for studying fundamental mechanisms of deformation and failure in metals and alloys because the relevant defects (dislocations, cracks, etc.) are far above the scales accessible to first-principles studies. Existing potentials for non-fcc metals and nearly all alloys are, however, not sufficiently quantitative for many crucial phenomena. Here machine learning in the Behler-Parrinello neural-network framework is used to create a broadly applicable potential for pure hcp magnesium (Mg). Lightweight Mg and its alloys are technologically important while presenting a diverse range of slip systems and crystal surfaces relevant to both plasticity and fracture that present a significant challenge for any potential. The machine learning potential is trained on first-principles density-functional theory (DFT) computable metallurgically relevant properties and is then shown to well predict metallurgically crucial dislocation and crack structures and competing phenomena. Extensive comparisons to an existing very good modified embedded atom method potential are made. These results demonstrate that a single machine learning potential can represent the wide scope of phenomena required for metallurgical studies. The DFT database is openly available for use in any other machine learning method. The method is naturally extendable to alloys, which are necessary for engineering applications but where ductility and fracture are controlled by complex atomic-scale mechanisms that are not well predicted by existing potentials. read less NOT USED (high confidence) H. Tanaka, “Liquid-liquid transition and polyamorphism.,” The Journal of chemical physics. 2020. link Times cited: 76 Abstract: Two or more liquid states may exist even for single-componen… read moreAbstract: Two or more liquid states may exist even for single-component substances, which is known as liquid polymorphism, and the transition between them is called liquid-liquid transition (LLT). On the other hand, the existence of two or more amorphous states is called polyamorphism, and the transition between them is called amorphous-amorphous transition (AAT). Recently, we have accumulated a lot of experimental and numerical evidence for LLT and AAT. These intriguing phenomena provide crucial information on the fundamental nature of liquid and amorphous states. Here, we review the recent progress in this field and discuss how we can physically rationalize the existence of two or more liquids (glasses) for a single-component substance. We also discuss the relationship between liquid-, amorphous-, and crystal-polymorphisms, putting a particular focus on the roles of thermodynamics, mechanics, and kinetics. read less NOT USED (high confidence) D. A. Conyuh and Y. Beltukov, “Universal Vibrational Properties of Disordered Systems in Terms of the Theory of Random Correlated Matrices,” JETP Letters. 2020. link Times cited: 2 NOT USED (high confidence) Z. Shui and G. Karypis, “Heterogeneous Molecular Graph Neural Networks for Predicting Molecule Properties,” 2020 IEEE International Conference on Data Mining (ICDM). 2020. link Times cited: 42 Abstract: As they carry great potential for modeling complex interacti… read moreAbstract: As they carry great potential for modeling complex interactions, graph neural network (GNN)-based methods have been widely used to predict quantum mechanical properties of molecules. Most of the existing methods treat molecules as molecular graphs in which atoms are modeled as nodes. They characterize each atom's chemical environment by modeling its pairwise interactions with other atoms in the molecule. Although these methods achieve a great success, limited amount of works explicitly take many-body interactions, i.e., interactions between three and more atoms, into consideration. In this paper, we introduce a novel graph representation of molecules, heterogeneous molecular graph (HMG) in which nodes and edges are of various types, to model many-body interactions. HMGs have the potential to carry complex geometric information. To leverage the rich information stored in HMGs for chemical prediction problems, we build heterogeneous molecular graph neural networks (HMGNN) on the basis of a neural message passing scheme. HMGNN incorporates global molecule representations and an attention mechanism into the prediction process. The predictions of HMGNN are invariant to translation and rotation of atom coordinates, and permutation of atom indices. Our model achieves state-of-the-art performance in 9 out of 12 tasks on the QM9 dataset. read less NOT USED (high confidence) L. B’etermin, M. Friedrich, and U. Stefanelli, “Stability of Z2 configurations in 3D,” Nonlinearity. 2020. link Times cited: 0 Abstract: Inspired by the issue of stability of molecular structures, … read moreAbstract: Inspired by the issue of stability of molecular structures, we investigate the strict minimality of point sets with respect to configurational energies featuring two- and three-body contributions. Our main focus is on characterizing those configurations which cannot be deformed without changing distances between first neighbours or angles formed by pairs of first neighbours. Such configurations are called angle-rigid. We tackle this question in the class of finite configurations in Z2 , seen as planar three-dimensional point sets. A sufficient condition preventing angle-rigidity is presented. This condition is also proved to be necessary when restricted to specific subclasses of configurations. read less NOT USED (high confidence) K. Parisis, F. Shuang, B. Wang, P. Hu, A. Giannakoudakis, and A. Konstantinidis, “From Gradient Elasticity to Gradient Interatomic Potentials: The Case-Study of Gradient London Potential,” Journal of Applied Mathematics and Physics. 2020. link Times cited: 1 Abstract: Motivated by the special theory of gradient elasticity (Grad… read moreAbstract: Motivated by the special theory of gradient elasticity (GradEla), a proposal is advanced for extending it to construct gradient models for interatomic potentials, commonly used in atomistic simulations. Our focus is on London’s quantum mechanical potential which is an analytical expression valid until a certain characteristic distance where “attractive” molecular interactions change character and become “repulsive” and cannot be described by the classical form of London’s potential. It turns out that the suggested internal length gradient (ILG) generalization of London’s potential generates both an “attractive” and a “repulsive” branch, and by adjusting the corresponding gradient parameters, the behavior of the empirical Lennard-Jones potentials is theoretically captured. read less NOT USED (high confidence) H. Luo, A. Gravouil, V. Giordano, W. Schirmacher, and A. Tanguy, “Continuum constitutive laws to describe acoustic attenuation in glasses.,” Physical review. E. 2020. link Times cited: 3 Abstract: Nowadays metamaterials are at the focus of an intense resear… read moreAbstract: Nowadays metamaterials are at the focus of an intense research as promising for thermal and acoustic engineering. However, the computational cost associated to the large system size required for correctly simulating them imposes the use of finite-elements simulations, developing continuum models, able to grasp the physics at play without entering in the atomistic details. Still, a correct description should be able to reproduce not only the extrinsic scattering sources on waves propagation, as introduced by the metamaterial microstructure, but also the intrinsic wave attenuation of the material itself. This becomes dramatically important when the metamaterial is made out of a glass, which is intrinsically highly dissipative and with a wave attenuation strongly dependent on frequency. Here we propose a continuum mechanical model for a viscoelastic medium, able to bridge atomic and macroscopic scale in amorphous materials and describe phonon attenuation due to atomistic mechanisms, characterized by a defined frequency dependence. This represents a first decisive step for investigating the effect of a complex nano- or microstructure on acoustic attenuation, while including the atomistic contribution as well. read less NOT USED (high confidence) S. Ciarella et al., “Soft Particles at Liquid Interfaces: From Molecular Particle Architecture to Collective Phase Behavior.,” Langmuir : the ACS journal of surfaces and colloids. 2020. link Times cited: 17 Abstract: Soft particles such as microgels can undergo significant and… read moreAbstract: Soft particles such as microgels can undergo significant and anisotropic deformations when adsorbed to a liquid interface. This, in turn, leads to a complex phase behavior upon compression. To date, experimental efforts have predominantly provided phenomenological links between microgel structure and resulting interfacial behavior, while simulations have not been entirely successful in reproducing experiments or predicting the minimal requirements for the desired phase behavior. Here, we develop a multiscale framework to link the molecular particle architecture to the resulting interfacial morphology and, ultimately, to the collective interfacial phase behavior. To this end, we investigate interfacial morphologies of different poly(N-isopropylacrylamide) particle systems using phase-contrast atomic force microscopy and correlate the distinct interfacial morphology with their bulk molecular architecture. We subsequently introduce a new coarse-grained simulation method that uses augmented potentials to translate this interfacial morphology into the resulting phase behavior upon compression. The main novelty of this method is the possibility to efficiently encode multibody interactions, the effects of which are key to distinguishing between heterostructural (anisotropic collapse) and isostructural (isotropic collapse) phase transitions. Our approach allows us to qualitatively resolve existing discrepancies between experiments and simulations. Notably, we demonstrate the first in silico account of the two-dimensional isostructural transition, which is frequently found in experiments but elusive in simulations. In addition, we provide the first experimental demonstration of a heterostructural transition to a chain phase in a single-component system, which has been theoretically predicted decades ago. Overall, our multiscale framework provides a phenomenological bridge between physicochemical soft-particle characteristics at the molecular scale and nanoscale and the collective self-assembly phenomenology at the macroscale, serving as a stepping stone toward an ultimately more quantitative and predictive design approach. read less NOT USED (high confidence) K. González-López, M. Shivam, Y. Zheng, M. Ciamarra, and E. Lerner, “Mechanical disorder of sticky-sphere glasses. I. Effect of attractive interactions.,” Physical review. E. 2020. link Times cited: 24 Abstract: Recent literature indicates that attractive interactions bet… read moreAbstract: Recent literature indicates that attractive interactions between particles of a dense liquid play a secondary role in determining its bulk mechanical properties. Here we show that, in contrast with their apparent unimportance to the bulk mechanics of dense liquids, attractive interactions can have a major effect on macro- and microscopic elastic properties of glassy solids. We study several broadly applicable dimensionless measures of stability and mechanical disorder in simple computer glasses, in which the relative strength of attractive interactions-referred to as "glass stickiness"-can be readily tuned. We show that increasing glass stickiness can result in the decrease of various quantifiers of mechanical disorder, on both macro- and microscopic scales, with a pair of intriguing exceptions to this rule. Interestingly, in some cases strong attractions can lead to a reduction of the number density of soft, quasilocalized modes, by up to an order of magnitude, and to a substantial decrease in their core size, similar to the effects of thermal annealing on elasticity observed in recent works. Contrary to the behavior of canonical glass models, we provide compelling evidence indicating that the stabilization mechanism in our sticky-sphere glasses stems predominantly from the self-organized depletion of interactions featuring large, negative stiffnesses. Finally, we establish a fundamental link between macroscopic and microscopic quantifiers of mechanical disorder, which we motivate via scaling arguments. Future research directions are discussed. read less NOT USED (high confidence) W. Jiang, Y. Zhang, L. Zhang, and H. Wang, “Accurate Deep Potential model for the Al–Cu–Mg alloy in the full concentration space*,” arXiv: Materials Science. 2020. link Times cited: 24 Abstract: Combining first-principles accuracy and empirical-potential … read moreAbstract: Combining first-principles accuracy and empirical-potential efficiency for the description of the potential energy surface (PES) is the philosopher's stone for unraveling the nature of matter via atomistic simulation. This has been particularly challenging for multi-component alloy systems due to the complex and non-linear nature of the associated PES. In this work, we develop an accurate PES model for the Al-Cu-Mg system by employing Deep Potential (DP), a neural network based representation of the PES, and DP Generator (DP-GEN), a concurrent-learning scheme that generates a compact set of ab initio data for training. The resulting DP model gives predictions consistent with first-principles calculations for various binary and ternary systems on their fundamental energetic and mechanical properties, including formation energy, equilibrium volume, equation of state, interstitial energy, vacancy and surface formation energy, as well as elastic moduli. Extensive benchmark shows that the DP model is ready and will be useful for atomistic modeling of the Al-Cu-Mg system within the full range of concentration. read less NOT USED (high confidence) M. Aleksandrovych, G. Castanet, S. Burian, F. Lemoine, D. Lacroix, and M. Isaiev, “Effect of Surface Nano-Texturing on Wetting Properties: Molecular Dynamics Study,” Ukrainian Journal of Physics. 2020. link Times cited: 0 Abstract: Molecular dynamics simulations describing the equilibrium sh… read moreAbstract: Molecular dynamics simulations describing the equilibrium shape of a nanodroplet located on the solid substrate are presented for the cases of a "cylindrical water droplet" on silicon substrates. Several examples of the structuration of the solid substrate surface are simulated, i.e.: atomistic flat substrate and substrates with ordered nanopillars and nanopores. The adhesives forces between molecules of the substrate and the fluid are modified to change the wettability. Three wetting configurations are considered in this work for the smooth surface: (i) hydrophilic (θ= 30°), (ii) hydrophobic (θ= 136°), and (iii) an intermediate regime (θ= 80°). Further, the dependence of the wetting angle as a function of the surface state is studied in details for the above-mentioned configurations read less NOT USED (high confidence) M. Morita and T. Shiga, “Surface phonons limit heat conduction in thin films,” Physical Review B. 2020. link Times cited: 3 Abstract: Understanding microscopic heat conduction in thin films is im… read moreAbstract: Understanding microscopic heat conduction in thin films is important for nano/micro heat transfer and thermal management for advanced electronics. As the thickness of thin films is comparable to or shorter than a phonon wavelength, phonon dispersion relations and transport properties are significantly modulated, which should be taken into account for heat conduction in thin films. Although phonon confinement and depletion effects have been considered, it should be emphasized that surface-localized phonons (surface phonons) arise whose influence on heat conduction may not be negligible due to the high surface-to-volume ratio. However, the role of surface phonons in heat conduction has received little attention thus far. In the present work, we performed anharmonic lattice dynamics calculations to investigate the thickness and temperature dependence of in-plane thermal conductivity of silicon thin films with sub-10-nm thickness in terms of surface phonons. Through systematic analysis of the influences of surface phonons, we found that anharmonic coupling between surface and internal phonons localized in thin films significantly suppresses overall in-plane heat conduction in thin films. We also discovered that specific low-frequency surface phonons significantly contribute to surface–internal phonon scattering and heat conduction suppression. Our findings are beneficial for the thermal management of electronics and phononic devices and may lead to surface phonon engineering for thermal conductivity control. read less NOT USED (high confidence) M. Alam, L. Lymperakis, and J. Neugebauer, “Phase diagram of grain boundary facet and line junctions in silicon,” Physical Review Materials. 2020. link Times cited: 1 Abstract: The presence of facets and line junctions connecting facets … read moreAbstract: The presence of facets and line junctions connecting facets on grain boundaries (GBs) has a strong impact on the properties of structural, functional, and optoelectronic materials: They govern the mobility of interfaces, the segregation of impurities, as well the electronic properties. In the present paper, we employ density-functional theory and modified embedded atom method calculations to systematically investigate the energetics and thermodynamic stability of these defects. As a prototype system, we consider (cid:2) 3 tilt GBs in Si. By analyzing the energetics of different faceted GBs, we derive a diagram that describes and predicts the reconstruction of these extended defects as a function of facet length and boundary inclination angle. The phase diagram sheds light upon the fundamental mechanisms causing GB faceting phenomena. It demonstrates that the properties of faceting are not determined solely by anisotropic GB energies but by a complex interplay between geometry and microstructure, boundary energies as well as long-range strain interactions. read less NOT USED (high confidence) L. Miao and L.-wang Wang, “Liquid to crystal Si growth simulation using machine learning force field.,” The Journal of chemical physics. 2020. link Times cited: 4 Abstract: Machine learning force field (ML-FF) has emerged as a potent… read moreAbstract: Machine learning force field (ML-FF) has emerged as a potential promising approach to simulate various material phenomena for large systems with ab initio accuracy. However, most ML-FFs have been used to study the phenomena relatively close to the equilibrium ground states. In this work, we have studied a far from equilibrium system of liquid to crystal Si growth using ML-FF. We found that our ML-FF based on ab initio decomposed atomic energy can reproduce all the aspects of ab initio simulated growth, from local energy fluctuations to transition temperatures, to diffusion constant, and growth rates. We have also compared the growth simulation with the Stillinger-Weber classical force field and found significant differences. A procedure is also provided to correct a systematic fitting bias in the ML-FF training process, which exists in all training models, otherwise critical results like transition temperature will be wrong. read less NOT USED (high confidence) Y. Cui, M. Li, and Y. Hu, “Emerging interface materials for electronics thermal management: experiments, modeling, and new opportunities,” Journal of Materials Chemistry C. 2020. link Times cited: 63 Abstract: Thermal management is becoming a critical technology challen… read moreAbstract: Thermal management is becoming a critical technology challenge for modern electronics with decreasing device size and increasing power density. One key materials innovation is the development of advanced thermal interfaces in electronic packaging to enable efficient heat dissipation and improve device performance, which has attracted intensive research efforts from both academia and industry over the past several decades. Here we review the recent progress in both theory and experiment for developing high-performance thermal interface materials. First, the basic theories and computational frameworks for interface energy transport are discussed, ranging from atomistic interface scattering to multiscale disorders that contributed to thermal boundary resistance. Second, state-of-the-art experimental techniques including steady-state and transient thermal measurements are discussed and compared. Moreover, the important structure design, requirements, and property factors for thermal interface materials depending on different applications are summarized and exemplified with the recent literature. Finally, emerging new semiconductors and polymers with high thermal conductivity are briefly reviewed and opportunities for future research are discussed. read less NOT USED (high confidence) M. S. Marques, E. Lomba, E. Noya, D. González-Salgado, and M. Barbosa, “Modeling the temperature of maximum density of aqueous tert-butanol solutions.,” arXiv: Soft Condensed Matter. 2020. link Times cited: 1 NOT USED (high confidence) H. Chen, N. Zarkevich, V. Levitas, D. D. Johnson, and X. Zhang, “Fifth-degree elastic energy for predictive continuum stress–strain relations and elastic instabilities under large strain and complex loading in silicon,” npj Computational Materials. 2020. link Times cited: 14 NOT USED (high confidence) D. A. Conyuh and Y. Beltukov, “Random matrix approach to the boson peak and Ioffe-Regel criterion in amorphous solids,” arXiv: Disordered Systems and Neural Networks. 2020. link Times cited: 6 Abstract: We show that the correlated Wishart ensemble can be used to … read moreAbstract: We show that the correlated Wishart ensemble can be used to study general vibrational properties of stable amorphous solids with translational invariance. Using the random matrix theory, we found the vibrational density of states and the dynamical structure factor. We demonstrate the presence of the Ioffe-Regel crossover between low-frequency propagating phonons and diffusons at higher frequencies. The reduced vibrational density of states shows the boson peak, which frequency is close to the Ioffe-Regel crossover. read less NOT USED (high confidence) D. Mora‐Fonz et al., “Real and virtual polymorphism of titanium selenide with robust interatomic potentials,” Journal of Materials Chemistry A. 2020. link Times cited: 5 Abstract: The first successful pairwise potential for a layered materi… read moreAbstract: The first successful pairwise potential for a layered material, TiSe2, has been parameterised to fit the experimental data, using a genetic algorithm as the optimisation tool for the parameters of the interatomic potential. read less NOT USED (high confidence) A. Genoese, A. Genoese, and G. Salerno, “In-plane and out-of-plane tensile behaviour of single-layer graphene sheets: a new interatomic potential,” Acta Mechanica. 2020. link Times cited: 7 NOT USED (high confidence) R. Yokogawa et al., “Anomalous low energy phonon dispersion in bulk silicon-germanium observed by inelastic x-ray scattering,” Applied Physics Letters. 2020. link Times cited: 7 Abstract: We report on an anomalous mode distinct from both optical an… read moreAbstract: We report on an anomalous mode distinct from both optical and acoustic modes in phonon dispersion curves of bulk Si1−xGex alloy with x taking the values of 0.16, 0.32, 0.45, and 0.72. The anomalous mode at approximately 13 meV was observed directly using inelastic x-ray scattering along the Γ–X ([00q]) direction. The phonon dispersion relations of the anomalous mode indicate that there was no momentum dependence, similar to those of the longitudinal and transverse optical modes (Ge–Ge, Si–Ge, and Si–Si modes). In contrast to the acoustic and optical phonon modes, the energy of the anomalous mode shows no Ge fraction dependence. The molecular dynamics simulation corroborates that the Ge–Ge pairs or Ge atom clusters, which are surrounded by Si atoms, provide the anomalous mode, which is unique to the alloy structure. It has been suggested that such a localized vibration mode with no propagation significantly affects the acoustic modes, leading to low thermal conductivity in the SiGe alloy. read less NOT USED (high confidence) A. Hamedani et al., “Insights into the primary radiation damage of silicon by a machine learning interatomic potential,” Materials Research Letters. 2020. link Times cited: 14 Abstract: ABSTRACT We develop a silicon Gaussian approximation machine… read moreAbstract: ABSTRACT We develop a silicon Gaussian approximation machine learning potential suitable for radiation effects, and use it for the first ab initio simulation of primary damage and evolution of collision cascades. The model reliability is confirmed by good reproduction of experimentally measured threshold displacement energies and sputtering yields. We find that clustering and recrystallization of radiation-induced defects, propagation pattern of cascades, and coordination defects in the heat spike phase show striking differences to the widely used analytical potentials. The results reveal that small defect clusters are predominant and show new defect structures such as a vacancy surrounded by three interstitials. GRAPHICAL ABSTRACT Impact statement Quantum-mechanical level of accuracy in simulation of primary damage was achieved by a silicon machine learning potential. The results show quantitative and qualitative differences from the damage predicted by any previous models. read less NOT USED (high confidence) G.-B. Jong, P. Song, and H.-S. Jin, “Phonon and thermodynamic properties of bcc transition metals using MEAM potentials,” Indian Journal of Physics. 2020. link Times cited: 6 NOT USED (high confidence) A. Genoese, A. Genoese, and G. Salerno, “In-plane and out-of-plane tensile behaviour of single-layer graphene sheets: a new interatomic potential,” Acta Mechanica. 2020. link Times cited: 0 NOT USED (high confidence) R. Chen, Z. Wang, S. Li, and H. Du, “A novel degradation mechanism of the elastic modulus of wet polymer substrates under nanoindentation.,” Soft matter. 2020. link Times cited: 2 Abstract: We demonstrated that the formation and solidification of a c… read moreAbstract: We demonstrated that the formation and solidification of a continuous confined water film played a very important role in changing the elastic modulus of the wet polymer substrate in a nanoindentation process by a coarse-grained molecular dynamics simulation of this process. It was found that as the water content increased, the elastic modulus of the wet polymer substrate showed a non-monotonic change. Relative to the dry polymer substrate, the elastic modulus of the wet polymer first decreased. This is because the appearance of a confined water film caused the force between the polymer substrate and the indenter to change from repulsion to attraction. Subsequently, as the confined water film gradually solidified and then weakened, the elastic modulus of the wet polymer slowly increased and then rapidly increased due to a large number of interstitial water molecules gradually penetrating the polymer substrate. Therefore, it is unreasonable to explain the wet polymer degradation during nanoindentation only from the plasticization and anti-plasticization effects based on the hydrogen bond breaking and formation during stretching. The above-mentioned results will help to more comprehensively understand the degradation mechanism of the polymers' encounter with water, thus promoting further practical applications for polymers. read less NOT USED (high confidence) P. Desmarchelier, K. Termentzidis, and A. Tanguy, “Vibrational density of states of free and embedded semiconducting GaN nanoparticles,” Semiconductor Science and Technology. 2020. link Times cited: 2 Abstract: The impact of the size of free and embedded GaN nanoparticle… read moreAbstract: The impact of the size of free and embedded GaN nanoparticles on vibrational properties has been studied using three different numerical methods. The thermal conductivity of free nanoparticles was also estimated with equilibrium molecular dynamics. Important discrepancies between the vibrational density of states of small nanoparticles compared to the bulk are observed, such as the presence of modes in the bandgap related to the surface modes, the optical peaks decrease, and the redshift of the transverse acoustic peak. When these nanoparticles are embedded in a SiO2 matrix, the peaks in the bandgap disappear and the transverse acoustic modes are shifted back to the bulk frequencies. These differences between the free and the embedded nanoparticles tend to disappear for nanoparticles with diameters larger than 5 nm. Finally, the thermal conductivity for free nanoparticles is computed, showing a non-linear augmentation upon the increase of the size of nanoparticles. The latter results could be useful in effective medium models used to estimate the thermal conductivity of nanocomposites. read less NOT USED (high confidence) M. Schiebl and I. Romero, “Energy-momentum conserving integration schemes for molecular dynamics,” Computational Mechanics. 2020. link Times cited: 4 NOT USED (high confidence) A. Utkin and V. Fomin, “Molecular Dynamic Calculation of the Bulk Modulus for Silicon and Silicon Carbide,” Doklady Physics. 2020. link Times cited: 2 NOT USED (high confidence) H. Li et al., “Experimental and numerical analysis of the effects of ion bombardment in silicon oxide (SiO2) plasma enhanced atomic layer deposition (PEALD) processes,” Japanese Journal of Applied Physics. 2020. link Times cited: 5 Abstract: Reactions between a precursor-absorbed SiO2 surface and ener… read moreAbstract: Reactions between a precursor-absorbed SiO2 surface and energetic ion species, i.e. Ar+ or O+ ions, in a plasma enhanced atomic layer deposition (PEALD) process were investigated using an in situ X-ray photoelectron spectrometer system and a molecular dynamics (MD) simulation. Both the experiment and simulation results showed that N and/or C atoms originating from the precursor molecules remained on the surface as amorphous carbon and/or cyanide after 50 eV ion bombardment. The precursor-originated atoms as well as the SiO2 film were removed by the incident ions when its energy increased to 100 eV, and exceedingly small amount remained on the surface. The MD simulation results showed that chemical effects had a more obvious effect on the removal of C atoms at lower incident energies, while purely physical effects dominated at high O+ ion incident energies. These results indicated the importance of ion energy in PEALD processes in terms of film quality. read less NOT USED (high confidence) X. Wei, C.-M. Wu, and Y.-R. Li, “Molecular insight into the formation of adsorption clusters based on the zeta isotherm.,” Physical chemistry chemical physics : PCCP. 2020. link Times cited: 7 Abstract: This work presents a series of molecular dynamics simulation… read moreAbstract: This work presents a series of molecular dynamics simulations of argon adsorption on a silicon substrate with different lattice orientations. From the simulation results, the density profiles are discussed and the amount of adsorbed particles is obtained at different pressures. It is found that the solid surface orientation has a great influence on the density distributions and atomic arrangements near the surface. With the collected data, the thermal constants derived from the expression of zeta adsorption isotherms are determined. The calculated isotherms agree well with the simulation results. Also, from a microscopic point of view, the molecular insights show that the structures of the adsorbates are present as clusters with different numbers of particles. The size of the clusters changes with pressure. At a relatively small pressure ratio, most of the clusters consist of a single molecule. As the pressure ratio increases, larger sized clusters appear, forming various cluster-types. The molecular cluster distributions are closely consistent with the basic approximation of the zeta adsorption isotherm. Furthermore, the surface adsorption sites determined from molecular dynamics simulation show good agreement with that predicted by the zeta isotherm model, which reaffirms the effectiveness of the theoretical model. When the isotherm is extended to a pressure ratio greater than unity, a finite amount of adsorption is predicted and the wetting conditions are obtained. Affected by the solid surface orientations, the pressure ratio at wetting for the silicon substrate with the (111) surface plane is larger than those of the (100) and (110) surfaces, indicating that a higher subcooling is required for the wetting transition. read less NOT USED (high confidence) V. V. Hoang, N. H. Giang, and T. Q. Dong, “Amorphous and ‘crystalline’ penta-silicene,” Philosophical Magazine. 2020. link Times cited: 2 Abstract: ABSTRACT Atomic structure, thermodynamic and mechanical beha… read moreAbstract: ABSTRACT Atomic structure, thermodynamic and mechanical behaviours of the penta-silicene (p-silicene) obtained by cooling from the melt are studied by the molecular dynamics (MD) simulations. We find that p-silicene can ‘naturally’ form from the liquid state using the appropriate interatomic potential, density and buckling. The charge-optimised many body (COMB) potential is employed. Depending on the cooling rate used in simulations, ‘crystalline’ or amorphous p-silicene can be obtained. ‘Crystallisation’ and glass transition temperatures ( and , respectively) have reasonable values compared to those of the hexa-silicene (h-silicene). We find that the Poisson’s ratio of the obtained ‘crystalline’ p-silicene is positive unlike the negative one found for the p-graphene. The reasons for the formation of p-silicene instead of tetra-silicene (t-silicene) are analysed and discussed, i.e. 2D liquid silicene with COMB potential has a significant fraction of pentagons which grow with decreasing temperature, unlike 2D liquid silicene with the Stillinger–Weber potential. read less NOT USED (high confidence) H. Hatami-Marbini, “A computational study of the behavior of colloidal gel networks at low volume fraction,” Journal of Physics: Condensed Matter. 2020. link Times cited: 1 Abstract: Colloidal gel networks appear in different scientific and in… read moreAbstract: Colloidal gel networks appear in different scientific and industrial applications because of their unique properties. Molecular dynamics simulations could reveal the relation between molecular level and macroscopic properties of these systems. Nevertheless, the predictions of numerical simulations might depend on the specific form and parameters of interaction potentials. In this paper, a new effective interaction potential is used for characterizing the mechanical behavior of low volume fraction colloidal gels under large shear deformation. The findings are compared with those obtained from other available forms of interaction potentials in order to determine gel characteristics that are interaction potential independent. Furthermore, the macroscopic stress–strain behavior is discussed in terms of the behavior of different terms of the proposed interaction potential. The correlation between the stretch of interparticle bonds and their alignment in the direction of the maximum principal stress is also computed in order to provide microscopic explanations for the initial strain softening behavior. It is concluded that, in addition to topology, local mechanical interactions between colloidal particles are important in defining the mechanical response of soft gels. read less NOT USED (high confidence) N. Takahashi, Y. Liu, and C. Kaneta, “Materials informatics approach for design of Si/Ge layered nanostructures with low thermal conductivity,” Japanese Journal of Applied Physics. 2020. link Times cited: 0 Abstract: We report an efficient method based on the materials informa… read moreAbstract: We report an efficient method based on the materials informatics approach to predict low thermal conductivity structures using a descriptor obtained by phonon mode calculations. For a small number of Si/Ge layered structures, we perform normal mode analysis to calculate the participation ratio for each phonon mode and calculations of thermal conductivity in the stacking direction using the perturbed molecular dynamics (MD) method. The descriptor for the thermal conductivity is defined using the participation ratios averaged in the acoustic phonon frequency ranges with their lower and upper limits independently optimized. By employing the descriptor and genetic algorithm, low thermal conductivity structures are recommended among a huge number of possible structures. The recommended structures are confirmed to have very small thermal conductivities from the results of the perturbed MD calculations. By employing the method, we can design Si/Ge layered structures with low thermal conductivity at very low computational cost. read less NOT USED (high confidence) E. Giessen et al., “Roadmap on multiscale materials modeling,” Modelling and Simulation in Materials Science and Engineering. 2020. link Times cited: 91 Abstract: Modeling and simulation is transforming modern materials sci… read moreAbstract: Modeling and simulation is transforming modern materials science, becoming an important tool for the discovery of new materials and material phenomena, for gaining insight into the processes that govern materials behavior, and, increasingly, for quantitative predictions that can be used as part of a design tool in full partnership with experimental synthesis and characterization. Modeling and simulation is the essential bridge from good science to good engineering, spanning from fundamental understanding of materials behavior to deliberate design of new materials technologies leveraging new properties and processes. This Roadmap presents a broad overview of the extensive impact computational modeling has had in materials science in the past few decades, and offers focused perspectives on where the path forward lies as this rapidly expanding field evolves to meet the challenges of the next few decades. The Roadmap offers perspectives on advances within disciplines as diverse as phase field methods to model mesoscale behavior and molecular dynamics methods to deduce the fundamental atomic-scale dynamical processes governing materials response, to the challenges involved in the interdisciplinary research that tackles complex materials problems where the governing phenomena span different scales of materials behavior requiring multiscale approaches. The shift from understanding fundamental materials behavior to development of quantitative approaches to explain and predict experimental observations requires advances in the methods and practice in simulations for reproducibility and reliability, and interacting with a computational ecosystem that integrates new theory development, innovative applications, and an increasingly integrated software and computational infrastructure that takes advantage of the increasingly powerful computational methods and computing hardware. read less NOT USED (high confidence) K. Momeni et al., “Multiscale computational understanding and growth of 2D materials: a review,” npj Computational Materials. 2020. link Times cited: 85 NOT USED (high confidence) G. Kacar, “Parametrizing hydrogen bond interactions in dissipative particle dynamics simulations: The case of water, methanol and their binary mixtures,” Journal of Molecular Liquids. 2020. link Times cited: 10 NOT USED (high confidence) C. Núñez, M. Saiz-Bretín, P. Orellana, L. Rosales, and F. Domínguez‐Adame, “Tuning the thermoelectric response of silicene nanoribbons with vacancies,” Journal of Physics: Condensed Matter. 2020. link Times cited: 2 Abstract: In this work, we present a thorough study of the thermoelect… read moreAbstract: In this work, we present a thorough study of the thermoelectric properties of silicene nanoribbons in the presence of a random distribution of atomic vacancies. By using a linear approach within the Landauer formalism, we calculate phonon and electron thermal conductances, the electric conductance, the Seebeck coefficient and the figure of merit of the nanoribbons. We found a sizable reduction of the phonon thermal conductance as a function of the vacancy concentration over a wide range of temperature. At the same time, the electric properties are not severely deteriorated, leading to an overall remarkable thermoelectric efficiency. We conclude that the incorporation of vacancies paves the way for designing better and more efficient nanoscale thermoelectric devices. read less NOT USED (high confidence) M. Kim, H. Yin, and G. Lin, “Multi-Fidelity Gaussian Process based Empirical Potential Development for Si: H Nanowires,” ArXiv. 2020. link Times cited: 2 NOT USED (high confidence) L. Fokin, “Analysis of Data on Zero and Negative Thermal Expansion Coefficients of Materials,” High Temperature. 2020. link Times cited: 3 NOT USED (high confidence) J. Ma, J.-J. Zheng, W. Li, D.-hong Wang, and B.-T. Wang, “Thermal transport properties of monolayer MoSe2 with defects.,” Physical chemistry chemical physics : PCCP. 2020. link Times cited: 11 Abstract: Two-dimensional (2D) molybdenum diselenide (MoSe2) as one of… read moreAbstract: Two-dimensional (2D) molybdenum diselenide (MoSe2) as one of the ultrathin transition metal dichalcogenides (TMDs) has attracted considerable attention because of its potential applications in thermoelectric and nano-electronic devices. Here, the thermal conductivity of monolayer MoSe2 and its responses to simulated size and defects are studied by nonequilibrium molecular dynamics simulations. With the increase of sample length, the thermal conductivity of monolayer MoSe2 nanoribbons exhibits an enhancement whereas it is insensitive to the width. At room temperature, the thermal conductivities of monolayer MoSe2 along armchair and zigzag directions are 17.758 and 18.932 W (m K)-1, respectively, which are consistent with previous results. The impact of defects on thermal conductivity has also been studied by varying the concentration of the vacancy from 0.1% to 0.5%. The results show that an increase of the defect concentration will greatly suppress the thermal conductivity. The 0.5% defect concentration with a Mo vacancy can result in a thermal conductivity reduction of ∼43%. Such a study would provide a good insight into the tunable thermal transport for potential applications of not only monolayer MoSe2, but also many other TMDs. read less NOT USED (high confidence) V. Vardanyan, Z. Zhang, I. A. Alhafez, and H. Urbassek, “Cutting of Al/Si bilayer systems: molecular dynamics study of twinning, phase transformation, and cracking,” The International Journal of Advanced Manufacturing Technology. 2020. link Times cited: 10 NOT USED (high confidence) C. Yi, C. Hu, M.-li Bai, J. Lv, and D. Tang, “Molecular dynamics study on the mechanical properties of multilayer MoS2 under different potentials,” Nanotechnology. 2020. link Times cited: 5 Abstract: Experiments and simulations have shown that molybdenum disul… read moreAbstract: Experiments and simulations have shown that molybdenum disulfide (MoS2) has unique mechanical and electrical properties that make it promising for application as a flexible material in microscopic and nanoscopic electronic devices. In this paper, the molecular dynamics method is used to study the mechanical properties of multilayer MoS2 during compression and stretching under different intra-layer and inter-layer potentials to choose the most suitable ones. The results show that the increase in the inter-layer repulsive force during compression was all provided by sulfur atoms in the adjacent layer. The two intra-layer potentials represented two forms of tensile fracture: plastic fracture with structural holes or lattice distortions, and brittle fracture with instantaneous destruction. The chosen inter-layer potential had a significant influence on the structure of the multilayer MoS2 but the effect of inter-layer potential during stretching was not prominent. By comparing these results with reference values, the most suitable intra-layer and inter-layer potentials for the multilayer MoS2 were selected, and can serve as a reliable reference for subsequent simulations. read less NOT USED (high confidence) T. Mueller, A. Hernandez, and C. Wang, “Machine learning for interatomic potential models.,” The Journal of chemical physics. 2020. link Times cited: 189 Abstract: The use of supervised machine learning to develop fast and a… read moreAbstract: The use of supervised machine learning to develop fast and accurate interatomic potential models is transforming molecular and materials research by greatly accelerating atomic-scale simulations with little loss of accuracy. Three years ago, Jörg Behler published a perspective in this journal providing an overview of some of the leading methods in this field. In this perspective, we provide an updated discussion of recent developments, emerging trends, and promising areas for future research in this field. We include in this discussion an overview of three emerging approaches to developing machine-learned interatomic potential models that have not been extensively discussed in existing reviews: moment tensor potentials, message-passing networks, and symbolic regression. read less NOT USED (high confidence) H. Hatami-Marbini and J. Coulibaly, “Colloidal particle gel models using many-body potential interactions.,” Physical review. E. 2020. link Times cited: 2 Abstract: Many-body effective interactions are commonly used in a mole… read moreAbstract: Many-body effective interactions are commonly used in a molecular dynamics simulation study of gel networks formed by colloidal particles. Here we report an interaction potential that can be used to investigate the mechanical response of colloidal gel networks under shear deformation. We then investigate the dependence of the numerical simulation results on the form of mathematical expression used to define the interparticle interactions. This work reveals insight into particle gel models by discussing the physical origins of their mechanical response. read less NOT USED (high confidence) T. Jarrin, A. Jay, M. Raine, N. Mousseau, A. Hémeryck, and N. Richard, “Simulation of Single Particle Displacement Damage in Si₁₋ₓGeₓ Alloys—Interaction of Primary Particles With the Material and Generation of the Damage Structure,” IEEE Transactions on Nuclear Science. 2020. link Times cited: 4 Abstract: Primary simulations of neutron interactions are performed on… read moreAbstract: Primary simulations of neutron interactions are performed on Si 1−xGe x alloys with a Monte Carlo (MC) code using the binary collision approximation (BCA). Then, a statistical study of the collision cascades development in Si 0.8Ge 0.2, Si 0.7Ge 0.3, and Si 0.5Ge 0.5 is carried out using molecular dynamics (MD), starting from both Si and Ge primary knock-on atoms (PKAs) of 1, 5, and 10 keV. The well-known Stillinger–Weber (SW) MD potential, which can be used to study Si, Ge, and Si 1−xGe x, is coupled to the Ziegler–Biersack–Littmark (ZBL) universal potential to better describe the collisions between atoms. To account for the stopping power of the electrons, the two-temperature model (TTM) is combined with MD. Similar studies are performed on pure Si and pure Ge in order to be able to compare our Si–Ge alloys damaged structures with reference materials. Moreover, data obtained by TTM-MD on Si, Ge, and Si 1−xGe x are compared with collision cascades statistical data from MC codes. read less NOT USED (high confidence) S. Hu, L. Feng, C. Shao, I. Strelnikov, Y. Kosevich, and J. Shiomi, “Two-path phonon interference resonance induces a stop band in a silicon crystal matrix with a multilayer array of embedded nanoparticles,” Physical Review B. 2020. link Times cited: 9 Abstract: In this work, we report a mechanism of stop-band formation i… read moreAbstract: In this work, we report a mechanism of stop-band formation in a multilayer array of germanium nanoparticles embedded in a crystalline silicon matrix. When only a single layer of nanoparticles is embedded, the local resonance, induced by the destructive interference between two different phonon wave paths, gives rise to several sharp and significant transmittance dips. On the other hand, when the number of the layers of embedded nanoparticles further increases to ten, a stop band with complete phonon reflection is formed due to the two-path resonance Bragg-type phonon interference. The wave packet simulations further uncover that the stop band originates from the collective phonon resonances in the embedded nanoparticles layers. Compared with the traditional stop-band formation mechanism that is the single-path Bragg reflection, the two-path phonon-interference resonance mechanism has a significant advantage in not requiring the strict periodicity in the embedded nanoparticles multilayer array. We also demonstrate that the stop band can significantly suppress thermal conductance in the low-frequency regime. Our work provides a robust, scalable, and easily modulable stop-band formation mechanism, which opens a degree of freedom for phononics-related heat control. read less NOT USED (high confidence) P. J. G’orski, K. O. Bochenina, J. Hołyst, and R. D’Souza, “Homophily based on few attributes can impede structural balance,” Physical review letters. 2020. link Times cited: 25 Abstract: Homophily between agents and structural balance in connected… read moreAbstract: Homophily between agents and structural balance in connected triads of agents are complementary mechanisms thought to shape social groups leading to, for instance, consensus or polarization. To capture both processes in a unified manner, we propose a model of pair and triadic interactions. We consider N fully connected agents, where each agent has G underlying attributes, and the similarity between agents in attribute space (i.e., homophily) is used to determine the link weight between them. For structural balance we use a triad-updating rule where only one attribute of one agent is changed intentionally in each update, but this also leads to accidental changes in link weights and even link polarities. The link weight dynamics in the limit of large G is described by a Fokker-Planck equation from which the conditions for a phase transition to a fully balanced state with all links positive can be obtained. This "paradise state" of global cooperation is, however, difficult to achieve requiring G>O(N^{2}) and p>0.5, where the parameter p captures a willingness for consensus. Allowing edge weights to be a consequence of attributes naturally captures homophily and reveals that many real-world social systems would have a subcritical number of attributes necessary to achieve structural balance. read less NOT USED (high confidence) F. Elahi, Z. Zhang, and Z. Hossain, “Toughness and strength anisotropy among high-symmetry directions in 3C-SiC,” Journal of Applied Physics. 2020. link Times cited: 8 Abstract: This paper presents a quantitative understanding of toughnes… read moreAbstract: This paper presents a quantitative understanding of toughness and strength anisotropy in 3 C-SiC under uniaxial deformation. We consider four high-symmetry crystallographic directions including [100], [110], [111], and [ 11 2 ¯ ] for loading, and find that both toughness and strength are the maximum along the [100] direction and the minimum along the [111] direction. The maximum anisotropy in crack nucleation-toughness is 145% and in fracture toughness 126%, relative to the [111] direction. The corresponding anisotropies in fracture strain and fracture strength are found to be 62% and 36%, respectively. An atomistic analysis shows that bonds deform uniformly for loading along the [100] direction, whereas for loading along the [110], [111], or [ 11 2 ¯] directions, bonds deform nonuniformly and it breaks the symmetry of the local atomic structure. The nonuniform bond deformation creates different sets of bond lengths and forms the atomistic basis for the direction-dependent mechanical behavior. The simulations are conducted with four different interatomic potentials including the Stillinger-Weber, Tersoff, Vashishta, and Environment Dependent Interatomic Potentials. It is found that only the Stillinger-Weber potential exhibits first-principles accurate strength and toughness as well as brittlelike fracture. Also, there is a sizeable difference among the potentials in terms of the crack nucleation toughness and strength. We find the difference to originate from the dissimilarity in the forcing function and its derivative in the nonlinear regime of mechanical deformation. A mathematical analysis suggests that it is essential for the forcing function to accurately represent the first-principles accurate forcing function, at least up to the maximum bond force, to produce accurate fracture properties and patterns. read less NOT USED (high confidence) J. Zhang et al., “Effects of interlayer interactions on the nanoindentation response of freely suspended multilayer gallium telluride,” Nanotechnology. 2019. link Times cited: 11 Abstract: Freestanding indentation is a widely used method to characte… read moreAbstract: Freestanding indentation is a widely used method to characterise the elastic properties of two-dimensional (2D) materials. However, many controversies and confusion remain in this field due to the lack of appropriate theoretical models in describing the indentation responses of 2D materials. Taking the multilayer gallium telluride (GaTe) as an example, in this paper we conduct a series of experiments and simulations to achieve a comprehensive understanding of its freestanding indentation behaviours. Specifically, the freestanding indentation experiments show that the elastic properties of the present multilayer GaTe with a relatively large thickness can only be extracted from the bending stage in the indentation process rather than the stretching stage widely utilised in the previous studies on thin 2D materials, since the stretching stage of thick 2D materials is inevitably accompanied with severe plastic deformations. In combination with existing continuum mechanical models and finite element simulations, an extremely small Young’s modulus of multilayer GaTe is obtained from the nanoindentation experiments, which is two orders of magnitude smaller than the value obtained from first principles calculations. Our molecular dynamics (MD) simulations reveal that this small Young’s modulus can be attributed to the significant elastic softening in the multilayer GaTe with increasing thickness and decreasing length. It is further revealed in MD simulations that this size-induced elastic softening originates from the synergistic effects of interlayer compression and interlayer shearing in the multilayer GaTe, both of which, however, are ignored in the existing indentation models. To consider these effects of interlayer interactions in the theoretical modelling of the freestanding indentation of multilayer GaTe, we propose here novel multiple-beam and multiple-plate models, which are found to agree well with MD results without any additional parameters fitting and thus can be treated as more precise theoretical models in characterising the freestanding indentation behaviours of 2D materials. read less NOT USED (high confidence) A. Pedersen, L. Pizzagalli, and H. Jónsson, “Atomic and electronic structures of a vacancy in amorphous silicon,” Physical Review B. 2019. link Times cited: 3 Abstract: Locally, the atomic structure in well-annealed amorphous sil… read moreAbstract: Locally, the atomic structure in well-annealed amorphous silicon appears similar to that of crystalline silicon. We address here the question whether a point defect, specifically a vacancy, in amorphous silicon also resembles that in the crystal. From density-functional theory calculations of a large number of nearly defect-free configurations, relaxed after an atom has been removed, we conclude that there is little similarity. The analysis is based on formation energy, relaxation energy, bond lengths, bond angles, Vorono\"{\i} volume, coordination, atomic charge, and electronic gap states. All these quantities span a large and continuous range in amorphous silicon and while the removal of an atom leads to the formation of one to two bond defects and to a lowering of the local atomic density, the relaxation of the bonding network is highly effective, and the signature of the vacancy generally unlike that of a vacancy in the crystal. read less NOT USED (high confidence) Y. D. Fomin, “Dispersion of acoustic excitations in tetrahedral liquids,” Journal of Physics: Condensed Matter. 2019. link Times cited: 2 Abstract: Investigation of the longitudinal and transverse excitations… read moreAbstract: Investigation of the longitudinal and transverse excitations in liquids is of great importance for understanding the fundamentals of the liquid state of matter. One of the important questions is the temperature and density dependence of the frequency of the excitations. In our recent works it was shown that while in simple liquids the frequency of longitudinal excitations increases when the temperature is increased isochorically, in water the frequency can anomalously decrease with the temperature increase. In the present manuscript we study the dispersion curves of longitudinal and transverse excitations of water and liquid silicon modelled by Stillinger–Weber (SW) potential. We show that both in liquid silicon and SW model of water the frequencies of longitudinal excitations slightly increase with temperature which is in contrast to the results for SPC/E model of water. read less NOT USED (high confidence) R. Li, E. Lee, and T. Luo, “A unified deep neural network potential capable of predicting thermal conductivity of silicon in different phases,” arXiv: Materials Science. 2019. link Times cited: 47 NOT USED (high confidence) M. Amsler et al., “FLAME: A library of atomistic modeling environments,” Comput. Phys. Commun. 2019. link Times cited: 19 NOT USED (high confidence) S. Lim, D. Jang, B. Park, and K.-Y. Han, “Optimized design of silicone pad for bended window lamination in organic light-emitting diodes,” Journal of Mechanical Science and Technology. 2019. link Times cited: 3 NOT USED (high confidence) X. W. Zhou et al., “Molecular dynamics discovery of an extraordinary ionic migration mechanism in dislocation-containing TlBr crystals.,” Physical chemistry chemical physics : PCCP. 2019. link Times cited: 0 Abstract: TlBr can surpass CZT as the leading semiconductor for γ- and… read moreAbstract: TlBr can surpass CZT as the leading semiconductor for γ- and X-radiation detection. Unfortunately, the optimum properties of TlBr quickly decay when an operating electrical field is applied. Quantum mechanical studies indicated that if this property degradation comes from the conventional mechanism of ionic migration of vacancies, then an unrealistically high vacancy concentration is required to account for the rapid aging of TlBr seen in experiments. In this work, we have applied large scale molecular dynamics simulations to study the effects of dislocations on ionic migration of TlBr crystals under electrical fields. We found that electrical fields can drive the motion of edge dislocations in both slip and climb directions. These combined motions eject enormous vacancies in the dislocation trail. Both dislocation motion and a high vacancy concentration can account for the rapid aging of the TlBr detectors. These findings suggest that strengthening methods to pin dislocations should be explored to increase the lifetimes of TlBr crystals. read less NOT USED (high confidence) A. Moradzadeh and N. Aluru, “Molecular Dynamics Properties without the Full Trajectory: A Denoising Autoencoder Network for Properties of Simple Liquids.,” The journal of physical chemistry letters. 2019. link Times cited: 18 Abstract: Molecular dynamics (MD) simulation is a popularly used compu… read moreAbstract: Molecular dynamics (MD) simulation is a popularly used computational tool to compute microscopic and macroscopic properties of a variety of systems including liquids, solids, biological systems, etc. To determine properties of atomic systems to a good level of accuracy with minimal noise or fluctuation, MD simulations are performed over a long time ranging from a few nanoseconds to several tens to hundreds of nanoseconds depending on the system and the properties of interest. In this study, by considering simple liquids, we explore the feasibility of significantly reducing the MD simulation time to compute various properties of monoatomic systems such as the structure, pressure and isothermal compressibility. To do so, extensive MD simulations are performed on 12000 distinct Lennard-Jones (LJ) systems at various thermodynamic states. Then, a deep denoising autoencoder network is trained to take the radial distribution function (RDF) from a single snapshot of a LJ liquid to compute the mean, temporally averaged RDF. We show that the method is not only successful in the prediction of RDF and other properties such as the pressure and isothermal compressibility that can be computed based on the RDF, for Lennard-Jones liquids at various thermodynamic states but also for various simple liquids described by exponential, Yukawa, and inverse-power-law pair potentials. read less NOT USED (high confidence) A. Sarikov, A. Marzegalli, L. Barbisan, E. Scalise, F. Montalenti, and L. Miglio, “Molecular dynamics simulations of extended defects and their evolution in 3C–SiC by different potentials,” Modelling and Simulation in Materials Science and Engineering. 2019. link Times cited: 11 Abstract: An important issue in the technology of cubic SiC (3C–SiC) m… read moreAbstract: An important issue in the technology of cubic SiC (3C–SiC) material for electronic device applications is to understand the behavior of extended defects such as partial dislocation complexes and stacking faults (SFs). Atomistic simulations using molecular dynamics (MD) are an efficient tool to tackle this issue for large systems at comparatively low computation cost. At this, proper choice of MD potential is imperative to ensure the reliability of the simulation predictions. In this work, we compare the evolution of extended defects in 3C–SiC obtained by MD simulations with Tersoff, analytical bond order, and Vashishta potentials. Key aspects of this evolution are considered including the dissociation of 60° perfect dislocations in pairs of 30° and 90° partials as well as the dependence of the partial dislocation velocity on the Burgers vector and the atomic composition of core. Tersoff potential has been found to be less appropriate in describing the dislocation behavior in 3C–SiC as compared to two other potentials, which in their turn provide qualitatively equivalent predictions. The Vashishta potential predicts much faster defect dynamics than the analytical bond order potential (ABOP). It can be applied therefore to describe the large-scale evolution of the dislocation systems and SFs. On the other hand, ABOP is more precise in predicting local atom arrangements and reconstructions of the dislocation core structures. In this respect, synergetic use of ABOP and Vashishta potential is suggested for the MD simulation study of the properties and evolution of extended defects in the 3C–SiC. read less NOT USED (high confidence) S. Hussain and A. Haji-Akbari, “Studying rare events using forward-flux sampling: Recent breakthroughs and future outlook.,” The Journal of chemical physics. 2019. link Times cited: 34 Abstract: Rare events are processes that occur upon the emergence of u… read moreAbstract: Rare events are processes that occur upon the emergence of unlikely fluctuations. Unlike what their name suggests, rare events are fairly ubiquitous in nature, as the occurrence of many structural transformations in biology and material sciences is predicated upon crossing large free energy barriers. Probing the kinetics and uncovering the molecular mechanisms of possible barrier crossings in a system is critical to predicting and controlling its structural and functional properties. Due to their activated nature, however, rare events are exceptionally difficult to study using conventional experimental and computational techniques. In recent decades, a wide variety of specialized computational techniques-known as advanced sampling techniques-have been developed to systematically capture improbable fluctuations relevant to rare events. In this perspective, we focus on a technique called forward flux sampling [Allen et al., J. Chem. Phys. 124, 024102 (2006)] and overview its recent methodological variants and extensions. We also provide a detailed overview of its application to study a wide variety of rare events and map out potential avenues for further explorations. read less NOT USED (high confidence) G. G. Vogiatzis, L. V. van Breemen, and M. Hütter, “Network Topology of the States Probed by a Glassy Polymer during Physical Aging,” Macromolecular Theory and Simulations. 2019. link Times cited: 4 Abstract: Trajectories of a long-chain atactic polystyrene system, obt… read moreAbstract: Trajectories of a long-chain atactic polystyrene system, obtained from long Molecular Dynamics simulations in the glassy state, are mapped onto a time series of inherent structures of the potential energy landscape. The topology of the network of states formed is analyzed by employing graph-theoretical concepts. It is found that the network of the inherent structures visited by the system in the course of physical aging has both a scale-free and a small-world character. There exist minima acting as highly connected hubs in the network and trench-like sequences of states driving the system from one hub to another. In contrast to previous studies of scale-free networks in other branches of science, where the topology results from the static connectivity of the network's entities, this network is created by adding one-by-one the inherent structures traversed by the system during its evolution in time. read less NOT USED (high confidence) A. Sycheva, E. Voronina, and A. Palov, “Analysis of the Results of Silicon Sputtering Simulation as Functions of Different Ar–Si Potentials,” Journal of Surface Investigation: X-ray, Synchrotron and Neutron Techniques. 2019. link Times cited: 2 NOT USED (high confidence) R. Maiti et al., “Strain-engineered high-responsivity MoTe2 photodetector for silicon photonic integrated circuits,” Nature Photonics. 2019. link Times cited: 148 NOT USED (high confidence) J. Bachler, P. Handle, N. Giovambattista, and T. Loerting, “Glass polymorphism and liquid-liquid phase transition in aqueous solutions: experiments and computer simulations.,” Physical chemistry chemical physics : PCCP. 2019. link Times cited: 24 Abstract: One of the most intriguing anomalies of water is its ability… read moreAbstract: One of the most intriguing anomalies of water is its ability to exist as distinct amorphous ice forms (glass polymorphism or polyamorphism). This resonates well with the possible first-order liquid-liquid phase transition (LLPT) in the supercooled state, where ice is the stable phase. In this Perspective, we review experiments and computer simulations that search for LLPT and polyamorphism in aqueous solutions containing salts and alcohols. Most studies on ionic solutes are devoted to NaCl and LiCl; studies on alcohols have mainly focused on glycerol. Less attention has been paid to protein solutions and hydrophobic solutes, even though they reveal promising avenues. While all solutions show polyamorphism and an LLPT only in dilute, sub-eutectic mixtures, there are differences regarding the nature of the transition. Isocompositional transitions for varying mole fractions are observed in alcohol but not in ionic solutions. This is because water can surround alcohol molecules either in a low- or high-density configuration whereas for ionic solutes, the water ion hydration shell is forced into high-density structures. Consequently, the polyamorphic transition and the LLPT are prevented near the ions, but take place in patches of water within the solutions. We highlight discrepancies and different interpretations within the experimental community as well as the key challenges that need consideration when comparing experiments and simulations. We point out where reinterpretation of past studies helps to draw a unified, consistent picture. In addition to the literature review, we provide original experimental results. A list of eleven open questions that need further consideration is identified. read less NOT USED (high confidence) A. Galashev, K. Ivanichkina, K. Katin, and M. Maslov, “Computational Study of Lithium Intercalation in Silicene Channels on a Carbon Substrate after Nuclear Transmutation Doping,” Comput. 2019. link Times cited: 10 Abstract: Silicene is considered to be the most promising anode materi… read moreAbstract: Silicene is considered to be the most promising anode material for lithium-ion batteries. In this work, we show that transmutation doping makes silicene substantially more suitable for use as an anode material. Pristine and modified bilayer silicene was simulated on a graphite substrate using the classical molecular dynamics method. The parameters of Morse potentials for alloying elements were determined using quantum mechanical calculations. The main advantage of modified silicene is its low deformability during lithium intercalation and its possibility of obtaining a significantly higher battery charge capacity. Horizontal and vertical profiles of the density of lithium as well as distributions of the most significant stresses in the walls of the channels were calculated both in undoped and doped systems with different gaps in silicene channels. The energies of lithium adsorption on silicene, including phosphorus-doped silicene, were determined. High values of the self-diffusion coefficient of lithium atoms in the silicene channels were obtained, which ensured a high cycling rate. The calculations showed that such doping increased the normal stress on the walls of the channel filled with lithium to 67% but did not provoke a loss of mechanical strength. In addition, doping achieved a greater battery capacity and higher charging/discharging rates. read less NOT USED (high confidence) L. Ma, T. Hao, and Z. Hossain, “Size-dependent toughness and strength in defective 3C-SiC nanowires,” Journal of Applied Physics. 2019. link Times cited: 3 Abstract: This paper presents an atomistic understanding of effective … read moreAbstract: This paper presents an atomistic understanding of effective toughness and strength in defective 3C-SiC nanowires of different diameters. We consider a set of high-symmetry vacancy defect clusters and employ a combination of density functional theory and molecular dynamics simulations to calculate stress in the nanowires, using an energy-based approach that does not require use of any macroscopic geometric information of the nanowire. Our results suggest that for defect-free nanowires, cracks nucleate from one of the corners of the hexagonal cross section, whereas for defective nanowires—regardless of the size of the defect core—cracks nucleate from the edge of the defect core. With increasing diameter, both strength and toughness increase in defective or defect-free nanowires. Furthermore, defects alter the size-dependent effective toughness and strength of the nanowire: the larger the size of the defect, the stronger the size-dependence of effective toughness and strength. A single vacancy in a 8.0 nm diameter nanowire reduces effective toughness and strength by around 16.5% and 3.4%, respectively. As diameter approaches ∞, effective stiffness approaches the bulk behavior—whereas neither strength nor toughness approaches the behavior of the bulk. This is primarily because of the presence of the surface and associated sustained stress-localization in the nanowire. Effective toughness and strength are, therefore, controlled by the local critical events and not by the macroscopic features of the nanowire. Additionally, both toughness and strength decrease nonlinearly with increasing temperature due to thermal softening of the material—and this thermal softening is, however, weakly dependent on the size of the defective regime. read less NOT USED (high confidence) S. Pozdnyakov, A. Oganov, E. Mazhnik, A. Mazitov, and I. Kruglov, “Fast general two- and three-body interatomic potential,” Physical Review B. 2019. link Times cited: 6 Abstract: We introduce a new class of machine learning interatomic pot… read moreAbstract: We introduce a new class of machine learning interatomic potentials - fast General Two- and Three-body Potential (GTTP) which are as fast as conventional empirical potentials and require computational time that remains constant with increasing fitting flexibility. GTTP does not contain any assumptions about functional form of two- and three-body interactions. These interactions can be modeled arbitrarily accurately potentially by thousands of parameters not affecting resulting computational cost. Time complexity is O(1) per every considered pair or triple of atoms. The fitting procedure is reduced to simple linear regression on ab initio calculated energies and forces and leads to effective two- and three-body potential which reproduces quantum many-body interactions as accurately as possible. Our potential can be made continuously differentiable any number of times at the expense of increased computational time. We made a number of performance tests on one-, two- and three-component systems. Flexibility of the introduced approach makes the potential transferable in terms of size and type of atomic systems. We show, that trained on randomly generated structures with just 8 atoms in the unit cell, it significantly outperforms common empirical interatomic potentials in the study of large systems, such as grain boundaries in polycrystalline materials. read less NOT USED (high confidence) C. van der Oord, G. Dusson, G. Csányi, and C. Ortner, “Regularised atomic body-ordered permutation-invariant polynomials for the construction of interatomic potentials,” Machine Learning: Science and Technology. 2019. link Times cited: 54 Abstract: We investigate the use of invariant polynomials in the const… read moreAbstract: We investigate the use of invariant polynomials in the construction of data-driven interatomic potentials for material systems. The ‘atomic body-ordered permutation-invariant polynomials’ comprise a systematic basis and are constructed to preserve the symmetry of the potential energy function with respect to rotations and permutations. In contrast to kernel based and artificial neural network models, the explicit decomposition of the total energy as a sum of atomic body-ordered terms allows to keep the dimensionality of the fit reasonably low, up to just 10 for the 5-body terms. The explainability of the potential is aided by this decomposition, as the low body-order components can be studied and interpreted independently. Moreover, although polynomial basis functions are thought to extrapolate poorly, we show that the low dimensionality combined with careful regularisation actually leads to better transferability than the high dimensional, kernel based Gaussian Approximation Potential. read less NOT USED (high confidence) J. Jiang, L. Wang, and Y. Zhang, “Free vibration of single-layered MoS2suspended over a circular hole,” Journal of Applied Physics. 2019. link Times cited: 8 Abstract: The vibrational behaviors of circular single-layered molybde… read moreAbstract: The vibrational behaviors of circular single-layered molybdenum disulfide (CSLMoS2) suspended over a concentric circular hole are investigated using a two-segment circular Kirchhoff plate (TSCKP) corresponding to different initial stresses and molecular dynamics (MD) simulations. An analytical solution is proposed to analyze the free vibrations of the TSCKP model. van der Waals (vdW) interaction coefficient between the single-layered MoS2 (SLMoS2) and the silicon substrate is derived theoretically. MD simulations show that the TSCKP model can give a good prediction to the vibrational behaviors of the CSLMoS2 suspended over a concentric circular hole. The effects of the overlapped width and radial initial stresses on the vibrational behaviors of the CSLMoS2s are investigated. The natural frequencies of the TSCKP model become much closer to those of a one-segment circular Kirchhoff plate with the clamped supported boundary (OSCKP-CC) as the radius of the inner-segment circular plate increases; however, the value predicted by the TSCKP model is always smaller than that predicted by the OSCKP-CC. The TSCKP model can also give a reasonable prediction to the vibrational behaviors of the square SLMoS2 suspended over a concentric circular hole when the overlapped widths between the circular and square SLMoS2s and elastic substrate along any radial direction are sufficiently large.The vibrational behaviors of circular single-layered molybdenum disulfide (CSLMoS2) suspended over a concentric circular hole are investigated using a two-segment circular Kirchhoff plate (TSCKP) corresponding to different initial stresses and molecular dynamics (MD) simulations. An analytical solution is proposed to analyze the free vibrations of the TSCKP model. van der Waals (vdW) interaction coefficient between the single-layered MoS2 (SLMoS2) and the silicon substrate is derived theoretically. MD simulations show that the TSCKP model can give a good prediction to the vibrational behaviors of the CSLMoS2 suspended over a concentric circular hole. The effects of the overlapped width and radial initial stresses on the vibrational behaviors of the CSLMoS2s are investigated. The natural frequencies of the TSCKP model become much closer to those of a one-segment circular Kirchhoff plate with the clamped supported boundary (OSCKP-CC) as the radius of the inner-segment circular plate increases; however, the ... read less NOT USED (high confidence) H. Yapicioglu, C. Sevik, and Y. Karaaslan, “OPTIMIZING THE THERMAL TRANSPORT PROPERTIES OF SINGLE LAYER (2D) TRANSITION METAL DICHALCOGENIDES (TMD),” Eskişehir Technical University Journal of Science and Technology A - Applied Sciences and Engineering. 2019. link Times cited: 4 Abstract: In order to characterize thermal dependent physical properti… read moreAbstract: In order to characterize thermal dependent physical properties of materials, potentially to be used in technological applications, an accurate interatomic-potential parameter set is a must. In general, conjugate-gradient methods and more recently, metaheuristics such as genetic algorithms are employed in determining these interatomic potentials, however, especially the use of metaheuristics specifically designed for optimization of real valued problems such as particle swarm and evaluation strategies are limited in the mentioned problem. In addition, some of these parameters are conflicting in nature, for which multi objective optimization procedures have a great potential for better understanding of these conflicts. In this respect, we aim to present a widely used interatomic potential parameter set, the Stillinger–Weber potential, obtained through three different optimization methods (particle swarm optimization, PSO, covariance matrix adaptation evolution strategies, CMA-ES, and non-dominated sorting genetic algorithm, NSGA-III) for two-dimensional materials MoS 2 , WS 2 , WSe 2 , and MoSe 2 . These two-dimensional transition metal dichalcogenides are considered as a case mainly due to their potential in a variety of promising technologies for next generation flexible and low-power nanoelectronics, (such as photonics, valleytronics, sensing, energy storage, and optoelectronic devices) as well as their excellent physical properties (such as electrical, mechanical, thermal, and optical properties) different from those of their bulk counterparts. The results show that the outputs of all optimization methods converge to ideal values with sufficiently long iterations and at different trials. However, when we consider the results of the statistical analyses of different trials under similar conditions, we observe that the method with the lowest error rate is the CMA-ES. read less NOT USED (high confidence) R. Mukuno and M. Ishimaru, “Application of the Tersoff interatomic potential to pressure-induced polyamorphism of silicon,” Japanese Journal of Applied Physics. 2019. link Times cited: 1 Abstract: Molecular-dynamics simulations of the pressure-induced struc… read moreAbstract: Molecular-dynamics simulations of the pressure-induced structural changes of amorphous Si have been performed using the Tersoff interatomic potential to examine the validity of this potential. Amorphous Si with a tetrahedral network was prepared by melt-quenching methods, and it was then compressed under isothermal–isobaric conditions. The changes of the atomic pair-distribution functions and static structure factors with increasing pressure were in agreement with those observed experimentally. The pressure-induced amorphous structures contained a short-range order similar to the β-tin and Imma structures. These results suggest that the Tersoff potential is suitable for describing the structural changes of amorphous Si under high pressure. read less NOT USED (high confidence) Z. Fan, Y. Wang, X. Gu, P. Qian, Y. Su, and T. Ala‐Nissila, “A minimal Tersoff potential for diamond silicon with improved descriptions of elastic and phonon transport properties,” Journal of Physics: Condensed Matter. 2019. link Times cited: 10 Abstract: Silicon is an important material and many empirical interato… read moreAbstract: Silicon is an important material and many empirical interatomic potentials have been developed for atomistic simulations of it. Among them, the Tersoff potential and its variants are the most popular ones. However, all the existing Tersoff-like potentials fail to reproduce the experimentally measured thermal conductivity of diamond silicon. Here we propose a modified Tersoff potential and develop an efficient open source code called GPUGA (graphics processing units genetic algorithm) based on the genetic algorithm and use it to fit the potential parameters against energy, virial and force data from quantum density functional theory calculations. This potential, which is implemented in the efficient open source GPUMD (graphics processing units molecular dynamics) code, gives significantly improved descriptions of the thermal conductivity and phonon dispersion of diamond silicon as compared to previous Tersoff potentials and at the same time well reproduces the elastic constants. Furthermore, we find that quantum effects on the thermal conductivity of diamond silicon at room temperature are non-negligible but small: using classical statistics underestimates the thermal conductivity by about 10% as compared to using quantum statistics. read less NOT USED (high confidence) M. H. Factorovich, P. M. Naullage, and V. Molinero, “Can clathrates heterogeneously nucleate ice?,” The Journal of chemical physics. 2019. link Times cited: 15 Abstract: Methane hydrates can be preserved at ambient pressure, beyon… read moreAbstract: Methane hydrates can be preserved at ambient pressure, beyond their region of thermodynamic stability, by storing them at temperatures from 240 to 270 K. The origin of this anomalous self-preservation is the formation of an ice coating that covers the clathrate particles and prevents further loss of gas. While there have been several studies on self-preservation, the question of what is the mechanism by which ice nucleates on the decomposing clathrate hydrates has not yet been fully explained. Here, we use molecular simulations, thermodynamic analysis, and nucleation theory to investigate possible scenarios for the nucleation of ice: heterogeneous nucleation at the clathrate/vapor or clathrate/liquid interfaces and homogeneous nucleation from supercooled water. Our results indicate that clathrates cannot heterogeneously nucleate ice and that ice nucleation is due to the cooling of water at the decomposing clathrate/liquid interface, which suffices to trigger homogeneous ice nucleation. We find that the (111) face of the sII structure clathrate can bind to the (111) plane of cubic ice or the basal plane of hexagonal ice through domain matching, resulting in a weak binding that-while insufficient to promote heterogeneous ice nucleation-suffices to produce epitaxy and alignment between these crystals. We use thermodynamic relations, theory, and the contact angles of ice at the (111) sII clathrate/liquid interface to determine-for the first time-the interfacial free energy of this most favorable ice-clathrate interface, 59 ± 5 mJ/m2. We discuss the implications of our results for the feasibility of heterogeneous nucleation of gas clathrates at ice/vapor interfaces. read less NOT USED (high confidence) M. Comin and L. J. Lewis, “Deep-learning approach to the structure of amorphous silicon,” Physical Review B. 2019. link Times cited: 6 Abstract: We present a deep-learning approach for modeling the atomic … read moreAbstract: We present a deep-learning approach for modeling the atomic structure of amorphous silicon ( a -Si). While accurate models of disordered systems require an ab initio description of the energy landscape which severely limits the attainable system size, large-scale models rely on empirical potentials, at the price of reduced reliability and a computational load that is still restricting for many purposes. In this paper, we explore an approach based on deep learning, particularly generative modeling that could reconcile both requirements of accuracy and efficiency by learning structural features from data. When trained on a set of observations, such models can generate new structures very efficiently with the desired level of accuracy, as determined by the data set. We first validate our approach by training a convolutional neural network to approximate the potential-energy surface of a -Si, as given by the Stillinger-Weber potential, which results in a root-mean-square error of 5.05 meV per atom—about 0 . 16% of the atomic energy. We then train a deep generative model, the Wasserstein autoencoder, for the generation of a -Si configurations. Our approach leads to models which exhibit some of the essential features of a -Si while possessing too much structural disorder, thus suggesting that the method is viable; we indicate avenues for improving it towards the generation of state-of-the-art structures. read less NOT USED (high confidence) V. L. Deringer, M. A. Caro, and G. Csányi, “Machine Learning Interatomic Potentials as Emerging Tools for Materials Science,” Advanced Materials. 2019. link Times cited: 245 Abstract: Atomic‐scale modeling and understanding of materials have ma… read moreAbstract: Atomic‐scale modeling and understanding of materials have made remarkable progress, but they are still fundamentally limited by the large computational cost of explicit electronic‐structure methods such as density‐functional theory. This Progress Report shows how machine learning (ML) is currently enabling a new degree of realism in materials modeling: by “learning” electronic‐structure data, ML‐based interatomic potentials give access to atomistic simulations that reach similar accuracy levels but are orders of magnitude faster. A brief introduction to the new tools is given, and then, applications to some select problems in materials science are highlighted: phase‐change materials for memory devices; nanoparticle catalysts; and carbon‐based electrodes for chemical sensing, supercapacitors, and batteries. It is hoped that the present work will inspire the development and wider use of ML‐based interatomic potentials in diverse areas of materials research. read less NOT USED (high confidence) I. Y. Zabavichev, A. A. Potehin, A. S. Puzanov, S. V. Obolenskiy, and V. Kozlov, “Simulation of the Formation of a Cascade of Displacements and Transient Ionization Processes in Silicon Semiconductor Structures under Neutron Exposure,” Semiconductors. 2019. link Times cited: 2 NOT USED (high confidence) C. Chen et al., “Vacancy-assisted core transformation and mobility modulation of a-type edge dislocations in wurtzite GaN,” Journal of Physics D: Applied Physics. 2019. link Times cited: 3 Abstract: In this study, core structure dependent dislocation dynamics… read moreAbstract: In this study, core structure dependent dislocation dynamics of a-type edge dislocation in three slip systems (basal, prismatic and pyramidal) of wurtzite GaN have been investigated using classical molecular dynamics simulations. All potential a-type edge dislocation cores in the shuffle and glide planes of the three slip systems have been identified, and the corresponding dislocation dynamics were examined. Our calculations reveal that for all of the three slip systems, all of the shuffle cores are planar glissile and mobile, while being non-planar sessile and immobile for all of the glide cores. We further show that vacancy can be used to activate the motion of glide cores via core transition from glide to shuffle, which is also valid for AlN and InN. The critical shear stresses for the motion of glide cores are also determined at various vacancy concentrations. Our study clarifies core structure dependent dislocation dynamics characteristics and provides ways in tuning dislocation motions in wurtzite crystals. read less NOT USED (high confidence) P. Gallo, “On the Crack‐Tip Region Stress Field in Molecular Systems: The Case of Ideal Brittle Fracture,” Advanced Theory and Simulations. 2019. link Times cited: 13 Abstract: Continuum‐based fracture mechanics breaks down at the nanosc… read moreAbstract: Continuum‐based fracture mechanics breaks down at the nanoscale where the discrete nature of atoms cannot be neglected. Intriguingly, this work shows that the concept of stress intensity factor is still valid if the atoms are modeled. Molecular statistics simulations are conducted on single‐edge cracked samples of ideal brittle silicon, varying the size until few nanometers. The local virial stress, derived as the functional derivative of the free energy of a molecular system with respect to the deformation tensor, is used as a measure of the mechanical stress at the atomic level. Then, stress intensity factor at failure is evaluated. The results show that regardless of the size, the atomistic stress field varies according to the classical 1/r0.5 relation, and discrete stress intensity factors can be derived for all the geometries. Continuum values, in contrast, fail to describe the fracture when the length of the singular stress field is smaller than 4–5 times the fracture process zone. Thus, this work shows that the stress intensity factor from atomic stress may be useful to describe the fracture criterion at extremely small dimensions, provided that virial stress is accepted as a representation of mechanical stress at the atomic level. read less NOT USED (high confidence) M. N. Esfahani, B. E. Alaca, and M. Jabbari, “Mechanical properties of honeycomb nanoporous silicon: a high strength and ductile structure,” Nanotechnology. 2019. link Times cited: 7 Abstract: There are remarkable studies geared towards developing mecha… read moreAbstract: There are remarkable studies geared towards developing mechanical analysis of nanoporous structures, while the size effect has been a major concern so far to improve strength or deformability. In this study, molecular dynamics simulations are utilized to study the pore shape effect on the mechanical behaviour of nanoporous silicon with circular, elliptical, square and hexagonal pore shapes. The influence of pore configuration on load transfer capabilities is studied for nanoporous silicon. A distinguished set of mechanical properties is observed on silicon with a hexagonal pore shape—resembling a honeycomb structure—with a high tensile strength and toughness. The study exhibits an improvement in the ductility through unique stress transformation in the hexagonal pore shape. In addition to the relative density, the potential to control the mechanical properties is demonstrated through the hexagon angle. Finally, a scaling law is developed for the mechanical behaviour of honeycomb nanoporous silicon. In addition to their outstanding mechanical properties, the work provides further insight into the capability of nanoporous structures in sensing applications due to their high surface-to-volume ratios. read less NOT USED (high confidence) E. J. Ragasa, C. J. O’Brien, R. G. Hennig, S. Foiles, and S. Phillpot, “Multi-objective optimization of interatomic potentials with application to MgO,” Modelling and Simulation in Materials Science and Engineering. 2019. link Times cited: 6 Abstract: The parameterization of a functional form for an interatomic… read moreAbstract: The parameterization of a functional form for an interatomic potential is treated as a problem in multi-objective optimization. An autonomous, machine-learning approach based on the identification of the Pareto hypersurface of errors in predicted properties allows the development of an ensemble of parameterizations with high materials fidelity and robustness. The efficacy of this approach is illustrated for the simple example of a Buckingham potential for MgO. This approach also provides a strong foundation for uncertainty quantification of potential parameterizations. read less NOT USED (high confidence) A. Giri and P. Hopkins, “A Review of Experimental and Computational Advances in Thermal Boundary Conductance and Nanoscale Thermal Transport across Solid Interfaces,” Advanced Functional Materials. 2019. link Times cited: 144 Abstract: Interfacial thermal resistance is the primary impediment to … read moreAbstract: Interfacial thermal resistance is the primary impediment to heat flow in materials and devices as characteristic lengths become comparable to the mean‐free paths of the energy carriers. This thermal boundary conductance across solid interfaces at the nanoscale can affect a plethora of applications. The recent experimental and computational advances that have led to significant atomistic insights into the nanoscopic thermal transport mechanisms at interfaces between various types of materials are summarized. The authors focus on discussions of works that have pushed the limits to interfacial heat transfer and drastically increased the understanding of thermal boundary conductance on the atomic and nanometer scales near solid/solid interfaces. Specifically, the role of localized interfacial modes on the energy conversion processes occurring at interfaces is emphasized in this review. The authors also focus on experiments and computational works that have challenged the traditionally used phonon gas models in interpreting the physical mechanisms driving interfacial energy transport. Finally, the authors discuss the future directions and avenues of research that can further the knowledge of heat transfer across systems with broken symmetries. read less NOT USED (high confidence) E. Zhang, Y.-H. Yao, T. Gao, D. Kang, J. Wu, and J. Dai, “The effect of external temperature gradients on thermal conductivity in non-equilibrium molecular dynamics simulations: From nanowires to bulk Si,” The Journal of Chemical Physics. 2019. link Times cited: 6 Abstract: Nonequilibrium molecular dynamics is widely used to calculat… read moreAbstract: Nonequilibrium molecular dynamics is widely used to calculate the thermal conductivity of various materials, but the influence of temperature gradient to thermal conductivity has received limited attention within current research studies. The purpose of this article is to explore the discrepancy between intrinsic and extrinsic thermal conductivities under different temperature gradients, which can be considered as external fields. The analyses of phonon density of states have shown that the temperature gradient plays a role in the external field, and a larger temperature gradient activates more low-frequency vibrational modes, which leads to larger thermal conductivities. Specially, the thermal conductivity increases linearly with the temperature gradient when using Stillinger-Weber (SW) potential. Moreover, a new formula was derived to satisfactorily fit the thermal conductivities of bulk Si and silicon nanowires (SiNWs) for various cell sizes, and the physical meaning of the formula was explained. It is shown that the SW potential and Tersoff potential of Si produce different thermal conductivities. By comparing the results of first principles simulations, the Tersoff potential gives rise to better description of vibrational modes. read less NOT USED (high confidence) F. Ricci, J. Palmer, Y. Goswami, S. Sastry, C. Angell, and P. Debenedetti, “A computational investigation of the thermodynamics of the Stillinger-Weber family of models at supercooled conditions,” Molecular Physics. 2019. link Times cited: 8 Abstract: The existence of metastable liquid-liquid phase transitions … read moreAbstract: The existence of metastable liquid-liquid phase transitions (LLPTs) in tetrahedral liquids such as water, silicon, and silica has been the subject of vigorous scientific debate. Because high crystallization rates hinder experimental investigation at deeply supercooled conditions, computer simulation has been widely employed to investigate the existence of LLPTs in molecular models of tetrahedral liquids. The Stillinger-Weber (SW) model of silicon (and more generally, the SW family of models) has been actively studied along these lines. Whereas some studies observe evidence of an LLPT in this model, others report that only a single metastable liquid exists under deeply supercooled conditions. Here, we perform extensive state-of-the-art free energy calculations to investigate the possibility of an LLPT in the SW model of silicon. A similar analysis is also presented for the generalized SW family of models constructed by varying the strength of the three-body energetic term. Our analysis does not show any evidence of an LLPT in SW silicon nor in the generalized family of SW models over the parameter ranges studied. Explanations for the aforementioned discrepancies between previous studies are provided, along with explicit demonstrations of how these discrepancies may have occurred. Outstanding ambiguities and directions for future work are also discussed. GRAPHICAL ABSTRACT read less NOT USED (high confidence) J. Schmidt, M. R. G. Marques, S. Botti, and M. A. L. Marques, “Recent advances and applications of machine learning in solid-state materials science,” npj Computational Materials. 2019. link Times cited: 1226 NOT USED (high confidence) X. Zhang, S. Sun, T. Xu, and T.-Y. Zhang, “Temperature dependent Grüneisen parameter,” Science China Technological Sciences. 2019. link Times cited: 12 NOT USED (high confidence) B. Huang, G. Li, X.-qiu Yang, and P. Zhai, “Capturing anharmonic and anisotropic natures in the thermotics and mechanics of Bi2Te3 thermoelectric material through an accurate and efficient potential,” Journal of Physics D: Applied Physics. 2019. link Times cited: 9 Abstract: Force-field-(FF)-based molecular simulation is essential but… read moreAbstract: Force-field-(FF)-based molecular simulation is essential but challenging in the theoretical research of complex thermoelectric (TE) materials. As they are general and crucial in TE semiconductors, the structural natures of anharmonicity and anisotropy can help us understand the inherent relation between thermal and mechanical behavior, and therefore the reliability of FF studies can be assessed. In this paper, given prior knowledge of the structural, mechanical and thermal properties as well as the limitations and necessary approximations of the FF method, a feasible and detailed FF modeling scheme and simulation has been designed for Bi2Te3, which is a typical high-performance TE material. Using the complementary approach combining quasi-harmonic lattice and molecular dynamics, the obtained potential is systematically confirmed to be accurate and efficient for the prediction of anharmonic and anisotropic behavior in thermotics and mechanics over a wide temperature range compared with the present Bi2Te3 models. This reveals that the intrinsic anisotropy and anharmonicity can measure the asymmetry of crystal lattices and the interatomic force in the current state. In addition, the significant distinction of temperature-dependent anharmonic effects in different directions of Bi2Te3 stems from its layered hierarchical structure, in which weak van der Waals bonding will probably be the key structural factor in comprehensively improving performance for mass production and wearable application. This prior-knowledge-based FF study is also suggested as a bridge between the theoretical understanding of micro-mechanisms and the experimental measurement of TE material properties, leading to a general framework of molecular simulation for other complex energy materials. read less NOT USED (high confidence) L. Deng, N. Zhou, S. Tang, and Y. Li, “Improved Dreiding force field for single layer black phosphorus.,” Physical chemistry chemical physics : PCCP. 2019. link Times cited: 7 Abstract: We present an improved Dreiding force field for single layer… read moreAbstract: We present an improved Dreiding force field for single layer black phosphorus (SLBP) obtained by first-principle calculations in conjunction with the particle swarm optimization algorithm and molecular dynamics (MD) simulations. The proposed Dreiding force field can describe material properties of the SLBP very well in comparison with first-principle calculations and the Stillinger-Weber potential, including Young's modulus, Poisson's ratio, shear modulus, bending stiffness and phonon spectrum. Through the improved Dreiding force field, the wetting of a water nanodroplet and the adsorption of a villin headpiece on SLBP under compressive deformation are also studied by MD simulations. The simulation results show that the microscopic contact angle increases with the level of compressive strain on the SLBP. Meanwhile, the compressive strain reduces disruption caused by SLBP to the structure of the villin headpiece. The proposed Dreiding force field shows great potential to describe the interaction between SLBP and water molecules. It can be further used to simulate the transport of water on SLBP, especially under mechanical deformation, and interactions between SLBP and biological systems. read less NOT USED (high confidence) J. Nie, S. Porowski, and P. Keblinski, “Using pressure to probe thermodynamic anomalies in tetrahedrally-bonded materials,” Journal of Applied Physics. 2019. link Times cited: 1 Abstract: Tetrahedrally-bonded materials, such as silicon, diamond, or… read moreAbstract: Tetrahedrally-bonded materials, such as silicon, diamond, or gallium nitride, are characterized by a low coordination number of 4 in the crystalline phase and, in general, can exhibit a liquid phase with higher density and coordination. This leads to interesting thermodynamic behavior, including the lowering of the melting temperature with increasing pressure and the possible existence of distinct low- and high-density liquid phases. Using molecular dynamics simulations, we explored the role of pressure and the degree of tetrahedrality on the structure and phase equilibria between the crystalline and liquid phases of tetrahedrally-bonded materials. In addition to the thermodynamic melting point, we determined the temperature of mechanical stability (spinodal temperature) as a function of pressure. The latter temperature is relevant to the laser pulse rapid melting of tetrahedrally-bonded materials. The results of our simulations indicate the possibility of the existence of a thermodynamically stable low-density liquid phase of silicon at high pressures. Our simulation also suggests that GaN is unlikely to exhibit anomalous thermodynamic behavior due to a high degree of tetragonality preventing the formation of high-density liquid, even at high pressures.Tetrahedrally-bonded materials, such as silicon, diamond, or gallium nitride, are characterized by a low coordination number of 4 in the crystalline phase and, in general, can exhibit a liquid phase with higher density and coordination. This leads to interesting thermodynamic behavior, including the lowering of the melting temperature with increasing pressure and the possible existence of distinct low- and high-density liquid phases. Using molecular dynamics simulations, we explored the role of pressure and the degree of tetrahedrality on the structure and phase equilibria between the crystalline and liquid phases of tetrahedrally-bonded materials. In addition to the thermodynamic melting point, we determined the temperature of mechanical stability (spinodal temperature) as a function of pressure. The latter temperature is relevant to the laser pulse rapid melting of tetrahedrally-bonded materials. The results of our simulations indicate the possibility of the existence of a thermodynamically stable low-d... read less NOT USED (high confidence) D. Fijan and M. Wilson, “The interactions between thermodynamic anomalies.,” The Journal of chemical physics. 2019. link Times cited: 4 Abstract: The origin of and interactions between key thermodynamic ano… read moreAbstract: The origin of and interactions between key thermodynamic anomalies are derived and analyzed, as are the interactions with the stability (or cavitation) limits. The conditions for interaction are derived from the underlying thermodynamic relations rather than using the more-commonly applied Taylor expansion method. As a result, we derive a general set of equations that govern the interactions between different lines of thermodynamic anomalies using standard manipulation of thermodynamic equations. The validity of the derivations is investigated by comparing them to numerical simulation data and previous Taylor expansion-based results. Simulations are performed using a modified Stillinger-Weber potential in which the balance of the two- and three-body interactions is varied and which serves to highlight the relationships between the various anomalies. The deeply supercooled regime is explored by employing replica exchange methods. The behavior of the anomalies is considered in terms of previously constructed thermodynamic "scenarios." Based on the newly uncovered interaction schemes, we propose a classification strategy for the thermodynamic anomalies (as first- or second-order) which could be extended to additional related anomalies. read less NOT USED (high confidence) L. A. S. de Oliveira and N. Neophytou, “Large-scale molecular dynamics investigation of geometrical features in nanoporous Si,” Physical Review B. 2019. link Times cited: 14 Abstract: Nanoporous materials are of broad interest for various appli… read moreAbstract: Nanoporous materials are of broad interest for various applications, in particular, advanced thermoelectric materials. The introduction of nanoscale porosity, even at modest levels, has been known to drastically reduce a material's thermal conductivity, in some cases even below its amorphous limit, thereby significantly increasing its thermoelectric figure of merit ZT. The details of the important attributes that drive these large reductions, however, are not yet clear. In this work, we employ large-scale equilibrium molecular dynamics to perform an exhaustive atomistic-scale investigation of the effect of porosity on thermal transport in nanoporous bulk silicon. Thermal transport is computed for over 50 different geometries, spanning a large number of geometrical degrees of freedom, such as cylindrical pores and voids, different porosities, diameters, neck sizes, pore/void numbers, and surface-to-volume ratios, placed in ordered fashion, or fully disordered. We thus quantify and compare the most important parameters that determine the thermal conductivity reductions in nanoporous materials. Ultimately, we find that, even at the nanoscale, the effect of merely reducing the line-of-sight of phonons, i.e., the clear pathways that phonons can utilize during transport, plays the most crucial role in reducing the thermal conductivity in nanoporous materials, beyond other metrics such as porosity and surface/boundary scattering. read less NOT USED (high confidence) R. Lot, F. Pellegrini, Y. Shaidu, and E. Küçükbenli, “PANNA: Properties from Artificial Neural Network Architectures,” Comput. Phys. Commun. 2019. link Times cited: 34 NOT USED (high confidence) E. Kocer, J. Mason, and H. Erturk, “Continuous and optimally complete description of chemical environments using Spherical Bessel descriptors,” AIP Advances. 2019. link Times cited: 18 Abstract: Recently, machine learning potentials have been advanced as … read moreAbstract: Recently, machine learning potentials have been advanced as candidates to combine the high-accuracy of quantum mechanical simulations with the speed of classical interatomic potentials. A crucial component of a machine learning potential is the description of local atomic environments by some set of descriptors. These should ideally be continuous throughout the specified local atomic environment, twice-differentiable with respect to atomic positions and complete in the sense of containing all possible information about the neighborhood. An updated version of the recently proposed Spherical Bessel descriptors satisfies all three of these properties, and moreover is optimally complete in the sense of encoding all configurational information with the smallest possible number of descriptors. The Smooth Overlap of Atomic Position descriptors that are frequently visited in the literature and the Zernike descriptors that are built upon a similar basis are included into the discussion as being the natural counterparts of the Spherical Bessel descriptors, and shown to be incapable of satisfying the full list of core requirements for an accurate description. Aside being mathematically and physically superior, the Spherical Bessel descriptors have also the advantage of allowing machine learning potentials of comparable accuracy that require roughly an order of magnitude less computation time per evaluation than the Smooth Overlap of Atomic Position descriptors, which appear to be the common choice of descriptors in recent studies. read less NOT USED (high confidence) I. Talyzin, M. V. Samsonov, V. Samsonov, M. Y. Pushkar,’ and V. V. Dronnikov, “Size Dependence of the Melting Point of Silicon Nanoparticles: Molecular Dynamics and Thermodynamic Simulation,” Semiconductors. 2019. link Times cited: 12 NOT USED (high confidence) S. Yesudasan, “Extended MARTINI water model for heat transfer studies,” Molecular Physics. 2019. link Times cited: 9 Abstract: The computationally efficient classical MARTINI model is ext… read moreAbstract: The computationally efficient classical MARTINI model is extended to simulate heat transfer simulations of water. The current MARTINI model, variations of it and other coarse grain water models focus on reproducing the thermodynamic properties below or at room temperature, hence making them unsuitable for studying high temperature simulations especially evaporation at . In this work, the MARTINI model is reparametrised using a combination of Genetic Algorithm, Artificial Neural Network and Nelder–Mead optimisation technique to match the phase equilibrium properties of water. The reparametrised model (MARTINI-E) accurately reproduces density, enthalpy of vaporisation and surface tension at and outperforms other leading coarse grain water models. The model is also validated using the energy conservation and enthalpy change due to latent heat in a lamellar system. This new water model can be used for simulating phase change phenomena, thin film evaporation and other energy transport mechanisms accurately. GRAPHICAL ABSTRACT read less NOT USED (high confidence) H. Hieu et al., “Structural and Thermomechanical Properties of Zincblende-Type ZnX (X = S, Se, Te),” Journal of Electronic Materials. 2019. link Times cited: 1 NOT USED (high confidence) O. Yenigun and M. Barisik, “Electric Field Controlled Heat Transfer Through Silicon and Nano-confined Water,” Nanoscale and Microscale Thermophysical Engineering. 2019. link Times cited: 9 Abstract: ABSTRACT Nanoscale heat transfer between two parallel silico… read moreAbstract: ABSTRACT Nanoscale heat transfer between two parallel silicon slabs filled with deionized water was studied under varying electric field in heat transfer direction. Two oppositely charged electrodes were embedded into the silicon walls to create a uniform electric field perpendicular to the surface, similar to electrowetting-on-dielectric technologies. Through the electrostatic interactions, (i) surface charge altered the silicon/water interface energy and (ii) electric field created orientation polarization of water by aligning dipoles to the direction of the electric field. We found that the first mechanism can manipulate the interface thermal resistance and the later can change the thermal conductivity of water. By increasing electric field, Kapitza length substantially decreased to 1/5 of its original value due to enhanced water layering, but also the water thermal conductivity lessened slightly since water dynamics were restricted; in this range of electric field, heat transfer was doubled. With a further increase of the electric field, electro-freezing (EF) developed as the aligned water dipoles formed a crystalline structure. During EF (0.53 V/nm), water thermal conductivity increased to 1.5 times of its thermodynamic value while Kapitza did not change; but once the EF is formed, both Kapitza and conductivity remained constant with increasing electric field. Overall, the heat transfer rate increased 2.25 times at 0.53 V/nm after which it remains constant with further increase of the electric field. read less NOT USED (high confidence) S. Abdullah, R. Aguirre, X. W. Zhou, and D. Zubia, “Growth Evolution of Polycrystalline CdTe/CdS with Atomic Scale Resolution via Molecular Dynamics,” 2019 IEEE 46th Photovoltaic Specialists Conference (PVSC). 2019. link Times cited: 1 Abstract: A new method to study polycrystalline growth of CdTe layers … read moreAbstract: A new method to study polycrystalline growth of CdTe layers has been developed using Molecular Dynamics (MD). The results show the creation of polycrystalline CdTe/CdS structures that closely recreate the morphology of experimental polycrystalline growth. The growth shows the nucleation and coalescence of grains at early stages for CdS on amorphous CdS and CdTe on polycrystalline CdS. read less NOT USED (high confidence) H. Dai, H. Du, J. Chen, and G. Chen, “Influence of elliptical vibration on the behavior of silicon during nanocutting,” The International Journal of Advanced Manufacturing Technology. 2019. link Times cited: 25 NOT USED (high confidence) M. Höhnerbach and P. Bientinesi, “Accelerating AIREBO: Navigating the Journey from Legacy to High‐Performance Code,” Journal of Computational Chemistry. 2019. link Times cited: 6 Abstract: Despite initiatives to improve the quality of scientific sof… read moreAbstract: Despite initiatives to improve the quality of scientific software, there still is a large presence of legacy code. The focus of such code is usually on domain‐science features, rather than maintainability or highest performance. Additionally, architecture specific optimizations often result in less maintainable code. In this article, we focus on the AIREBO potential from LAMMPS, which exhibits large and complex computational kernels, hindering any systematic optimization. We suggest an approach based on complexity‐reducing refactoring and hardware abstraction and present the journey from the C++ port of a previous Fortran code to performance‐portable, KNC‐hybrid, vectorized, scalable, and optimized code supporting full and reduced precision. The journey includes extensive testing that fixed bugs in the original code. Large‐scale, full‐precision runs sustain speedups of more than 4× (KNL) and 3× (Skylake). © 2019 Wiley Periodicals, Inc. read less NOT USED (high confidence) H. Babaei, R. Guo, A. Hashemi, and S. Lee, “Machine-learning-based interatomic potential for phonon transport in perfect crystalline Si and crystalline Si with vacancies,” Physical Review Materials. 2019. link Times cited: 30 Abstract: We report that single interatomic potential, developed using… read moreAbstract: We report that single interatomic potential, developed using Gaussian regression of density functional theory calculation data, has high accuracy and flexibility to describe phonon transport with ab initio accuracy in two different atomistic configurations: perfect crystalline Si and crystalline Si with vacancies. The high accuracy of second- and third-order force constants from the Gaussian approximation potential (GAP) are demonstrated with phonon dispersion, Gruneisen parameter, three-phonon scattering rate, phonon-vacancy scattering rate, and thermal conductivity, all of which are very close to the results from density functional theory calculation. We also show that the widely used empirical potentials (Stillinger-Weber and Tersoff) produce much larger errors compared to the GAP. The computational cost of GAP is higher than the two empirical potentials, but five orders of magnitude lower than the density functional theory calculation. Our work shows that GAP can provide a new opportunity for studying phonon transport in partially disordered crystalline phases with the high predictive power of ab initio calculation but at a feasible computational cost. read less NOT USED (high confidence) A. Glielmo, C. Zeni, ’A. Fekete, and A. Vita, “Building Nonparametric n-Body Force Fields Using Gaussian Process Regression,” Machine Learning Meets Quantum Physics. 2019. link Times cited: 8 NOT USED (high confidence) M. M. Huda, T. Yagasaki, M. Matsumoto, and H. Tanaka, “Negative Thermal Expansivity of Ice: Comparison of the Monatomic mW Model with the All-Atom TIP4P/2005 Water Model,” Crystals. 2019. link Times cited: 2 Abstract: We calculate the thermal expansivity of ice I for the monato… read moreAbstract: We calculate the thermal expansivity of ice I for the monatomic mW model using the quasi-harmonic approximation. It is found that the original mW model is unable to reproduce the negative thermal expansivity experimentally observed at low temperatures. A simple prescription is proposed to recover the negative thermal expansion by re-adjusting the so-called tetrahedrality parameter, λ. We investigate the relation between the λ value and the Grüneisen parameter to explain the origin of negative thermal expansion in the mW model and compare it with an all-atom water model that allows the examination of the effect of the rotational motions on the volume of ice. read less NOT USED (high confidence) E. Schmidt, “Atomistic modelling of precipitation in Ni-base superalloys.” 2019. link Times cited: 0 Abstract: The presence of the ordered γ ′ phase (Ni3Al) in Ni-base sup… read moreAbstract: The presence of the ordered γ ′ phase (Ni3Al) in Ni-base superalloys is fundamental to the performance of engineering components such as turbine disks and blades which operate at high temperatures and loads. Hence for these alloys it is important to optimize their microstructure and phase composition. This is typically done by varying their chemistry and heat treatment to achieve an appropriate balance between γ ′ content and other constituents such as carbides, borides, oxides and topologically close packed phases. In this work we have set out to investigate the onset of γ ′ ordering in Ni-Al single crystals and in Ni-Al bicrystals containing coincidence site lattice grain boundaries (GBs) and we do this at high temperatures, which are representative of typical heat treatment schedules including quenching and annealing. For this we use the atomistic simulation methods of molecular dynamics (MD) and density functional theory (DFT). In the first part of this work we develop robust Bayesian classifiers to identify the γ ′ phase in large scale simulation boxes at high temperatures around 1500 K. We observe significant γ ′ ordering in the simulations in the form of clusters of γ ′-like ordered atoms embedded in a γ host solid solution and this happens within 100 ns. Single crystals are found to exhibit the expected homogeneous ordering with slight indications of chemical composition change and a positive correlation between the Al concentration and the concentration of γ ′ phase. In general, the ordering is found to take place faster in systems with GBs and preferentially adjacent to the GBs. The sole exception to this is the Σ3 (111) tilt GB, which is a coherent twin. An analysis of the ensemble and time lag average displacements of the GBs reveals mostly ‘anomalous diffusion’ behaviour. Increasing the Al content from pure Ni to Ni 20 at.% Al was found to either consistently increase or decrease the mobility of the GB as seen from the changing slope of the time lag displacement average. The movement of the GB can then be characterized as either ‘super’ or ‘sub-diffusive’ and is interpreted in terms of diffusion induced grain boundary migration, which is posited as a possible precursor to the appearance of serrated edge grain boundaries. In the second part of this work we develop a method for the training of empirical interatomic read less NOT USED (high confidence) M. Marriott, L. Lupi, A. Kumar, and V. Molinero, “Following the nucleation pathway from disordered liquid to gyroid mesophase.,” The Journal of chemical physics. 2019. link Times cited: 3 Abstract: Mesophases have order intermediate between liquids and cryst… read moreAbstract: Mesophases have order intermediate between liquids and crystals and arise in systems with frustration, such as surfactants, block copolymers, and Janus nanoparticles. The gyroid mesophase contains two interpenetrated, nonintersecting chiral networks that give it properties useful for photonics. It is challenging to nucleate a gyroid from the liquid. Elucidating the reaction coordinate for gyroid nucleation could assist in designing additives that facilitate the formation of the mesophase. However, the complexity of the gyroid structure and the extreme weakness of the first-order liquid to gyroid transition make this a challenging quest. Here, we investigate the pathway and transition states for the nucleation of a gyroid from the liquid in molecular simulations with a mesogenic binary mixture. We find that the gyroid nuclei at the transition states have a large degree of positional disorder and are not compact, consistent with the low surface free energy of the liquid-gyroid interface. A combination of bond-order parameters for the minor component is best to describe the passage from liquid to gyroid, among those we consider. The committor analyses, however, show that this best coordinate is not perfect and suggests that accounting for the relative ordering of the two interpenetrated networks in infant nuclei, as well as for signatures of ordering in the major component of the mesophase, would improve the accuracy of the reaction coordinate for gyroid formation and its use to evaluate nucleation barriers. To our knowledge, this study is the first to investigate the reaction coordinate and critical nuclei for the formation of any mesophase from an amorphous phase. read less NOT USED (high confidence) V. Kuryliuk, O. Nepochatyi, P. Chantrenne, D. Lacroix, and M. Isaiev, “Thermal conductivity of strained silicon: Molecular dynamics insight and kinetic theory approach,” Journal of Applied Physics. 2019. link Times cited: 15 Abstract: In this work, we investigated tensile and compression forces… read moreAbstract: In this work, we investigated tensile and compression forces effect on the thermal conductivity of silicon. We used equilibrium molecular dynamics approach for the evaluation of thermal conductivity considering different interatomic potentials. More specifically, we tested Stillinger-Weber, Tersoff, Environment-Dependent Interatomic Potential and Modified Embedded Atom Method potentials for the description of silicon atom motion under different strain and temperature conditions. Additionally, we extracted phonon density of states and dispersion curves from molecular dynamics simulations. These data were used for direct calculations of thermal conductivity considering the kinetic theory approach. Comparison of molecular dynamics and kinetic theory simulations results as a function of strain and temperature allowed us to investigate the different factors affecting the thermal conductivity of strained silicon. read less NOT USED (high confidence) H. Dai, F. Zhang, Y. Zhou, and J. Chen, “Numerical study of three-body diamond abrasive nanoindentation of single-crystal Si by molecular dynamics simulation,” Applied Physics A. 2019. link Times cited: 11 NOT USED (high confidence) H. Dai, F. Zhang, Y. Zhou, and J. Chen, “Numerical study of three-body diamond abrasive nanoindentation of single-crystal Si by molecular dynamics simulation,” Applied Physics A. 2019. link Times cited: 0 NOT USED (high confidence) S. Prado, J. Rino, and E. D. Zanotto, “Successful test of the classical nucleation theory by molecular dynamic simulations of BaS,” Computational Materials Science. 2019. link Times cited: 23 NOT USED (high confidence) H. N. Pishkenari and P. Delafrouz, “Modeling Vibrational Behavior of Silicon Nanowires Using Accelerated Molecular Dynamics Simulations,” Scientia Iranica. 2019. link Times cited: 0 Abstract: The classical methods utilized for modeling the nano-scale s… read moreAbstract: The classical methods utilized for modeling the nano-scale systems are not practical because of the enlarged surface effects that appear at small dimensions. Contrarily, implementing more accurate methods results in prolonged computations as these methods are highly dependent on quantum and atomistic models and they can be employed for very small sizes in brief time periods. In order to speed up the molecular dynamics (MD) simulations of the silicon structures, coarse-graining (CG) models are put forward in this research. The procedure consists of establishing a map between the main structure’s atoms and the beads comprising the CG model and modifying the systems parameters such that the original and the CG models reach identical physical parameters. The accuracy and speed of this model is investigated by carrying out various static and dynamic simulations and assessing the effect of size. The simulations show that for a nanowire with thickness over 10a, where parameter a is the lattice constant of diamond structure, the Young modulus obtained by CG and MD models differs less than 5 percent. The results also show that the corresponding CG model behaves 190 time faster compared to the AA model. read less NOT USED (high confidence) E. Kocer, J. Mason, and H. Erturk, “A novel approach to describe chemical environments in high-dimensional neural network potentials.,” The Journal of chemical physics. 2019. link Times cited: 24 Abstract: A central concern of molecular dynamics simulations is the p… read moreAbstract: A central concern of molecular dynamics simulations is the potential energy surfaces that govern atomic interactions. These hypersurfaces define the potential energy of the system and have generally been calculated using either predefined analytical formulas (classical) or quantum mechanical simulations (ab initio). The former can accurately reproduce only a selection of material properties, whereas the latter is restricted to short simulation times and small systems. Machine learning potentials have recently emerged as a third approach to model atomic interactions, and are purported to offer the accuracy of ab initio simulations with the speed of classical potentials. However, the performance of machine learning potentials depends crucially on the description of a local atomic environment. A set of invariant, orthogonal, and differentiable descriptors for an atomic environment is proposed, implemented in a neural network potential for solid-state silicon, and tested in molecular dynamics simulations. Neural networks using the proposed descriptors are found to outperform ones using the Behler-Parinello and smooth overlap of atomic position descriptors in the literature. read less NOT USED (high confidence) J. Vandermause et al., “On-the-fly active learning of interpretable Bayesian force fields for atomistic rare events,” npj Computational Materials. 2019. link Times cited: 189 NOT USED (high confidence) J. Dorrell and L. B. Pártay, “Thermodynamics and the potential energy landscape: case study of small water clusters.,” Physical chemistry chemical physics : PCCP. 2019. link Times cited: 6 Abstract: We investigated the structure and the thermodynamic properti… read moreAbstract: We investigated the structure and the thermodynamic properties of small water clusters with the nested sampling computational technique, using two different water models, the coarse-grained mW (up to 25 molecules) and the flexible version of the TIP3P (up to 16 molecules). By mapping the entire potential energy landscape of the clusters, we calculated the heat capacity curves, located the structural transitions and identified those local minimum basins which contribute the most to the total partition function. We found that in the case of the mW model, trends in first-order-like and continuous-like transitions can be very well matched to the characteristics of the landscape: cluster sizes with fewer and narrower local minimum basins show a sharper 'melting' peak on the heat capacity curve. Trends in the case of the TIP3P model were not easily assigned to the changing occupation of basins, and the contribution of local minima was negligible, except for n = 7, 15 and 16. read less NOT USED (high confidence) J. Chen and B. Wang, “Existence criteria and validity of plate models for graphene-like materials,” Science China Physics, Mechanics & Astronomy. 2019. link Times cited: 5 NOT USED (high confidence) M. R. G. Marques, J. Wolff, C. Steigemann, and M. Marques, “Neural network force fields for simple metals and semiconductors: construction and application to the calculation of phonons and melting temperatures.,” Physical chemistry chemical physics : PCCP. 2019. link Times cited: 17 Abstract: We present a practical procedure to obtain reliable and unbi… read moreAbstract: We present a practical procedure to obtain reliable and unbiased neural network based force fields for solids. Training and test sets are efficiently generated from global structural prediction runs, at the same time assuring the structural variety and importance of sampling the relevant regions of phase space. The neural networks are trained to yield not only good formation energies, but also accurate forces and stresses, which are the quantities of interest for molecular dynamics simulations. Finally, we construct, as an example, several force fields for both semiconducting and metallic elements, and prove their accuracy for a variety of structural and dynamical properties. These are then used to study the melting of bulk copper and gold. read less NOT USED (high confidence) H.-H. Boltz, J. Kurchan, and A. J. Liu, “Fluctuation distributions of energy minima in complex landscapes,” Bulletin of the American Physical Society. 2019. link Times cited: 1 Abstract: We discuss the properties of the distributions of energies o… read moreAbstract: We discuss the properties of the distributions of energies of minima obtained by gradient descent in complex energy landscapes. We find strikingly similar phenomenology across several prototypical models. We particularly focus on the distribution of energies of minima in the analytically well-understood p-spin-interaction spin glass model. We numerically find non-Gaussian distributions that resemble the Tracy-Widom distributions often found in problems of random correlated variables, and non-trivial finite-size scaling. Based on this, we propose a picture of gradient descent dynamics that highlights the importance of a first-passage process in the eigenvalues of the Hessian. This picture provides a concrete link to problems in which the Tracy-Widom distribution is established. Aspects of this first-passage view of gradient-descent dynamics are generic for non-convex complex landscapes, rationalizing the commonality that we find across models. read less NOT USED (high confidence) J. Bennett, M. E. Raglione, S. M. Oburn, L. MacGillivray, M. Arnold, and S. Mason, “DFT Computed Dielectric Response and THz Spectra of Organic Co-Crystals and Their Constituent Components,” Molecules. 2019. link Times cited: 2 Abstract: Terahertz (THz) spectroscopy has been put forth as a non-con… read moreAbstract: Terahertz (THz) spectroscopy has been put forth as a non-contact, analytical probe to characterize the intermolecular interactions of biologically active molecules, specifically as a way to understand, better develop, and use active pharmaceutical ingredients. An obstacle towards fully utilizing this technique as a probe is the need to couple features in the THz regions to specific vibrational modes and interactions. One solution is to use density functional theory (DFT) methods to assign specific vibrational modes to signals in the THz region, coupling atomistic insights to spectral features. Here, we use open source planewave DFT packages that employ ultrasoft pseudopotentials to assess the infrared (IR) response of organic compounds and complex co-crystal formulations in the solid state, with and without dispersion corrections. We compare our DFT computed lattice parameters and vibrational modes to experiment and comment on how to improve the agreement between theory and modeling to allow for THz spectroscopy to be used as an analytical probe in complex biologically relevant systems. read less NOT USED (high confidence) B. Bauerhenne and M. E. Garcia, “Performance of state-of-the-art force fields for atomistic simulations of silicon at high electronic temperatures,” The European Physical Journal Special Topics. 2019. link Times cited: 5 NOT USED (high confidence) K. Li, X. Xian, J. Wang, and N. Yu, “First-principle study on honeycomb fluorated-InTe monolayer with large Rashba spin splitting and direct bandgap,” Applied Surface Science. 2019. link Times cited: 11 NOT USED (high confidence) J. Roth, E. Eisfeld, D. Klein, S. Hocker, H. Lipp, and H. Trebin, “IMD – the ITAP molecular dynamics simulation package,” The European Physical Journal Special Topics. 2019. link Times cited: 3 NOT USED (high confidence) E. Lerner, “Mechanical properties of simple computer glasses,” Journal of Non-Crystalline Solids. 2019. link Times cited: 33 NOT USED (high confidence) H. Dai, H. Du, J. Chen, and G. Chen, “Influence of elliptical vibration on the behavior of silicon during nanocutting,” The International Journal of Advanced Manufacturing Technology. 2019. link Times cited: 0 NOT USED (high confidence) S. Chavoshi and S. Xu, “Nanoindentation/scratching at finite temperatures: Insights from atomistic-based modeling,” Progress in Materials Science. 2019. link Times cited: 37 NOT USED (high confidence) Y. Lysogorskiy, T. Hammerschmidt, J. Janssen, J. Neugebauer, and R. Drautz, “Transferability of interatomic potentials for molybdenum and silicon,” Modelling and Simulation in Materials Science and Engineering. 2019. link Times cited: 14 Abstract: Interatomic potentials are widely used in computational mate… read moreAbstract: Interatomic potentials are widely used in computational materials science, in particular for simulations that are too computationally expensive for density functional theory (DFT). Most interatomic potentials have a limited application range and often there is very limited information available regarding their performance for specific simulations. We carried out high-throughput calculations for molybdenum and silicon with DFT and a number of interatomic potentials. We compare the DFT reference calculations and experimental data to the predictions of the interatomic potentials. We focus on a large number of basic materials properties, including the cohesive energy, atomic volume, elastic coefficients, vibrational properties, thermodynamic properties, surface energies and vacancy formation energies, which enables a detailed discussion of the performance of the different potentials. We further analyze correlations between properties as obtained from DFT calculations and how interatomic potentials reproduce these correlations, and suggest a general measure for quantifying the accuracy and transferability of an interatomic potential. From our analysis we do not establish a clearcut ranking of the potentials as each potential has its strengths and weaknesses. It is therefore essential to assess the properties of a potential carefully before application of the potential in a specific simulation. The data presented here will be useful for selecting a potential for simulations of Mo or Si. read less NOT USED (high confidence) T. Brink and J. Molinari, “Adhesive wear mechanisms in the presence of weak interfaces: Insights from an amorphous model system,” Physical Review Materials. 2019. link Times cited: 27 Abstract: Engineering wear models are generally empirical and lack con… read moreAbstract: Engineering wear models are generally empirical and lack connections to the physical processes of debris generation at the nanoscale to microscale. Here, we thus analyze wear particle formation for sliding interfaces in dry contact with full and reduced adhesion. Depending on the material and interface properties and the local slopes of the surfaces, we find that colliding surface asperities can either deform plastically, form wear particles, or slip along the contact junction surface without significant damage. We propose a mechanism map as a function of material properties and local geometry, and confirm it using quasi-two-dimensional and three-dimensional molecular dynamics and finite-element simulations on an amorphous, siliconlike model material. The framework developed in the present paper conceptually ties the regimes of weak and strong interfacial adhesion together and can explain that even unlubricated sliding contacts do not necessarily lead to catastrophic wear rates. A salient result of the present paper is an analytical expression of a critical length scale, which incorporates interface properties and roughness parameters. Therefore, our findings provide a theoretical framework and a quantitative map to predict deformation mechanisms at individual contacts. In particular, contact junctions of sizes above the critical length scale contribute to the debris formation. read less NOT USED (high confidence) F. Domínguez‐Adame, M. Martín‐González, D. Sánchez, and A. Cantarero, “Nanowires: A route to efficient thermoelectric devices,” Physica E: Low-dimensional Systems and Nanostructures. 2019. link Times cited: 39 NOT USED (high confidence) E. Teich, G. van Anders, and S. Glotzer, “Identity crisis in alchemical space drives the entropic colloidal glass transition,” Nature Communications. 2019. link Times cited: 17 NOT USED (high confidence) L. Wang, W. Yu, and S. Shen, “Revisiting the structures and energies of silicon 〈110〉 symmetric tilt grain boundaries,” Journal of Materials Research. 2019. link Times cited: 19 Abstract: Atomistic simulations of 18 silicon 〈110〉 symmetric tilt gra… read moreAbstract: Atomistic simulations of 18 silicon 〈110〉 symmetric tilt grain boundaries are performed using Stillinger Weber, Tersoff, and the optimized Modified Embedded Atom Method potentials. We define a novel structural unit classification through dislocation core analysis to characterize the relaxed GB structures. GBs with the misorientation angle θ ranging from 13.44° to 70.53° are solely composed of Lomer dislocation cores. For GBs with θ less than but close to 70.53°, GB ‘step’ appears and the equilibrated states with lowest GB energies can be attained only when such GB ‘step’ is located in the middle of each single periodic GB structure. For the misorientation angles in the range of 93.37° ≤ θ ≤ 148.41°, GB structures become complicated since they contain multiple types of dislocation cores. This work not only facilitates the structural characterization of silicon 〈110〉 STGBs, but also may provide new insights into mirco-structure design in multicrystalline silicon. read less NOT USED (high confidence) D. Prasad and N. Mitra, “An atomistic study of phase transition in cubic diamond Si single crystal subjected to static compression,” Computational Materials Science. 2019. link Times cited: 7 NOT USED (high confidence) G. Almyras, D. Sangiovanni, and K. Sarakinos, “Semi-Empirical Force-Field Model for the Ti1−xAlxN (0 ≤ x ≤ 1) System,” Materials. 2019. link Times cited: 21 Abstract: We present a modified embedded atom method (MEAM) semi-empir… read moreAbstract: We present a modified embedded atom method (MEAM) semi-empirical force-field model for the Ti1−xAlxN (0 ≤ x ≤ 1) alloy system. The MEAM parameters, determined via an adaptive simulated-annealing (ASA) minimization scheme, optimize the model’s predictions with respect to 0 K equilibrium volumes, elastic constants, cohesive energies, enthalpies of mixing, and point-defect formation energies, for a set of ≈40 elemental, binary, and ternary Ti-Al-N structures and configurations. Subsequently, the reliability of the model is thoroughly verified against known finite-temperature thermodynamic and kinetic properties of key binary Ti-N and Al-N phases, as well as properties of Ti1−xAlxN (0 < x < 1) alloys. The successful outcome of the validation underscores the transferability of our model, opening the way for large-scale molecular dynamics simulations of, e.g., phase evolution, interfacial processes, and mechanical response in Ti-Al-N-based alloys, superlattices, and nanostructures. read less NOT USED (high confidence) D. Limbu, R. Atta-Fynn, and P. Biswas, “Atomistic simulation of nearly defect-free models of amorphous silicon: An information-based approach,” MRS Advances. 2019. link Times cited: 3 Abstract: We present an information-based total-energy optimization me… read moreAbstract: We present an information-based total-energy optimization method to produce nearly defect-free structural models of amorphous silicon. Using geometrical, structural, and topological information from disordered tetrahedral networks, we have shown that it is possible to generate structural configurations of amorphous silicon, which are superior than the models obtained from conventional reverse Monte Carlo and molecular dynamics simulations. The new data-driven hybrid approach presented here is capable of producing atomistic models with structural and electronic properties which are on a par with those obtained from the modified Wooten-Winer-Weaire (WWW) models of amorphous silicon. Structural, electronic, and thermodynamic properties of the hybrid models are compared with the best dynamical models obtained from using machine-intelligence-based algorithms and efficient classical molecular dynamics simulations, reported in the recent literature. We have shown that, together with the WWW models, our hybrid models represent one of the best structural models so far produced by total-energy-based Monte Carlo methods in conjunction with experimental diffraction data. read less NOT USED (high confidence) B. Bauerhenne, V. Lipp, T. Zier, E. S. Zijlstra, and M. E. Garcia, “Self-Learning Method for Construction of Analytical Interatomic Potentials to Describe Laser-Excited Materials.,” Physical review letters. 2018. link Times cited: 12 Abstract: Large-scale simulations using interatomic potentials provide… read moreAbstract: Large-scale simulations using interatomic potentials provide deep insight into the processes occurring in solids subject to external perturbations. The atomistic description of laser-induced ultrafast nonthermal phenomena, however, constitutes a particularly difficult case and has so far not been possible on experimentally accessible length scales and timescales because of two main reasons: (i) ab initio simulations are restricted to a very small number of atoms and ultrashort times and (ii) simulations relying on electronic temperature- (T_{e}) dependent interatomic potentials do not reach the necessary ab initio accuracy. Here we develop a self-learning method for constructing T_{e}-dependent interatomic potentials which permit ultralarge-scale atomistic simulations of systems suddenly brought to extreme nonthermal states with density-functional theory (DFT) accuracy. The method always finds the global minimum in the parameter space. We derive a highly accurate analytical T_{e}-dependent interatomic potential Φ(T_{e}) for silicon that yields a remarkably good description of laser-excited and -unexcited Si bulk and Si films. Using Φ(T_{e}) we simulate the laser excitation of Si nanoparticles and find strong damping of their breathing modes due to nonthermal melting. read less NOT USED (high confidence) A. Bandura, S. I. Lukyanov, R. Evarestov, and D. D. Kuruch, “Calculation of Young’s Modulus of MoS2-Based Single-Wall Nanotubes Using Force-Field and Hybrid Density Functional Theory,” Physics of the Solid State. 2018. link Times cited: 3 NOT USED (high confidence) P. Cao et al., “Mechanical properties of bi- and poly-crystalline ice,” AIP Advances. 2018. link Times cited: 13 Abstract: A sound knowledge of fundamental mechanical properties of wa… read moreAbstract: A sound knowledge of fundamental mechanical properties of water ice is of crucial importance to address a wide range of applications in earth science, engineering, as well as ice sculpture and winter sports, such as ice skating, ice fishing, ice climbing, bobsleighs, and so on. Here, we report large-scale molecular dynamics (MD) simulations of mechanical properties of bi- and poly-crystalline hexagonal ice (Ih) under mechanical loads. Results show that bicrystals, upon tension, exhibit either brittle or ductile fracture, depending on the microstructure of grain boundaries (GBs), whereas they show ductile fracture by amorphization and crystallographic slips emitted from GBs under compression. Under shearing, the strength of bicrystals exhibits a characteristic plateau or sawtooth behavior drawn out the initial elastic strains. Nanograined polycrystals are destabilized by strain-induced amorphization and collective GB sliding. Their mechanical responses depend on the grain size. Both tensile and compressive strengths decrease as grain size decreases, showing inverse Hall-Petch weakening behavior. Large fraction of amorphous water structure in polycrystals with small grain size is mainly responsible for the inverse Hall-Petch softening. Dislocation nucleation and propagation are also identified in nanograined ice, which is in good agreement with experimental measurements. Beyond the elastic strain, a combination of GB sliding, grain rotation, amorphization and recrystallization, phase transformation, and dislocation nucleation dominate the plastic deformation in both bicrystals and polycrystals. read less NOT USED (high confidence) N. Bernstein, B. Bhattarai, G. Csányi, D. A. Drabold, S. Elliott, and V. L. Deringer, “Quantifying Chemical Structure and Machine‐Learned Atomic Energies in Amorphous and Liquid Silicon,” Angewandte Chemie (International Ed. in English). 2018. link Times cited: 43 Abstract: Amorphous materials are being described by increasingly powe… read moreAbstract: Amorphous materials are being described by increasingly powerful computer simulations, but new approaches are still needed to fully understand their intricate atomic structures. Here, we show how machine‐learning‐based techniques can give new, quantitative chemical insight into the atomic‐scale structure of amorphous silicon (a‐Si). We combine a quantitative description of the nearest‐ and next‐nearest‐neighbor structure with a quantitative description of local stability. The analysis is applied to an ensemble of a‐Si networks in which we tailor the degree of ordering by varying the quench rates down to 1010 K s−1. Our approach associates coordination defects in a‐Si with distinct stability regions and it has also been applied to liquid Si, where it traces a clear‐cut transition in local energies during vitrification. The method is straightforward and inexpensive to apply, and therefore expected to have more general significance for developing a quantitative understanding of liquid and amorphous states of matter. read less NOT USED (high confidence) T. Ahmed, Z. Zhang, C. McDermitt, and Z. Hossain, “Strength and toughness anisotropy in hexagonal boron nitride: An atomistic picture,” Journal of Applied Physics. 2018. link Times cited: 13 Abstract: Strength and toughness are two crucial mechanical properties… read moreAbstract: Strength and toughness are two crucial mechanical properties of a solid that determine its ability to function reliably without undergoing failure in extreme conditions. While hexagonal boron nitride (hBN) is known to be elastically isotropic in the linear regime of mechanical deformation, its directional response to extreme mechanical loading remains less understood. Here, using a combination of density functional theory calculations and molecular dynamics simulations, we show that strength and crack nucleation toughness of pristine hBN are strongly anisotropic and chirality dependent. They vary nonlinearly with the chirality of the lattice under symmetry breaking deformation, and the anisotropic behavior is retained over a large temperature range with a decreasing trend at higher temperatures. An atomistic analysis reveals that bond deformation and associated distortion of electron density are nonuniform in the nonlinear regime of mechanical deformation, irrespective of the loading direction. This nonuniformity forms the physical basis for the observed anisotropy under static conditions, whereas reduction in nonuniformity and thermal softening reduce anisotropy at higher temperatures. The chirality-dependent anisotropic effects are well predicted by inverse cubic polynomials.Strength and toughness are two crucial mechanical properties of a solid that determine its ability to function reliably without undergoing failure in extreme conditions. While hexagonal boron nitride (hBN) is known to be elastically isotropic in the linear regime of mechanical deformation, its directional response to extreme mechanical loading remains less understood. Here, using a combination of density functional theory calculations and molecular dynamics simulations, we show that strength and crack nucleation toughness of pristine hBN are strongly anisotropic and chirality dependent. They vary nonlinearly with the chirality of the lattice under symmetry breaking deformation, and the anisotropic behavior is retained over a large temperature range with a decreasing trend at higher temperatures. An atomistic analysis reveals that bond deformation and associated distortion of electron density are nonuniform in the nonlinear regime of mechanical deformation, irrespective of the loading direction. This nonun... read less NOT USED (high confidence) L. Martín, I. Santos, P. López, L. Marqués, M. Aboy, and L. Pelaz, “Modeling SiGe Through Classical Molecular Dynamics Simulations: Chasing an Appropriate Empirical Potential,” 2018 Spanish Conference on Electron Devices (CDE). 2018. link Times cited: 2 Abstract: We used classical molecular dynamics simulations to reproduc… read moreAbstract: We used classical molecular dynamics simulations to reproduce basic properties of Si, Ge and SiGe using different empirical potentials available in the literature. The empirical potential that offered the better compromise with experimental data was used to study the surface stability of these materials. We considered the (100), $(100)2\times 1$ and (111) surfaces, and we found the processing temperature range to avoid the structural degradation of studied surfaces. read less NOT USED (high confidence) S. Chavoshi and S. Xu, “Twinning effects in the single/nanocrystalline cubic silicon carbide subjected to nanoindentation loading,” Materialia. 2018. link Times cited: 9 NOT USED (high confidence) L. Huang, R. Wang, and S. Wang, “A new reconstruction core of the 30° partial dislocation in silicon,” Philosophical Magazine. 2018. link Times cited: 3 Abstract: ABSTRACT The partial dislocation in silicon is investigated … read moreAbstract: ABSTRACT The partial dislocation in silicon is investigated theoretically in the framework of the fully discrete Peierls–Nabarro model and first-principles calculations. A new reconstructed core composed of a periodic arrangement of one tetragon and two heptagons (477-core) is proposed. Similar to the partial dislocation, we find that there are actually two types of reconstructed cores for the partial dislocation, namely, a well-known 558-core and a new 477-core. The energy of the 477-core is 0.137 eV/Å higher than that of the 558-core. However, from the molecular dynamics simulation, we found that the 477-core may have a macroscopic lifetime for temperature below 30 K. The full kinks and the partial kinks due to the appearance of the 477-core are also studied. Remarkably, it is found that formation and migration of the global kinks deeply involve with the partial kinks, and the creation and motion of partial kinks can be attributed to the rotation of a single bond. Our results are helpful in understanding the mechanism of kink nucleation and the plasticity of silicon. read less NOT USED (high confidence) A. Sycheva, E. Voronina, and T. Rakhimova, “Molecular Dynamics Simulation of Physical Sputtering of Nanoporous Silicon-Based Materials with Low Energy Argon,” Journal of Surface Investigation: X-ray, Synchrotron and Neutron Techniques. 2018. link Times cited: 6 NOT USED (high confidence) P. A. Santos-Flórez, C. Ruestes, and M. de Koning, “Uniaxial-deformation behavior of ice I h as described by the TIP4P/Ice and mW water models.,” The Journal of chemical physics. 2018. link Times cited: 9 Abstract: Using molecular dynamics simulations, we assess the uniaxial… read moreAbstract: Using molecular dynamics simulations, we assess the uniaxial deformation response of ice I h as described by two popular water models, namely, the all-atom TIP4P/Ice potential and the coarse-grained mW model. In particular, we investigate the response to both tensile and compressive uniaxial deformations along the [0001] and [ 0 1 ¯ 10 ] crystallographic directions for a series of different temperatures. We classify the respective failure mechanisms and assess their sensitivity to strain rate and cell size. While the TIP4P/Ice model fails by either brittle cleavage under tension at low temperatures or large-scale amorphization/melting, the mW potential behaves in a much more ductile manner, displaying numerous cases in which stress relief involves the nucleation and subsequent activity of lattice dislocations. Indeed, the fact that mW behaves in such a malleable manner even at strain rates that are substantially higher than those applied in typical experiments indicates that the mW description of ice I h is excessively ductile. One possible contribution to this enhanced malleability is the absence of explicit protons in the mW model, disregarding the fundamental asymmetry of the hydrogen bond that plays an important role in the nucleation and motion of lattice dislocations in ice I h . read less NOT USED (high confidence) Y. Wang, X. Zhou, and M. Kou, “Three-dimensional numerical study on the failure characteristics of intermittent fissures under compressive-shear loads,” Acta Geotechnica. 2018. link Times cited: 124 NOT USED (high confidence) D. Kilymis, C. Gérard, J. Amodeo, U. Waghmare, and L. Pizzagalli, “Uniaxial compression of silicon nanoparticles: An atomistic study on the shape and size effects,” Acta Materialia. 2018. link Times cited: 35 NOT USED (high confidence) P. Du, S. Rick, and R. Kumar, “Towards a coarse-grained model of the peptoid backbone: the case of N,N-dimethylacetamide.,” Physical chemistry chemical physics : PCCP. 2018. link Times cited: 5 Abstract: In this study, a coarse-grained (CG) model for N,N-dimethyla… read moreAbstract: In this study, a coarse-grained (CG) model for N,N-dimethylacetamide (DMA), which represents the polypeptoid backbone, is developed as a step towards establishing a CG model of the complex polypeptoid system. Polypeptoids or poly N-substituted glycines are a type of peptidomimetic polymers that are highly tunable, and hence an ideal model system to study self-assembly as a function of chemical groups in aqueous soft matter systems. The DMA CG model is parameterized to reproduce the structural properties of DMA liquid as well as a dilute aqueous solution of DMA using a reference all atom model, namely the OPLS-AA force-field. The intermolecular forces are represented by the Stillinger-Weber potential, that consists of both two- and three-body terms that are very short-ranged. The model is validated on thermodynamic properties of liquid and aqueous DMA, as well as the vapor-liquid interface of liquid DMA and the structure of a concentrated aqueous solution of DMA in water as well as a simple peptoid in water. Without long-ranged interactions and the absence of interaction sites on hydrogen atoms, the CG DMA model is an order of magnitude faster than the higher resolution all-atom (AA) model. read less NOT USED (high confidence) O. Sluis et al., “Advances in delamination modeling of metal/polymer systems: atomistic aspects.” 2018. link Times cited: 3 NOT USED (high confidence) D. D. Alix-Williams and M. Falk, “Shear band broadening in simulated glasses,” Physical Review E. 2018. link Times cited: 20 Abstract: Two models are proposed to predict the evolution of shear ba… read moreAbstract: Two models are proposed to predict the evolution of shear band width as a function of applied strain for simulated glasses mechanically deformed in simple shear. The first model arises from dimensional analysis and an assumption that band broadening is controlled by the strain rate inside the shear band. The second model describes the shear band as a pulled front propagating into an unsteady state, the dynamics of which are described using the effective temperature shear transformation zone (ET-STZ) theory. Both models are compared to three simulated systems: a two-dimensional binary Lennard-Jones glass, a Cu64Zr36 glass modeled using an embedded atom method (EAM) potential, and a Si glass modeled using the Stillinger-Weber potential. Shear bands form in all systems across a variety of quench rates. Depending on the case these bands either appear to broaden indefinitely or to saturate to a finite width. The shear band strain rate model appears to apply only when band growth is unconstrained, indicating the dominance of a single time scale in the early stages of band development. The front propagation model, which reduces to the other model in the early stages of band broadening, also applies to cases in which the band width saturates, suggesting that competition between the rate of shear-induced configurational disordering and thermal relaxation sets a maximum width for shear bands in a variety of materials systems. read less NOT USED (high confidence) J. Palmer, P. H. Poole, F. Sciortino, and P. Debenedetti, “Advances in Computational Studies of the Liquid-Liquid Transition in Water and Water-Like Models.,” Chemical reviews. 2018. link Times cited: 140 Abstract: There has been uninterrupted interest in supercooled water e… read moreAbstract: There has been uninterrupted interest in supercooled water ever since the pioneering experiments of Speedy and Angell revealed sharp increases in this substance's response functions upon supercooling. One intriguing hypothesis that was formulated to explain this behavior involves the existence of a metastable liquid-liquid transition (LLT) at deeply supercooled conditions. The preponderance of experimental evidence is consistent with this hypothesis, although no definitive proof exists to date. Computational studies have played an important role in this area, because ice nucleation can in principle be controlled in silico. It has been claimed, controversially, that the LLT is a misinterpreted liquid-solid transition in all models of water. Recent studies disprove this viewpoint by providing unambiguous counter-examples of distinct liquid-liquid and liquid-crystal transitions in tetrahedral models. In one, state-of-the-art sampling methods were used to compute the free energy surface of a molecular model of water and revealed the existence of two liquid phases in metastable equilibrium with each other and a stable crystal phase, at the same, deeply supercooled thermodynamic conditions. Further studies showed that, by tuning the potential parameters of a model tetrahedral system, it is possible to make the LLT evolve continuously from metastability to being thermodynamically stable with respect to crystallization. Most recently, it has been shown that the simulation code used to challenge the hypothesis of an LLT contains conceptual errors that invalidate the results on which the challenge was based, definitively resolving the controversy. The debate has vastly expanded the range of fundamental questions being pursued about phase transitions in metastable systems and ushered the use of increasingly sophisticated computational methods to explore the possible existence of LLTs in model systems. read less NOT USED (high confidence) S. Nahid, S. Nahian, M. Motalab, T. Rakib, S. Mojumder, and M. M. Islam, “Tuning the mechanical properties of silicene nanosheet by auxiliary cracks: a molecular dynamics study,” RSC Advances. 2018. link Times cited: 17 Abstract: Silicene has become a topic of interest nowadays due to its … read moreAbstract: Silicene has become a topic of interest nowadays due to its potential application in various electro-mechanical nanodevices. In our previous work on silicene, fracture stresses of single crystal and polycrystalline silicene have been investigated. Existence of defects in the form of cracks reduces the fracture strength of silicene nanosheets to a great extent. In this study, an engineering way has been proposed for improving the fracture stress of silicene nanosheets with a pre-existing crack by incorporating auxiliary cracks symmetrically in a direction perpendicular to the main crack. We call this mechanism the “Failure shielding mechanism”. An extensive molecular dynamics simulation based analysis has been performed to capture the atomic level auxiliary crack-main crack interactions. It is found that the main crack tip stress distribution is significantly changed with the presence of auxiliary cracks for loading along both armchair and zigzag directions. The effects of temperature and the crack propagation speed of silicene have also been studied. Interestingly, in the case of loading along the zigzag direction, SW defect formation is observed at the tip of main crack. This leads to a reduction of the tip stress resulting in a more prominent failure shielding in case of zigzag loading than in armchair loading. Moreover, the position and length of the cracks as well as the loading directions have significant impacts on the tip stress distribution. Finally, this study opens the possibilities of strain engineering for silicene by proposing an engineering way to tailor the fracture strength of silicene. read less NOT USED (high confidence) N. Pingua and P. A. Apte, “Increase in local crystalline order across the limit of stability leads to cubic-hexagonal stacking in supercooled monatomic (mW) water.,” The Journal of chemical physics. 2018. link Times cited: 1 Abstract: At the limit of stability of a supercooled tetrahedral liqui… read moreAbstract: At the limit of stability of a supercooled tetrahedral liquid modeled by monatomic (mW) water potential, it was recently shown that relaxation occurs across a unique value of per particle potential energy (ϕmid ), which corresponds to a dynamical (non-stationary) condition of Gibbs free energy function G(T, P, N, ϕ): [∂2(G/N)/∂ϕ2 = 0] and [∂(G/N)/∂ϕ ≠ 0]. In this work, we explore the inherent structures responsible for the formation of the amorphous states through such a mechanism of relaxation of mW liquid. We first identify 6-member boat and chair shaped rings using a criterion based on the internal dihedral angles. We then consider the stacking of the cubic diamond (10-atom cluster with 4 chair shaped rings) and hexagonal wurtzite (12-atom cluster with 3 boat and 2 chair shaped rings) units through a shared chair ring. We find that the local crystalline (tetrahedral) order is exhibited by the eclipsed bond particles of the laterally connected wurtzite units which are stacked from both sides with the diamond units (DWD stacking). Increasingly longer range crystalline order is obtained as the number of stacked wurtzite layers increases: the particles shared by the stacked (laterally connected) wurtzite layers in DWWD show a longer range crystalline order. An even longer range crystalline order is exhibited by the eclipsed bond particles of the middle (laterally connected) wurtzite layer of DWWWD stacking. We find that cubic-hexagonal stacking occurs primarily in the form of DWD layers across the limit of stability. The local tetrahedral order of the purely cubic (diamond) network particles (which are not shared with wurtzite units) deviates significantly from that of the hexagonal crystal. Nonetheless, the average length of the bonds in the purely cubic network approaches that in the hexagonal crystal very closely. Thus a large increase in the purely cubic ice across the instability also leads to an increase in the local crystalline order in the form of bond-lengths. Our results are consistent with previous experimental and simulation studies which find a significant fraction of cubic ice along with cubic-hexagonal stacking layers in deeply supercooled water. read less NOT USED (high confidence) I. Novikov and A. Shapeev, “Improving accuracy of interatomic potentials: more physics or more data? A case study of silica,” Materials Today Communications. 2018. link Times cited: 35 NOT USED (high confidence) X. Mei, W. Mohamed, and J. Eapen, “Approach to local thermodynamic equilibrium and the evolution to a glassy core following neutron/ion radiation impact,” Philosophical Magazine. 2018. link Times cited: 2 Abstract: ABSTRACT Using molecular dynamics simulations and statistica… read moreAbstract: ABSTRACT Using molecular dynamics simulations and statistical-mechanical metrics, we make quantitative predictions on the local thermodynamic and dynamic states following an ion or neutron impact in three materials – copper, silicon and solid argon. Through a two-energy distribution, we first capture the non-equilibrium temperature evolution and the approach to the local thermal equilibrium in three generic stages. By examining the time-resolved van Hove self-correlator, we then demonstrate that the impact core of all the three materials shows the dynamic characteristics of a jammed or glassy state. We delineate a dynamic atom-hopping mechanism that attests to a rapid defect recovery stage in copper; silicon, on the contrary, accommodates only small displacements which resist recovery. The dissimilitude between copper with a close-packed structure and silicon with an open network structure is further drawn out through an isoconfigurational analysis of displacements, which shows a compact dendritic-like condensation front for the mobile atoms in copper through atom hopping. In contrast, silicon portrays larger-scale spatial oscillations of dynamically separated regions, which appear to be a precursor to dynamic lattice instability and eventual amorphisation. read less NOT USED (high confidence) C. Zhang, Z. Liu, and P. Deng, “Using molecular dynamics to unravel phase composition behavior of nano-size pores in frozen soils: Does Young–Laplace equation apply in low temperature range?,” Canadian Geotechnical Journal. 2018. link Times cited: 8 Abstract: The phase composition curve of frozen soils is a fundamental… read moreAbstract: The phase composition curve of frozen soils is a fundamental relationship in understanding permafrost and seasonally frozen soils. However, due to the complex interplay between adsorption and capillarity, a clear physically based understanding of the phase composition curve in the low temperature range, i.e., <265 K, is still absent. Especially, it is unclear whether the Young–Laplace equation corresponding to capillarity still holds in nano-size pores where adsorption could dominate. In this paper, a framework based on molecular dynamics was developed to investigate the phase transition behavior of water confined in nano-size pores. A series of simulations was conducted to unravel the effects of the pore size and wettability on the freezing and melting of pore water. This is the first time that the phase composition behavior of frozen soils is analyzed using molecular dynamics. It is found that the Young–Laplace equation may not apply in the low temperature range. read less NOT USED (high confidence) A. U. H. Meem, O. Chowdhury, and A. M. Morshed, “Effects of vacancy defects location on thermal conductivity of silicon nanowire: a molecular dynamics study,” Micro & Nano Letters. 2018. link Times cited: 1 Abstract: The improvement of thermoelectric figure of merit of silicon… read moreAbstract: The improvement of thermoelectric figure of merit of silicon nanowire (SiNW) can be achieved by lowering its thermal conductivity. In this work, non-equilibrium molecular dynamics method was used to demonstrate that the thermal conductivity of bulk silicon crystal is drastically reduced when it is crafted as SiNW and that it can be reduced remarkably by including vacancy defects. It has been found that ‘centre vacancy defect’ contributes much more in reducing the thermal conductance than ‘surface vacancy defect’. The lowest thermal conductivity that occurs is about 52.1% of that of pristine SiNW, when 2% vacancy defect is introduced in the nanowire. The vibrational density of states analysis was performed to understand the nature of this reduction and it has been found that the various boundary scatterings of phonon significantly reduce the thermal conductivity. Also, larger mass difference due to voids induces smaller thermal conductivity values. These results indicate that the inclusion of vacancy defects can enhance the thermoelectric performance of SiNWs. read less NOT USED (high confidence) D. Gobrecht, S. Bromley, J. Plane, L. Decin, and S. Cristallo, “On the onset of dust formation in AGB stars,” Proceedings of the International Astronomical Union. 2018. link Times cited: 0 Abstract: A promising candidate to initiate dust formation in oxygen-r… read moreAbstract: A promising candidate to initiate dust formation in oxygen-rich AGB stars is alumina (Al2O3) showing an emission feature around ∼13μm attributed to Al−O stretching and bending modes (Posch+99,Sloan+03). The counterpart to alumina in carbon-rich AGB atmospheres is the highly refractory silicon carbide (SiC) showing a characteristic feature around 11.3μm (Treffers74). Alumina and SiC grains are thought to represent the first condensates to emerge in AGB stellar atmospheres. We follow a bottom-up approach, starting with the smallest stoichiometric clusters (i.e. Al4O6, Si2C2), successively building up larger-sized clusters. We present new results of quantum-mechanical structure calculations of (Al2O3)n, n = 1−10 and (SiC)n clusters with n = 1−16, including potential energies, rotational constants, and structure-specific vibrational spectra. We demonstrate the energetic viability of homogeneous nucleation scenarios where monomers (Al2O3 and SiC) or dimers (Al4O6 and Si2C2) are successively added. We find significant differences between our quantum theory based results and nanoparticle properties derived from (classical) nucleation theory. read less NOT USED (high confidence) A. Palov, “Elastic Scattering of Mo-Mo, Mo-S and S-S Atomic Pairs in the Relative Kinetic Energy Range of 2–200 eV,” Technical Physics Letters. 2018. link Times cited: 1 NOT USED (high confidence) Z. Zhang, I. A. Alhafez, and H. Urbassek, “Scratching an Al/Si Interface: Molecular Dynamics Study of a Composite Material,” Tribology Letters. 2018. link Times cited: 20 NOT USED (high confidence) L. N. Abdulkadir, K. Abou-El-Hossein, A. I. Jumare, M. Liman, T. A. Olaniyan, and P. B. Odedeyi, “Review of molecular dynamics/experimental study of diamond-silicon behavior in nanoscale machining,” The International Journal of Advanced Manufacturing Technology. 2018. link Times cited: 38 NOT USED (high confidence) L. N. Abdulkadir, K. Abou-El-Hossein, A. I. Jumare, M. Liman, T. A. Olaniyan, and P. B. Odedeyi, “Review of molecular dynamics/experimental study of diamond-silicon behavior in nanoscale machining,” The International Journal of Advanced Manufacturing Technology. 2018. link Times cited: 0 NOT USED (high confidence) R. Agnese et al., “Energy loss due to defect formation from 206Pb recoils in SuperCDMS germanium detectors,” Applied Physics Letters. 2018. link Times cited: 7 Abstract: The Super Cryogenic Dark Matter Search experiment at the Sou… read moreAbstract: The Super Cryogenic Dark Matter Search experiment at the Soudan Underground Laboratory studied energy loss associated with defect formation in germanium crystals at mK temperatures using in situ 210Pb sources. We examine the spectrum of 206Pb nuclear recoils near its expected 103 keV endpoint energy and determine an energy loss of (6:08 ± 0:18)%, which we attribute to defect formation. From this result and using TRIM simulations, we extract the first experimentally determined average displacement threshold energy of 19.7−0.5+0.6 eV for germanium. This has implications for the analysis thresholds of future germanium-based dark matter searches.The Super Cryogenic Dark Matter Search experiment at the Soudan Underground Laboratory studied energy loss associated with defect formation in germanium crystals at mK temperatures using in situ 210Pb sources. We examine the spectrum of 206Pb nuclear recoils near its expected 103 keV endpoint energy and determine an energy loss of (6:08 ± 0:18)%, which we attribute to defect formation. From this result and using TRIM simulations, we extract the first experimentally determined average displacement threshold energy of 19.7−0.5+0.6 eV for germanium. This has implications for the analysis thresholds of future germanium-based dark matter searches. read less NOT USED (high confidence) A. Giri, B. F. Donovan, and P. Hopkins, “Localization of vibrational modes leads to reduced thermal conductivity of amorphous heterostructures,” Physical Review Materials. 2018. link Times cited: 24 Abstract: Ashutosh Giri,1,* Brian F. Donovan,2 and Patrick E. Hopkins1… read moreAbstract: Ashutosh Giri,1,* Brian F. Donovan,2 and Patrick E. Hopkins1,3,4,† 1Department of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, Virginia 22904, USA 2Department of Physics, United States Naval Academy, Annapolis, Maryland 21042, USA 3Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22904, USA 4Department of Physics, University of Virginia, Charlottesville, Virginia 22904, USA read less NOT USED (high confidence) M. El-Genk, K. Talaat, and B. Cowen, “Thermal conductivity of silicon using reverse non-equilibrium molecular dynamics,” Journal of Applied Physics. 2018. link Times cited: 13 Abstract: Simulations are performed using the reverse non-equilibrium … read moreAbstract: Simulations are performed using the reverse non-equilibrium molecular dynamics (rNEMD) method and the Stillinger-Weber (SW) potential to determine the input parameters for achieving ±1% convergence of the calculated thermal conductivity of silicon. These parameters are then used to investigate the effects of the interatomic potentials of SW, Tersoff II, Environment Dependent Interatomic Potential (EDIP), Second Nearest Neighbor, Modified Embedded-Atom Method (MEAM), and Highly Optimized Empirical Potential MEAM on determining the bulk thermal conductivity as a function of temperature (400–1000 K). At temperatures > 400 K, data collection and swap periods of 15 ns and 150 fs, system size ≥6 × 6 UC2 and system lengths ≥192 UC are adequate for ±1% convergence with all potentials, regardless of the time step size (0.1–0.5 fs). This is also true at 400 K, except for the SW potential, which requires a data collection period ≥30 ns. The calculated bulk thermal conductivities using the rNEMD method and the EDIP potential are close to, but lower than experimental values. The 10% difference at 400 K increases gradually to 20% at 1000 K.Simulations are performed using the reverse non-equilibrium molecular dynamics (rNEMD) method and the Stillinger-Weber (SW) potential to determine the input parameters for achieving ±1% convergence of the calculated thermal conductivity of silicon. These parameters are then used to investigate the effects of the interatomic potentials of SW, Tersoff II, Environment Dependent Interatomic Potential (EDIP), Second Nearest Neighbor, Modified Embedded-Atom Method (MEAM), and Highly Optimized Empirical Potential MEAM on determining the bulk thermal conductivity as a function of temperature (400–1000 K). At temperatures > 400 K, data collection and swap periods of 15 ns and 150 fs, system size ≥6 × 6 UC2 and system lengths ≥192 UC are adequate for ±1% convergence with all potentials, regardless of the time step size (0.1–0.5 fs). This is also true at 400 K, except for the SW potential, which requires a data collection period ≥30 ns. The calculated bulk thermal conductivities using the rNEMD method and the EDIP... read less NOT USED (high confidence) J. Russo, F. Romano, and H. Tanaka, “Glass Forming Ability in Systems with Competing Orderings,” Physical Review X. 2018. link Times cited: 51 Abstract: Some liquids, if cooled rapidly enough to avoid crystallizat… read moreAbstract: Some liquids, if cooled rapidly enough to avoid crystallization, can be frozen into a nonergodic glassy state. The tendency for a material to form a glass when quenched is called “glass-forming ability,” and it is of key significance both fundamentally and for materials science applications. Here, we consider liquids with competing orderings, where an increase in the glass-forming ability is signaled by a depression of the melting temperature towards its minimum at triple or eutectic points. With simulations of two model systems where glass-forming ability can be tuned by an external parameter, we are able to interpolate between crystal-forming and glass-forming behavior. We find that the enhancement of the glass-forming ability is caused by an increase in the structural difference between liquid and crystal: stronger competition in orderings towards the melting point minimum makes a liquid structure more disordered (more complex). This increase in the liquid-crystal structure difference can be described by a single adimensional parameter, i.e., the interface energy cost scaled by the thermal energy, which we call the “thermodynamic interface penalty.” Our finding may provide a general physical principle for not only controlling the glass-forming ability but also the emergence of glassy behavior of various systems with competing orderings, including orderings of structural, magnetic, electronic, charge, and dipolar origin. read less NOT USED (high confidence) A. Bartók, J. Kermode, N. Bernstein, and G. Csányi, “Machine Learning a General-Purpose Interatomic Potential for Silicon,” Physical Review X. 2018. link Times cited: 291 Abstract: The success of first principles electronic structure calcula… read moreAbstract: The success of first principles electronic structure calculation for predictive modeling in chemistry, solid state physics, and materials science is constrained by the limitations on simulated length and time scales due to computational cost and its scaling. Techniques based on machine learning ideas for interpolating the Born-Oppenheimer potential energy surface without explicitly describing electrons have recently shown great promise, but accurately and efficiently fitting the physically relevant space of configurations has remained a challenging goal. Here we present a Gaussian Approximation Potential for silicon that achieves this milestone, accurately reproducing density functional theory reference results for a wide range of observable properties, including crystal, liquid, and amorphous bulk phases, as well as point, line, and plane defects. We demonstrate that this new potential enables calculations that would be extremely expensive with a first principles electronic structure method, such as finite temperature phase boundary lines, self-diffusivity in the liquid, formation of the amorphous by slow quench, and dynamic brittle fracture. We show that the uncertainty quantification inherent to the Gaussian process regression framework gives a qualitative estimate of the potential's accuracy for a given atomic configuration. The success of this model shows that it is indeed possible to create a useful machine-learning-based interatomic potential that comprehensively describes a material, and serves as a template for the development of such models in the future. read less NOT USED (high confidence) Z. Fan, H. Dong, A. Harju, and T. Ala‐Nissila, “Homogeneous nonequilibrium molecular dynamics method for heat transport and spectral decomposition with many-body potentials,” Physical Review B. 2018. link Times cited: 51 Abstract: The standard equilibrium Green--Kubo and nonequilibrium mole… read moreAbstract: The standard equilibrium Green--Kubo and nonequilibrium molecular dynamics (MD) methods for computing thermal transport coefficients in solids typically require relatively long simulation times and large system sizes. To this end, we revisit here the homogeneous nonequilibrium MD method by Evans [Phys. Lett. A 91, 457 (1982)] and generalize it to many-body potentials that are required for more realistic materials modeling. We also propose a method for obtaining spectral conductivity and phonon mean-free path from the simulation data. This spectral decomposition method does not require lattice dynamics calculations and can find important applications in spatially complex structures. We benchmark the method by calculating thermal conductivities of three-dimensional silicon, two-dimensional graphene, and a quasi-one-dimensional carbon nanotube and show that the method is about one to two orders of magnitude more efficient than the Green--Kubo method. We apply the spectral decomposition method to examine the long-standing dispute over thermal conductivity convergence vs divergence in carbon nanotubes. read less NOT USED (high confidence) M. Faruq, A. Villesuzanne, and G. Shao, “Molecular-dynamics simulations of binary Pd-Si metal alloys: Glass formation, crystallisation and cluster properties,” Journal of Non-crystalline Solids. 2018. link Times cited: 22 NOT USED (high confidence) M. Vohra, A. Nobakht, S. Shin, and S. Mahadevan, “Uncertainty quantification in non-equilibrium molecular dynamics simulations of thermal transport,” International Journal of Heat and Mass Transfer. 2018. link Times cited: 14 NOT USED (high confidence) R. C. Remsing, M. Klein, and J. Sun, “Refined description of liquid and supercooled silicon from ab initio simulations,” Physical Review B. 2018. link Times cited: 6 Abstract: Despite silicon being of great technological importance, an … read moreAbstract: Despite silicon being of great technological importance, an understanding of its behavior across the phase diagram is still lacking, especially near liquid-solid coexistence. The difficulty in describing silicon near coexistence from first principles lies in discriminating between the metallic and covalent bonds present in the material. Using the strongly constrained and appropriately normed (SCAN) density functional, which can describe a wide variety of bonds with quantitative accuracy, we report a thorough investigation of liquid silicon in the vicinity of liquid-solid coexistence using ab initio molecular dynamics simulations. We observe a structural transition in the supercooled regime that is rooted in a change in the electronic structure of the material. This transition is found to occur at a higher temperature than previous predictions. We also discuss implications of the observed change in interatomic interactions for empirical models of transitions between two distinct liquids. read less NOT USED (high confidence) A. Bourque and G. Rutledge, “Empirical potential for molecular simulation of graphene nanoplatelets.,” The Journal of chemical physics. 2018. link Times cited: 8 Abstract: A new empirical potential for layered graphitic materials is… read moreAbstract: A new empirical potential for layered graphitic materials is reported. Interatomic interactions within a single graphene sheet are modeled using a Stillinger-Weber potential. Interatomic interactions between atoms in different sheets of graphene in the nanoplatelet are modeled using a Lennard-Jones interaction potential. The potential is validated by comparing molecular dynamics simulations of tensile deformation with the reported elastic constants for graphite. The graphite is found to fracture into graphene nanoplatelets when subjected to ∼15% tensile strain normal to the basal surface of the graphene stack, with an ultimate stress of 2.0 GPa and toughness of 0.33 GPa. This force field is useful to model molecular interactions in an important class of composite systems comprising 2D materials like graphene and multi-layer graphene nanoplatelets. read less NOT USED (high confidence) H. Urbassek, M. L. Nietiadi, R. M. Bradley, and G. Hobler, “Sputtering of Si c Ge 1 -c nanospheres,” Physical Review B. 2018. link Times cited: 8 NOT USED (high confidence) J. Rimsza, R. Jones, and L. Criscenti, “Crack propagation in silica from reactive classical molecular dynamics simulations,” Journal of the American Ceramic Society. 2018. link Times cited: 32 NOT USED (high confidence) J. Russo, K. Akahane, and H. Tanaka, “Water-like anomalies as a function of tetrahedrality,” Proceedings of the National Academy of Sciences of the United States of America. 2018. link Times cited: 52 Abstract: Significance Water is the most common and yet least understo… read moreAbstract: Significance Water is the most common and yet least understood material on Earth. Despite its simplicity, water tends to form tetrahedral order locally by directional hydrogen bonding. This structuring is known to be responsible for a vast array of unusual properties, e.g., the density maximum at 4 °C, which play a fundamental role in countless natural and technological processes, with the Earth’s climate being one of the most important examples. By systematically tuning the degree of tetrahedrality, we succeed in continuously interpolating between water-like behavior and simple liquid-like behavior. Our approach reveals what physical factors make water so anomalous and special even compared with other tetrahedral liquids. Tetrahedral interactions describe the behavior of the most abundant and technologically important materials on Earth, such as water, silicon, carbon, germanium, and countless others. Despite their differences, these materials share unique common physical behaviors, such as liquid anomalies, open crystalline structures, and extremely poor glass-forming ability at ambient pressure. To reveal the physical origin of these anomalies and their link to the shape of the phase diagram, we systematically study the properties of the Stillinger–Weber potential as a function of the strength of the tetrahedral interaction λ. We uncover a unique transition to a reentrant spinodal line at low values of λ, accompanied with a change in the dynamical behavior, from non-Arrhenius to Arrhenius. We then show that a two-state model can provide a comprehensive understanding on how the thermodynamic and dynamic anomalies of this important class of materials depend on the strength of the tetrahedral interaction. Our work establishes a deep link between the shape of the phase diagram and the thermodynamic and dynamic properties through local structural ordering in liquids and hints at why water is so special among all substances. read less NOT USED (high confidence) Y. Bi, E. Xu, T. Strobel, and T. Li, “Formation of inclusion type silicon phases induced by inert gases,” Communications Chemistry. 2018. link Times cited: 6 NOT USED (high confidence) Y. Beltukov, D. Parshin, V. Giordano, and A. Tanguy, “Propagative and diffusive regimes of acoustic damping in bulk amorphous material.,” Physical review. E. 2018. link Times cited: 27 Abstract: In amorphous solids, a non-negligible part of thermal conduc… read moreAbstract: In amorphous solids, a non-negligible part of thermal conductivity results from phonon scattering on the structural disorder. The conversion of acoustic energy into thermal energy is often measured by the dynamical dtructure factor (DSF) thanks to inelastic neutron or x-ray scattering. The DSF is used to quantify the dispersion relation of phonons, together with their damping. However, the connection of the dynamical structure factor with dynamical attenuation of wave packets in glasses is still a matter of debate. We focus here on the analysis of wave-packet propagation in numerical models of amorphous silicon. We show that the damped harmonic oscillator model fits of the dynamical structure factors give a good estimate of the wave packets mean free path, only below the Ioffe-Regel frequency. Above the Ioffe-Regel frequency and below the mobility edge, a pure diffusive regime without a definite mean free path is observed. The high-frequency mobility edge is characteristic of a transition to localized vibrations. Below the Ioffe-Regel frequency, a mixed regime is evidenced at intermediate frequencies, with a coexistence of propagative and diffusive wave fronts. The transition between these different regimes is analyzed in detail and reveals a complex dynamics for energy transport, thus raising the question of the correct modeling of thermal transport in amorphous materials. read less NOT USED (high confidence) F. Grigoriev, V. Sulimov, and A. Tikhonravov, “Simulation of the optical coating deposition,” Advanced Optical Technologies. 2018. link Times cited: 5 Abstract: A brief review of the mathematical methods of thin-film grow… read moreAbstract: A brief review of the mathematical methods of thin-film growth simulation and results of their applications is presented. Both full-atomistic and multi-scale approaches that were used in the studies of thin-film deposition are considered. The results of the structural parameter simulation including density profiles, roughness, porosity, point defect concentration, and others are discussed. The application of the quantum level methods to the simulation of the thin-film electronic and optical properties is considered. Special attention is paid to the simulation of the silicon dioxide thin films. read less NOT USED (high confidence) M. Verdier et al., “Influence of amorphous layers on the thermal conductivity of phononic crystals,” Physical Review B. 2018. link Times cited: 16 Abstract: The impact of amorphous phases around the holes and at the u… read moreAbstract: The impact of amorphous phases around the holes and at the upper and lower free surfaces on thermal transport in silicon phononic membranes is studied. By means of molecular dynamics and Monte Carlo simulations, we explore the impact of the amorphous phase (oxidation and amorphous silicon), surfaces roughness, and a series of geometric parameters on thermal transport. We show that the crystalline phase drives the phenomena; the two main parameters are (i) the crystalline fraction between two holes and (ii) the crystalline thickness of the membranes. We reveal the hierarchical impact of nanostructurations on the thermal conductivity, namely, from the most resistive to the less resistive: the creation of holes, the amorphous phase around them, and the amorphization of the membranes edges. The surfaces or interfaces perpendicular to the heat flow hinder the thermal conductivity to a much greater extent than those parallel to the heat flow. read less NOT USED (high confidence) Y. Hong, J. Zhang, and X. Zeng, “Thermal transport in phosphorene and phosphorene-based materials: A review on numerical studies,” Chinese Physics B. 2018. link Times cited: 19 NOT USED (high confidence) A. Mobaraki, A. Kandemir, H. Yapicioglu, O. Gulseren, and C. Sevik, “Validation of inter-atomic potential for WS2 and WSe2 crystals through assessment of thermal transport properties,” Computational Materials Science. 2018. link Times cited: 31 NOT USED (high confidence) L. Zhang, J. Han, H. Wang, R. Car, and W. E, “DeePCG: Constructing coarse-grained models via deep neural networks.,” The Journal of chemical physics. 2018. link Times cited: 140 Abstract: We introduce a general framework for constructing coarse-gra… read moreAbstract: We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called the Deep Coarse-Grained Potential (abbreviated DeePCG), exploits a carefully crafted neural network to construct a many-body coarse-grained potential. The network is trained with full atomistic data in a way that preserves the natural symmetries of the system. The resulting model is very accurate and can be used to sample the configurations of the coarse-grained variables in a much faster way than with the original atomistic model. As an application, we consider liquid water and use the oxygen coordinates as the coarse-grained variables, starting from a full atomistic simulation of this system at the ab initio molecular dynamics level. We find that the two-body, three-body, and higher-order oxygen correlation functions produced by the coarse-grained and full atomistic models agree very well with each other, illustrating the effectiveness of the DeePCG model on a rather challenging task. read less NOT USED (high confidence) G. Fugallo and L. Colombo, “Calculating lattice thermal conductivity: a synopsis,” Physica Scripta. 2018. link Times cited: 41 Abstract: We provide a tutorial introduction to the modern theoretical… read moreAbstract: We provide a tutorial introduction to the modern theoretical and computational schemes available to calculate the lattice thermal conductivity in a crystalline dielectric material. While some important topics in thermal transport will not be covered (including thermal boundary resistance, electronic thermal conduction, and thermal rectification), we aim at: (i) framing the calculation of thermal conductivity within the general non-equilibrium thermodynamics theory of transport coefficients, (ii) presenting the microscopic theory of thermal conduction based on the phonon picture and the Boltzmann transport equation, and (iii) outlining the molecular dynamics schemes to calculate heat transport. A comparative and critical addressing of the merits and drawbacks of each approach will be discussed as well. read less NOT USED (high confidence) M. Friedrich and U. Stefanelli, “Graphene ground states,” Zeitschrift für angewandte Mathematik und Physik. 2018. link Times cited: 7 NOT USED (high confidence) C. Zhang and Z. Liu, “Freezing of water confined in porous materials: role of adsorption and unfreezable threshold,” Acta Geotechnica. 2018. link Times cited: 25 NOT USED (high confidence) L. Rovigatti, J. Russo, and F. Romano, “How to simulate patchy particles,” The European Physical Journal E. 2018. link Times cited: 32 NOT USED (high confidence) M. Z. Hossain, T. Hao, and B. Silverman, “Stillinger–Weber potential for elastic and fracture properties in graphene and carbon nanotubes,” Journal of Physics: Condensed Matter. 2018. link Times cited: 42 Abstract: This paper presents a new framework for determining the Stil… read moreAbstract: This paper presents a new framework for determining the Stillinger–Weber (SW) potential parameters for modeling fracture in graphene and carbon nanotubes. In addition to fitting the equilibrium material properties, the approach allows fitting the potential to the forcing behavior as well as the mechanical strength of the solid, without requiring ad hoc modification of the nearest-neighbor interactions for avoiding artificial stiffening of the lattice at larger deformation. Consistent with the first-principles results, the potential shows the Young’s modulus of graphene to be isotropic under symmetry-preserving and symmetry-breaking deformation conditions. It also shows the Young’s modulus of carbon nanotubes to be diameter-dependent under symmetry-breaking loading conditions. The potential addresses the key deficiency of existing empirical potentials in reproducing experimentally observed glass-like brittle fracture in graphene and carbon nanotubes. In simulating the entire deformation process leading to fracture, the SW-potential costs several factors less computational time compared to the state-of-the-art interatomic potentials that enables exploration of the fracture processes in large atomistic systems which are inaccessible otherwise. read less NOT USED (high confidence) J. Zhang, “Piezoelectric effect on the thermal conductivity of monolayer gallium nitride,” Journal of Applied Physics. 2018. link Times cited: 9 Abstract: Using molecular dynamics and density functional theory simul… read moreAbstract: Using molecular dynamics and density functional theory simulations, in this work, we find that the heat transport property of the monolayer gallium nitride (GaN) can be efficiently tailored by external electric field due to its unique piezoelectric characteristic. As the monolayer GaN possesses different piezoelectric properties in armchair and zigzag directions, different effects of the external electric field on thermal conductivity are observed when it is applied in the armchair and zigzag directions. Our further study reveals that due to the elastoelectric effect in the monolayer GaN, the external electric field changes the Young's modulus and therefore changes the phonon group velocity. Also, due to the inverse piezoelectric effect, the applied electric field induces in-plane stress in the monolayer GaN subject to a length constraint, which results in the change in the lattice anharmonicity and therefore affects the phonon mean free path. Furthermore, for relatively long GaN monolayers, the in-plane ... read less NOT USED (high confidence) A. Glielmo, C. Zeni, and A. Vita, “Efficient nonparametric n -body force fields from machine learning,” Physical Review B. 2018. link Times cited: 92 Abstract: The authors present a scheme to construct classical $n$-body… read moreAbstract: The authors present a scheme to construct classical $n$-body force fields using Gaussian Process (GP) Regression, appropriately mapped over explicit n-body functions (M-FFs). The procedure is possible, and will yield accurate forces, whenever prior knowledge allows to restrict the interactions to a finite order $n$, so that the ``universal approximator'' resolving power of standard GPs or Neural Networks is not needed. Under these conditions, the proposed construction preserves flexibility of training, systematically improvable accuracy, and a clear framework for validation of the underlying machine learning technique. Moreover, the M-FFs are as fast as classical parametrized potentials, since they avoid lengthy summations over database entries or weight parameters. read less NOT USED (high confidence) Y. Han, J. Jin, J. Wagner, and G. Voth, “Quantum theory of multiscale coarse-graining.,” The Journal of chemical physics. 2018. link Times cited: 13 Abstract: Coarse-grained (CG) models serve as a powerful tool to simul… read moreAbstract: Coarse-grained (CG) models serve as a powerful tool to simulate molecular systems at much longer temporal and spatial scales. Previously, CG models and methods have been built upon classical statistical mechanics. The present paper develops a theory and numerical methodology for coarse-graining in quantum statistical mechanics, by generalizing the multiscale coarse-graining (MS-CG) method to quantum Boltzmann statistics. A rigorous derivation of the sufficient thermodynamic consistency condition is first presented via imaginary time Feynman path integrals. It identifies the optimal choice of CG action functional and effective quantum CG (qCG) force field to generate a quantum MS-CG (qMS-CG) description of the equilibrium system that is consistent with the quantum fine-grained model projected onto the CG variables. A variational principle then provides a class of algorithms for optimally approximating the qMS-CG force fields. Specifically, a variational method based on force matching, which was also adopted in the classical MS-CG theory, is generalized to quantum Boltzmann statistics. The qMS-CG numerical algorithms and practical issues in implementing this variational minimization procedure are also discussed. Then, two numerical examples are presented to demonstrate the method. Finally, as an alternative strategy, a quasi-classical approximation for the thermal density matrix expressed in the CG variables is derived. This approach provides an interesting physical picture for coarse-graining in quantum Boltzmann statistical mechanics in which the consistency with the quantum particle delocalization is obviously manifest, and it opens up an avenue for using path integral centroid-based effective classical force fields in a coarse-graining methodology. read less NOT USED (high confidence) A. Mrózek, W. Kuś, and T. Burczynski, “Modelling of molybdenum-based 2D materials.” 2018. link Times cited: 1 Abstract: The flat, two dimensional materials play important role in t… read moreAbstract: The flat, two dimensional materials play important role in the research and industrial applications in the last 15 years. The new materials with flat atomic structures are discovered almost every month. The focus of the paper is on the discrete modeling of the single layer molybdenum disulphide based material (SLMoS2). Two methods, based on the molecular statics and molecular dynamics of estimation of material properties and numerical simulations at the nanolevel are described and discussed. read less NOT USED (high confidence) M. Wen, S. Shirodkar, P. Plecháč, E. Kaxiras, R. Elliott, and E. Tadmor, “A force-matching Stillinger-Weber potential for MoS2: Parameterization and Fisher information theory based sensitivity analysis,” Journal of Applied Physics. 2017. link Times cited: 25 Abstract: Two-dimensional molybdenum disulfide (MoS2) is a promising m… read moreAbstract: Two-dimensional molybdenum disulfide (MoS2) is a promising material for the next generation of switchable transistors and photodetectors. In order to perform large-scale molecular simulations of the mechanical and thermal behavior of MoS2-based devices, an accurate interatomic potential is required. To this end, we have developed a Stillinger-Weber potential for monolayer MoS2. The potential parameters are optimized to reproduce the geometry (bond lengths and bond angles) of MoS2 in its equilibrium state and to match as closely as possible the forces acting on the atoms along a dynamical trajectory obtained from ab initio molecular dynamics. Verification calculations indicate that the new potential accurately predicts important material properties including the strain dependence of the cohesive energy, the elastic constants, and the linear thermal expansion coefficient. The uncertainty in the potential parameters is determined using a Fisher information theory analysis. It is found that the parameters are... read less NOT USED (high confidence) X. W. Zhou, R. Jones, and K. Chu, “Polymorphic improvement of Stillinger-Weber potential for InGaN,” Journal of Applied Physics. 2017. link Times cited: 4 Abstract: A Stillinger-Weber potential is computationally very efficie… read moreAbstract: A Stillinger-Weber potential is computationally very efficient for molecular dynamics simulations. Despite its simple mathematical form, the Stillinger-Weber potential can be easily parameterized to ensure that crystal structures with tetrahedral bond angles (e.g., diamond-cubic, zinc-blende, and wurtzite) are stable and have the lowest energy. As a result, the Stillinger-Weber potential has been widely used to study a variety of semiconductor elements and alloys. When studying an A-B binary system, however, the Stillinger-Weber potential is associated with two major drawbacks. First, it significantly overestimates the elastic constants of elements A and B, limiting its use for systems involving both compounds and elements (e.g., an A/AB multilayer). Second, it prescribes equal energy for zinc-blende and wurtzite crystals, limiting its use for compounds with large stacking fault energies. Here, we utilize the polymorphic potential style recently implemented in LAMMPS to develop a modified Stillinger-Weber potential for InGaN that overcomes these two problems.A Stillinger-Weber potential is computationally very efficient for molecular dynamics simulations. Despite its simple mathematical form, the Stillinger-Weber potential can be easily parameterized to ensure that crystal structures with tetrahedral bond angles (e.g., diamond-cubic, zinc-blende, and wurtzite) are stable and have the lowest energy. As a result, the Stillinger-Weber potential has been widely used to study a variety of semiconductor elements and alloys. When studying an A-B binary system, however, the Stillinger-Weber potential is associated with two major drawbacks. First, it significantly overestimates the elastic constants of elements A and B, limiting its use for systems involving both compounds and elements (e.g., an A/AB multilayer). Second, it prescribes equal energy for zinc-blende and wurtzite crystals, limiting its use for compounds with large stacking fault energies. Here, we utilize the polymorphic potential style recently implemented in LAMMPS to develop a modified Stillinger-Weber... read less NOT USED (high confidence) J. Luo, A. Alateeqi, L. Liu, and T. Sinno, “Atomistic simulations of carbon diffusion and segregation in liquid silicon,” Journal of Applied Physics. 2017. link Times cited: 9 Abstract: The diffusivity of carbon atoms in liquid silicon and their … read moreAbstract: The diffusivity of carbon atoms in liquid silicon and their equilibrium distribution between the silicon melt and crystal phases are key, but unfortunately not precisely known parameters for the global models of silicon solidification processes. In this study, we apply a suite of molecular simulation tools, driven by multiple empirical potential models, to compute diffusion and segregation coefficients of carbon at the silicon melting temperature. We generally find good consistency across the potential model predictions, although some exceptions are identified and discussed. We also find good agreement with the range of available experimental measurements of segregation coefficients. However, the carbon diffusion coefficients we compute are significantly lower than the values typically assumed in continuum models of impurity distribution. Overall, we show that currently available empirical potential models may be useful, at least semi-quantitatively, for studying carbon (and possibly other impurity) trans... read less NOT USED (high confidence) X. Wu and X. Li, “Simulations of micron-scale fracture using atomistic-based boundary element method,” Modelling and Simulation in Materials Science and Engineering. 2017. link Times cited: 3 Abstract: A new formulation of a boundary element method (BEM) is prop… read moreAbstract: A new formulation of a boundary element method (BEM) is proposed in this paper to simulate cracks at the micron scale. The main departure from the traditional BEMs is that the current model is derived from the underlying atomistic model, which involves the interactions of atoms at the scale of Angstroms. By using the lattice Green’s function, the new BEM formulation eliminates the excessive atomic degrees of freedom away from crack tips, and directly couples the process zones with the physical boundary conditions. We show that with such a drastic reduction, one can simulate brittle fracture process on the scale of microns, for which the entire system consists of a few billion atoms. We discuss several numerical issues to make the implementation more efficient. Examples will be presented for cracks in the bcc iron system. read less NOT USED (high confidence) P. M. Naullage, L. Lupi, and V. Molinero, “Molecular Recognition of Ice by Fully Flexible Molecules,” Journal of Physical Chemistry C. 2017. link Times cited: 57 Abstract: Cold acclimatized organisms produce antifreeze proteins that… read moreAbstract: Cold acclimatized organisms produce antifreeze proteins that prevent ice growth and recrystallization at subfreezing conditions. Flatness and rigidity of the ice-binding sites of antifreeze proteins are considered key for their recognition of ice. However, the most potent synthetic ice recrystallization inhibitor (IRI) found to date is poly(vinyl alcohol) (PVA), a fully flexible molecule. The ability to tune the architecture and functionalization of PVA makes it a promising candidate to replace antifreeze proteins in industrial applications ranging from cryopreservation of organs to deicing of turbine blades. However, an understanding of how does PVA recognize ice remains elusive, hampering the design of more effective IRIs. Here we use large-scale molecular simulations to elucidate the mechanism by which PVA recognizes ice. We find that the polymer selectively binds to the prismatic faces of ice through a cooperative zipper mechanism. The binding is driven by hydrogen bonding, facilitated by distance mat... read less NOT USED (high confidence) M. L. Nietiadi, P. Umstätter, I. A. Alhafez, Y. Rosandi, E. Bringa, and H. Urbassek, “Collision‐Induced Melting in Collisions of Water Ice Nanograins: Strong Deformations and Prevention of Bouncing,” Geophysical Research Letters. 2017. link Times cited: 11 Abstract: Collisions between ice grains are ubiquitous in the outer so… read moreAbstract: Collisions between ice grains are ubiquitous in the outer solar system. The mechanics of such collisions is traditionally described by the elastic contact theory of adhesive spheres. Here we use molecular dynamics simulations to study collisions between nanometer‐sized amorphous water ice grains. We demonstrate that the collision‐induced heating leads to grain melting in the interface of the colliding grains. The large lateral deformations and grain sticking induced considerably modify available macroscopic collision models. We report on systematic increases of the contact radius, strong grain deformations, and the prevention of grain bouncing. read less NOT USED (high confidence) T. Gao et al., “Microstructural properties and evolution of nanoclusters in liquid Si during a rapid cooling process,” JETP Letters. 2017. link Times cited: 2 NOT USED (high confidence) N. Ning, L. Couedel, C. Arnas, and S. Khrapak, “Computational Prediction of Rate Constants for Reactions Involved in Al Clustering.,” The journal of physical chemistry. A. 2017. link Times cited: 2 Abstract: Aluminum (Al) clustering processes via three types of associ… read moreAbstract: Aluminum (Al) clustering processes via three types of association reactions are herein studied using classical molecular dynamics trajectory calculations. The simulations were carried out under realistic experimental conditions. The dependence of rate constants on temperature and cluster size was obtained. The association reactions have a very small activation barrier, and the activation energy increases with increasing temperature. Our prediction of reaction rate constants can be of interest for the study of Al nanoparticle growth using kinetic models. read less NOT USED (high confidence) E. Mainini, H. Murakawa, P. Piovano, and U. Stefanelli, “Carbon-Nanotube Geometries as Optimal Configurations,” Multiscale Model. Simul. 2017. link Times cited: 12 Abstract: The fine geometry of carbon nanotubes is investigated from t… read moreAbstract: The fine geometry of carbon nanotubes is investigated from the viewpoint of molecular mechanics. Actual nanotube configurations are characterized as locally minimizers of a given configurational energy, including both two- and three-body contributions. By focusing on so-called zigzag and armchair topologies, we prove that the configurational energy is strictly minimized within specific, one-parameter families of periodic configurations. Such optimal configurations are checked to be stable with respect to a large class of small nonperiodic perturbations and do not coincide with classical rolled-up nor polyhedral geometries. read less NOT USED (high confidence) V. R. Ardham and F. Leroy, “Communication: Is a coarse-grained model for water sufficient to compute Kapitza conductance on non-polar surfaces?,” The Journal of chemical physics. 2017. link Times cited: 5 Abstract: Coarse-grained models have increasingly been used in large-s… read moreAbstract: Coarse-grained models have increasingly been used in large-scale particle-based simulations. However, due to their lack of degrees of freedom, it is a priori unlikely that they straightforwardly represent thermal properties with the same accuracy as their atomistic counterparts. We take a first step in addressing the impact of liquid coarse-graining on interfacial heat conduction by showing that an atomistic and a coarse-grained model of water may yield similar values of the Kapitza conductance on few-layer graphene with interactions ranging from hydrophobic to mildly hydrophilic. By design the water models employed yield similar liquid layer structures on the graphene surfaces. Moreover, they share common vibration properties close to the surfaces and thus couple with the vibrations of graphene in a similar way. These common properties explain why they yield similar Kapitza conductance values despite their bulk thermal conductivity differing by more than a factor of two. read less NOT USED (high confidence) M. Lauricella, G. Ciccotti, N. J. English, B. Peters, and S. Meloni, “Mechanisms and Nucleation Rate of Methane Hydrate by Dynamical Nonequilibrium Molecular Dynamics,” Journal of Physical Chemistry C. 2017. link Times cited: 28 Abstract: We investigate the effects of high solvated-methane concentr… read moreAbstract: We investigate the effects of high solvated-methane concentration on methane-hydrate nucleation at 250 K and 500 atm. We consider solutions at four levels of methane molar fraction in the initial H2O–CH4 solution, χCH4 = 0.038, 0.044, 0.052, and 0.058, which are higher than (metastable) bulk supersaturation. χCH4 is controlled independently of the temperature and pressure thanks to the use of special simulation techniques [Phys. Chem. Chem. Phys. 2011, 13, 13177]. These conditions mimic a possible increase of local methane concentration beyond supersaturation induced, for example, by freeze concentration or thermal fluctuations. The nucleation mechanism and kinetics are investigated using the dynamical approach to nonequilibrium molecular dynamics. We demonstrate a hydrate-forming/-ordering process of solvated methane and water molecules in a manner consistent with both the “blob” hypothesis and “cage adsorption hypothesis”: the system initially forms an amorphous nucleus at high methane concentration, wh... read less NOT USED (high confidence) S. Hashimoto et al., “Enhanced nickelidation rate in silicon nanowires with interfacial lattice disorder,” Journal of Applied Physics. 2017. link Times cited: 5 Abstract: We demonstrate that the nickelidation (nickel silicidation) … read moreAbstract: We demonstrate that the nickelidation (nickel silicidation) reaction rate of silicon nanowires (SiNWs) surrounded by a thermally grown silicon dioxide (SiO2) film is enhanced by post-oxidation annealing (POA). The SiNWs are fabricated by electron beam lithography, and some of the SiNWs are subjected to the POA process. The nickelidation reaction rate of the SiNWs is enhanced in the samples subjected to the POA treatment. Ultraviolet Raman spectroscopy measurements reveal that POA enhances compressive strain and lattice disorder in the SiNWs. By considering these experimental results in conjunction with our molecular dynamics simulation analysis, we conclude that the oxide-induced lattice disorder is the dominant origin of the increase in the nickelidation rate in smaller width SiNWs. This study sheds light on the pivotal role of lattice disorders in controlling metallic contact formation in SiNW devices. read less NOT USED (high confidence) A. Nobakht, S. Shin, K. Kihm, D. C. Marable, and W. Lee, “Heat flow diversion in supported graphene nanomesh,” Carbon. 2017. link Times cited: 20 NOT USED (high confidence) N. Lubbers, J. S. Smith, and K. Barros, “Hierarchical modeling of molecular energies using a deep neural network.,” The Journal of chemical physics. 2017. link Times cited: 225 Abstract: We introduce the Hierarchically Interacting Particle Neural … read moreAbstract: We introduce the Hierarchically Interacting Particle Neural Network (HIP-NN) to model molecular properties from datasets of quantum calculations. Inspired by a many-body expansion, HIP-NN decomposes properties, such as energy, as a sum over hierarchical terms. These terms are generated from a neural network-a composition of many nonlinear transformations-acting on a representation of the molecule. HIP-NN achieves the state-of-the-art performance on a dataset of 131k ground state organic molecules and predicts energies with 0.26 kcal/mol mean absolute error. With minimal tuning, our model is also competitive on a dataset of molecular dynamics trajectories. In addition to enabling accurate energy predictions, the hierarchical structure of HIP-NN helps to identify regions of model uncertainty. read less NOT USED (high confidence) M. Tomita, M. Ogasawara, T. Terada, and T. Watanabe, “Development of interatomic potential of Ge(1−x−y)SixSny ternary alloy semiconductors for classical lattice dynamics simulation,” Japanese Journal of Applied Physics. 2017. link Times cited: 9 Abstract: We provide the parameters of Stillinger–Weber potentials for… read moreAbstract: We provide the parameters of Stillinger–Weber potentials for GeSiSn ternary mixed systems. These parameters can be used in molecular dynamics (MD) simulations to reproduce phonon properties and thermal conductivities. The phonon dispersion relation is derived from the dynamical structure factor, which is calculated by the space-time Fourier transform of atomic trajectories in an MD simulation. The phonon properties and thermal conductivities of GeSiSn ternary crystals calculated using these parameters mostly reproduced both the findings of previous experiments and earlier calculations made using MD simulations. The atomic composition dependence of these properties in GeSiSn ternary crystals obtained by previous studies (both experimental and theoretical) and the calculated data were almost exactly reproduced by our proposed parameters. Moreover, the results of the MD simulation agree with the previous calculations made using a time-independent phonon Boltzmann transport equation with complicated scattering mechanisms. These scattering mechanisms are very important in complicated nanostructures, as they allow the heat-transfer properties to be more accurately calculated by MD simulations. This work enables us to predict the phonon- and heat-related properties of bulk group IV alloys, especially ternary alloys. read less NOT USED (high confidence) K. Ono, N. Nakazaki, H. Tsuda, Y. Takao, and K. Eriguchi, “Surface morphology evolution during plasma etching of silicon: roughening, smoothing and ripple formation,” Journal of Physics D: Applied Physics. 2017. link Times cited: 14 Abstract: Atomic- or nanometer-scale roughness on feature surfaces has… read moreAbstract: Atomic- or nanometer-scale roughness on feature surfaces has become an important issue to be resolved in the fabrication of nanoscale devices in industry. Moreover, in some cases, smoothing of initially rough surfaces is required for planarization of film surfaces, and controlled surface roughening is required for maskless fabrication of organized nanostructures on surfaces. An understanding, under what conditions plasma etching results in surface roughening and/or smoothing and what are the mechanisms concerned, is of great technological as well as fundamental interest. In this article, we review recent developments in the experimental and numerical study of the formation and evolution of surface roughness (or surface morphology evolution such as roughening, smoothing, and ripple formation) during plasma etching of Si, with emphasis being placed on a deeper understanding of the mechanisms or plasma–surface interactions that are responsible for. Starting with an overview of the experimental and theoretical/numerical aspects concerned, selected relevant mechanisms are illustrated and discussed primarily on the basis of systematic/mechanistic studies of Si etching in Cl-based plasmas, including noise (or stochastic roughening), geometrical shadowing, surface reemission of etchants, micromasking by etch inhibitors, and ion scattering/chanelling. A comparison of experiments (etching and plasma diagnostics) and numerical simulations (Monte Carlo and classical molecular dynamics) indicates a crucial role of the ion scattering or reflection from microscopically roughened feature surfaces on incidence in the evolution of surface roughness (and ripples) during plasma etching; in effect, the smoothing/non-roughening condition is characterized by reduced effects of the ion reflection, and the roughening-smoothing transition results from reduced ion reflections caused by a change in the predominant ion flux due to that in plasma conditions. Smoothing of initially rough surfaces as well as non-roughening of initially planar surfaces during etching (normal ion incidence) and formation of surface ripples by plasma etching (off-normal ion incidence) are also presented and discussed in this context. read less NOT USED (high confidence) K. Cai, J. Shi, L. Liu, and Q. Qin, “Fabrication of an ideal nanoring from a black phosphorus nanoribbon upon movable bundling carbon nanotubes,” Nanotechnology. 2017. link Times cited: 11 Abstract: As a low dimensional material, black phosphorus (BP) continu… read moreAbstract: As a low dimensional material, black phosphorus (BP) continues to attract much attention from researchers due to its excellent electric properties. In particular, the one-dimensional material, in the form of a ring or tube formed from BP, has been extensively studied and found to be a perfect semiconductor. But the BP ring has never been reported in laboratories. To form an ideal ring from a rectangular BP ribbon, we choose a carbon nanotube (CNT) bundle to attract the ribbon and move one or more CNTs in the bundle to induce the unsaturated ends of the BP ribbon to become covalently bonded. Numerical experiments are applied to BP ribbons with lengths either equal to, shorter, or longer than the perimeter of the CNT bundle, to investigate the formation of a BP ring. Experiments show that if one end of the BP ribbon is attracted by a CNT, moving the other CNTs away endows the ribbon with high probability of forming an ideal ring. The conclusions drawn from these results will benefit future in situ experiments involving forming a ring from a BP ribbon. read less NOT USED (high confidence) U. Stefanelli, “Stable carbon configurations,” Bollettino dell’Unione Matematica Italiana. 2017. link Times cited: 8 NOT USED (high confidence) M. Stein, “A fast, parallel algorithm for distant-dependent calculation of crystal properties,” Comput. Phys. Commun. 2017. link Times cited: 3 NOT USED (high confidence) Z. Zhang, Y. Zhao, and G. Ouyang, “Strain Modulation of Electronic Properties of Monolayer Black Phosphorus,” Journal of Physical Chemistry C. 2017. link Times cited: 33 Abstract: Recent advances in the fabrication of monolayer black phosph… read moreAbstract: Recent advances in the fabrication of monolayer black phosphorus (MBP) call for a detailed understanding of the physics underlying the electronic structure and related modulation by the method of strain engineering. Here, we present an analytic study to explore the uniaxial strain effect of band structure in MBP based on the first-principles calculations and atomic-bond-relaxation correlation mechanism. It was found that the stress responses of MBP show evident anisotropy due to different edge type structures. The electronic band structure of MBP can be tuned by the applied strain. Moreover, we propose an analytic expression for the variation of the bandgap induced by the uniaxial strain from the perspective of atomistic origin, which suggests an effective bridge between the measurable quantities and the atomic bond identities of MBP. The underlying mechanism on the strain-dependent band offset can be attributed to the variation of crystal potential induced by the changes of bond length, strength, and ang... read less NOT USED (high confidence) A. Gautam, N. Pingua, A. Goyal, and P. A. Apte, “Dynamical Instability Causes the Demise of a Supercooled Tetrahedral Liquid,” Journal of Statistical Physics. 2017. link Times cited: 5 NOT USED (high confidence) K. Eriguchi, “Modeling of defect generation during plasma etching and its impact on electronic device performance—plasma-induced damage,” Journal of Physics D: Applied Physics. 2017. link Times cited: 23 Abstract: The increasing demand for the higher performance of ultra-la… read moreAbstract: The increasing demand for the higher performance of ultra-large-scale integration (ULSI) circuits requires the aggressive shrinkage of device feature sizes in accordance with the scaling law. Plasma processing plays an important role in achieving fine patterns with anisotropic features in metal–oxide–semiconductor field-effect transistors (MOSFETs). This article comprehensively addresses the negative aspects of plasma processing, i.e. plasma process-induced damage, in particular, the defect creation induced by ion bombardment in Si substrates during plasma etching. The ion bombardment damage forms a surface modified region and creates localized defect structures. Modeling and characterization techniques of the ion bombardment damage in Si substrates are overviewed. The thickness of the modified region, i.e. the damaged layer, is modeled by a modified range theory and the density of defects is characterized by photoreflectance spectroscopy (PRS) and the capacitance–voltage technique. The effects of plasma-induced damage (PID) on MOSFET performance are presented. In addition, some of the emerging topics—the enhanced parameter variability in ULSI circuits and recovery of the damage—are discussed as future perspectives. read less NOT USED (high confidence) S. Bergmann, K. Albe, E. Flegel, D. Barragan-Yani, and B. Wagner, “Anisotropic solid–liquid interface kinetics in silicon: an atomistically informed phase-field model,” Modelling and Simulation in Materials Science and Engineering. 2017. link Times cited: 10 Abstract: We present an atomistically informed parametrization of a ph… read moreAbstract: We present an atomistically informed parametrization of a phase-field model for describing the anisotropic mobility of liquid–solid interfaces in silicon. The model is derived from a consistent set of atomistic data and thus allows to directly link molecular dynamics and phase field simulations. Expressions for the free energy density, the interfacial energy and the temperature and orientation dependent interface mobility are systematically fitted to data from molecular dynamics simulations based on the Stillinger–Weber interatomic potential. The temperature-dependent interface velocity follows a Vogel–Fulcher type behavior and allows to properly account for the dynamics in the undercooled melt. read less NOT USED (high confidence) J. Dérès, M. David, K. Alix, C. Hébert, D. Alexander, and L. Pizzagalli, “Properties of helium bubbles in covalent systems at the nanoscale: A combined numerical and experimental study,” Physical Review B. 2017. link Times cited: 16 Abstract: The properties of nanometric-sized helium bubbles in silicon… read moreAbstract: The properties of nanometric-sized helium bubbles in silicon have been investigated using both spatially resolved electron-energy-loss spectroscopy combined with a recently developed method, and molecular-dynamics simulations. The experiments allowed for an accurate determination of size, aspect ratio, and helium density for a large number of single bubbles, whose diameters ranged from 6 to 20 nm. Very high helium densities, from 60 to 180 He nm(-3), have been measured depending on the conditions, in stark contrast with previous investigations of helium bubbles in metal with similar sizes. To supplement experiments on a smaller scale, and to obtain insights into the silicon matrix state, atomistic calculations have been performed for helium bubbles in the diameter range 1-13 nm. Molecular-dynamics simulations revealed that the maximum attainable helium density is critically related to the strength of the silicon matrix, which tends to yield by amorphization at the highest density levels. Calculations give helium density values for isolated single bubbles that are typically lower than measurements. However, excellent agreement is recovered when the interactions between bubbles and the presence of helium interstitials in the matrix are taken into account. Both experiments and numerical simulations suggest that the Laplace-Young law cannot be used to predict helium density in nanometric-sized bubbles in a covalent material such as silicon. read less NOT USED (high confidence) V. Mazhukin, A. V. Shapranov, V. E. Perezhigin, O. Koroleva, and A. Mazhukin, “Kinetic melting and crystallization stages of strongly superheated and supercooled metals,” Mathematical Models and Computer Simulations. 2017. link Times cited: 17 NOT USED (high confidence) A. Rohskopf, H. Seyf, K. Gordiz, T. Tadano, and A. Henry, “Empirical interatomic potentials optimized for phonon properties,” npj Computational Materials. 2017. link Times cited: 35 NOT USED (high confidence) V. Mazhukin, A. V. Shapranov, V. E. Perezhigin, O. Koroleva, and A. Mazhukin, “Kinetic melting and crystallization stages of strongly superheated and supercooled metals,” Mathematical Models and Computer Simulations. 2017. link Times cited: 0 NOT USED (high confidence) X. Chen, J. Ding, C. Jiang, Z. Liu, and N. Yuan, “Microstructure evolution of polycrystalline silicon by molecular dynamics simulation,” AIP Advances. 2017. link Times cited: 2 Abstract: Polycrystalline silicon is the dominant material in solar ce… read moreAbstract: Polycrystalline silicon is the dominant material in solar cells and plays an important role in photovoltaic industry. It is important for not only the conventional production of silicon ingots but also the direct growth of silicon wafers to control crystallization for obtaining the desired polycrystalline silicon. To the best of our knowledge, few studies have systematically reported about the effects of crystalline planes on the solidification behavior of liquid silicon and the analysis of the microstructural features of the polysilicon structure. In this study, molecular dynamics simulations were employed to investigate the solidification and microstructure evolution of polysilicon, with focus on the effects of the seed distribution and cooling rate on the growth of polycrystalline silicon. The (110), (111), and (112) planes were extruded by the (100) plane and formed the inclusion shape. The crystallization of silicon consisted of diamond-type structures is relatively high at a low cooling rate. The si... read less NOT USED (high confidence) R.-peng Chen, E. Lascaris, and J. Palmer, “Liquid-liquid phase transition in an ionic model of silica.,” The Journal of chemical physics. 2017. link Times cited: 27 Abstract: Recent equation of state calculations [E. Lascaris, Phys. Re… read moreAbstract: Recent equation of state calculations [E. Lascaris, Phys. Rev. Lett. 116, 125701 (2016)] for an ionic model of silica suggest that it undergoes a density-driven, liquid-liquid phase transition (LLPT) similar to the controversial transition hypothesized to exist in deeply supercooled water. Here, we perform extensive free energy calculations to scrutinize the model's low-temperature phase behavior and confirm the existence of a first-order phase transition between two liquids with identical compositions but different densities. The low-density liquid (LDL) exhibits tetrahedral order, which is partially disrupted in the high-density liquid (HDL) by the intrusion of additional particles into the primary neighbor shell. Histogram reweighting methods are applied to locate conditions of HDL-LDL coexistence and the liquid spinodals that bound the two-phase region. Spontaneous liquid-liquid phase separation is also observed directly in large-scale molecular dynamics simulations performed inside the predicted two-phase region. Given its clear LLPT, we anticipate that this model may serve as a paradigm for understanding whether similar transitions occur in water and other tetrahedral liquids. read less NOT USED (high confidence) P. Saidi, R. Freitas, T. Frolov, M. Asta, and J. Hoyt, “Free energy of steps at faceted (1 1 1) solid-liquid interfaces in the Si-Al system calculated using capillary fluctuation method,” Computational Materials Science. 2017. link Times cited: 8 NOT USED (high confidence) M. Friedrich, E. Mainini, P. Piovano, and U. Stefanelli, “Characterization of Optimal Carbon Nanotubes Under Stretching and Validation of the Cauchy–Born Rule,” Archive for Rational Mechanics and Analysis. 2017. link Times cited: 9 NOT USED (high confidence) A. Bartók et al., “Machine learning unifies the modeling of materials and molecules,” Science Advances. 2017. link Times cited: 497 Abstract: Statistical learning based on a local representation of atom… read moreAbstract: Statistical learning based on a local representation of atomic structures provides a universal model of chemical stability. Determining the stability of molecules and condensed phases is the cornerstone of atomistic modeling, underpinning our understanding of chemical and materials properties and transformations. We show that a machine-learning model, based on a local description of chemical environments and Bayesian statistical learning, provides a unified framework to predict atomic-scale properties. It captures the quantum mechanical effects governing the complex surface reconstructions of silicon, predicts the stability of different classes of molecules with chemical accuracy, and distinguishes active and inactive protein ligands with more than 99% reliability. The universality and the systematic nature of our framework provide new insight into the potential energy surface of materials and molecules. read less NOT USED (high confidence) T. Rodríguez-López, Y. Khalak, and M. Karttunen, “Non-conformal coarse-grained potentials for water.,” The Journal of chemical physics. 2017. link Times cited: 8 Abstract: Water is a notoriously difficult substance to model both acc… read moreAbstract: Water is a notoriously difficult substance to model both accurately and efficiently. Here, we focus on descriptions with a single coarse-grained particle per molecule using the so-called approximate non-conformal and generalized Stockmayer potentials as the starting points. They are fitted using the radial distribution function and the liquid-gas density profile of the atomistic extended simple point charge (SPC/E) model by downhill simplex optimization. We compare the results with monatomic water (mW), ELBA, and direct iterative Boltzmann inversion of SPC/E. The results show that symmetrical potentials result in non-transferable models, that is, they need to be reparametrized for new state points. This indicates that transferability may require more complex models. Furthermore, the results also show that the addition of a point dipole is not sufficient to make the potentials accurate and transferable to different temperatures (300 K-500 K) and pressures without an appropriate choice of properties as targets during model optimization. read less NOT USED (high confidence) P. Seeberger and J. Vidal, “On the ab initio calculation of vibrational formation entropy of point defect: the case of the silicon vacancy.” 2017. link Times cited: 7 Abstract: Formation entropy of point defects is one of the last crucia… read moreAbstract: Formation entropy of point defects is one of the last crucial elements required to fully describe the temperature dependence of point defect formation. However, while many attempts have been made to compute them for very complicated systems, very few works have been carried out such as to assess the different effects of finite size effects and precision on such quantity. Large discrepancies can be found in the literature for a system as primitive as the silicon vacancy. In this work, we have proposed a systematic study of formation entropy for silicon vacancy in its 3 stable charge states: neutral, +2 and –2 for supercells with size not below 432 atoms. Rationalization of the formation entropy is presented, highlighting importance of finite size error and the difficulty to compute such quantities due to high numerical requirement. It is proposed that the direct calculation of formation entropy of V Si using first principles methods will be plagued by very high computational workload (or large numerical errors) and finite size dependent results. read less NOT USED (high confidence) Y. Furukawa and Y. Matsushita, “Analysis of single and composite structural defects in pure amorphous silicon: a first-principles study.” 2017. link Times cited: 3 NOT USED (high confidence) H. Ko, A. Kaczmarowski, I. Szlufarska, and D. Morgan, “Data for: Optimization of self-interstitial clusters in 3C-SiC with Genetic Algorithm.” 2017. link Times cited: 9 NOT USED (high confidence) J. Gruber, X. W. Zhou, R. Jones, S. R. Lee, and G. Tucker, “Molecular dynamics studies of defect formation during heteroepitaxial growth of InGaN alloys on (0001) GaN surfaces.,” Journal of applied physics. 2017. link Times cited: 25 Abstract: We investigate the formation of extended defects during mole… read moreAbstract: We investigate the formation of extended defects during molecular-dynamics (MD) simulations of GaN and InGaN growth on (0001) and ([Formula: see text]) wurtzite-GaN surfaces. The simulated growths are conducted on an atypically large scale by sequentially injecting nearly a million individual vapor-phase atoms towards a fixed GaN surface; we apply time-and-position-dependent boundary constraints that vary the ensemble treatments of the vapor-phase, the near-surface solid-phase, and the bulk-like regions of the growing layer. The simulations employ newly optimized Stillinger-Weber In-Ga-N-system potentials, wherein multiple binary and ternary structures are included in the underlying density-functional-theory training sets, allowing improved treatment of In-Ga-related atomic interactions. To examine the effect of growth conditions, we study a matrix of >30 different MD-growth simulations for a range of In x Ga 1-x N-alloy compositions (0 ≤ x ≤ 0.4) and homologous growth temperatures [0.50 ≤ T/T*m (x) ≤ 0.90], where T*m (x) is the simulated melting point. Growths conducted on polar (0001) GaN substrates exhibit the formation of various extended defects including stacking faults/polymorphism, associated domain boundaries, surface roughness, dislocations, and voids. In contrast, selected growths conducted on semi-polar ([Formula: see text]) GaN, where the wurtzite-phase stacking sequence is revealed at the surface, exhibit the formation of far fewer stacking faults. We discuss variations in the defect formation with the MD growth conditions, and we compare the resulting simulated films to existing experimental observations in InGaN/GaN. While the palette of defects observed by MD closely resembles those observed in the past experiments, further work is needed to achieve truly predictive large-scale simulations of InGaN/GaN crystal growth using MD methodologies. read less NOT USED (high confidence) J. Zhang et al., “Phonon Thermal Properties of Transition-Metal Dichalcogenides MoS2 and MoSe2 Heterostructure,” Journal of Physical Chemistry C. 2017. link Times cited: 37 Abstract: Two prototype transition-metal dichalcogenide (TMDC) materia… read moreAbstract: Two prototype transition-metal dichalcogenide (TMDC) materials, MoS2 and MoSe2, have attracted growing attention as promising 2D semiconductors. The heterostructure created by stacking the 2D monolayers in the out-of-plane direction exhibits peculiar properties that can be utilized in electronic applications. The lateral and flexural phonon transport behaviors in MoS2/MoSe2 heterobilayer are comprehensively investigated using classical molecular dynamics simulations. In-plane thermal conductivity (κ) and out-of-plane interfacial thermal resistance (R) are calculated by nonequilibrium molecular dynamics (NEMD) and transient pump–probe methods, respectively. Thermal conductivity of MoS2/MoSe2 bilayer 2D sheet is characterized as 28.8 W/m·K, which preserves the high thermal conductivity of most TMDC materials. The maximum κ reductions of MoS2, MoSe2, and heterobilayer amount to 83.0, 68.9, and 77.1%, respectively, with increasing temperatures from 100 to 500 K. It is also found that the basal-plane thermal p... read less NOT USED (high confidence) Z. Fan, J. Ding, Q. J. Li, and E. Ma, “Correlating the properties of amorphous silicon with its flexibility volume,” Physical Review B. 2017. link Times cited: 16 Abstract: For metallic glasses, “flexibility volume” has recently been… read moreAbstract: For metallic glasses, “flexibility volume” has recently been introduced as a property-revealing indicator of the structural state the glass is in. This parameter incorporates the atomic volume and the vibrational mean square displacement, to combine both static structure and dynamics information. Flexibility volume was shown to quantitatively correlate with the properties of metallic glasses [J. Ding et al. Nat. Comm. 7, 13733 (2016)]. However, it remains to be examined if this parameter is useful for other types of glasses with bonding characteristics, atomic packing structures as well as properties that are distinctly different read less NOT USED (high confidence) D. Gobrecht, S. Cristallo, L. Piersanti, and S. Bromley, “Nucleation of Small Silicon Carbide Dust Clusters in AGB Stars,” The Astrophysical Journal. 2017. link Times cited: 23 Abstract: Silicon carbide (SiC) grains are a major dust component in c… read moreAbstract: Silicon carbide (SiC) grains are a major dust component in carbon-rich asymptotic giant branch stars. However, the formation pathways of these grains are not fully understood. We calculate ground states and energetically low-lying structures of (SiC)n, n = 1, 16 clusters by means of simulated annealing and Monte Carlo simulations of seed structures and subsequent quantum-mechanical calculations on the density functional level of theory. We derive the infrared (IR) spectra of these clusters and compare the IR signatures to observational and laboratory data. According to energetic considerations, we evaluate the viability of SiC cluster growth at several densities and temperatures, characterizing various locations and evolutionary states in circumstellar envelopes. We discover new, energetically low-lying structures for Si4C4, Si5C5, Si15C15, and Si16C16 and new ground states for Si10C10 and Si15C15. The clusters with carbon-segregated substructures tend to be more stable by 4–9 eV than their bulk-like isomers with alternating Si–C bonds. However, we find ground states with cage geometries resembling buckminsterfullerens (“bucky-like”) for Si12C12 and Si16C16 and low-lying stable cage structures for n ≥ 12. The latter findings thus indicate a regime of cluster sizes that differ from small clusters as well as from large-scale crystals. Thus—and owing to their stability and geometry—the latter clusters may mark a transition from a quantum-confined cluster regime to a crystalline, solid bulk-material. The calculated vibrational IR spectra of the ground-state SiC clusters show significant emission. They include the 10–13 μm wavelength range and the 11.3 μm feature inferred from laboratory measurements and observations, respectively, although the overall intensities are rather low. read less NOT USED (high confidence) H. T.-T. Vu, H. Pham, T. V. Nguyen, and H. K. Ho, “Pressure effects on the thermodynamic and mechanical properties of zinc-blende ZnTe compound,” The European Physical Journal B. 2017. link Times cited: 2 NOT USED (high confidence) F. Kadribasic, N. Mirabolfathi, K. Nordlund, A. Sand, E. Holmström, and F. Djurabekova, “Directional Sensitivity in Light-Mass Dark Matter Searches with Single-Electron-Resolution Ionization Detectors.,” Physical review letters. 2017. link Times cited: 34 Abstract: We propose a method using solid state detectors with directi… read moreAbstract: We propose a method using solid state detectors with directional sensitivity to dark matter interactions to detect low-mass weakly interacting massive particles (WIMPs) originating from galactic sources. In spite of a large body of literature for high-mass WIMP detectors with directional sensitivity, no available technique exists to cover WIMPs in the mass range <1 GeV/c^{2}. We argue that single-electron-resolution semiconductor detectors allow for directional sensitivity once properly calibrated. We examine the commonly used semiconductor material response to these low-mass WIMP interactions. read less NOT USED (high confidence) Y.-S. Song, J. Kim, and S. Jhi, “Pair potential modeling of atomic rearrangement in GeTe-Sb2Te3 superlattice via first-principles calculations,” Journal of Applied Physics. 2017. link Times cited: 8 Abstract: We study the nature of atomic rearrangement during the phase… read moreAbstract: We study the nature of atomic rearrangement during the phase-change processes in the superlattice of GeTe and Sb2Te3 by developing a new approach combining the first-principles calculations and a pair-potential model. We investigate the phase-change process in terms of energy changes from individual pairs or atoms by applying the pair (atom)-projection analysis to the intermediate structures between the initial and final states obtained from the climbing-image nudged elastic band method. Among the prototypical steps that can lead to the atomic layer rearrangement, we find that the required energy for the phase change is dominated by specific atoms responsible for the intrinsic energy barrier and the response to external pressure. Our approach of combining the first-principles methods and pair potential model with the projecting analysis can be a very efficient method in revealing the detailed atomic motions and the mechanism of fast atomic transition of the phase-change materials.We study the nature of atomic rearrangement during the phase-change processes in the superlattice of GeTe and Sb2Te3 by developing a new approach combining the first-principles calculations and a pair-potential model. We investigate the phase-change process in terms of energy changes from individual pairs or atoms by applying the pair (atom)-projection analysis to the intermediate structures between the initial and final states obtained from the climbing-image nudged elastic band method. Among the prototypical steps that can lead to the atomic layer rearrangement, we find that the required energy for the phase change is dominated by specific atoms responsible for the intrinsic energy barrier and the response to external pressure. Our approach of combining the first-principles methods and pair potential model with the projecting analysis can be a very efficient method in revealing the detailed atomic motions and the mechanism of fast atomic transition of the phase-change materials. read less NOT USED (high confidence) T. D. Nguyen, “GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations,” Comput. Phys. Commun. 2017. link Times cited: 44 NOT USED (high confidence) Y. Yu, H. Zhao, and G. Li, “A quasi-continuum thermomechanical model for phonon damping analysis of single crystal silicon nano-resonators,” International Journal of Heat and Mass Transfer. 2017. link Times cited: 4 NOT USED (high confidence) S. Sarangi, P. V. Satyam, S. Nayak, and S. Mahanti, “Molecular dynamics simulation studies of gold nano-cluster on silicon (001) surface,” Indian Journal of Physics. 2017. link Times cited: 5 NOT USED (high confidence) B. N. Galimzyanov and A. Mokshin, “Surface tension of water droplets upon homogeneous droplet nucleation in water vapor,” Colloid Journal. 2017. link Times cited: 5 NOT USED (high confidence) X. W. Zhou, R. Jones, and J. Gruber, “Molecular dynamics simulations of substitutional diffusion,” Computational Materials Science. 2017. link Times cited: 23 NOT USED (high confidence) D. Kaiser, S. Han, and T. Sinno, “Parametric analysis of mechanically driven compositional patterning in SiGe substrates,” Journal of Applied Physics. 2017. link Times cited: 4 Abstract: A recently demonstrated approach for creating structured com… read moreAbstract: A recently demonstrated approach for creating structured compositional gradients in the near-surface region of SiGe substrates is studied parametrically using a multiresolution coarse-grained lattice kinetic Monte Carlo simulation method. In the “stress patterning” process, a patterned elastic stress field is generated in the SiGe substrate by pressing an array of micro-indenters into it. The stressed substrate is then thermally annealed to drive the atomic diffusion in which the larger Ge atoms are pushed away from the areas of compressive stress. By varying a subset of the parameters that characterize the high-dimensional input space of the process (e.g., indenter spacing, indenter tip shape, and indenter array symmetry) we show that technologically interesting compositional configurations may be readily generated. In particular, we show that it is theoretically possible to generate arrays of well-delineated nanoscale regions of high Ge content surrounded by essentially pure Si. Such configurations may ... read less NOT USED (high confidence) P. Biswas, D. Paudel, R. Atta-Fynn, D. A. Drabold, and S. Elliott, “Morphology and Number Density of Voids In Hydrogenated Amorphous Silicon: An Ab Initio Study,” Physical review applied. 2017. link Times cited: 21 NOT USED (high confidence) C. Desgranges, P. Anderson, and J. Delhommelle, “Classical and quantum many-body effects on the critical properties and thermodynamic regularities of silicon,” Journal of Physics: Condensed Matter. 2017. link Times cited: 3 Abstract: Using molecular simulation, we determine the critical proper… read moreAbstract: Using molecular simulation, we determine the critical properties of Si as well as the loci for several remarkable thermodynamic contours spanning the supercritical region of the phase diagram. We consider a classical three-body potential as well as a quantum (tight-binding) many-body model, and determine the loci for the ideality contours, including the Zeno line and the H line of ideal enthalpy. The two strategies (classical or quantum) lead to strongly asymmetric binodals and to critical properties in good agreement with each other. The Zeno and H lines are found to remain linear over a wide temperature interval, despite the changes in electronic structure undergone by the fluid along these contours. We also show that the classical and quantum model yield markedly different results for the parameters defining the H line, the exponents for the power-laws underlying the line of minima for the isothermal enthalpy and for the density required to achieve ideal behavior, most notably for the enthalpy. read less NOT USED (high confidence) P. López et al., “Evaluation of energy barriers for topological transitions of Si self-interstitial clusters by classical molecular dynamics and the kinetic activation-relaxation technique,” 2017 Spanish Conference on Electron Devices (CDE). 2017. link Times cited: 0 Abstract: The modeling of self-interstitial defects evolution is key f… read moreAbstract: The modeling of self-interstitial defects evolution is key for process and device optimization. For a self-interstitial cluster of a given size, several configurations or topologies exist, but conventional models assume that the minimum energy one is instantaneously reached. The existence of significant energy barriers for configurational transitions may change the picture of defect evolution in non-equilibrium processes (such as ion implantation), and contribute to explain anomalous defect observations. In this work, we present a method to determine the energy barriers for topological transitions among small self-interstitial defects, which is applied to characterize the Si self-interstitial and the di-interstitial cluster. read less NOT USED (high confidence) K. Termentzidis, M. Verdier, and D. Lacroix, “Effect of Amorphisation on the Thermal Properties of Nanostructured Membranes,” Zeitschrift für Naturforschung A. 2017. link Times cited: 3 Abstract: The majority of the silicon devices contain amorphous phase … read moreAbstract: The majority of the silicon devices contain amorphous phase and amorphous/crystalline interfaces which both considerably affect the transport of energy carriers as phonons and electrons. In this article, we investigate the impact of amorphous phases (both amorphous silicon and amorphous SiO2) of silicon nanoporous membranes on their thermal properties via molecular dynamics simulations. We show that a small fraction of amorphous phase reduces dramatically the thermal transport. One can even create nanostructured materials with subamorphous thermal conductivity, while keeping an important crystalline fraction. In general, the a-SiO2 shell around the pores reduces the thermal conductivity by a factor of five to ten compared to a-Si shell. The phonon density of states for several systems is also given to give the impact of the amorphisation on the phonon modes. read less NOT USED (high confidence) K. Choudhary, F. Y. Congo, T. Liang, C. Becker, R. Hennig, and F. Tavazza, “Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface,” Scientific Data. 2017. link Times cited: 21 NOT USED (high confidence) A. Stukowski, E. Fransson, M. Mock, and P. Erhart, “Atomicrex—a general purpose tool for the construction of atomic interaction models,” Modelling and Simulation in Materials Science and Engineering. 2017. link Times cited: 17 Abstract: We introduce atomicrex, an open-source code for constructing… read moreAbstract: We introduce atomicrex, an open-source code for constructing interatomic potentials as well as more general types of atomic-scale models. Such effective models are required to simulate extended materials structures comprising many thousands of atoms or more, because electronic structure methods become computationally too expensive at this scale. atomicrex covers a wide range of interatomic potential types and fulfills many needs in atomistic model development. As inputs, it supports experimental property values as well as ab initio energies and forces, to which models can be fitted using various optimization algorithms. The open architecture of atomicrex allows it to be used in custom model development scenarios beyond classical interatomic potentials while thanks to its Python interface it can be readily integrated e.g., with electronic structure calculations or machine learning algorithms. read less NOT USED (high confidence) A. Bourque, C. Locker, and G. Rutledge, “Heterogeneous Nucleation of an n-Alkane on Tetrahedrally Coordinated Crystals.,” The journal of physical chemistry. B. 2017. link Times cited: 24 Abstract: Heterogeneous nucleation refers to the propensity for phase … read moreAbstract: Heterogeneous nucleation refers to the propensity for phase transformations to initiate preferentially on foreign surfaces, such as vessel walls, dust particles, or formulation additives. In crystallization, the form of the initial nucleus has ramifications for the crystallographic form, morphology, and properties of the resulting solid. Nevertheless, the discovery and design of nucleating agents remains a matter of trial and error because of the very small spatiotemporal scales over which the critical nucleus is formed and the extreme difficulty of examining such events empirically. Using molecular dynamics simulations, we demonstrate a method for the rapid screening of entire families of materials for activity as nucleating agents and for characterizing their mechanism of action. The method is applied to the crystallization of n-pentacontane, a model surrogate for polyethylene, on the family of tetrahedrally coordinated crystals, including diamond and silicon. A systematic variation of parameters in the interaction potential permits a comprehensive, physically based screening of nucleating agents in this class of materials, including both real and hypothetical candidates. The induction time for heterogeneous nucleation is shown to depend strongly on crystallographic registry between the nucleating agent and the critical nucleus, indicative of an epitaxial mechanism in this class of materials. Importantly, the severity of this registry requirement weakens with decreasing rigidity of the substrate and increasing strength of attraction to the surface of the nucleating agent. Employing this method, a high-throughput computational screening of nucleating agents becomes possible, facilitating the discovery of novel nucleating agents within a broad "materials genome" of possible additives. read less NOT USED (high confidence) J. Shi, H. Cai, K. Cai, and Q. Qin, “Dynamic behavior of a black phosphorus and carbon nanotube composite system,” Journal of Physics D: Applied Physics. 2017. link Times cited: 23 Abstract: A double walled nanotube composite is constructed by placing… read moreAbstract: A double walled nanotube composite is constructed by placing a black-phosphorene-based nanotube (BPNT) in a carbon nanotube (CNT). When driving the CNT to rotate by stators in a thermal driven rotary nanomotor, the BPNT behaves differently from the CNT. For instance, the BPNT can be actuated to rotate by the CNT, but its rotational acceleration differs from that of the CNT. The BPNT oscillates along the tube axis when it is longer than the CNT. The results obtained indicate that the BPNT functions with high structural stability when acting as a rotor with rotational frequency of ~20 GHz at 250 K. If at a higher temperature than 250 K, say 300 K, the rotating BPNT shows weaker structural stability than its status at 250 K. When the two tubes in the rotor are of equal length, the rotational frequency of the BPNT drops rapidly after the BPNT is collapsed, owing to more broken P–P bonds. When the black-phosphorene nanotube is longer than the CNT, it rotates synchronously with the CNT even if it is collapsed. Hence, in the design of a nanomotor with a rotor from BPNT, the working rotational frequency should be lower than a certain threshold at a higher temperature. read less NOT USED (high confidence) P. Norouzzadeh and D. J. Singh, “Thermal conductivity of single-layer WSe2 by a Stillinger–Weber potential,” Nanotechnology. 2017. link Times cited: 33 Abstract: In this study, we present the parameters of the Stillinger–W… read moreAbstract: In this study, we present the parameters of the Stillinger–Weber (SW) potential for single-layer WSe2 and calculate its in-plane thermal conductivity using a reverse non-equilibrium molecular dynamics simulation. The parameters are fitted to the phonon dispersion curves from literature density functional perturbation theory and experimental structural properties. The set reproduces the phonon dispersion well. The in-plane thermal conductivity of single-layer WSe2 and its dependency on sample length and temperature are calculated and the results are in good agreement with experimental values. Our developed SW-type potential facilitates further investigations on thermal, mechanical and other properties of WSe2. read less NOT USED (high confidence) F. Sciortino, “Three-body potential for simulating bond swaps in molecular dynamics,” The European Physical Journal E. 2017. link Times cited: 39 NOT USED (high confidence) J. Schneider et al., “ATK-ForceField: a new generation molecular dynamics software package,” Modelling and Simulation in Materials Science and Engineering. 2017. link Times cited: 63 Abstract: ATK-ForceField is a software package for atomistic simulatio… read moreAbstract: ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal. read less NOT USED (high confidence) J. Lu, L. C. Jacobson, Y. A. P. Sirkin, and V. Molinero, “High-Resolution Coarse-Grained Model of Hydrated Anion-Exchange Membranes that Accounts for Hydrophobic and Ionic Interactions through Short-Ranged Potentials.,” Journal of chemical theory and computation. 2017. link Times cited: 26 Abstract: Molecular simulations provide a versatile tool to study the … read moreAbstract: Molecular simulations provide a versatile tool to study the structure, anion conductivity, and stability of anion-exchange membrane (AEM) materials and can provide a fundamental understanding of the relation between structure and property of membranes that is key for their use in fuel cells and other applications. The quest for large spatial and temporal scales required to model the multiscale structure and transport processes in the polymer electrolyte membranes, however, cannot be met with fully atomistic models, and the available coarse-grained (CG) models suffer from several challenges associated with their low-resolution. Here, we develop a high-resolution CG force field for hydrated polyphenylene oxide/trimethylamine chloride (PPO/TMACl) membranes compatible with the mW water model using a hierarchical parametrization approach based on Uncertainty Quantification and reference atomistic simulations modeled with the Generalized Amber Force Field (GAFF) and TIP4P/2005 water. The parametrization weighs multiple properties, including coordination numbers, radial distribution functions (RDFs), self-diffusion coefficients of water and ions, relative vapor pressure of water in the solution, hydration enthalpy of the tetramethylammonium chloride (TMACl) salt, and cohesive energy of its aqueous solutions. We analyze the interdependence between properties and address how to compromise between the accuracies of the properties to achieve an overall best representability. Our optimized CG model FFcomp quantitatively reproduces the diffusivities and RDFs of the reference atomistic model and qualitatively reproduces the experimental relative vapor pressure of water in solutions of tetramethylammonium chloride. These properties are of utmost relevance for the design and operation of fuel cell membranes. To our knowledge, this is the first CG model that includes explicitly each water and ion and accounts for hydrophobic, ionic, and intramolecular interactions explicitly parametrized to reproduce multiple properties of interest for hydrated polyelectrolyte membranes. The CG model of hydrated PPO/TMACl water is about 100 times faster than the reference atomistic GAFF-TIP4P/2005 model. The strategy implemented here can be used in the parametrization of CG models for other substances, such as biomolecular systems and membranes for desalination, water purification, and redox flow batteries. We anticipate that the large spatial and temporal simulations made possible by the CG model will advance the quest for anion-exchange membranes with improved transport and mechanical properties. read less NOT USED (high confidence) K. Gordiz and A. Henry, “Phonon transport at interfaces between different phases of silicon and germanium,” Journal of Applied Physics. 2017. link Times cited: 52 Abstract: Current knowledge and understanding of phonon transport at i… read moreAbstract: Current knowledge and understanding of phonon transport at interfaces are wholly based on the phonon gas model (PGM). However, it is difficult to rationalize the usage of the PGM for disordered materials, such as amorphous materials. Thus, there is essentially no intuition regarding interfaces with amorphous materials. Given this gap in understanding, herein we investigated heat conduction at different crystalline and amorphous Si/Ge interfaces using the recently developed interface conductance modal analysis method, which does not rely on the PGM and can therefore treat an interface with a disordered material. The results show that contrary to arguments based on lower mean free paths in amorphous materials, the interface conductances are quite high. The results also show that the interfacial modes of vibration in the frequency region of 12–13 THz are so important that perturbing the natural vibrations with velocity rescaling heat baths (i.e., in non-equilibrium molecular dynamics simulations) affects the... read less NOT USED (high confidence) H. Dai and G. Chen, “A molecular dynamics investigation into the mechanisms of material removal and subsurface damage of nanoscale high speed laser-assisted machining,” Molecular Simulation. 2017. link Times cited: 22 Abstract: Molecular dynamics is employed to study the mechanism of mat… read moreAbstract: Molecular dynamics is employed to study the mechanism of material removal and subsurface damage of monocrystalline silicon when it is under a nanoscale high-speed laser-assisted grinding of a diamond tip. Laser-assisted machining (LAM) is that the workpiece is locally heated by an intense laser beam before material removal. The effects of laser moving speed, laser pulse intensity and laser spot radius are thoroughly investigated in terms of atomic trajectories, phase transformation, temperature distribution, grinding temperature, grinding force and friction coefficient. The investigation shows that a higher laser moving speed reduces the subsurface damage and improves the material remove rate because of fewer atoms with five and six coordination atoms and more chips. Besides, both tangential grinding force (Fx) and normal grinding force (Fy) decrease as the laser moving speed increases. The distribution of high-temperature zone strongly depends upon the effect of laser pulse intensity and laser spot radius. Larger laser pulse intensity can make the material more fully softened before being removed. Moreover, as the laser pulse intensity becomes larger, the friction coefficients became smaller, the material remove rate improves and the depth of grinding increases. However, larger laser pulse intensity may result in a larger thermal deformation of workpiece. A larger laser spot radius reduces the grinding depth but increases the width of laser irradiation zone on machined surface. Thus, a suitable laser spot radius can improve the material removal rate. These results indicate that it is possible to control and adjust the laser parameters according to laser moving speed, laser pulse intensity and laser spot radius, and it provides a potential technology to improve a surface integrity and a smoothness of ground surface. read less NOT USED (high confidence) A. Gooneie, S. Schuschnigg, and C. Holzer, “A Review of Multiscale Computational Methods in Polymeric Materials,” Polymers. 2017. link Times cited: 131 Abstract: Polymeric materials display distinguished characteristics wh… read moreAbstract: Polymeric materials display distinguished characteristics which stem from the interplay of phenomena at various length and time scales. Further development of polymer systems critically relies on a comprehensive understanding of the fundamentals of their hierarchical structure and behaviors. As such, the inherent multiscale nature of polymer systems is only reflected by a multiscale analysis which accounts for all important mechanisms. Since multiscale modelling is a rapidly growing multidisciplinary field, the emerging possibilities and challenges can be of a truly diverse nature. The present review attempts to provide a rather comprehensive overview of the recent developments in the field of multiscale modelling and simulation of polymeric materials. In order to understand the characteristics of the building blocks of multiscale methods, first a brief review of some significant computational methods at individual length and time scales is provided. These methods cover quantum mechanical scale, atomistic domain (Monte Carlo and molecular dynamics), mesoscopic scale (Brownian dynamics, dissipative particle dynamics, and lattice Boltzmann method), and finally macroscopic realm (finite element and volume methods). Afterwards, different prescriptions to envelope these methods in a multiscale strategy are discussed in details. Sequential, concurrent, and adaptive resolution schemes are presented along with the latest updates and ongoing challenges in research. In sequential methods, various systematic coarse-graining and backmapping approaches are addressed. For the concurrent strategy, we aimed to introduce the fundamentals and significant methods including the handshaking concept, energy-based, and force-based coupling approaches. Although such methods are very popular in metals and carbon nanomaterials, their use in polymeric materials is still limited. We have illustrated their applications in polymer science by several examples hoping for raising attention towards the existing possibilities. The relatively new adaptive resolution schemes are then covered including their advantages and shortcomings. Finally, some novel ideas in order to extend the reaches of atomistic techniques are reviewed. We conclude the review by outlining the existing challenges and possibilities for future research. read less NOT USED (high confidence) J. Guénolé, A. Prakash, and E. Bitzek, “Influence of intrinsic strain on irradiation induced damage: the role of threshold displacement and surface binding energies,” Materials & Design. 2016. link Times cited: 10 NOT USED (high confidence) D. Dhabal, C. Chakravarty, V. Molinero, and H. K. Kashyap, “Comparison of liquid-state anomalies in Stillinger-Weber models of water, silicon, and germanium.,” The Journal of chemical physics. 2016. link Times cited: 38 Abstract: We use molecular dynamics simulations to compare and contras… read moreAbstract: We use molecular dynamics simulations to compare and contrast the liquid-state anomalies in the Stillinger-Weber models of monatomic water (mW), silicon (Si), and germanium (Ge) over a fairly wide range of temperatures and densities. The relationships between structure, entropy, and mobility, as well as the extent of the regions of anomalous behavior, are discussed as a function of the degree of tetrahedrality. We map out the cascade of density, structural, pair entropy, excess entropy, viscosity, and diffusivity anomalies for these three liquids. Among the three liquids studied here, only mW displays anomalies in the thermal conductivity, and this anomaly is evident only at very low temperatures. Diffusivity and viscosity, on the other hand, show pronounced anomalous regions for the three liquids. The temperature of maximum density of the three liquids shows re-entrant behavior consistent with either singularity-free or liquid-liquid critical point scenarios proposed to explain thermodynamic anomalies. The order-map, which shows the evolution of translational versus tetrahedral order in liquids, is different for Ge than for Si and mW. We find that although the monatomic water reproduces several thermodynamic and dynamic properties of rigid-body water models (e.g., SPC/E, TIP4P/2005), its sequence of anomalies follows, the same as Si and Ge, the silica-like hierarchy: the region of dynamic (diffusivity and viscosity) anomalies encloses the region of structural anomalies, which in turn encloses the region of density anomaly. The hierarchy of the anomalies based on excess entropy and Rosenfeld scaling, on the other hand, reverses the order of the structural and dynamic anomalies, i.e., predicts that the three Stillinger-Weber liquids follow a water-like hierarchy of anomalies. We investigate the scaling of diffusivity, viscosity, and thermal conductivity with the excess entropy of the liquid and find that for dynamical properties that present anomalies there is no universal scaling of the reduced property with excess entropy for the whole range of temperatures and densities. Instead, Rosenfeld's scaling holds for all the three liquids at high densities and high temperatures, although deviations from simple exponential dependence are observed for diffusivity and viscosity at lower temperatures and intermediate densities. The slope of the scaling of transport properties obtained for Ge is comparable to that obtained for simple liquids, suggesting that this low tetrahedrality liquid, although it stabilizes a diamond crystal, is already close to simple liquid behavior for certain properties. read less NOT USED (high confidence) S. Ciarella, O. Gang, and F. Sciortino, “Toward the observation of a liquid-liquid phase transition in patchy origami tetrahedra: a numerical study,” The European Physical Journal E. 2016. link Times cited: 8 NOT USED (high confidence) S. T. John and G. Csányi, “Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials.,” The journal of physical chemistry. B. 2016. link Times cited: 93 Abstract: We introduce a computational framework that is able to descr… read moreAbstract: We introduce a computational framework that is able to describe general many-body coarse-grained (CG) interactions of molecules and use it to model the free energy surface of molecular liquids as a cluster expansion in terms of monomer, dimer, and trimer terms. The contributions to the free energy due to these terms are inferred from all-atom molecular dynamics (MD) data using Gaussian Approximation Potentials, a type of machine-learning model that employs Gaussian process regression. The resulting CG model is much more accurate than those possible using pair potentials. Though slower than the latter, our model can still be faster than all-atom simulations for solvent-free CG models commonly used in biomolecular simulations. read less NOT USED (high confidence) D. Olson, X. Li, C. Ortner, and B. V. Koten, “Force-based atomistic/continuum blending for multilattices,” Numerische Mathematik. 2016. link Times cited: 7 NOT USED (high confidence) S.-J. Sun, P.-Y. Yang, S. Ju, and Z.-M. Lai, “Electronic and structural properties of ultrathin germanium nanowires by density functional theory calculations,” Journal of Applied Physics. 2016. link Times cited: 4 Abstract: Employing the basin-hopping method with the Stillinger–Weber… read moreAbstract: Employing the basin-hopping method with the Stillinger–Weber potential and penalty function, four germanium nanowires with the most stable energies were obtained at cross-section radii of 1.8 A, 2.0 A, 2.4 A, and 2.9 A, respectively. Because the coordination numbers and orbital hybridizations of Ge atoms in these nanostructures are different from bulk Ge, their density of states (DOS) profiles are distinctly different from that of bulk. Besides, the discrepancies of DOS among these nanowires arising from different electron density overlaps induce the different Coulomb interactions. Furthermore, the enhanced Coulomb interaction and the quantum confinement in germanium nanowires cause the original p-orbitals below Fermi-level shift up to cross the Fermi-level, which leads Ge nanowires to be conductors. read less NOT USED (high confidence) P. Zhang, R. Zhu, M. Jiang, Y. Song, D. Zhang, and Y. Cui, “Molecular dynamics study on the thermal conductivity of multiple layers in semiconductor disk laser,” SPIE/COS Photonics Asia. 2016. link Times cited: 0 Abstract: Thermal properties of multiple layers including distributed … read moreAbstract: Thermal properties of multiple layers including distributed Bragg reflector (DBR) and multiple quantum wells (MQWs) used in the semiconductor gain element are crucial for the performance of a semiconductor disk laser (SDL). For the purpose of more reasonable semiconductor wafer design, so to improve the thermal management of SDLs, accurate thermal conductivity value of a DBR is under considerable requirement. By the use of equilibrium molecular dynamics (EMD) method, thermal conductivities of AlAs/GaAs DBRs, which were widely employed in 1μm wavelength SDLs, were calculated, and simulated results were compared with reported data. Influences of the Al composition, and the layer thickness on the thermal conductivities were focused and analyzed. read less NOT USED (high confidence) M. Radek, H. Bracht, B. Liedke, R. Böttger, and M. Posselt, “Ion-beam induced atomic mixing in isotopically controlled silicon multilayers,” Journal of Applied Physics. 2016. link Times cited: 5 Abstract: Implantation of germanium (Ge), gallium (Ga), and arsenic (A… read moreAbstract: Implantation of germanium (Ge), gallium (Ga), and arsenic (As) into crystalline and preamorphized isotopically controlled silicon (Si) multilayer structures at temperatures between 153 K and 973 K was performed to study the mechanisms mediating ion-beam induced atomic mixing. Secondary-ion-mass-spectrometry was applied to determine concentration-depth profiles of the stable isotopes before and after ion implantation. The intermixing is analytically described by a depth-dependent displacement function. The maximum displacement is found to depend not only on temperature and microstructure but also on the doping type of the implanted ion. Molecular dynamics calculations evaluate the contribution of cascade mixing, i.e., thermal-spike mixing, to the overall observed atomic mixing. Calculated and experimental results on the temperature dependence of ion-beam mixing in the amorphous and crystalline structures provide strong evidence for ion-beam induced enhanced crystallization and enhanced self-diffusion, resp... read less NOT USED (high confidence) E. Davoli, P. Piovano, and U. Stefanelli, “Wulff shape emergence in graphene,” Mathematical Models and Methods in Applied Sciences. 2016. link Times cited: 28 Abstract: Graphene samples are identified as minimizers of configurati… read moreAbstract: Graphene samples are identified as minimizers of configurational energies featuring both two- and three-body atomic-interaction terms. This variational viewpoint allows for a detailed description of ground-state geometries as connected subsets of a regular hexagonal lattice. We investigate here how these geometries evolve as the number n of carbon atoms in the graphene sample increases. By means of an equivalent characterization of minimality via a discrete isoperimetric inequality, we prove that ground states converge to the ideal hexagonal Wulff shape as n →∞. Precisely, ground states deviate from such hexagonal Wulff shape by at most Kn3/4 + o(n3/4) atoms, where both the constant K and the rate n3/4 are sharp. read less NOT USED (high confidence) M. Wilson, “Structure and dynamics in network-forming materials,” Journal of Physics: Condensed Matter. 2016. link Times cited: 9 Abstract: The study of the structure and dynamics of network-forming m… read moreAbstract: The study of the structure and dynamics of network-forming materials is reviewed. Experimental techniques used to extract key structural information are briefly considered. Strategies for building simulation models, based on both targeting key (experimentally-accessible) materials and on systematically controlling key model parameters, are discussed. As an example of the first class of materials, a key target system, SiO2, is used to highlight how the changing structure with applied pressure can be effectively modelled (in three dimensions) and used to link to both experimental results and simple structural models. As an example of the second class the topology of networks of tetrahedra in the MX2 stoichiometry are controlled using a single model parameter linked to the M–X–M bond angles. The evolution of ordering on multiple length-scales is observed as are the links between the static structure and key dynamical properties. The isomorphous relationship between the structures of amorphous Si and SiO2 is discussed as are the similarities and differences in the phase diagrams, the latter linked to potential polyamorphic and ‘anomalous’ (e.g. density maxima) behaviour. Links to both two-dimensional structures for C, Si and Ge and near-two-dimensional bilayers of SiO2 are discussed. Emerging low-dimensional structures in low temperature molten carbonates are also uncovered. read less NOT USED (high confidence) J. Rimsza, J. Yeon, A. Duin, and J. Du, “Water Interactions with Nanoporous Silica: Comparison of ReaxFF and ab Initio based Molecular Dynamics Simulations,” Journal of Physical Chemistry C. 2016. link Times cited: 77 Abstract: Detailed understanding of the reactions and processes which … read moreAbstract: Detailed understanding of the reactions and processes which govern silicate–water interactions is critical to geological, materials, and environmental sciences. Interactions between water and nanoporous silica were studied using classical molecular dynamics with a Reactive Force Field (ReaxFF), and the results were compared with density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations. Two versions of ReaxFF Si/O/H parametrizations (Yeon et al. J. Phys. Chem. C 2016, 120, 305 and Fogarty et al. J. Chem. Phys. 2010, 132, 174704) were compared with AIMD results to identify differences in local structures, water dissociation mechanisms, energy barriers, and diffusion behaviors. Results identified reaction mechanisms consisting of two different intermediate structures involved in the removal of high energy two-membered ring (2-Ring) defects on complex nanoporous silica surfaces. Intermediate defects lifetimes affect hydroxylation and 2-Ring defect removal. Additionally, the limite... read less NOT USED (high confidence) V. Mazhukin, A. V. Shapranov, M. Demin, and N. Kozlovskaya, “Temperature dependence of the kinetics rate of the melting and crystallization of aluminum,” Bulletin of the Lebedev Physics Institute. 2016. link Times cited: 12 NOT USED (high confidence) I. Chepkasov, Y. Gafner, S. Gafner, and S. P. Bardahanov, “Condensation of Cu nanoparticles from the gas phase,” The Physics of Metals and Metallography. 2016. link Times cited: 8 NOT USED (high confidence) C. Zhang, Z. Liu, and P. Deng, “Atomistic‐scale investigation of effective stress principle of saturated porous materials by molecular dynamics,” Geophysical Research Letters. 2016. link Times cited: 5 Abstract: The effective stress principle is one of the most fundamenta… read moreAbstract: The effective stress principle is one of the most fundamental concepts in the mechanics of porous materials. Several mathematical expressions have been proposed for this fundamental principle, leading to unsettled debates on the validity and applicability of the principle and its mathematical descriptions. Recent developments in atomistic modeling techniques make it possible to understand multiphase systems at the atomistic scale. In this paper, molecular dynamics simulation is explored as a tool to investigate the stress formulation in porous materials. A molecular dynamics framework, including molecular models of phases, interatomic potentials, initial configuration, and simulation procedure, is presented. Numerical simulations based on the framework preliminarily show the validity of the effective stress principle at the atomistic scale. Furthermore, the effectiveness of typical expressions for the principle is investigated. read less NOT USED (high confidence) M. Friedrich, P. Piovano, and U. Stefanelli, “The Geometry of C_60,” Siam Journal on Applied Mathematics. 2016. link Times cited: 8 Abstract: Molecular Mechanics describes molecules as particle configur… read moreAbstract: Molecular Mechanics describes molecules as particle configurations interacting via classical potentials. These configurational energies usually consist of the sum of different phenomenological terms which are tailored to the description of specific bonding geometries. This approach is followed here to model the fullerene $C_{60}$, an allotrope of carbon corresponding to a specific hollow spherical structure of sixty atoms. We rigorously address different modeling options and advance a set of minimal requirements on the configurational energy able to deliver an accurate prediction of the fine three-dimensional geometry of $C_{60}$ as well as of its remarkable stability. In particular, the experimentally observed truncated-icosahedron structure with two different bond lengths is shown to be a strict local minimizer. read less NOT USED (high confidence) U. Stefanelli, “Stable carbon configurations,” Bollettino dell’Unione Matematica Italiana. 2016. link Times cited: 0 NOT USED (high confidence) J. Gong, L. Thompson, and G. Li, “A semi-analytical approach for calculating the equilibrium structure and radial breathing mode frequency of single-walled carbon nanotubes,” Acta Mechanica Sinica. 2016. link Times cited: 3 NOT USED (high confidence) J. Gong, L. Thompson, and G. Li, “A semi-analytical approach for calculating the equilibrium structure and radial breathing mode frequency of single-walled carbon nanotubes,” Acta Mechanica Sinica. 2016. link Times cited: 0 NOT USED (high confidence) J. Burg and R. Dauskardt, “Elastic and thermal expansion asymmetry in dense molecular materials.,” Nature materials. 2016. link Times cited: 19 NOT USED (high confidence) K. Akahane, J. Russo, and H. Tanaka, “A possible four-phase coexistence in a single-component system,” Nature Communications. 2016. link Times cited: 18 NOT USED (high confidence) J. M. Stevenson, “All-atom modeling for solution-processed solar cell.” 2016. link Times cited: 0 NOT USED (high confidence) T. Zohdi, “On progressive blast envelope evolution of charged particles in electromagnetic fields,” Computer Methods in Applied Mechanics and Engineering. 2016. link Times cited: 5 NOT USED (high confidence) M. K. Bushehri, A. Mohebbi, and H. H. Rafsanjani, “Prediction of thermal conductivity and viscosity of nanofluids by molecular dynamics simulation,” Journal of Engineering Thermophysics. 2016. link Times cited: 30 NOT USED (high confidence) H. Dai, G. Chen, Q. Fang, and J. Yin, “The effect of tool geometry on subsurface damage and material removal in nanometric cutting single-crystal silicon by a molecular dynamics simulation,” Applied Physics A. 2016. link Times cited: 56 NOT USED (high confidence) H. Dai, G. Chen, Q. Fang, and J. Yin, “The effect of tool geometry on subsurface damage and material removal in nanometric cutting single-crystal silicon by a molecular dynamics simulation,” Applied Physics A. 2016. link Times cited: 0 NOT USED (high confidence) M. Siddiqui and A. Arif, “Generalized Effective Medium Theory for Particulate Nanocomposite Materials,” Materials. 2016. link Times cited: 24 Abstract: The thermal conductivity of particulate nanocomposites is st… read moreAbstract: The thermal conductivity of particulate nanocomposites is strongly dependent on the size, shape, orientation and dispersion uniformity of the inclusions. To correctly estimate the effective thermal conductivity of the nanocomposite, all these factors should be included in the prediction model. In this paper, the formulation of a generalized effective medium theory for the determination of the effective thermal conductivity of particulate nanocomposites with multiple inclusions is presented. The formulated methodology takes into account all the factors mentioned above and can be used to model nanocomposites with multiple inclusions that are randomly oriented or aligned in a particular direction. The effect of inclusion dispersion non-uniformity is modeled using a two-scale approach. The applications of the formulated effective medium theory are demonstrated using previously published experimental and numerical results for several particulate nanocomposites. read less NOT USED (high confidence) Y. Mankelevich et al., “Multi-step reaction mechanism for F atom interactions with organosilicate glass and SiOx films,” Journal of Physics D: Applied Physics. 2016. link Times cited: 20 Abstract: An ab initio approach with the density functional theory (DF… read moreAbstract: An ab initio approach with the density functional theory (DFT) method was used to study F atom interactions with organosilicate glass (OSG)-based low-k dielectric films. Because of the complexity and significant modifications of the OSG surface structure during the interaction with radicals and etching, a variety of reactions between the surface groups and thermal F atoms can happen. For OSG film etching and damage, we propose a multi-step mechanism based on DFT static and dynamic simulations, which is consistent with the previously reported experimental observations. The important part of the proposed mechanism is the formation of pentavalent Si atoms on the OSG surface due to a quasi-chemisorption of the incident F atoms. The revealed mechanism of F atom incorporation into the OSG matrix explains the experimentally observed phenomena of fast fluorination without significant modification of the chemical structure. We demonstrate that the pentavalent Si states induce the weakening of adjacent Si–O bonds and their breaking under F atom flux. The calculated results allow us to propose a set of elementary chemical reactions of successive removal of CH3 and CH2 groups and fluorinated SiOx matrix etching. read less NOT USED (high confidence) M. Isaiev, S. Burian, L. Bulavin, M. Gradeck, F. Lemoine, and K. Termentzidis, “Efficient tuning of potential parameters for liquid–solid interactions,” Molecular Simulation. 2016. link Times cited: 31 Abstract: Spherical and cylindrical water droplets on silicon surface … read moreAbstract: Spherical and cylindrical water droplets on silicon surface are studied to tune the silicon–oxygen interaction. We use molecular dynamics simulations to estimate the contact angle of two different shaped droplets. We found that the cylindrical droplets are independent of the line tension as their three phases curvature is equal zero. Additionally, we compare an analytical model, taking into account or not the Tolman length and we show that for spherical small size droplets, this length is important to be included, in contrast to cylindrical droplets in which the influence of the Tolman length is negligible. We demonstrate that the usual convenient way to exclude linear tension in the general case can give wrong results. Here, we consider cylindrical droplets, since their contact angle does not depend on the droplet size in the range of few to 10ths of nanometres. The droplets are stabilised due to the periodic boundary conditions. This allows us to propose a new parameterisation for nanoscale droplets, which is independent the size of the droplets or its shape, minimising at the same time the calculation procedure. With the proposed methodology, we can extract the epsilon parameter of the interaction potential between a liquid and a solid from the nanoscaled molecular simulation with only as input the macrosized experimental wetting angle for a given temperature. read less NOT USED (high confidence) N. Onofrio, D. Guzman, and A. Strachan, “Atomistic simulations of electrochemical metallization cells: mechanisms of ultra-fast resistance switching in nanoscale devices.,” Nanoscale. 2016. link Times cited: 13 Abstract: We describe a new method that enables reactive molecular dyn… read moreAbstract: We describe a new method that enables reactive molecular dynamics (MD) simulations of electrochemical processes and apply it to study electrochemical metallization cells (ECMs). The model, called EChemDID, extends the charge equilibration method to capture the effect of external electrochemical potential on partial atomic charges and describes its equilibration over connected metallic structures, on-the-fly, during the MD simulation. We use EChemDID to simulate resistance switching in nanoscale ECMs; these devices consist of an electroactive metal separated from an inactive electrode by an insulator and can be reversibly switched to a low-resistance state by the electrochemical formation of a conducting filament between electrodes. Our structures use Cu as the active electrode and SiO2 as the dielectric and have dimensions at the foreseen limit of scalability of the technology, with a dielectric thickness of approximately 1 nm. We explore the effect of device geometry on switching timescales and find that nanowires with an electroactive shell, where ions migrate towards a smaller inactive electrode core, result in faster switching than planar devices. We observe significant device-to-device variability in switching timescales and intermittent switching for these nanoscale devices. To characterize the evolution in the electronic structure of the dielectric as dissolved metallic ions switch the device, we perform density functional theory calculations on structures obtained from an EChemDID MD simulation. These results confirm the appearance of states around the Fermi energy as the metallic filament bridges the electrodes and show that the metallic ions and not defects in the dielectric contribute to the majority of those states. read less NOT USED (high confidence) K. Cai, J. Wan, L. Yang, N. Wei, J. Shi, and Q. Qin, “Buckling behaviour of composites with double walled nanotubes from carbon and phosphorus.,” Physical chemistry chemical physics : PCCP. 2016. link Times cited: 14 Abstract: Due to weak interactions among phosphorus atoms in black pho… read moreAbstract: Due to weak interactions among phosphorus atoms in black phosphorene, a nanotube obtained by curling single-layer black phosphorus is not as stable as a carbon nanotube (CNT) at finite temperature. In the present work, we recommend a new 1D composite material with a double-walled nanotube (DWNT) from a black phosphorus nanotube (BPNT) and a CNT. The dynamic response of the composite DWNTs is simulated using a molecular dynamics approach. Effects of the factors including temperature, slenderness and configurations of DWNTs on dynamic behavior of the composite are discussed. Compared with a single-walled BPNT, the composite DWNTs under uniaxial compression show some unique properties. When a BPNT is embedded in a CNT which will not only isolate the BPNT from the ambient conditions, but also improve the capability of axial deformation of the BPNT, the system will not collapse rapidly even if the BPNT has been buckled. read less NOT USED (high confidence) S. Xiong, K. Sääskilahti, Y. Kosevich, H. Han, D. Donadio, and S. Volz, “Blocking Phonon Transport by Structural Resonances in Alloy-Based Nanophononic Metamaterials Leads to Ultralow Thermal Conductivity.,” Physical review letters. 2016. link Times cited: 134 Abstract: Understanding the design rules to obtain materials that enab… read moreAbstract: Understanding the design rules to obtain materials that enable a tight control of phonon transport over a broad range of frequencies would aid major developments in thermoelectric energy harvesting, heat management in microelectronics, and information and communication technology. Using atomistic simulations we show that the metamaterials approach relying on localized resonances is very promising to engineer heat transport at the nanoscale. Combining designed resonant structures to alloying can lead to extremely low thermal conductivity in silicon nanowires. The hybridization between resonant phonons and propagating modes greatly reduces the group velocities and the phonon mean free paths in the low frequency acoustic range below 4 THz. Concurrently, alloy scattering hinders the propagation of high frequency thermal phonons. Our calculations establish a rationale between the size, shape, and period of the resonant structures, and the thermal conductivity of the nanowire, and demonstrate that this approach is even effective to block phonon transport in wavelengths much longer than the size and period of the surface resonant structures. A further consequence of using resonant structures is that they are not expected to scatter electrons, which is beneficial for thermoelectric applications. read less NOT USED (high confidence) M. K. Bushehri, A. Mohebbi, and H. H. Rafsanjani, “Prediction of thermal conductivity and viscosity of nanofluids by molecular dynamics simulation,” Journal of Engineering Thermophysics. 2016. link Times cited: 0 NOT USED (high confidence) E. Voyiatzis and M. Böhm, “Atomic and global mechanical properties of systems described by the Stillinger–Weber potential,” Journal of Physics: Condensed Matter. 2016. link Times cited: 0 Abstract: Analytical expressions for the stress and elasticity tensors… read moreAbstract: Analytical expressions for the stress and elasticity tensors of materials, in which the interactions are described by the Stillinger–Weber potential, are derived in the context of the stress fluctuation formalism. The derived formulas can be used both in Monte Carlo and molecular dynamics simulations. As an example of possible applications, they are employed to calculate the influence of the temperature and system size on the mechanical properties of crystalline cubic boron nitride. The system has been studied by molecular dynamics simulations. The computed mechanical properties are in good agreement with available experimental data and first principle calculations. In the studied crystalline cubic boron nitride system, the employed formalism is of higher accuracy than the ‘small-strain’ non-equilibrium method. The dominant contributions to the elastic constants stem from the Born and stress fluctuation terms. An increase in the system size reduces the statistical uncertainties in the computation of the mechanical properties. A rise of the temperature leads to a slight increase in the observed uncertainties. The derived expressions for the stress and elasticity tensors are further decomposed into sums of atomic level stress and atomic level elasticity tensors. The developed factorization enables us (i) to quantify the contribution of the various chemical groups, in the case under consideration of the different atoms, to the observed mechanical properties and (ii) to determine the elastic constants with reduced computational uncertainties. The reason is that the exact values of some terms of the proposed factorization can be determined theoretically beforehand. Thus, they can be substituted in the derived formulas leading to an enhanced convergence. read less NOT USED (high confidence) F. Saiz and M. Gamero-Castaño, “Molecular dynamics of nanodroplet impact: The effect of the projectile’s molecular mass on sputtering,” AIP Advances. 2016. link Times cited: 8 Abstract: The impact of electrosprayed nanodroplets on ceramics at sev… read moreAbstract: The impact of electrosprayed nanodroplets on ceramics at several km/s alters the atomic order of the target, causing sputtering, surface amorphization and cratering. The molecular mass of the projectile is known to have a strong effect on the impact phenomenology, and this article aims to rationalize this dependency using molecular dynamics. To achieve this goal, the article models the impact of four projectiles with molecular masses between 45 and 391 amu, and identical diameters and kinetic energies, 10 nm and 63 keV, striking a silicon target. In agreement with experiments, the simulations show that the number of sputtered atoms strongly increases with molecular mass. This is due to the increasing intensity of collision cascades with molecular mass: when the fixed kinetic energy of the projectile is distributed among fewer, more massive molecules, their collisions with the target produce knock-on atoms with higher energies, which in turn generate more energetic and larger numbers of secondary and tertiary knock-on atoms. The more energetic collision cascades intensify both knock-on sputtering and, upon thermalization, thermal sputtering. Besides enhancing sputtering, heavier molecules also increase the fraction of the projectile’s energy that is transferred to the target, as well as the fraction of this energy that is dissipated. read less NOT USED (high confidence) J. Lu, C. Chakravarty, and V. Molinero, “Relationship between the line of density anomaly and the lines of melting, crystallization, cavitation, and liquid spinodal in coarse-grained water models.,” The Journal of chemical physics. 2016. link Times cited: 30 Abstract: Liquid water has several anomalous properties, including a n… read moreAbstract: Liquid water has several anomalous properties, including a non-monotonous dependence of density with temperature and an increase of thermodynamic response functions upon supercooling. Four thermodynamic scenarios have been proposed to explain the anomalies of water, but it is not yet possible to decide between them from experiments because of the crystallization and cavitation of metastable liquid water. Molecular simulations provide a versatile tool to study the anomalies and phase behavior of water, assess their agreement with the phenomenology of water under conditions accessible to experiments, and provide insight into the behavior of water in regions that are challenging to probe in the laboratory. Here we investigate the behavior of the computationally efficient monatomic water models mW and mTIP4P/2005(REM), with the aim of unraveling the relationships between the lines of density extrema in the p-T plane, and the lines of melting, liquid-vapor spinodal and non-equilibrium crystallization and cavitation. We focus particularly on the conditions for which the line of density maxima (LDM) in the liquid emerges and disappears as the pressure is increased. We find that these models present a retracing LDM, same as previously found for atomistic water models and models of other tetrahedral liquids. The low-pressure end of the LDM occurs near the pressure of maximum of the melting line, a feature that seems to be general to models that produce tetrahedrally coordinated crystals. We find that the mW water model qualitatively reproduces several key properties of real water: (i) the LDM is terminated by cavitation at low pressures and by crystallization of ice Ih at high pressures, (ii) the LDM meets the crystallization line close to the crossover in crystallization from ice Ih to a non-tetrahedral four-coordinated crystal, and (iii) the density of the liquid at the crossover in crystallization from ice Ih to a four-coordinated non-tetrahedral crystal coincides with the locus of maximum in diffusivity as a function of pressure. The similarities in equilibrium and non-equilibrium phase behavior between the mW model and real water provide support to the quest to find a compressibility extremum, and determine whether it presents a maximum, in the doubly metastable region. read less NOT USED (high confidence) A. Arab, A. V. Davydov, D. Papaconstantopoulos, and Q. Li, “Monolayer MoS2 Nanoribbons as a Promising Material for Both n-type and p-type Legs in Thermoelectric Generators,” Journal of Electronic Materials. 2016. link Times cited: 9 NOT USED (high confidence) D. Kaiser, S. Ghosh, S. Han, and T. Sinno, “Modeling and simulation of compositional engineering in SiGe films using patterned stress fields.” 2016. link Times cited: 2 Abstract: Semiconductor alloys such as silicon–germanium (SiGe) offer … read moreAbstract: Semiconductor alloys such as silicon–germanium (SiGe) offer attractive environments for engineering quantum-confined structures that are the basis for a host of current and future optoelectronic devices. Although vertical stacking of such structures is routinely achieved via heteroepitaxy, lateral manipulation has proven much more challenging. We have recently demonstrated that a patterned elastic stress field applied, with an array of nanoscale indenters, to an initially compositionally uniform SiGe substrate will drive atomic interdiffusion leading to compositional patterns in the near-surface region of the substrate. While this approach may offer a potentially efficient and robust pathway to producing laterally ordered arrays of quantum-confined structures, optimizing it with respect to the various process parameters, such as indenter array geometry, annealing history, and SiGe substrate thickness and composition, is highly challenging. Here, a mesoscopic model based on coarse-grained lattice kinetic Monte Carlo simulation is presented that describes quantitatively the atomic interdiffusion processes in SiGe alloy films subjected to applied stress. We first show that the model provides predictions that are quantitatively consistent with experimental measurements. Then, the model is used to investigate the impact of several process parameters such as indenter shape and pitch. We find that certain indenter configurations produce compositional patterns that are favorable for engineering lateral arrays of quantum-confined structures. read less NOT USED (high confidence) E. Hahn, S. Zhao, E. Bringa, E. Bringa, and M. A. Meyers, “Supersonic Dislocation Bursts in Silicon,” Scientific Reports. 2016. link Times cited: 23 NOT USED (high confidence) Y. A. P. Sirkin, M. H. Factorovich, V. Molinero, and D. Scherlis, “Vapor Pressure of Aqueous Solutions of Electrolytes Reproduced with Coarse-Grained Models without Electrostatics.,” Journal of chemical theory and computation. 2016. link Times cited: 19 Abstract: The vapor pressure of water is a key property in a large cla… read moreAbstract: The vapor pressure of water is a key property in a large class of applications from the design of membranes for fuel cells and separations to the prediction of the mixing state of atmospheric aerosols. Molecular simulations have been used to compute vapor pressures, and a few studies on liquid mixtures and solutions have been reported on the basis of the Gibbs Ensemble Monte Carlo method in combination with atomistic force fields. These simulations are costly, making them impractical for the prediction of the vapor pressure of complex materials. The goal of the present work is twofold: (1) to demonstrate the use of the grand canonical screening approach ( Factorovich , M. H. J. Chem. Phys. 2014 , 140 , 064111 ) to compute the vapor pressure of solutions and to extend the methodology for the treatment of systems without a liquid-vapor interface and (2) to investigate the ability of computationally efficient high-resolution coarse-grained models based on the mW monatomic water potential and ions described exclusively with short-range interactions to reproduce the relative vapor pressure of aqueous solutions. We find that coarse-grained models of LiCl and NaCl solutions faithfully reproduce the experimental relative pressures up to high salt concentrations, despite the inability of these models to predict cohesive energies of the solutions or the salts. A thermodynamic analysis reveals that the coarse-grained models achieve the experimental activity coefficients of water in solution through a compensation of severely underestimated hydration and vaporization free energies of the salts. Our results suggest that coarse-grained models developed to replicate the hydration structure and the effective ion-ion attraction in solution may lead to this compensation. Moreover, they suggest an avenue for the design of coarse-grained models that accurately reproduce the activity coefficients of solutions. read less NOT USED (high confidence) D. Pan, T.-C. Wang, C. Wang, W. Guo, and Y. Yao, “Self-assembled chiral phosphorus nanotubes from phosphorene: a molecular dynamics study,” RSC Advances. 2016. link Times cited: 15 Abstract: Controlled syntheses in nanoscale structures should be expec… read moreAbstract: Controlled syntheses in nanoscale structures should be expected and phosphorous nanotubes with predefined chiralities are important in electronic devices with tunable bandgap. Here, incorporating molecular dynamics simulations with theoretical analyses, we show that a zigzag phosphorene nanoribbon can self-assemble and form a corresponding chiral phosphorous nanotube surrounding a template armchair phosphorous nanotube. The van der Waals potential between the nanoribbon and the nanotube is transformed to the intrinsic deformed and chemical bonding energies of the synthesized tube together with partial kinetic energy. The self-assembly process has an apparent temperature dependence and size effect and the formed chiral tube is thermodynamically stable. Also, the chirality and measurement can be tuned by the radius of template tube and the aspect ratio of raw ribbon. The study suggests a novel and feasible approach for controlled synthesis of phosphorous nanotubes and thus is of great interest for semiconductor device applications. read less NOT USED (high confidence) M. Schöberl, N. Zabaras, and P. Koutsourelakis, “Predictive coarse-graining,” J. Comput. Phys. 2016. link Times cited: 32 NOT USED (high confidence) D. Varshney, S. Jain, S. Shriya, and R. Khenata, “High-pressure and temperature-induced structural, elastic, and thermodynamical properties of strontium chalcogenides,” Journal of Theoretical and Applied Physics. 2016. link Times cited: 12 NOT USED (high confidence) S. Sarikurt et al., “Tailoring thermal conductivity of silicon/germanium nanowires utilizing core-shell architecture,” Journal of Applied Physics. 2016. link Times cited: 10 Abstract: Low-dimensional nanostructured materials show large variatio… read moreAbstract: Low-dimensional nanostructured materials show large variations in their thermal transport properties. In this work, we investigate the influence of the core-shell architecture on nanowire (1D) thermal conductivity and evaluate its validity as a strategy to achieve a better thermoelectric performance. To obtain the thermal conductivity values, equilibrium molecular dynamics simulations are conducted for core-shell nanowires of silicon and germanium. To explore the parameter space, we have calculated thermal conductivity values of the Si-core/Ge-shell and Ge-core/Si-shell nanowires having different cross-sectional sizes and core contents at several temperatures. Our results indicate that (1) increasing the cross-sectional area of pristine Si and pristine Ge nanowires increases the thermal conductivity, (2) increasing the Ge core size in the Ge-core/Si-shell structure results in a decrease in the thermal conductivity at 300 K, (3) the thermal conductivity of the Si-core/Ge-shell nanowires demonstrates a mini... read less NOT USED (high confidence) W. Jiang, Y.-H. Zeng, Q. Qin, and Q. Luo, “A novel oscillator based on heterogeneous carbon@MoS2 nanotubes,” Nano Research. 2016. link Times cited: 15 NOT USED (high confidence) M. Friedrich, P. Piovano, and U. Stefanelli, “The Geometry of C60: A Rigorous Approach via Molecular Mechanics,” SIAM J. Appl. Math. 2016. link Times cited: 5 Abstract: Molecular Mechanics describes molecules as particle configur… read moreAbstract: Molecular Mechanics describes molecules as particle configurations interacting via classical potentials. These {\it configurational energies} usually consist of the sum of different phenomenological terms which are tailored to the description of specific bonding geometries. This approach is followed here to model the fullerene $C_{60}$, an allotrope of carbon corresponding to a specific hollow spherical structure of sixty atoms. We rigorously address different modeling options and advance a set of minimal requirements on the configurational energy able to deliver an accurate prediction of the fine three-dimensional geometry of $C_{60}$ as well as of its remarkable stability. In particular, the experimentally observed truncated-icosahedron structure with two different bond lengths is shown to be a strict local minimizer. read less NOT USED (high confidence) C. Desgranges and J. Delhommelle, “Evaluation of the grand-canonical partition function using expanded Wang-Landau simulations. IV. Performance of many-body force fields and tight-binding schemes for the fluid phases of silicon.,” The Journal of chemical physics. 2016. link Times cited: 20 Abstract: We extend Expanded Wang-Landau (EWL) simulations beyond clas… read moreAbstract: We extend Expanded Wang-Landau (EWL) simulations beyond classical systems and develop the EWL method for systems modeled with a tight-binding Hamiltonian. We then apply the method to determine the partition function and thus all thermodynamic properties, including the Gibbs free energy and entropy, of the fluid phases of Si. We compare the results from quantum many-body (QMB) tight binding models, which explicitly calculate the overlap between the atomic orbitals of neighboring atoms, to those obtained with classical many-body (CMB) force fields, which allow to recover the tetrahedral organization in condensed phases of Si through, e.g., a repulsive 3-body term that favors the ideal tetrahedral angle. Along the vapor-liquid coexistence, between 3000 K and 6000 K, the densities for the two coexisting phases are found to vary significantly (by 5 orders of magnitude for the vapor and by up to 25% for the liquid) and to provide a stringent test of the models. Transitions from vapor to liquid are predicted to occur for chemical potentials that are 10%-15% higher for CMB models than for QMB models, and a ranking of the force fields is provided by comparing the predictions for the vapor pressure to the experimental data. QMB models also reveal the formation of a gap in the electronic density of states of the coexisting liquid at high temperatures. Subjecting Si to a nanoscopic confinement has a dramatic effect on the phase diagram with, e.g. at 6000 K, a decrease in liquid densities by about 50% for both CMB and QMB models and an increase in vapor densities between 90% (CMB) and 170% (QMB). The results presented here provide a full picture of the impact of the strategy (CMB or QMB) chosen to model many-body effects on the thermodynamic properties of the fluid phases of Si. read less NOT USED (high confidence) C. Hou, J. Xu, W. Ge, and J. Li, “Molecular dynamics simulation overcoming the finite size effects of thermal conductivity of bulk silicon and silicon nanowires,” Modelling and Simulation in Materials Science and Engineering. 2016. link Times cited: 13 Abstract: Nonequilibrium molecular dynamics simulation has been a powe… read moreAbstract: Nonequilibrium molecular dynamics simulation has been a powerful tool for studying the thermophysical properties of bulk silicon and silicon nanowires. Nevertheless, usually limited by the capacity and capability of computational resources, the traditional longitudinal and transverse simulation sizes are evidently restricted in a narrow range much less than the experimental scales, which seriously hinders the exploration of the thermal properties. In this research, based on a powerful and efficient molecular dynamics (MD) simulation method, the computation of thermal conductivity beyond the known Casimir size limits is realized. The longitudinal dimensions of the simulations significantly exceed the micrometer scale. More importantly, the lateral characteristic sizes are much larger than 10 nanometers, explicitly comparable with the silicon nanowires fabricated and measured experimentally, whereas the traditional simulation size is several nanometers. The powerful virtual experimental measurement provided in our simulations achieves the direct prediction of the thermal conductivity of bulk silicon and real-scale silicon nanowires, and delineates the complete longitudinal size dependence of their thermal conductivities, especially at the elusive mesoscopic scale. Furthermore, the presented measurement paves an exciting and promising way to explore in depth the thermophysical properties of other bulk covalent solids and their low-dimensional structures, such as nanowires and nanosheets. read less NOT USED (high confidence) J. Hattori, V. Poborchii, and T. Tada, “Axial strain effects on ballistic phonon thermal transport in silicon nanowires,” Japanese Journal of Applied Physics. 2016. link Times cited: 1 Abstract: We study the effects of axial strain on phonon thermal trans… read moreAbstract: We study the effects of axial strain on phonon thermal transport in silicon nanowires (Si NWs). The thermal conductance of strained Si NWs in the ballistic regime is evaluated with the phonon dispersion relation derived through an atomistic approach. Compressive strain increases the ballistic thermal conductance of [100]-oriented Si NWs having a square cross section with a side length of about 3 nm. In contrast, tensile strain reduces it. These strain effects mainly result from two factors: a change in the phonon energy per unit length of a NW directly due to the length change of the NW, and a change in the phonon group velocity. We also investigate the relationships of the strain effects with the wire size, surface orientation, and wire orientation. Among the three factors, the wire orientation has the most significant effect on the strain effects. read less NOT USED (high confidence) A. France-Lanord, P. Soukiassian, C. Glattli, and E. Wimmer, “Ab initio parameterization of a charge optimized many-body forcefield for Si-SiO2: Validation and thermal transport in nanostructures.,” The Journal of chemical physics. 2016. link Times cited: 13 Abstract: In an effort to extend the reach of current ab initio calcul… read moreAbstract: In an effort to extend the reach of current ab initio calculations to simulations requiring millions of configurations for complex systems such as heterostructures, we have parameterized the third-generation Charge Optimized Many-Body (COMB3) potential using solely ab initio total energies, forces, and stress tensors as input. The quality and the predictive power of the new forcefield are assessed by computing properties including the cohesive energy and density of SiO2 polymorphs, surface energies of alpha-quartz, and phonon densities of states of crystalline and amorphous phases of SiO2. Comparison with data from experiments, ab initio calculations, and molecular dynamics simulations using published forcefields including BKS (van Beest, Kramer, and van Santen), ReaxFF, and COMB2 demonstrates an overall improvement of the new parameterization. The computed temperature dependence of the thermal conductivity of crystalline alpha-quartz and the Kapitza resistance of the interface between crystalline Si(001) and amorphous silica is in excellent agreement with experiment, setting the stage for simulations of complex nanoscale heterostructures. read less NOT USED (high confidence) S. Zhao, E. Hahn, B. Kad, B. Remington, E. Bringa, and M. Meyers, “Shock compression of [001] single crystal silicon,” The European Physical Journal Special Topics. 2016. link Times cited: 4 NOT USED (high confidence) S. Taioli, R. Gabbrielli, S. Simonucci, N. Pugno, and A. Iorio, “Lobachevsky crystallography made real through carbon pseudospheres,” Journal of Physics: Condensed Matter. 2016. link Times cited: 24 Abstract: We realize Lobachevsky geometry in a simulation lab, by prod… read moreAbstract: We realize Lobachevsky geometry in a simulation lab, by producing a carbon-based energetically stable molecular structure, arranged in the shape of a Beltrami pseudosphere. We find that this structure: (i) corresponds to a non-Euclidean crystallographic group, namely a loxodromic subgroup of SL(2,Z) ?>; (ii) has an unavoidable singular boundary, that we fully take into account. Our approach, substantiated by extensive numerical simulations of Beltrami pseudospheres of different size, might be applied to other surfaces of constant negative Gaussian curvature, and points to a general procedure to generate them. Our results also pave the way to test certain scenarios of the physics of curved spacetimes owing to graphene’s unique properties. read less NOT USED (high confidence) T. Zohdi, “A discrete element and ray framework for rapid simulation of acoustical dispersion of microscale particulate agglomerations,” Computational Mechanics. 2016. link Times cited: 9 NOT USED (high confidence) R. Frieling, S. Eon, D. Wolf, and H. Bracht, “Molecular dynamics simulations of thermal transport in isotopically modulated semiconductor nanostructures,” physica status solidi (a). 2016. link Times cited: 9 Abstract: In this paper, we investigate the effect of isotopic modulat… read moreAbstract: In this paper, we investigate the effect of isotopic modulation on the thermal conductivity of semiconductor nanostructures. The isotope doping is of particular interest for the application of semiconductors as thermoelectric materials as it leaves the electronic properties practically unaffected while the phononic transport is retarded. This approach could increase the figure of merit of thermoelectric generators by decreasing the thermal conductivity of semiconductors. We use non‐equilibrium molecular dynamics simulations to examine thermal transport in isotopically engineered semiconductors. The temperature profiles along the sample region deduced from the simulations allow the extraction of thermal conductivities. The reliability of the MD‐predicted thermal conductivities is studied by analyzing the influence of the input parameters on the results. The first set of samples are isotopically modified silicon samples. The influence of temperature, isotopic composition, and ordering of isotopic defects on the thermal conductivity of silicon is studied. The second material system under investigation is silicon germanium alloys. The influence of isotopic modulation on the thermal conductivity of Si–Ge alloys is examined for varying chemical composition. The thermal conductivities predicted by MD are compared to results derived from the solution of the Boltzmann transport equation in the relaxation time approach. read less NOT USED (high confidence) S. Pant and P. Ghorai, “Structural anomaly of core-softened fluid confined in single walled carbon nanotube: a molecular dynamics simulation investigation,” Molecular Physics. 2016. link Times cited: 5 Abstract: ABSTRACT Thermodynamic and structural properties of core-sof… read moreAbstract: ABSTRACT Thermodynamic and structural properties of core-softened fluid inside a (6,6) carbon nanotube (CNT) nanopore with tunable well depth, temperature and density have been carried out by molecular dynamic simulations. Methods of analysis include the radial distribution function, translational order parameter, excess entropy and derivative of excess entropy with respect to the density. We observe strong positional ordering of core-softened fluid inside the CNT and this ordering strongly depends on temperature and density of the system. On increasing density, we observe new peaks in the positional ordering. Translational order parameter and excess entropy indicate presence of a new anomalous region. On increasing the well depth and change in slope between the attractive well and repulsive shoulder in the potential, we hardly observe any change in the anomalous regions that are drastically different from that of the bulk core-softened fluids. read less NOT USED (high confidence) R. S. Singh, J. Biddle, P. Debenedetti, and M. Anisimov, “Two-state thermodynamics and the possibility of a liquid-liquid phase transition in supercooled TIP4P/2005 water.,” The Journal of chemical physics. 2016. link Times cited: 148 Abstract: Water shows intriguing thermodynamic and dynamic anomalies i… read moreAbstract: Water shows intriguing thermodynamic and dynamic anomalies in the supercooled liquid state. One possible explanation of the origin of these anomalies lies in the existence of a metastable liquid-liquid phase transition (LLPT) between two (high and low density) forms of water. While the anomalies are observed in experiments on bulk and confined water and by computer simulation studies of different water-like models, the existence of a LLPT in water is still debated. Unambiguous experimental proof of the existence of a LLPT in bulk supercooled water is hampered by fast ice nucleation which is a precursor of the hypothesized LLPT. Moreover, the hypothesized LLPT, being metastable, in principle cannot exist in the thermodynamic limit (infinite size, infinite time). Therefore, computer simulations of water models are crucial for exploring the possibility of the metastable LLPT and the nature of the anomalies. In this work, we present new simulation results in the NVT ensemble for one of the most accurate classical molecular models of water, TIP4P/2005. To describe the computed properties and explore the possibility of a LLPT, we have applied two-structure thermodynamics, viewing water as a non-ideal mixture of two interconvertible local structures ("states"). The results suggest the presence of a liquid-liquid critical point and are consistent with the existence of a LLPT in this model for the simulated length and time scales. We have compared the behavior of TIP4P/2005 with other popular water-like models, namely, mW and ST2, and with real water, all of which are well described by two-state thermodynamics. In view of the current debate involving different studies of TIP4P/2005, we discuss consequences of metastability and finite size in observing the liquid-liquid separation. We also address the relationship between the phenomenological order parameter of two-structure thermodynamics and the microscopic nature of the low-density structure. read less NOT USED (high confidence) T. Zohdi, “Modeling and efficient simulation of the deposition of particulate flows onto compliant substrates,” International Journal of Engineering Science. 2016. link Times cited: 17 NOT USED (high confidence) K. Prasai, P. Biswas, and D. A. Drabold, “Electronically designed amorphous carbon and silicon,” physica status solidi (a). 2016. link Times cited: 4 Abstract: We present a new approach to modeling materials. We show tha… read moreAbstract: We present a new approach to modeling materials. We show that Hellmann–Feynman forces associated with gap states may be used to drive the system to a preferred electronic structure that is also a total energy minimum. We use a priori information about the electronic gap to construct realistic models of tetrahedral amorphous carbon and silicon. We show that our method can be used to obtain continuously tunable concentration of tetrahedrally bonded carbon atoms in models of amorphous carbon. The method is carried out in the tight‐binding approximation to produce computer‐models of amorphous silicon that have fewer structural and optical defects than their conventional MD counterparts. We end by presenting a first test‐case for the ab initio (plane‐wave LDA) implementation of the method. read less NOT USED (high confidence) J. Andrejevic, J. M. Stevenson, and P. Clancy, “Simple Molecular Reactive Force Field for Metal-Organic Synthesis.,” Journal of chemical theory and computation. 2016. link Times cited: 2 Abstract: For colloidal quantum dots to transition from research labor… read moreAbstract: For colloidal quantum dots to transition from research laboratories to deployment as optical and electronic products, there will be a need to scale-up their production to large-scale manufacturing processes. This demand increases the need to understand their formation via a molecular representation of the nucleation of lead sulfide (PbS) quantum dot systems passivated by lead oleate complexes. We demonstrate the effectiveness of a new type of reactive potential, custom-made for this system, that is drawn from simple Morse, Lennard-Jones, and Coulombic components, which can reproduce reactions across a broad range of PbS quantum dot sizes with good accuracy. We validate the capability of this model to capture reactive systems by comparison to ab initio calculations for a reaction between two dots. read less NOT USED (high confidence) F. van Swol, X. W. Zhou, S. R. Challa, and J. E. Martin, “Thermodynamic properties of model CdTe/CdSe mixtures,” Molecular Simulation. 2016. link Times cited: 3 Abstract: We report on the thermodynamic properties of binary compound… read moreAbstract: We report on the thermodynamic properties of binary compound mixtures of model groups II–VI semiconductors. We use the recently introduced Stillinger–Weber Hamiltonian to model binary mixtures of CdTe and CdSe. We use molecular dynamics simulations to calculate the volume and enthalpy of mixing as a function of mole fraction. The lattice parameter of the mixture closely follows Vegard's law: a linear relation. This implies that the excess volume is a cubic function of mole fraction. A connection is made with hard sphere models of mixed fcc and zincblende structures. The potential energy exhibits a positive deviation from ideal soluton behaviour; the excess enthalpy is nearly independent of temperatures studied (300 and 533 K) and is well described by a simple cubic function of the mole fraction. Using a regular solution approach (combining non-ideal behaviour for the enthalpy with ideal solution behaviour for the entropy of mixing), we arrive at the Gibbs free energy of the mixture. The Gibbs free energy results indicate that the CdTe and CdSe mixtures exhibit phase separation. The upper consolute temperature is found to be 335 K. Finally, we provide the surface energy as a function of composition. It roughly follows ideal solution theory, but with a negative deviation (negative excess surface energy). This indicates that alloying increases the stability, even for nano-particles. read less NOT USED (high confidence) N. Nakazaki, Y. Takao, K. Eriguchi, and K. Ono, “Molecular dynamics simulations of Si etching in Cl- and Br-based plasmas: Cl+ and Br+ ion incidence in the presence of Cl and Br neutrals,” Journal of Applied Physics. 2015. link Times cited: 17 Abstract: Classical molecular dynamics (MD) simulations have been perf… read moreAbstract: Classical molecular dynamics (MD) simulations have been performed for Cl+ and Br+ ions incident on Si(100) surfaces with Cl and Br neutrals, respectively, to gain a better understanding of the ion-enhanced surface reaction kinetics during Si etching in Cl- and Br-based plasmas. The ions were incident normally on surfaces with translational energies in the range Ei = 20–500 eV, and low-energy neutrals of En = 0.01 eV were also incident normally thereon with the neutral-to-ion flux ratio in the range Γn0/Γi0 = 0–100, where an improved Stillinger--Weber potential form was employed for the interatomic potential concerned. The etch yields and thresholds presently simulated were in agreement with the experimental results previously reported for Si etching in Cl2 and Br2 plasmas as well as in Cl+, Cl2+, and Br+ beams, and the product stoichiometry simulated was consistent with that observed during Ar+ beam incidence on Si in Cl2. Moreover, the surface coverage of halogen atoms, halogenated layer thickness, surface stoichiometry, and depth profile of surface products simulated for Γn0/Γi0 = 100 were in excellent agreement with the observations depending on Ei reported for Si etching in Cl2 plasmas. The MD also indicated that the yield, coverage, and surface layer thickness are smaller in Si/Br than in Si/Cl system, while the percentage of higher halogenated species in product and surface stoichiometries is larger in Si/Br. The MD further indicated that in both systems, the translational energy distributions of products and halogen adsorbates desorbed from surfaces are approximated by two Maxwellians of temperature T1 ≈ 2500 K and T2 ≈ 7000–40 000 K. These energy distributions are discussed in terms of the desorption or evaporation from hot spots formed through chemically enhanced physical sputtering and physically enhanced chemical sputtering, which have so far been speculated to both occur in the ion-enhanced surface reaction kinetics of plasma etching. read less NOT USED (high confidence) S. Bringuier, V. Manga, K. Runge, P. Deymier, and K. Muralidharan, “An atomic scale characterization of coupled grain boundary motion in silicon bicrystals,” Philosophical Magazine. 2015. link Times cited: 7 Abstract: The mechanical response of symmetric tilt grain boundaries (… read moreAbstract: The mechanical response of symmetric tilt grain boundaries (GBs) in silicon bicrystals under shear loading are characterized using molecular dynamics simulations. It is seen that under shear, high-angle GBs namely Σ5 and Σ13 having a rotation axis [0 0 1] demonstrate coupled GB motion, such that the displacement of grains parallel to the GB interface is accompanied by normal GB motion. An atomic-scale characterization revealed that concerted rotations of silicon tetrahedra within the GB are the primary mechanisms leading to the coupled GB motion. Interestingly, so far, this phenomenon has only been examined in detail for metallic systems. A distinguishing feature of the coupled GB motion observed for the silicon symmetric tilt bicrystals as compared to metallic bicrystals is the fact that in the absence of shear, spontaneous coupled motion is not observed at high temperatures. read less NOT USED (high confidence) M. Pluciński and J. Zwanziger, “Topological constraints and the Makishima-Mackenzie model,” Journal of Non-crystalline Solids. 2015. link Times cited: 22 NOT USED (high confidence) M. Moqadam, E. Riccardi, T. T. Trinh, P. Åstrand, and T. S. van Erp, “A test on reactive force fields for the study of silica dimerization reactions.,” The Journal of chemical physics. 2015. link Times cited: 15 Abstract: We studied silica dimerization reactions in the gas and aque… read moreAbstract: We studied silica dimerization reactions in the gas and aqueous phase by density functional theory (DFT) and reactive force fields based on two parameterizations of ReaxFF. For each method (both ReaxFF force fields and DFT), we performed constrained geometry optimizations, which were subsequently evaluated in single point energy calculations using the other two methods. Standard fitting procedures typically compare the force field energies and geometries with those from quantum mechanical data after a geometry optimization. The initial configurations for the force field optimization are usually the minimum energy structures of the ab initio database. Hence, the ab initio method dictates which structures are being examined and force field parameters are being adjusted in order to minimize the differences with the ab initio data. As a result, this approach will not exclude the possibility that the force field predicts stable geometries or low transition states which are realistically very high in energy and, therefore, never considered by the ab initio method. Our analysis reveals the existence of such unphysical geometries even at unreactive conditions where the distance between the reactants is large. To test the effect of these discrepancies, we launched molecular dynamics simulations using DFT and ReaxFF and observed spurious reactions for both ReaxFF force fields. Our results suggest that the standard procedures for parameter fitting need to be improved by a mutual comparative method. read less NOT USED (high confidence) B. Shen et al., “Dynamics and Diffusion Mechanism of Low-Density Liquid Silicon.,” The journal of physical chemistry. B. 2015. link Times cited: 2 Abstract: A first-order phase transition from a high-density liquid to… read moreAbstract: A first-order phase transition from a high-density liquid to a low-density liquid has been proposed to explain the various thermodynamic anomies of water. It also has been proposed that such liquid-liquid phase transition would exist in supercooled silicon. Computer simulation studies show that, across the transition, the diffusivity drops roughly 2 orders of magnitude, and the structures exhibit considerable tetrahedral ordering. The resulting phase is a highly viscous, low-density liquid silicon. Investigations on the atomic diffusion of such a novel form of liquid silicon are of high interest. Here we report such diffusion results from molecular dynamics simulations using the classical Stillinger-Weber (SW) potential of silicon. We show that the atomic diffusion of the low-density liquid is highly correlated with local tetrahedral geometries. We also show that atoms diffuse through hopping processes within short ranges, which gradually accumulate to an overall random motion for long ranges as in normal liquids. There is a close relationship between dynamical heterogeneity and hopping process. We point out that the above diffusion mechanism is closely related to the strong directional bonding nature of the distorted tetrahedral network. Our work offers new insights into the complex behavior of the highly viscous low density liquid silicon, suggesting similar diffusion behaviors in other tetrahedral coordinated liquids that exhibit liquid-liquid phase transition such as carbon and germanium. read less NOT USED (high confidence) E. Malolepsza and T. Keyes, “Water Freezing and Ice Melting.,” Journal of chemical theory and computation. 2015. link Times cited: 17 Abstract: The generalized replica exchange method (gREM) is designed t… read moreAbstract: The generalized replica exchange method (gREM) is designed to sample states with coexisting phases and thereby to describe strong first order phase transitions. The isobaric MD version of the gREM is presented and applied to the freezing of liquid water and the melting of hexagonal and cubic ice. It is confirmed that coexisting states are well-sampled. The statistical temperature as a function of enthalpy, TS(H), is obtained. Hysteresis between freezing and melting is observed and discussed. The entropic analysis of phase transitions is applied and equilibrium transition temperatures, latent heats, and surface tensions are obtained for hexagonal ice ↔ liquid and cubic ice ↔ liquid with excellent agreement with published values. A new method is given to assign water molecules among various symmetry types. Pathways for water freezing, ultimately leading to hexagonal ice, are found to contain intermediate layered structures built from hexagonal and cubic ice. read less NOT USED (high confidence) M. Marder, “Particle methods in the study of fracture,” International Journal of Fracture. 2015. link Times cited: 5 NOT USED (high confidence) Y. Ye.A. et al., “Theoretical and Experimental Researches of Methanol Clusters in Low-Temperature Matrices,” Ukrainian Journal of Physics. 2015. link Times cited: 6 NOT USED (high confidence) D. Ma et al., “Nano-cross-junction effect on phonon transport in silicon nanowire cages,” Physical Review B. 2015. link Times cited: 92 Abstract: Wave effects of phonons can give rise to controllability of … read moreAbstract: Wave effects of phonons can give rise to controllability of heat conduction in nanostructures beyond that by particle scattering at surfaces and interfaces. In this paper, we propose a new class of three-dimensional nanostructures: a silicon-nanowire-cage (SiNWC) structure consisting of silicon nanowires (SiNWs) connected by nano-cross-junctions. We perform equilibrium molecular dynamics simulations and find an ultralow value of thermal conductivity of SiNWC, $0.173\phantom{\rule{0.16em}{0ex}}\mathrm{W}{\mathrm{m}}^{\ensuremath{-}1}\phantom{\rule{0.16em}{0ex}}{\mathrm{K}}^{\ensuremath{-}1}$, which is one order lower than that of SiNWs. By further modal analysis and atomistic Green's function calculations, we identify that the large reduction is due to significant phonon localization induced by the phonon local resonance and hybridization at the junction part in a wide range of phonon modes. This localization effect does not require the cage to be periodic, unlike the phononic crystals, and can be realized in structures that are easier to synthesize, for instance in a form of randomly oriented SiNW network. read less NOT USED (high confidence) D. Dhabal et al., “Excess entropy and crystallization in Stillinger-Weber and Lennard-Jones fluids.,” The Journal of chemical physics. 2015. link Times cited: 33 Abstract: Molecular dynamics simulations are used to contrast the supe… read moreAbstract: Molecular dynamics simulations are used to contrast the supercooling and crystallization behaviour of monatomic liquids that exemplify the transition from simple to anomalous, tetrahedral liquids. As examples of simple fluids, we use the Lennard-Jones (LJ) liquid and a pair-dominated Stillinger-Weber liquid (SW16). As examples of tetrahedral, water-like fluids, we use the Stillinger-Weber model with variable tetrahedrality parameterized for germanium (SW20), silicon (SW21), and water (SW(23.15) or mW model). The thermodynamic response functions show clear qualitative differences between simple and water-like liquids. For simple liquids, the compressibility and the heat capacity remain small on isobaric cooling. The tetrahedral liquids in contrast show a very sharp rise in these two response functions as the lower limit of liquid-phase stability is reached. While the thermal expansivity decreases with temperature but never crosses zero in simple liquids, in all three tetrahedral liquids at the studied pressure, there is a temperature of maximum density below which thermal expansivity is negative. In contrast to the thermodynamic response functions, the excess entropy on isobaric cooling does not show qualitatively different features for simple and water-like liquids; however, the slope and curvature of the entropy-temperature plots reflect the heat capacity trends. Two trajectory-based computational estimation methods for the entropy and the heat capacity are compared for possible structural insights into supercooling, with the entropy obtained from thermodynamic integration. The two-phase thermodynamic estimator for the excess entropy proves to be fairly accurate in comparison to the excess entropy values obtained by thermodynamic integration, for all five Lennard-Jones and Stillinger-Weber liquids. The entropy estimator based on the multiparticle correlation expansion that accounts for both pair and triplet correlations, denoted by S(trip), is also studied. S(trip) is a good entropy estimator for liquids where pair and triplet correlations are important such as Ge and Si, but loses accuracy for purely pair-dominated liquids, like LJ fluid, or near the crystallization temperature (T(thr)). Since local tetrahedral order is compatible with both liquid and crystalline states, the reorganisation of tetrahedral liquids is accompanied by a clear rise in the pair, triplet, and thermodynamic contributions to the heat capacity, resulting in the heat capacity anomaly. In contrast, the pair-dominated liquids show increasing dominance of triplet correlations on approaching crystallization but no sharp rise in either the pair or thermodynamic heat capacities. read less NOT USED (high confidence) U. Monteverde et al., “Ripples, phonons and bandgap in strained graphene,” 2015 International Conference on Numerical Simulation of Optoelectronic Devices (NUSOD). 2015. link Times cited: 1 Abstract: Using a novel interatomic force field, called MMP, we study … read moreAbstract: Using a novel interatomic force field, called MMP, we study the morphology of Graphene layers under a variety of strain conditions. We report that strain induced ripples possess the “right” kind of elastic deformation that is necessary in order to produce appreciable bandgap opening, which we calculate using Tight Binding, even for low enough strain that can be accessed through realistic means. At the same time the vibrational properties, calculated from analytic derivatives of the MMP force field and used within the dynamics matrix method, can be easily linked to strain obtained from Molecular Dynamics, opening the way for accurate modelling of Raman data. We also show that our models have allowed us to realize in practice novel devices based on our predictions. read less NOT USED (high confidence) Y. Lü, X. X. Zhang, M. Chen, and J. Jiang, “Exploring the nature of the liquid-liquid transition in silicon: a non-activated transformation.,” Physical chemistry chemical physics : PCCP. 2015. link Times cited: 2 Abstract: In contrast to other glass formers, silicon exhibits a therm… read moreAbstract: In contrast to other glass formers, silicon exhibits a thermodynamic discontinuity between its liquid and amorphous solid states. Some researchers have conjectured that a first-order phase transition occurs between two forms of liquid silicon: the high-density liquid (HDL) and the low-density liquid (LDL). Despite the fact that several computer simulations have supported a liquid-liquid phase transition (LLPT) in silicon, recent work based on surface free energy calculations contradicts its existence and the authors of this work have argued that the proposed LLPT has been mistakenly interpreted [J. Chem. Phys., 2013, 138, 214504]. A similar controversy has also arisen in the case of water because of discrepancies in the calculation of its free energy surface [Nature, 2014, 510, 385; J. Chem. Phys., 2013, 138, 214504]. Current evidence supporting or not supporting the LLPT is mostly derived from the thermodynamic stability of the LDL phase. Provided that the HDL-LDL transition is a first-order transition, the formation of LDL silicon should be an activated process. Following this idea, the nature of the LLPT should be clarified by tracing the kinetic path toward LDL silicon. In this work, we focus on the transformation process from HDL to LDL phases and use the mean first passage time (MFPT) method to examine thermodynamic and dynamic trajectories. The MFPT results show that the presumed HDL-LDL transition is not characterized by a thermodynamic activated process but by a continuous dynamic transformation. LDL silicon is actually a mixture of the high-density liquid and a low-density tetrahedral network. We show that the five-membered Si-Si rings in the LDL network play a critical role in stabilizing the low-density network and suppressing the crystallization. read less NOT USED (high confidence) K. Mizotani, M. Isobe, K. Karahashi, and S. Hamaguchi, “Numerical Simulation of Atomic Layer Oxidation of Silicon by Oxygen Gas Cluster Beams,” Plasma and Fusion Research. 2015. link Times cited: 1 Abstract: A gas cluster is a collection of atoms or molecules weakly b… read moreAbstract: A gas cluster is a collection of atoms or molecules weakly bound by van der Waals forces. Gas clusters may form by the adiabatic expansion of gases. In this study, it is demonstrated by molecular dynamics simulations that a low-energy beam of oxygen gas clusters may be used to oxidize the top surface layer of silicon (Si) substrates without affecting its deeper layers. An incident oxygen gas cluster with sufficiently low incident energy may stick to the Si surface and expose a large number of oxygen molecules to the surface Si atoms for extended periods until the cluster sublimates. This may cause the formation of Si–O bonds only on the top Si surface. This is in contrast to the oxidation of Si by oxygen ion beams or plasmas, where deeper layers of the Si surface are typically oxidized by the energetic incident oxygen ions. An oxidized single Si layer may be chemically removed; therefore, this nearly single-layer oxidation process by oxygen gas cluster beams may lead to the development of a new atomic layer etching technology for Si. read less NOT USED (high confidence) J. Jalkanen and M. Müser, “Systematic analysis and modification of embedded-atom potentials: case study of copper,” Modelling and Simulation in Materials Science and Engineering. 2015. link Times cited: 10 Abstract: In this study, we evaluate the functionals of different embe… read moreAbstract: In this study, we evaluate the functionals of different embedded-atom methods (EAM) by fitting their free parameters to ab-initio results for copper. Our emphasis lies on testing the transferability of the potentials between systems which vary in their spatial dimension and geometry. The model structures encompass zero-dimensional clusters, one-dimensional chains, two-dimensional tilings, and three-dimensional bulk systems. To avoid having to mimic charge transfer, which is outside the scope of conventional EAM potentials, we focus on structures, in which all atoms are symmetrically equivalent. We find that the simple, four-parameter Gupta EAM potential is overall satisfactory. Adding complexity to it decreases the errors on our set of structures only by marginal amounts, unless EAM is modified to depend also on density gradients, higher-order derivatives, or related terms. All tested conventional EAM functions reveal similar problems: the binding energy of closed-packed systems is overestimated in comparison to open or planar geometries, and structures with small coordination tend to be too rigid. These deficiencies can be fixed in terms of a systematically modified embedded-atom method (SMEAM), which reproduces DFT results on bond lengths, binding energies, and stiffnesses or bulk moduli by typically O(1%), O(5%), and O(15%) accuracy, respectively. SMEAM also predicts the radial distribution function of liquid copper quite accurately. Yet, it does not overcome the difficulty to reproduce the elastic tensor elements of a hypothetical diamond lattice. read less NOT USED (high confidence) X. W. Zhou, D. Ward, and M. E. Foster, “An analytical bond‐order potential for carbon,” Journal of Computational Chemistry. 2015. link Times cited: 38 Abstract: Carbon is the most widely studied material today because it … read moreAbstract: Carbon is the most widely studied material today because it exhibits special properties not seen in any other materials when in nano dimensions such as nanotube and graphene. Reduction of material defects created during synthesis has become critical to realize the full potential of carbon structures. Molecular dynamics (MD) simulations, in principle, allow defect formation mechanisms to be studied with high fidelity, and can, therefore, help guide experiments for defect reduction. Such MD simulations must satisfy a set of stringent requirements. First, they must employ an interatomic potential formalism that is transferable to a variety of carbon structures. Second, the potential needs to be appropriately parameterized to capture the property trends of important carbon structures, in particular, diamond, graphite, graphene, and nanotubes. Most importantly, the potential must predict the crystalline growth of the correct phases during direct MD simulations of synthesis to achieve a predictive simulation of defect formation. Because an unlimited number of structures not included in the potential parameterization are encountered, the literature carbon potentials are often not sufficient for growth simulations. We have developed an analytical bond order potential for carbon, and have made it available through the public MD simulation package LAMMPS. We demonstrate that our potential reasonably captures the property trends of important carbon phases. Stringent MD simulations convincingly show that our potential accounts not only for the crystalline growth of graphene, graphite, and carbon nanotubes but also for the transformation of graphite to diamond at high pressure. © 2015 Wiley Periodicals, Inc. read less NOT USED (high confidence) P. Dagenais, L. J. Lewis, and S. Roorda, “Dominant structural defects in amorphous silicon,” Journal of Physics: Condensed Matter. 2015. link Times cited: 1 Abstract: The nature of disorder in amorphous silicon (a-Si) is explor… read moreAbstract: The nature of disorder in amorphous silicon (a-Si) is explored by investigating the spatial arrangement and energies of coordination defects in a numerical model. Spatial correlations between structural defects are examined on the basis of a parameter that quantifies the probability for two sites to share a bond. Pentacoordinated atoms are found to be the dominant coordination defects. They show a tendency to cluster, and about 17% of them are linked through three-membered rings. As for tricoordinated sites, they are less numerous, and tend to be distant by at least two bond lengths. Typical local geometries associated to under and overcoordinated atoms are extracted from the model and described using partial bond angle distributions. An estimate of the formation energies of structural defects is provided. Using molecular-dynamics calculations, we simulate the implantation of high-energy atoms in the initial structure in order to study the effect of relaxation on the coordination defects and their environments. read less NOT USED (high confidence) V. Rashidi and K. Pipe, “Contributions of strain relaxation and interface modes to thermal transport in superlattices,” Computational Materials Science. 2015. link Times cited: 4 NOT USED (high confidence) Y. Beltukov, C. Fusco, A. Tanguy, and D. Parshin, “Transverse and longitudinal vibrations in amorphous silicon,” Journal of Physics: Conference Series. 2015. link Times cited: 8 Abstract: We show that harmonic vibrations in amorphous silicon can be… read moreAbstract: We show that harmonic vibrations in amorphous silicon can be decomposed to transverse and longitudinal components in all frequency range even in the absence of the well defined wave vector q. For this purpose we define the transverse component of the eigenvector with given ω as a component, which does not change the volumes of Voronoi cells around atoms. The longitudinal component is the remaining orthogonal component. We have found the longitudinal and transverse components of the vibrational density of states for numerical model of amorphous silicon. The vibrations are mostly transverse below 7 THz and above 15 THz. In the frequency interval in between the vibrations have a longitudinal nature. Just this sudden transformation of vibrations at 7 THz from almost transverse to almost longitudinal ones explains the prominent peak in the diffusivity of the amorphous silicon just above 7 THz. read less NOT USED (high confidence) J. Behler, “Constructing high‐dimensional neural network potentials: A tutorial review,” International Journal of Quantum Chemistry. 2015. link Times cited: 544 Abstract: A lot of progress has been made in recent years in the devel… read moreAbstract: A lot of progress has been made in recent years in the development of atomistic potentials using machine learning (ML) techniques. In contrast to most conventional potentials, which are based on physical approximations and simplifications to derive an analytic functional relation between the atomic configuration and the potential-energy, ML potentials rely on simple but very flexible mathematical terms without a direct physical meaning. Instead, in case of ML potentials the topology of the potential-energy surface is “learned” by adjusting a number of parameters with the aim to reproduce a set of reference electronic structure data as accurately as possible. Due to this bias-free construction, they are applicable to a wide range of systems without changes in their functional form, and a very high accuracy close to the underlying first-principles data can be obtained. Neural network potentials (NNPs), which have first been proposed about two decades ago, are an important class of ML potentials. Although the first NNPs have been restricted to small molecules with only a few degrees of freedom, they are now applicable to high-dimensional systems containing thousands of atoms, which enables addressing a variety of problems in chemistry, physics, and materials science. In this tutorial review, the basic ideas of NNPs are presented with a special focus on developing NNPs for high-dimensional condensed systems. A recipe for the construction of these potentials is given and remaining limitations of the method are discussed. © 2015 Wiley Periodicals, Inc. read less NOT USED (high confidence) G. Zhao, Y. J. Yu, and X. Tan, “Nature of the first-order liquid-liquid phase transition in supercooled silicon.,” The Journal of chemical physics. 2015. link Times cited: 10 Abstract: The first-order liquid-liquid phase transition in supercoole… read moreAbstract: The first-order liquid-liquid phase transition in supercooled Si is revisited by long-time first-principle molecular dynamics simulations. As the focus of the present paper, its nature is revealed by analyzing the inherent structures of low-density liquid (LDL) and high-density liquid (HDL). Our results show that it is a transition between a sp(3)-hybridization LDL and a white-tin-like HDL. This uncovers the origin of the semimetal-metal transition accompanying it and also proves that HDL is the metastable extension of high temperature equilibrium liquid into the supercooled regime. The pressure-temperature diagram of supercooled Si thus can be regarded in some respects as shifted reflection of its crystalline phase diagram. read less NOT USED (high confidence) Y. Fu and J. H. Song, “Heat flux expressions that satisfy the conservation laws in atomistic system involving multibody potentials,” J. Comput. Phys. 2015. link Times cited: 11 NOT USED (high confidence) J. Godet, F. A. E. Nabi, S. Brochard, and L. Pizzagalli, “Surface effects on the mechanical behavior of silicon nanowires: Consequence on the brittle to ductile transition at low scale and low temperature,” physica status solidi (a). 2015. link Times cited: 15 Abstract: Understanding the origin of the brittle to ductile transitio… read moreAbstract: Understanding the origin of the brittle to ductile transition at low scale in Si requires the characterization of the elementary mechanisms governing crack formation or dislocation nucleation. By molecular dynamics simulations, we have investigated the role of three surface states of silicon nanowires (NWs), fresh cut, reconstructed by annealing at 300 K and amorphized, for the activation of plastic mechanisms under tensile and compressive strains. We show that the onset of crack formation identified as wedge‐shaped defect on the surface was only observed in fresh‐cut NWs in tension. These NWs present high yield strain due to the high symmetry of the surface and the absence of surface defects favoring dislocation nucleation as for the other surface states. This result seems to confirm that the crack formation in nanostructures could be linked to dislocations interactions on intersecting glide planes as experimentally observed rather than direct crack opening. read less NOT USED (high confidence) O. Trushin et al., “Minimum energy path for the nucleation of misfit dislocations in Ge/Si(0 0 1) heteroepitaxy,” Modelling and Simulation in Materials Science and Engineering. 2015. link Times cited: 9 Abstract: A possible mechanism for the formation of a 90° misfit dislo… read moreAbstract: A possible mechanism for the formation of a 90° misfit dislocation at the Ge/Si(0 0 1) interface through homogeneous nucleation is identified from atomic scale calculations where a minimum energy path connecting the coherent epitaxial state and a final state with a 90° misfit dislocation is found using the nudged elastic band method. The initial path is generated using a repulsive bias activation procedure in a model system including 75 000 atoms. The energy along the path exhibits two maxima in the energy. The first maximum occurs as a 60° dislocation nucleates. The intermediate minimum corresponds to an extended 60° dislocation. The subsequent energy maximum occurs as a second 60° dislocation nucleates in a complementary, mirror glide plane, simultaneously starting from the surface and from the first 60° dislocation. The activation energy of the nucleation of the second dislocation is 30% lower than that of the first one showing that the formation of the second 60° dislocation is aided by the presence of the first one. The simulations represent a step towards unraveling the formation mechanism of 90° dislocations, an important issue in the design of growth procedures for strain released Ge overlayers on Si(1 0 0) surfaces, and more generally illustrate an approach that can be used to gain insight into the mechanism of complex nucleation paths of extended defects in solids. read less NOT USED (high confidence) D. Vasileska, “Modeling self-heating in nanoscale devices,” 2015 IEEE 15th International Conference on Nanotechnology (IEEE-NANO). 2015. link Times cited: 7 Abstract: In this paper, a review is presented on the self-heating mod… read moreAbstract: In this paper, a review is presented on the self-heating modeling efforts performed at Arizona State University. In the analysis, first simple SOI Devices are being considered from different technology generations to illustrate what we call “Thermal Landauer picture”. Namely, it is demonstrated via numerical simulations that in the shortest devices the hot spot does not occur in the channel (as it was speculated in previous works), but occurs in the drain contact due to the largely ballistic nature of the carrier transport. Impact of self-heating effects is also examined in dual-gate devices and silicon nanowire transistors. read less NOT USED (high confidence) L. Yang, J. Bian, H. Zhang, X. Niu, and G. Wang, “Size-dependent deformation mechanisms in hollow silicon nanoparticles,” AIP Advances. 2015. link Times cited: 22 Abstract: Even inherently brittle hollow silicon nanoparticles (NPs) c… read moreAbstract: Even inherently brittle hollow silicon nanoparticles (NPs) can withstand larger strain to failure than solid NPs. However, the influence of wall thickness on the mechanical behavior of hollow Si NPs is not fully understood. Using molecular dynamics simulations, we investigate the compressive behavior of hollow Si NPs. Three distinct failure mechanisms of hollow NPs are uncovered, and their strength and deformability are analyzed quantitatively. For extra-thick-walled NPs, dislocations will nucleate below the contact area and cut through the particles till failure. For mid-thick-walled NPs, however, dislocations will emit from the inner surface and slip towards the outer surface. For thin-walled NPs, elastic buckling is the cause of failure. Compared to solid NPs, hollow NPs with wall thickness being around half of its outer radius can achieve significant improvement in both strength and deformability. read less NOT USED (high confidence) Y. Qiu and Y. Chen, “Counterions and water molecules in charged silicon nanochannels: the influence of surface charge discreteness,” Molecular Simulation. 2015. link Times cited: 5 Abstract: In order to detect the effect of the surface charge discrete… read moreAbstract: In order to detect the effect of the surface charge discreteness on the properties at the solid–liquid interface, a molecular dynamics simulation model considering the vibration of wall atoms was used to investigate the performance of ion and water under different charge distributions. Through the comparison between simulation results and the theoretical prediction, it was found that, with the increasing degree of discreteness, much more counterions were attracted to the surface. These ions formed a denser accumulating layer which was located much nearer to the surface and caused charge inversion. The ions in this layer were non-hydrated or partially hydrated. When a voltage was applied across the nanochannel, this dense accumulating layer did not move unlike the ions near the uniformly charged surface. From the water density profiles obtained in nanochannels with different surface charge distributions, the influence of the surface charge discreteness on water distributions could be neglected. read less NOT USED (high confidence) J. Oh, M. Jang, H. Kim, S. Moon, and M. Shin, “Suppression of phonon transport in multiple Si/PtSi heterostructures,” Journal of Applied Physics. 2015. link Times cited: 2 Abstract: Using a Green function method based on an atomic vibration m… read moreAbstract: Using a Green function method based on an atomic vibration model, herein we report the results from our investigation of phonon transport through multiple Si/PtSi layered structures. In contrast with values predicted using elastic wave theory and an impedance mismatch method, we find that a detailed atomic-vibration approach exhibits significantly suppressed phonon transport and leads to a 30-times reduction of the thermal conductance, compared to that of Si bulk. We attribute the origin of the suppression to the lack of PtSi phonon modes in the energy range of 20–30 meV, and to the effects of interface scattering between Si and PtSi layers. read less NOT USED (high confidence) K. Jolley, R. Smith, and K. Joseph, “Borosilicate glass potentials for radiation damage simulations,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2015. link Times cited: 13 NOT USED (high confidence) W.-T. Xu, L. Zhu, Y. Cai, G. Zhang, and B. Li, “Direction dependent thermal conductivity of monolayer phosphorene: parameterization of Stillinger-Weber potential and molecular dynamics study,” arXiv: Mesoscale and Nanoscale Physics. 2015. link Times cited: 70 Abstract: A Stillinger-Weber interatomic potential is parameterized fo… read moreAbstract: A Stillinger-Weber interatomic potential is parameterized for phosphorene. It well reproduces the crystal structure, cohesive energy and phonon dispersion predicted by first-principles calculations. The thermal conductivity of phosphorene is further explored by equilibrium molecular dynamics simulations adopting the optimal set of potential parameters. At room temperature, the intrinsic thermal conductivities along zigzag and armchair directions are about 152.7 and 33.0 W/mK, respectively, with a large anisotropy ratio of five. The remarkably directional dependence of thermal conductivity in phosphorene, consistent with previous reports, is mainly due to the strong anisotropy of phonon group velocities, and weak anisotropy of phonon lifetimes as revealed by lattice dynamics calculations. Moreover, the effective phonon mean free paths at zigzag and armchair directions are about 141.4 and 43.4nm, respectively. read less NOT USED (high confidence) K. Das, H. Johnson, and J. Freund, “Atomic-scale thermocapillary flow in focused ion beam milling,” Physics of Fluids. 2015. link Times cited: 4 Abstract: Focused ion beams provide a means of nanometer-scale manufac… read moreAbstract: Focused ion beams provide a means of nanometer-scale manufacturing and material processing, which is used for applications such as forming nanometer-scale pores in thin films for DNA sequencing. We investigate such a configuration with Ga+ bombardment of a Si thin-film target using molecular dynamics simulation. For a range of ion intensities in a realistic configuration, a recirculating melt region develops, which is seen to flow with a symmetrical pattern, counter to how it would flow were it driven by the ion momentum flux. Such flow is potentially important for the shape and composition of the formed structures. Relevant stress scales and estimated physical properties of silicon under these extreme conditions support the importance thermocapillary effects. A flow model with Marangoni forcing, based upon the temperature gradient and geometry from the atomistic simulation, indeed reproduces the flow and thus could be used to anticipate such flows and their influence in applications. read less NOT USED (high confidence) S. Kerdsongpanya, “Design of Transition-Metal Nitride Thin Films for Thermoelectrics.” 2015. link Times cited: 0 Abstract: Thermoelectric devices are one of the promising energy harve… read moreAbstract: Thermoelectric devices are one of the promising energy harvesting technologies, because of their ability to convert heat (temperature gradient) to electricity by the Seebeck effect. Furthermore, th ... read less NOT USED (high confidence) N. Onofrio and A. Strachan, “Voltage equilibration for reactive atomistic simulations of electrochemical processes.,” The Journal of chemical physics. 2015. link Times cited: 37 Abstract: We introduce electrochemical dynamics with implicit degrees … read moreAbstract: We introduce electrochemical dynamics with implicit degrees of freedom (EChemDID), a model to describe electrochemical driving force in reactive molecular dynamics simulations. The method describes the equilibration of external electrochemical potentials (voltage) within metallic structures and their effect on the self-consistent partial atomic charges used in reactive molecular dynamics. An additional variable assigned to each atom denotes the local potential in its vicinity and we use fictitious, but computationally convenient, dynamics to describe its equilibration within connected metallic structures on-the-fly during the molecular dynamics simulation. This local electrostatic potential is used to dynamically modify the atomic electronegativities used to compute partial atomic changes via charge equilibration. Validation tests show that the method provides an accurate description of the electric fields generated by the applied voltage and the driving force for electrochemical reactions. We demonstrate EChemDID via simulations of the operation of electrochemical metallization cells. The simulations predict the switching of the device between a high-resistance to a low-resistance state as a conductive metallic bridge is formed and resistive currents that can be compared with experimental measurements. In addition to applications in nanoelectronics, EChemDID could be useful to model electrochemical energy conversion devices. read less NOT USED (high confidence) J.-W. Jiang, “Parametrization of Stillinger–Weber potential based on valence force field model: application to single-layer MoS2 and black phosphorus,” Nanotechnology. 2015. link Times cited: 223 Abstract: We propose parametrizing the Stillinger–Weber potential for … read moreAbstract: We propose parametrizing the Stillinger–Weber potential for covalent materials starting from the valence force-field model. All geometrical parameters in the Stillinger–Weber potential are determined analytically according to the equilibrium condition for each individual potential term, while the energy parameters are derived from the valence force-field model. This parametrization approach transfers the accuracy of the valence force field model to the Stillinger–Weber potential. Furthermore, the resulting Stilliinger–Weber potential supports stable molecular dynamics simulations, as each potential term is at an energy-minimum state separately at the equilibrium configuration. We employ this procedure to parametrize Stillinger–Weber potentials for single-layer MoS2 and black phosphorous. The obtained Stillinger–Weber potentials predict an accurate phonon spectrum and mechanical behaviors. We also provide input scripts of these Stillinger–Weber potentials used by publicly available simulation packages including GULP and LAMMPS. read less NOT USED (high confidence) X. W. Zhou et al., “A prediction of dislocation‐free CdTe/CdS photovoltaic multilayers via nano‐patterning and composition grading,” Progress in Photovoltaics: Research and Applications. 2015. link Times cited: 12 Abstract: Defects in multilayered films have long been a performance‐l… read moreAbstract: Defects in multilayered films have long been a performance‐limiting problem for the semiconductor industry. For instance, CdTe/CdS solar cell efficiencies have had significant improvement in the past 15years or more without addressing the problem of high misfit dislocation densities. Overcoming this stagnation requires a fundamental understanding of interfacial defect formation. Herein, we demonstrate a new first principles‐based CdTe bond‐order approach that enables efficient molecular dynamics to approach the fidelity of density functional theory. Stringent quantum‐mechanical verification and experimental validation tests reveal that our new approach provides an accurate prediction of defects that earlier methods cannot. Using this new capability, we show that misfit dislocations in CdTe/CdS multilayers can be significantly reduced via nano‐patterning and composition grading and more importantly, dislocation‐free multilayers naturally arise when the pattern dimension is reduced below 90nm. Our predictive methods are generally applicable to other materials, highlighting a rational approach towards low‐defect semiconductor films. Copyright © 2015 John Wiley & Sons, Ltd. read less NOT USED (high confidence) T.-H. Chen, R. Xu, and Q. Li, “Effect of Strain Rate on Tensile Strength of Defective Silicon Nanorods,” Acta Mechanica Solida Sinica. 2015. link Times cited: 4 NOT USED (high confidence) K. Mizotani, M. Isobe, M. Fukasawa, K. Nagahata, T. Tatsumi, and S. Hamaguchi, “Molecular dynamics simulation of silicon oxidation enhanced by energetic hydrogen ion irradiation,” Journal of Physics D: Applied Physics. 2015. link Times cited: 13 Abstract: Molecular dynamics numerical simulations have been performed… read moreAbstract: Molecular dynamics numerical simulations have been performed to clarify the mechanism of enhanced oxidation in Si during silicon gate etching by HBr/O2 plasmas. Such enhanced oxidation sometimes manifests itself as Si recess during gate etching processes. When a Si substrate is subject to energetic ion bombardment together with a flux of radical species, our study has identified the cause of such enhanced oxidation in Si as enhanced O diffusion arising from the momentum transfer from energetic H atoms to O atoms on the surface or in the subsurface of the Si substrate. No chemical effect such as hydrogenation of Si plays a role for the enhanced oxidation. Simulation results are found to be in good agreement with earlier experimental observations of ion-irradiation-enhanced oxidation obtained by beam experiments. read less NOT USED (high confidence) Z. Fan, L. Pereira, H. Q. Wang, J.-C. Zheng, D. Donadio, and A. Harju, “Force and heat current formulas for many-body potentials in molecular dynamics simulations with applications to thermal conductivity calculations,” Physical Review B. 2015. link Times cited: 166 Abstract: Author(s): Fan, Z; Pereira, LFC; Wang, HQ; Zheng, JC; Donadi… read moreAbstract: Author(s): Fan, Z; Pereira, LFC; Wang, HQ; Zheng, JC; Donadio, D; Harju, A | Abstract: © 2015 American Physical Society. We derive expressions of interatomic force and heat current for many-body potentials such as the Tersoff, the Brenner, and the Stillinger-Weber potential used extensively in molecular dynamics simulations of covalently bonded materials. Although these potentials have a many-body nature, a pairwise force expression that follows Newton's third law can be found without referring to any partition of the potential. Based on this force formula, a stress applicable for periodic systems can be unambiguously defined. The force formula can then be used to derive the heat current formulas using a natural potential partitioning. Our heat current formulation is found to be equivalent to most of the seemingly different heat current formulas used in the literature, but to deviate from the stress-based formula derived from two-body potential. We validate our formulation numerically on various systems described by the Tersoff potential, namely three-dimensional silicon and diamond, two-dimensional graphene, and quasi-one-dimensional carbon nanotube. The effects of cell size and production time used in the simulation are examined. read less NOT USED (high confidence) S. Neogi and D. Donadio, “Thermal transport in free-standing silicon membranes: influence of dimensional reduction and surface nanostructures,” The European Physical Journal B. 2015. link Times cited: 24 NOT USED (high confidence) B. Liu et al., “Thermal transport in a graphene–MoS2 bilayer heterostructure: a molecular dynamics study,” RSC Advances. 2015. link Times cited: 77 Abstract: With the availability of various types of two-dimensional ma… read moreAbstract: With the availability of various types of two-dimensional materials such as graphene (GE) and MoS2, intensive efforts have been devoted to their van der Waals heterostructures obtained by vertically stacking them together for novel functionalities and applications. The thermal transport behavior of these heterostructures plays a pivotal role in determining their functional performance. This work studies the thermal transport in a GE–MoS2 bilayer heterostructure via molecular dynamics simulation. It is found that the in-plane thermal conductivity λB of the GE–MoS2 bilayer can be approximated by that of an isolated monolayer GE. The λB of an infinitely long GE–MoS2 bilayer is calculated to be 1037 W m−1 K−1, while its out-of-plane interface thermal conductance G is obtained as 5.81 MW m−2 K−1. The increase in the interface coupling strengths can dramatically increase G but has little effect on λB. On the other hand, G also increases with temperature because of the enhanced phonon coupling between GE and MoS2. This study is helpful for understanding the interface thermal transport behaviors of novel van der Waals heterostructures and could provide guidance for optimal design and control of their thermal properties. read less NOT USED (high confidence) Z. Li, J. Kermode, and A. D. Vita, “Molecular dynamics with on-the-fly machine learning of quantum-mechanical forces.,” Physical review letters. 2015. link Times cited: 420 Abstract: We present a molecular dynamics scheme which combines first-… read moreAbstract: We present a molecular dynamics scheme which combines first-principles and machine-learning (ML) techniques in a single information-efficient approach. Forces on atoms are either predicted by Bayesian inference or, if necessary, computed by on-the-fly quantum-mechanical (QM) calculations and added to a growing ML database, whose completeness is, thus, never required. As a result, the scheme is accurate and general, while progressively fewer QM calls are needed when a new chemical process is encountered for the second and subsequent times, as demonstrated by tests on crystalline and molten silicon. read less NOT USED (high confidence) K. Garcez and A. Antonelli, “Polyamorphism in tetrahedral substances: Similarities between silicon and ice.,” The Journal of chemical physics. 2015. link Times cited: 1 Abstract: Tetrahedral substances, such as silicon, water, germanium, a… read moreAbstract: Tetrahedral substances, such as silicon, water, germanium, and silica, share various unusual phase behaviors. Among them, the so-called polyamorphism, i.e., the existence of more than one amorphous form, has been intensively investigated in the last three decades. In this work, we study the metastable relations between amorphous states of silicon in a wide range of pressures, using Monte Carlo simulations. Our results indicate that the two amorphous forms of silicon at high pressures, the high density amorphous (HDA) and the very high density amorphous (VHDA), can be decompressed from high pressure (∼20 GPa) down to the tensile regime, where both convert into the same low density amorphous. Such behavior is also observed in ice. While at high pressure (∼20 GPa), HDA is less stable than VHDA, at the pressure of 10 GPa both forms exhibit similar stability. On the other hand, at much lower pressure (∼5 GPa), HDA and VHDA are no longer the most stable forms, and, upon isobaric annealing, an even less dense form of amorphous silicon emerges, the expanded high density amorphous, again in close similarity to what occurs in ice. read less NOT USED (high confidence) W.-L. Lv and A. Henry, “Direct calculation of modal contributions to thermal conductivity via Green–Kubo modal analysis,” New Journal of Physics. 2015. link Times cited: 115 Abstract: We derived a new method for direct calculation of the modal … read moreAbstract: We derived a new method for direct calculation of the modal contributions to thermal conductivity, which is termed Green–Kubo modal analysis (GKMA). The GKMA method combines the lattice dynamics formalism with the Green–Kubo formula for thermal conductivity, such that the thermal conductivity becomes a direct summation of modal contributions, where one need not define the phonon velocity. As a result, the GKMA method can be applied to any material/group of atoms, where the atoms vibrate around stable equilibrium positions, which includes non-stoichiometric compounds, random alloys, amorphous materials and even rigid molecules. By using molecular dynamics simulations to obtain the time history of each mode’s contribution to the heat current, one naturally includes anharmonicity to full order and can obtain insight into the interactions between different modes through the cross-correlations. As an example, we applied the GMKA method to crystalline and amorphous silicon. The modal contributions at each frequency result from the analysis and thereby allow one to apply a quantum correction to the mode heat capacity to determine the temperature dependence of thermal conductivity. The predicted temperature dependent thermal conductivity for amorphous silicon shows the best agreement with experiments to date. The GKMA method provides new insight into the nature of phonon transport, as it casts the problem in terms of mode–mode correlation instead of scattering, and provides a general unified formalism that can be used to understand phonon–phonon interactions in essentially any class of materials or structures where the atoms vibrate around stable equilibrium sites. read less NOT USED (high confidence) C. Angell, “Forty Years of Silica Simulations. Which Way Now,” International Journal of Applied Glass Science. 2015. link Times cited: 10 Abstract: Ten years after Aneesur Rahman’s seminal 1964 paper on simul… read moreAbstract: Ten years after Aneesur Rahman’s seminal 1964 paper on simulating liquid argon using computer simulations of atoms interacting with continuous potentials, Woodcock and Singer published the first study of ionic liquids using the same classical mechanical approach. With tongue-in-cheek, Woodcock and Angell with student Cheeseman then studied SiO2 in a simple ionic model using Tosi-Fumi type potentials and were surprised by the degree of similarity to the unusual properties of the “real” silica, liquid, and glassy, they were able to obtain. Since that time, many advances have been made and the field of ionic liquids now embraces geochemical in addition to complex inorganic glass systems. Now it seems that some “silica” models may exhibit water-like second critical points, and then liquid‐liquid transitions, and so may serve as new model liquids for liquid polyamorphism studies. Current studies using the realistic van Beest-Kramer-van Santen(BKS) and the simpler Woodcock-Angell-Cheeseman(WAC) potential models will be described. We provide background on silica’s role as a “strong” liquid, and on the criterion for ergodicity breaking which requires the relation Qds/dT ! 1 to hold at the hysteresis peak Tp (coincides with three common definitions of Tg). read less NOT USED (high confidence) K. Joseph, K. Jolley, and R. Smith, “Iron phosphate glasses: structure determination and displacement energy thresholds, using a fixed charge potential model,” Journal of Non-crystalline Solids. 2015. link Times cited: 38 NOT USED (high confidence) D. Hou, T. Zhao, Z. Jin, H. Ma, and Z. Li, “Molecular Simulation of Calcium Silicate Composites: Structure, Dynamics, and Mechanical Properties,” Journal of the American Ceramic Society. 2015. link Times cited: 14 Abstract: Calcium silicate composite (CaO)x(SiO2)1−x has significant a… read moreAbstract: Calcium silicate composite (CaO)x(SiO2)1−x has significant applications in the bioactive materials in medical treatment and cementitious materials in construction engineering. In this study, to unravel the role of calcium atoms on the silicate composite, the molecular dynamics (MD) technique was used to simulate the structures, dynamics, and mechanical properties of (CaO)x(SiO2)1−x systems, with x varying from 0 to 0.6. The Feuston–Garofalini model was employed to describe the interatomic interactions in the systems. Q species, the connectivity factor, shows that the increase in calcium content in the silicate composite can lead to the depolymerization of the silicate network. Due to the high diffusion rate, the presence of Ca atoms also weakens the stability of the chemical bonds in the system. With the increasing calcium content, the molecular structure of the silicate skeleton is transformed from an integrity network to separated short chains, which significantly decreases the stiffness and cohesive force of the calcium silicate composites. On the other hand, the uniaxial tension response of the calcium silicate composites suggests that at the postfailure stage, Ca atoms associate with the nonbridging oxygen atoms and the reconstructed Ca–O connection slows down the irreversible damage of the composite, hereby enhancing the plasticity. read less NOT USED (high confidence) S. Li and W. Qi, “Unification of Two Different Melting Mechanisms of Nanovoids,” Journal of Physical Chemistry C. 2015. link Times cited: 7 Abstract: Void melting in solids is a very complicated process, while … read moreAbstract: Void melting in solids is a very complicated process, while the mechanism is far from understood. In this paper, we studied the void melting in Pd and Si solids using a molecular dynamics simulation method. It is found that there exist two different melting mechanisms for nanovoid, nucleation melting and non-nucleation melting; although void melting in Pd follows the former mechanism, that in Si follows the latter (unless the nanovoid size decreases to a critically small value). For nucleation melting, there will be liquid nucleate at the surface of the nanovoid, and then the liquid fills the void before the temperature reaches the melting point of the solids. For non-nucleation melting, there will be local stiffening around the nanovoid, and the nanovoid always exists until the whole matrix comes to melt. For these two different melting mechanisms, the inner surface atoms will behave totally differently. We find the most exciting thing to be that the two mechanisms can be well unified based on surface me... read less NOT USED (high confidence) K. Das, J. Freund, and H. Johnson, “Mechanisms of material removal and mass transport in focused ion beam nanopore formation,” Journal of Applied Physics. 2015. link Times cited: 8 Abstract: Despite the widespread use of focused ion beam (FIB) process… read moreAbstract: Despite the widespread use of focused ion beam (FIB) processing as a material removal method for applications ranging from electron microscope sample preparation to nanopore processing for DNA sequencing, the basic material removal mechanisms of FIB processing are not well understood. We present the first complete atomistic simulation of high-flux FIB using large-scale parallel molecular dynamics (MD) simulations of nanopore fabrication in freestanding thin films. We focus on the root mechanisms of material removal and rearrangement and describe the role of explosive boiling in forming nanopores. FIB nanopore fabrication is typically understood to occur via sputter erosion. This can be shown to be the case in low flux systems, where individual ion impacts are sufficiently separated in time that they may be considered as independent events. But our detailed MD simulations show that in high flux FIB processing, above a threshold level at which thermal effects become significant, the primary mechanism of mat... read less NOT USED (high confidence) K. Mizotani, M. Isobe, and S. Hamaguchi, “Molecular dynamic simulation of damage formation at Si vertical walls by grazing incidence of energetic ions in gate etching processes,” Journal of Vacuum Science and Technology. 2015. link Times cited: 7 Abstract: During gate etching processes of multigate fin-type field ef… read moreAbstract: During gate etching processes of multigate fin-type field effect transistors (finFETs), energetic ions may hit the vertical walls at grazing angles and form damaged layers there. Such damages, if formed, can affect the device performance since part of the Si vertical walls of a finFET structure is used as a conductive channel. In this article, possible damage formation mechanisms at a Si vertical wall by energetic incidence of hydrogen ions (H+) and other heavier ions are discussed based on molecular dynamics simulation. In typical plasma processing conditions, incident ions are highly directional toward the wafer surface and therefore ions that hit such a vertical wall do so only at nearly grazing angles. It has been found in this study that the penetration depth of H+ into a Si substrate is weakly dependent on the incident angle and therefore ions at grazing incidence can form deep damage. The results indicate that, in gate etching processes with HBr plasmas or other plasmas with hydrogen, control of en... read less NOT USED (high confidence) G. Jeanmairet, M. Levesque, V. Sergiievskyi, and D. Borgis, “Molecular density functional theory for water with liquid-gas coexistence and correct pressure.,” The Journal of chemical physics. 2015. link Times cited: 34 Abstract: The solvation of hydrophobic solutes in water is special bec… read moreAbstract: The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular density functional theory, coexistence is not taken into account. Hydration structures and energies of nanometer-scale hydrophobic solutes are thus incorrect. In this article, we propose a bridge functional that corrects this thermodynamic inconsistency by introducing a metastable gas phase for the homogeneous solvent. We show how this can be done by a third order expansion of the functional around the bulk liquid density that imposes the right pressure and the correct second order derivatives. Although this theory is not limited to water, we apply it to study hydrophobic solvation in water at room temperature and pressure and compare the results to all-atom simulations. The solvation free energy of small molecular solutes like n-alkanes and hard sphere solutes whose radii range from angstroms to nanometers is now in quantitative agreement with reference all atom simulations. The macroscopic liquid-gas surface tension predicted by the theory is comparable to experiments. This theory gives an alternative to the empirical hard sphere bridge correction used so far by several authors. read less NOT USED (high confidence) J.-W. Jiang, “Graphene versus MoS2: A short review,” Frontiers of Physics. 2015. link Times cited: 52 NOT USED (high confidence) C. Vega, “Water: one molecule, two surfaces, one mistake,” Molecular Physics. 2015. link Times cited: 51 Abstract: In order to rigorously evaluate the energy and dipole moment… read moreAbstract: In order to rigorously evaluate the energy and dipole moment of a certain configuration of molecules, one needs to solve the Schrödinger equation. Repeating this for many different configurations allows one to determine the potential energy surface (PES) and the dipole moment surface (DMS). Since the early days of computer simulation, it has been implicitly accepted that for empirical potentials the charges used to fit the PES should also be used to describe the DMS. This is a mistake. Partial charges are not observable magnitudes. They should be regarded as adjustable fitting parameters. Optimal values used to describe the PES are not necessarily the best to describe the DMS. One could use two fits: one for the PES and the other for the DMS. This is a common practice in the quantum chemistry community, but not used so often by the community performing computer simulations. This idea affects all types of modelling of water (with the exception of ab initio calculations) from coarse-grained to non-polarisable and polarisable models. We anticipate that an area that will benefit dramatically from having both, a good PES and a good DMS, is the modelling of water in the presence of electric fields. read less NOT USED (high confidence) X. W. Zhou, D. Ward, M. Foster, and J. Zimmerman, “An analytical bond-order potential for the copper–hydrogen binary system,” Journal of Materials Science. 2015. link Times cited: 18 NOT USED (high confidence) F. A. E. Nabi, J. Godet, S. Brochard, and L. Pizzagalli, “Onset of ductility and brittleness in silicon nanowires mediated by dislocation nucleation,” Modelling and Simulation in Materials Science and Engineering. 2015. link Times cited: 16 Abstract: Most studies show that materials at the nano-scale have diff… read moreAbstract: Most studies show that materials at the nano-scale have different mechanical properties than in the bulk state. Semiconductors like silicon and germanium are brittle in the bulk state, but when their size is reduced to the nano-scale they appear to be ductile. Under tensile loading, we performed molecular dynamics simulations on silicon crystalline nanowires of different lengths. We present the details of the obtained mechanisms that led to ductility and brittleness. In the case of ductility, dislocation nucleation was observed with a signature of surface step formation on the surface and in the case of brittleness a cavity was formed after the distinct formation of a wedge-like shape on the surface. Interestingly, a common mechanism taking place behind ductility and brittleness is dislocation nucleation. We believe that the observed mechanisms reveal interesting information for understanding and explaining the size dependent brittle to ductile transition. read less NOT USED (high confidence) S. Gupta, K. K. Sreeja, and S. Thakur, “Autonomous movement of a chemically powered vesicle.,” Physical review. E, Statistical, nonlinear, and soft matter physics. 2015. link Times cited: 11 Abstract: We investigate the diffusio-phoretic motion of a deformable … read moreAbstract: We investigate the diffusio-phoretic motion of a deformable vesicle. A vesicle is built from the linked catalytic and noncatalytic vertices that consumes fuel in the environment and utilize the resulting self-generated concentration gradient to exhibit propulsive motion. Under nonequilibrium conditions it is found that the self-propulsion velocity of the vesicle depends on its shape, which in turn is controlled by the bending rigidity of the membrane and solvent density around it. The self-propulsion velocity of the vesicle for different shapes has been calculated and the factors which affect the velocity are identified. read less NOT USED (high confidence) R. Ranganathan, K. Sasikumar, and P. Keblinski, “Realizing tunable molecular thermal devices based on photoisomerism—Is it possible?,” Journal of Applied Physics. 2015. link Times cited: 5 Abstract: In this work, we address the question if it is possible to t… read moreAbstract: In this work, we address the question if it is possible to tune the thermal conductance through photoisomerism-capable molecular junctions. Using non-equilibrium molecular dynamics simulations, we study heat flow due to phonons between two silicon leads connected via two classes of photoisomeric molecules—(a) azobenzene and (b) Spiropyran (SP)–Merocyanine (MC) isomers. For the case of azobenzene, isomeric states with different conformations are realized via mechanical strain, while in the case of SP-MC, via a hybridization change. Based on the phononic contribution to thermal conductance, we observe that the thermal conductance of both junctions is rather insensitive to the isomeric state, thereby rendering the tunability of molecular thermal devices rather difficult. Consistent with these observations, the vibrational density of states for different configurations yields very similar spectra. We note that including the effect of electronic contribution to thermal conductance could enhance the tunability ... read less NOT USED (high confidence) G. P. Srivastava, “Tuning phonon properties in thermoelectric materials,” Reports on Progress in Physics. 2015. link Times cited: 21 Abstract: This review article presents a discussion of theoretical pro… read moreAbstract: This review article presents a discussion of theoretical progress made over the past several decades towards our understanding of thermoelectric properties of materials. Particular emphasis is placed upon describing recent progress in ‘tuning’ phonon properties of nanocomposite materials for gaining enhancement of the thermoelectric figure of merit. read less NOT USED (high confidence) G. K. Lockwood and S. Garofalini, “Proton Dynamics at the Water–Silica Interface via Dissociative Molecular Dynamics,” Journal of Physical Chemistry C. 2014. link Times cited: 33 Abstract: A robust and accurate dissociative potential that reproduces… read moreAbstract: A robust and accurate dissociative potential that reproduces the structural and dynamic properties of bulk and nanoconfined water, and proton transport similar to ab initio calculations in bulk water, is used for reactive molecular dynamics simulations of the proton dynamics at the silica/water interface. The simulations are used to evaluate the lifetimes of protonated sites at the interfaces of water with planar amorphous silica surfaces and cylindrical pores in amorphous silica with different densities of water confined in the pores. In addition to lifetimes, the donor/acceptor sites are evaluated and discussed in terms of local atomistic structure. The results of the lifetimes of the protonated sites, including H3O+, SiOH, SiOH2+, and Si–(OH+)–Si sites, are considered. The lifetime of the hydronium ion, H3O+, is considerably shorter near the interface than in bulk water, as are the lifetimes of the other protonated sites. The results indicate the beneficial effect of the amorphous silica surface in enh... read less NOT USED (high confidence) A. Dongare, “Quasi-coarse-grained dynamics: modelling of metallic materials at mesoscales,” Philosophical Magazine. 2014. link Times cited: 26 Abstract: A computationally efficient modelling method called quasi-co… read moreAbstract: A computationally efficient modelling method called quasi-coarse-grained dynamics (QCGD) is developed to expand the capabilities of molecular dynamics (MD) simulations to model behaviour of metallic materials at the mesoscales. This mesoscale method is based on solving the equations of motion for a chosen set of representative atoms from an atomistic microstructure and using scaling relationships for the atomic-scale interatomic potentials in MD simulations to define the interactions between representative atoms. The scaling relationships retain the atomic-scale degrees of freedom and therefore energetics of the representative atoms as would be predicted in MD simulations. The total energetics of the system is retained by scaling the energetics and the atomic-scale degrees of freedom of these representative atoms to account for the missing atoms in the microstructure. This scaling of the energetics renders improved time steps for the QCGD simulations. The success of the QCGD method is demonstrated by the prediction of the structural energetics, high-temperature thermodynamics, deformation behaviour of interfaces, phase transformation behaviour, plastic deformation behaviour, heat generation during plastic deformation, as well as the wave propagation behaviour, as would be predicted using MD simulations for a reduced number of representative atoms. The reduced number of atoms and the improved time steps enables the modelling of metallic materials at the mesoscale in extreme environments. read less NOT USED (high confidence) V. Lipp, B. Rethfeld, M. E. Garcia, and D. Ivanov, “Atomistic-continuum modeling of short laser pulse melting of Si targets,” Physical Review B. 2014. link Times cited: 41 Abstract: We present an atomistic-continuum model to simulate ultrasho… read moreAbstract: We present an atomistic-continuum model to simulate ultrashort laser-induced melting processes in semiconductor solids on the example of silicon. The kinetics of transient non-equilibrium phase transition mechanisms is addressed with a Molecular Dynamics method at atomic level, whereas the laser light absorption, strong generated electron-phonon non-equilibrium, fast diffusion and heat conduction due to photo-excited free carriers are accounted for in the continuum. We give a detailed description of the model, which is then applied to study the mechanism of short laser pulse melting of free standing Si films. The effect of laser-induced pressure and temperature of the lattice on the melting kinetics is investigated. Two competing melting mechanisms, heterogeneous and homogeneous, were identified. Apart of classical heterogeneous melting mechanism, the nucleation of the liquid phase homogeneously inside the material significantly contributes to the melting process. The simulations showed, that due to the open diamond structure of the crystal, the laser-generated internal compressive stresses reduce the crystal stability against the homogeneous melting. Consequently, the latter can take a massive character within several picoseconds upon the laser heating. Due to negative volume of melting of modeled Si material, -7.5%, the material contracts upon the phase transition, relaxes the compressive stresses and the subsequent melting proceeds heterogeneously until the excess of thermal energy is consumed. The threshold fluence value, at which homogeneous nucleation of liquid starts contributing to the classical heterogeneous propagation of the solid-liquid interface, is found from the series of simulations at different laser input fluences. On the example of Si, the laser melting kinetics of semiconductors was found to be noticeably different from that of metals with fcc crystal structure. read less NOT USED (high confidence) B. Nuñez-Moraleda et al., “Preferential sites for InAsP/InP quantum wire nucleation using molecular dynamics,” The European Physical Journal B. 2014. link Times cited: 0 NOT USED (high confidence) D. Dhabal, M. P. Singh, K. T. Wikfeldt, and C. Chakravarty, “Triplet correlation functions in liquid water.,” The Journal of chemical physics. 2014. link Times cited: 24 Abstract: Triplet correlations have been shown to play a crucial role … read moreAbstract: Triplet correlations have been shown to play a crucial role in the transformation of simple liquids to anomalous tetrahedral fluids [M. Singh, D. Dhabal, A. H. Nguyen, V. Molinero, and C. Chakravarty, Phys. Rev. Lett. 112, 147801 (2014)]. Here we examine triplet correlation functions for water, arguably the most important tetrahedral liquid, under ambient conditions, using configurational ensembles derived from molecular dynamics (MD) simulations and reverse Monte Carlo (RMC) datasets fitted to experimental scattering data. Four different RMC data sets with widely varying hydrogen-bond topologies fitted to neutron and x-ray scattering data are considered [K. T. Wikfeldt, M. Leetmaa, M. P. Ljungberg, A. Nilsson, and L. G. M. Pettersson, J. Phys. Chem. B 113, 6246 (2009)]. Molecular dynamics simulations are performed for two rigid-body effective pair potentials (SPC/E and TIP4P/2005) and the monatomic water (mW) model. Triplet correlation functions are compared with other structural measures for tetrahedrality, such as the O-O-O angular distribution function and the local tetrahedral order distributions. In contrast to the pair correlation functions, which are identical for all the RMC ensembles, the O-O-O triplet correlation function can discriminate between ensembles with different degrees of tetrahedral network formation with the maximally symmetric, tetrahedral SYM dataset displaying distinct signatures of tetrahedrality similar to those obtained from atomistic simulations of the SPC/E model. Triplet correlations from the RMC datasets conform closely to the Kirkwood superposition approximation, while those from MD simulations show deviations within the first two neighbour shells. The possibilities for experimental estimation of triplet correlations of water and other tetrahedral liquids are discussed. read less NOT USED (high confidence) V. V. Vasisht, J. Mathew, S. Sengupta, and S. Sastry, “Nesting of thermodynamic, structural, and dynamic anomalies in liquid silicon.,” The Journal of chemical physics. 2014. link Times cited: 24 Abstract: Anomalous behaviour in density, diffusivity, and structural … read moreAbstract: Anomalous behaviour in density, diffusivity, and structural order is investigated for silicon modeled by the Stillinger-Weber potential by performing molecular dynamics simulations. As previously reported in the case of water [J. R. Errington and P. G. Debenedetti, Nature (London) 409, 318 (2001)] and silica [M. S. Shell, P. G. Debenedetti, and A. Z. Panagiotopoulos, Phys. Rev. E 66, 011202 (2002)], a cascading of thermodynamic, dynamic, and structural anomalous regions is also observed in liquid silicon. The region of structural anomaly includes the region of diffusivity anomaly, which in turn encompasses the region of density anomaly (which is unlike water but similar to silica). In the region of structural anomaly, a tight correlation between the translational and tetrahedrality order parameter is found, but the correlation is weaker when a local orientational order parameter (q3) is used as a measure of tetrahedrality. The total excess entropy and the pair correlation entropy are computed across the phase diagram and the correlation between the excess entropy and the regions of anomalies in the phase diagram of liquid silicon is examined. Scaling relations associating the excess entropy with the diffusion coefficient show considerable deviation from the quasi-universal behaviour observed in hard-sphere and Lennard-Jones liquids and some liquid metals. Excess entropy based criteria for diffusivity and structural anomalies fail to capture the observed regions of anomaly. read less NOT USED (high confidence) J.-W. Jiang, T. Rabczuk, and H. S. Park, “A Stillinger-Weber potential for single-layered black phosphorus, and the importance of cross-pucker interactions for a negative Poisson’s ratio and edge stress-induced bending.,” Nanoscale. 2014. link Times cited: 76 Abstract: The distinguishing structural feature of single-layered blac… read moreAbstract: The distinguishing structural feature of single-layered black phosphorus is its puckered structure, which leads to many novel physical properties. In this work, we first present a new parameterization of the Stillinger-Weber potential for single-layered black phosphorus. In doing so, we reveal the importance of a cross-pucker interaction term in capturing its unique mechanical properties, such as a negative Poisson's ratio. In particular, we show that the cross-pucker interaction enables the pucker to act as a re-entrant hinge, which expands in the lateral direction when it is stretched in the longitudinal direction. As a consequence, single-layered black phosphorus has a negative Poisson's ratio in the direction perpendicular to the atomic plane. As an additional demonstration of the impact of the cross-pucker interaction, we show that it is also the key factor that enables capturing the edge stress-induced bending of single-layered black phosphorus that has been reported in ab initio calculations. read less NOT USED (high confidence) X. Zhou, M. E. Foster, F. Swol, J. E. Martin, and B. M. Wong, “Analytical Bond-Order Potential for the Cd–Te–Se Ternary System,” Journal of Physical Chemistry C. 2014. link Times cited: 13 NOT USED (high confidence) A. Haji-Akbari, R. S. DeFever, S. Sarupria, and P. Debenedetti, “Suppression of sub-surface freezing in free-standing thin films of a coarse-grained model of water.,” Physical chemistry chemical physics : PCCP. 2014. link Times cited: 55 Abstract: Freezing in the vicinity of water-vapor interfaces is of con… read moreAbstract: Freezing in the vicinity of water-vapor interfaces is of considerable interest to a wide range of disciplines, most notably the atmospheric sciences. In this work, we use molecular dynamics and two advanced sampling techniques, forward flux sampling and umbrella sampling, to study homogeneous nucleation of ice in free-standing thin films of supercooled water. We use a coarse-grained monoatomic model of water, known as mW, and we find that in this model a vapor-liquid interface suppresses crystallization in its vicinity. This suppression occurs in the vicinity of flat interfaces where no net Laplace pressure in induced. Our free energy calculations reveal that the pre-critical crystalline nuclei that emerge near the interface are thermodynamically less stable than those that emerge in the bulk. We investigate the origin of this instability by computing the average asphericity of nuclei that form in different regions of the film, and observe that average asphericity increases closer to the interface, which is consistent with an increase in the free energy due to increased surface-to-volume ratios. read less NOT USED (high confidence) T. Sipkens et al., “In situ nanoparticle size measurements of gas-borne silicon nanoparticles by time-resolved laser-induced incandescence,” Applied Physics B. 2014. link Times cited: 68 NOT USED (high confidence) P. Norris, “Modeling Interfacial Thermal Boundary Conductance of Engineered Interfaces.” 2014. link Times cited: 2 Abstract: : The hypothesis that motivates this grant--that material ca… read moreAbstract: : The hypothesis that motivates this grant--that material can be added at an interface to enhance its effective thermal conductance--was first explored using simulations. Our primary tool was the classical molecular dynamics (MD) method. The first part of the simulation work demonstrated that an interfacial film can enhance conductance in simple systems. The second part laid the groundwork to extend those simulations to more complex material systems. To theoretically investigate the phonon transport underlying the conductance trends observed in our simulations, we used various theoretical approaches to understand fundamental phonon transport in interfacial structures: (1) semi-empirical methods such as the DMM, (2) the wavelet transform applied to MD simulations, (3) Green's functions, and (4) the interfering particle model (IPM). Finally, the findings from simulations and theoretical analysis were used to design a series of experimental measurements of hBD at interfaces with varying thicknesses of interfacial films. The findings have been published in the 16 archival journal papers and 3 conference proceeding papers cited here, not including publications still under preparation. Each of these publications acknowledged funding from the AFOSR. read less NOT USED (high confidence) E. Cieren, L. Colombet, S. Pitoiset, and R. Namyst, “ExaStamp: A Parallel Framework for Molecular Dynamics on Heterogeneous Clusters,” Euro-Par Workshops. 2014. link Times cited: 8 NOT USED (high confidence) A. Jain and A. McGaughey, “Thermal conductivity of compound semiconductors: Interplay of mass density and acoustic-optical phonon frequency gap,” Journal of Applied Physics. 2014. link Times cited: 34 Abstract: The thermal conductivities of model compound semiconductors,… read moreAbstract: The thermal conductivities of model compound semiconductors, where the two species differ only in mass, are predicted using lattice dynamics calculations and the Boltzmann transport equation. The thermal conductivity varies non-monotonically with mass ratio, with a maximum value that is four times higher than that of a monatomic semiconductor of the same density. The very high thermal conductivities are attributed to a reduction in the scattering of optical phonons when the acoustic-optical frequency gap in the phonon dispersion approaches the maximum acoustic phonon frequency. The model system predictions compare well to predictions for real compound semiconductors under appropriate scaling, suggesting a universal behavior and a strategy for efficient screening of materials for high thermal conductivity. read less NOT USED (high confidence) F. Saiz and M. Gamero-Castaño, “Atomistic modeling of the sputtering of silicon by electrosprayed nanodroplets,” Journal of Applied Physics. 2014. link Times cited: 11 Abstract: The hypervelocity impact of electrosprayed nanodroplets on s… read moreAbstract: The hypervelocity impact of electrosprayed nanodroplets on single-crystal silicon ejects a large number of atoms. Although sputtering by atomic, molecular, and gas cluster ions has been thoroughly studied, the significantly larger size of nanodroplets prevents a straightforward extrapolation of the physics governing the impact of these smaller projectiles. This motivates the present molecular dynamics simulations of nanodroplet impact on silicon, aimed at resolving the mechanisms and the effect of the projectile's size and velocity on sputtering. We find that both collision cascades and thermal sputtering contribute to the overall atom ejection, the former being active during the initial stages of the impact characterized by strong interactions between the molecules of the projectile and the atoms of the target, and the absence of partial thermodynamic equilibrium. In addition, for sufficiently large projectile diameters and impact velocities, conglomerates of atoms are ejected by hydrodynamic forces. The sputtering yield, defined as the average number of target atoms ejected per projectile's molecule, increases monotonically with the kinetic energy of the molecules and, at constant molecular kinetic energy, slightly decreases with projectile diameter as a result of enhanced backscattering of the ejected atoms by the projectile's molecules. For the ionic liquid considered in this study, sputtering is first observed at molecular energies near 12.7 eV and, at the highest energy simulated of 73 eV, the sputtering yield averages to 0.37. read less NOT USED (high confidence) J. Lu, Y. Qiu, R. Baron, and V. Molinero, “Coarse-Graining of TIP4P/2005, TIP4P-Ew, SPC/E, and TIP3P to Monatomic Anisotropic Water Models Using Relative Entropy Minimization.,” Journal of chemical theory and computation. 2014. link Times cited: 100 Abstract: Coarse-grained models are becoming a competitive alternative… read moreAbstract: Coarse-grained models are becoming a competitive alternative for modeling processes that occur over time and length scales beyond the reach of fully atomistic molecular simulations. Ideally, coarse-grained models should not only achieve high computational efficiency but also provide accurate predictions and fundamental insight into the role of molecular interactions, the characteristic behavior, and properties of the system they model. In this work we derive a series of monatomic coarse-grained water models mX(REM) from the most popular atomistic water models X = TIP3P, SPC/E, TIP4P-Ew, and TIP4P/2005, using the relative entropy minimization (REM) method. Each coarse-grained water molecule is represented by a single particle that interacts through short-ranged anisotropic interactions that encourage the formation of "hydrogen-bonded" structures. We systematically investigate the features of the coarse-grained models in reproducing over 20 structural, dynamic, and thermodynamic properties of the reference atomistic water models-including the existence and locus of the characteristic density anomaly. The mX(REM) coarse-grained models reproduce quite faithfully the radial and angular distribution function of water, produce a temperature of maximum density (TMD), and stabilize the ice I crystal. Moreover, the ratio between the TMD and the melting temperature of the crystal in the mX(REM) models and liquid-ice equilibrium properties show reasonable agreement with the results of the corresponding atomistic models. The mX(REM) models, however, severely underestimate the cohesive energy of the condensed water phases. We investigate which specific limitations of the coarse-grained models arise from the REM methodology, from the monatomic nature of the models, and from the Stillinger-Weber interaction potential form. Our analysis indicates that a small compromise in the accuracy of structural properties can result in a significant increase of the overall accuracy and representability of the coarse-grained water models. We evaluate the accuracy of the atomistic and the monatomic anisotropic coarse-grained water models, including the mW water model, in reproducing experimental water properties. We find that mW and mTIP4P/2005(REM) score closer to experiment than widely used atomistic water models. We conclude that monatomic models of water with short-range, anisotropic "hydrogen-bonding" three-body interactions can be competitive in accuracy with fully atomistic models for the study of a wide range of properties and phenomena at less than 1/100th of the computational cost. read less NOT USED (high confidence) N. Wang and K. Komvopoulos, “The effect of deposition energy of energetic atoms on the growth and structure of ultrathin amorphous carbon films studied by molecular dynamics simulations,” Journal of Physics D: Applied Physics. 2014. link Times cited: 14 Abstract: The growth and structure of ultrathin amorphous carbon films… read moreAbstract: The growth and structure of ultrathin amorphous carbon films was investigated by molecular dynamics simulations. The second-generation reactive-empirical-bond-order potential was used to model atomic interactions. Films with different structures were simulated by varying the deposition energy of carbon atoms in the range of 1–120 eV. Intrinsic film characteristics (e.g. density and internal stress) were determined after the system reached equilibrium. Short- and intermediate-range carbon atom ordering is examined in the context of atomic hybridization and ring connectivity simulation results. It is shown that relatively high deposition energy (i.e., 80 eV) yields a multilayer film structure consisting of an intermixing layer, bulk film and surface layer, consistent with the classical subplantation model. The highest film density (3.3 g cm−3), sp3 fraction (∼43%), and intermediate-range carbon atom ordering correspond to a deposition energy of ∼80 eV, which is in good agreement with experimental findings. read less NOT USED (high confidence) F. Soberon, “Surface activation of cyclo olefin polymer by oxygen plasma discharge: a molecular dynamics study,” Modelling and Simulation in Materials Science and Engineering. 2014. link Times cited: 3 Abstract: Thermoplastic substrates made of cyclo olefin polymer (COP) … read moreAbstract: Thermoplastic substrates made of cyclo olefin polymer (COP) are treated with oxygen plasma discharges to introduce polar groups at the surface. This is the first step in the process of surface functionalization of COP substrates used in biosensor devices. A molecular dynamics model of basic COP structure is implemented using the second-generation reactive empirical bond order (REBO) potentials for hydrocarbon–oxygen interactions. The model includes covalent bond and Van der Waals interactions. The bombardment of a COP surface with mono-energetic atomic oxygen ions, energy in the range 1-35 eV, is simulated and reported here. The dynamics of the substrate modification reveals that the substrate top layer is de-hydrogenated and subsequently builds up an oxygen–carbon matrix layer, ∼10 Å thick. Analysis of the modified substrates indicates that surface yield is predominantly peroxide groups. read less NOT USED (high confidence) P. Saidi, T. Frolov, J. Hoyt, and M. Asta, “An angular embedded atom method interatomic potential for the aluminum–silicon system,” Modelling and Simulation in Materials Science and Engineering. 2014. link Times cited: 19 Abstract: A modified version of the Stillinger–Weber (SW) interatomic … read moreAbstract: A modified version of the Stillinger–Weber (SW) interatomic potential for pure Si has been developed. In contrast to the original SW form, the modified version allows one to grow diamond cubic crystal structures from the melt at high temperatures. Now, the modified SW potential has been combined with an embedded atom (EAM) description of pure Al developed by Mendelev et al to formulate an Al–Si binary potential of the angular EAM type. The Al–Si potential reproduces quite well the experimental enthalpy of mixing in the liquid. It also predicts an Al–Si phase diagram with a eutectic concentration for the liquid that agrees with experimental values within 4 at% and a eutectic temperature that differs from experimental values by just 13 K. read less NOT USED (high confidence) C. Royall and S. R. Williams, “The role of local structure in dynamical arrest,” Physics Reports. 2014. link Times cited: 328 NOT USED (high confidence) T. Tadano, Y. Gohda, and S. Tsuneyuki, “Anharmonic force constants extracted from first-principles molecular dynamics: applications to heat transfer simulations,” Journal of Physics: Condensed Matter. 2014. link Times cited: 337 Abstract: A systematic method to calculate anharmonic force constants … read moreAbstract: A systematic method to calculate anharmonic force constants of crystals is presented. The method employs the direct-method approach, where anharmonic force constants are extracted from the trajectory of first-principles molecular dynamics simulations at high temperature. The method is applied to Si where accurate cubic and quartic force constants are obtained. We observe that higher-order correction is crucial to obtain accurate force constants from the trajectory with large atomic displacements. The calculated harmonic and anharmonic force constants are, then, combined with the Boltzmann transport equation (BTE) and non-equilibrium molecular dynamics (NEMD) methods in calculating the thermal conductivity. The BTE approach successfully predicts the lattice thermal conductivity of bulk Si, whereas NEMD shows considerable underestimates. To evaluate the linear extrapolation method employed in NEMD to estimate bulk values, we analyze the size dependence in NEMD based on BTE calculations. We observe strong nonlinearity in the size dependence of NEMD in Si, which can be ascribed to acoustic phonons having long mean-free-paths and carrying considerable heat. Subsequently, we also apply the whole method to a thermoelectric material Mg2Si and demonstrate the reliability of the NEMD method for systems with low thermal conductivities. read less NOT USED (high confidence) Y. Magnin, G. D. Förster, F. Rabilloud, F. Calvo, A. Zappelli, and C. Bichara, “Thermal expansion of free-standing graphene: benchmarking semi-empirical potentials,” Journal of Physics: Condensed Matter. 2014. link Times cited: 55 Abstract: The thermodynamical properties of free-standing graphene hav… read moreAbstract: The thermodynamical properties of free-standing graphene have been investigated under constant zero pressure as a function of temperature using Monte Carlo simulations. A variety of atomistic models have been used, including the simple three-body Stillinger potential and a series of bond-order many-body potentials based on the Tersoff–Brenner seminal models, with recent reparametrizations dedicated to graphene, extensions to medium-range or long-range dispersion corrections. In addition, we have also tested a tight-binding potential in the fourth-moment approximation. The simulations reveal significant discrepancies in the in-plane lattice parameter and the thermal expansion coefficient, which despite showing monotonically increasing variations with temperature, can be positive, negative or change sign at moderate temperature depending on the potential. Comparison with existing experimental and theoretical data obtained from complementary approaches indicates that empirical potentials limited to nearest-neighbour interactions give rather dispersed results, and that van der Waals corrections generally tend to flatten the variations of the in-plane lattice constant, in contradiction with experiment. Only the medium-range corrected potentials of Los and Fasolino, as well as the tight-binding model in the fourth-moment approximation, are reasonably close to the reference results near room temperature. Our results suggest that classical potentials should be used with caution for thermal properties. read less NOT USED (high confidence) T. Zohdi, “Embedded electromagnetically sensitive particle motion in functionalized fluids,” Computational Particle Mechanics. 2014. link Times cited: 45 NOT USED (high confidence) L. Marqués, M. Aboy, K. Dudeck, G. Botton, A. Knights, and R. Gwilliam, “Modeling and experimental characterization of stepped and v-shaped 311 defects in silicon,” Journal of Applied Physics. 2014. link Times cited: 7 Abstract: We propose an atomistic model to describe extended {311} def… read moreAbstract: We propose an atomistic model to describe extended {311} defects in silicon. It is based on the combination of interstitial and bond defect chains. The model is able to accurately reproduce not only planar {311} defects but also defect structures that show steps, bends, or both. We use molecular dynamics techniques to show that these interstitial and bond defect chains spontaneously transform into extended {311} defects. Simulations are validated by comparing with precise experimental measurements on actual {311} defects. The excellent agreement between the simulated and experimentally derived structures, regarding individual atomic positions and shape of the distinct structural {311} defect units, provides strong evidence for the robustness of the proposed model. read less NOT USED (high confidence) J. J. Möller and E. Bitzek, “Comparative study of embedded atom potentials for atomistic simulations of fracture in α-iron,” Modelling and Simulation in Materials Science and Engineering. 2014. link Times cited: 50 Abstract: Atomistic simulations play a crucial role in advancing our u… read moreAbstract: Atomistic simulations play a crucial role in advancing our understanding of the crack-tip processes that take place during fracture of semi-brittle materials like α-iron. As with all atomistic simulations, the results of such simulations however depend critically on the underlying atomic interaction model. Here, we present a systematic study of eight α-iron embedded atom method potentials used to model cracks subjected to plane strain mode-I loading conditions in six different crystal orientations. Molecular statics simulations are used to determine the fracture behavior (cleavage, dislocation emission, twinning) and the critical stress intensity factor KIc. The structural transformations in front of the crack tips, and in particular the occurrence of {1 1 0} planar faults, are analyzed in detail and related to the strain-dependent generalized stacking fault energy curve. The simulation results are discussed in terms of theoretical fracture criteria and compared to recent experimental data. The different potentials are ranked according to their capability to model the experimentally observed fracture behavior. read less NOT USED (high confidence) X. Gu and R. Yang, “First-principles prediction of phononic thermal conductivity of silicene: A comparison with graphene,” Journal of Applied Physics. 2014. link Times cited: 199 Abstract: There has been great interest in two-dimensional materials, … read moreAbstract: There has been great interest in two-dimensional materials, beyond graphene, for both fundamental sciences and technological applications. Silicene, a silicon counterpart of graphene, has been shown to possess some better electronic properties than graphene. However, its thermal transport properties have not been fully studied. In this paper, we apply the first-principles-based phonon Boltzmann transport equation to investigate the thermal conductivity of silicene as well as the phonon scattering mechanisms. Although both graphene and silicene are two-dimensional crystals with similar crystal structure, we find that phonon transport in silicene is quite different from that in graphene. The thermal conductivity of silicene shows a logarithmic increase with respect to the sample size due to the small scattering rates of acoustic in-plane phonon modes, while that of graphene is finite. Detailed analysis of phonon scattering channels shows that the linear dispersion of the acoustic out-of-plane (ZA) phonon modes, which is induced by the buckled structure, makes the long-wavelength longitudinal acoustic phonon modes in silicene not as efficiently scattered as that in graphene. Compared with graphene, where most of the heat is carried by the acoustic out-of-plane (ZA) phonon modes, the ZA phonon modes in silicene only have ∼10% contribution to the total thermal conductivity, which can also be attributed to the buckled structure. This systematic comparison of phonon transport and thermal conductivity of silicene and graphene using the first-principle-based calculations shed some light on other two-dimensional materials, such as two-dimensional transition metal dichalcogenides. read less NOT USED (high confidence) Z. Li, D. Chen, J. Wang, and L. Shao, “Molecular dynamics simulation of Coulomb explosion, melting and shock wave creation in silicon after an ionization pulse,” Journal of Applied Physics. 2014. link Times cited: 3 Abstract: Strong electronic stopping power of swift ions in a semicond… read moreAbstract: Strong electronic stopping power of swift ions in a semiconducting or insulating substrate can lead to localized electron stripping. The subsequent repulsive interactions among charged target atoms can cause Coulomb explosion. Using molecular dynamics simulation, we simulate Coulomb explosion in silicon by introducing an ionization pulse lasting for different periods, and at different substrate temperatures. We find that the longer the pulse period, the larger the melting radius. The observation can be explained by a critical energy density model assuming that melting required thermal energy density is a constant value and the total thermal energy gained from Coulomb explosion is linearly proportional to the ionization period. Our studies also show that melting radius is larger at higher substrate temperatures. The temperature effect is explained due to a longer structural relaxation above the melting temperature at original ionization boundary due to lower heat dissipation rates. Furthermore, simulations show the formation of shock waves, created due to the compression from the melting core. read less NOT USED (high confidence) A. Vasin, O. Vikhrova, and M. Vasilevskiy, “Effects of alloy disorder and confinement on phonon modes and Raman scattering in SixGe1-x nanocrystals : a microscopic modeling,” Journal of Applied Physics. 2014. link Times cited: 6 Abstract: Confinement and alloy disorder effects on the lattice dynami… read moreAbstract: Confinement and alloy disorder effects on the lattice dynamics and Raman scattering in Si1−xGex nanocrystals (NCs) are investigated numerically employing two different empirical inter-atomic potentials. Relaxed NCs of different compositions (x) were built using the Molecular Dynamics method and applying rigid boundary conditions mimicking the effect of surrounding matrix. The resulting variation of bond lengths with x was checked against Vegard's law and the NC phonon modes were calculated using the same inter-atomic potential. The localization of the principal Raman-active (Si-Si, Si-Ge, and Ge-Ge) modes is investigated by analysing representative eigenvectors and their inverse participation ratio. The dependence of the position and intensity of these modes upon x and NC size is presented and compared to previous calculated results and available experimental data. In particular, it is argued that the composition dependence of the intensity of the Si-Ge and Ge-Ge modes does not follow the fraction of the ... read less NOT USED (high confidence) L. C. Jacobson, R. Kirby, and V. Molinero, “How short is too short for the interactions of a water potential? Exploring the parameter space of a coarse-grained water model using uncertainty quantification.,” The journal of physical chemistry. B. 2014. link Times cited: 57 Abstract: Coarse-grained models are becoming increasingly popular due … read moreAbstract: Coarse-grained models are becoming increasingly popular due to their ability to access time and length scales that are prohibitively expensive with atomistic models. However, as a result of decreasing the degrees of freedom, coarse-grained models often have diminished accuracy, representability, and transferability compared with their finer grained counterparts. Uncertainty quantification (UQ) can help alleviate this challenge by providing an efficient and accurate method to evaluate the effect of model parameters on the properties of the system. This method is useful in finding parameter sets that fit the model to several experimental properties simultaneously. In this work we use UQ as a tool for the evaluation and optimization of a coarse-grained model. We efficiently sample the five-dimensional parameter space of the coarse-grained monatomic water (mW) model to determine what parameter sets best reproduce experimental thermodynamic, structural and dynamical properties of water. Generalized polynomial chaos (gPC) was used to reconstruct the analytical surfaces of density, enthalpy of vaporization, radial and angular distribution functions, and diffusivity of liquid water as a function of the input parameters. With these surfaces, we evaluated the sensitivity of these properties to perturbations of the model input parameters and the accuracy and representability of the coarse-grained models. In particular, we investigated what is the optimum length scale of the water-water interactions needed to reproduce the properties of liquid water with a monatomic model with two- and three-body interactions. We found that there is an optimum cutoff length of 4.3 Å, barely longer than the size of the first neighbor shell in water. As cutoffs deviate from this optimum value, the ability of the model to simultaneously reproduce the structure and thermodynamics is severely diminished. read less NOT USED (high confidence) E. Mainini and U. Stefanelli, “Crystallization in Carbon Nanostructures,” Communications in Mathematical Physics. 2014. link Times cited: 57 NOT USED (high confidence) J. Farrell and D. Wales, “Clusters of coarse-grained water molecules.,” The journal of physical chemistry. A. 2014. link Times cited: 4 Abstract: Global optimization for molecular clusters can be significan… read moreAbstract: Global optimization for molecular clusters can be significantly more difficult than for atomic clusters because of the coupling between orientational and translational degrees of freedom. A coarse-grained representation of the potential can reduce the complexity of this problem, while retaining the essential features of the intermolecular interactions. In this study, we use a basin-hopping algorithm to locate putative global minima for clusters of coarse-grained water molecules modeled using a monatomic water potential for cluster sizes 3 ≤ N ≤ 55. We characterize these structures and identify structural trends using ideas from graph theory. The agreement with atomistic results and experiment is rather patchy, which we attribute to the tetrahedral bias in the three-body potential that results in too few nearest neighbor contacts and premature emergence of bulk-like structure. In spite of this issue, the results offer further useful insight into the relationship between the structure of clusters and bulk phases, and the mathematical form of a widely used model potential. read less NOT USED (high confidence) P. Brichon, E. Despiau-Pujo, and O. Joubert, “MD simulations of low energy Clx+ ions interaction with ultrathin silicon layers for advanced etch processes,” Journal of Vacuum Science and Technology. 2014. link Times cited: 26 Abstract: Molecular dynamics simulations of low-energy (5–100 eV) Cl+ … read moreAbstract: Molecular dynamics simulations of low-energy (5–100 eV) Cl+ and Cl2+ bombardment on (100) Si surfaces are performed to investigate the impact of plasma dissociation and very low-energy ions (5–10 eV) in chlorine pulsed plasmas used for silicon etch applications. Ion bombardment leads to an initial rapid chlorination of the Si surface followed by the formation of a stable SiClx mixed layer and a constant etch yield at steady state. The SiClx layer thickness increases with ion energy (from 0.7 ± 0.2 nm at 5 eV to 4 ± 0.5 nm at 100 eV) but decreases for Cl2+ bombardment (compared to Cl+), due to the fragmentation of Cl2+ molecular ions into atomic Cl species with reduced energies [one X eV Cl + two 2X eV Cl2+]. The Si etch yield is larger for Cl2+ than Cl+ bombardment at high-energy (Ei > 25 eV) but larger for Cl+ than Cl2+ bombardment at low-energy (Ei two 2X eV Cl2+]. The Si etch yield is larger for Cl2+ than Cl+ bombardment at high-energy (Ei > 25 eV) but larger for Cl+ than Cl2+ bombardment at low-energy (Ei < 25 eV) due to threshold effects. And the higher the ion energy, the less saturated the etch products. Results suggest that weakly dissociated chlorine ... read less NOT USED (high confidence) B. Deng, A. Chernatynskiy, M. Khafizov, D. Hurley, and S. Phillpot, “Kapitza resistance of Si/SiO2 interface,” Journal of Applied Physics. 2014. link Times cited: 61 Abstract: A phonon wave packet dynamics method is used to characterize… read moreAbstract: A phonon wave packet dynamics method is used to characterize the Kapitza resistance of a Si/SiO2 interface in a Si/SiO2/Si heterostructure. By varying the thickness of SiO2 layer sandwiched between two Si layers, we determine the Kapitza resistance for the Si/SiO2 interface from both wave packet dynamics and a direct, non-equilibrium molecular dynamics approach. The good agreement between the two methods indicates that they have each captured the anharmonic phonon scatterings at the interface. Moreover, detailed analysis provides insights as to how individual phonon mode scatters at the interface and their contribution to the Kapitza resistance. read less NOT USED (high confidence) L. Lupi and V. Molinero, “Does hydrophilicity of carbon particles improve their ice nucleation ability?,” The journal of physical chemistry. A. 2014. link Times cited: 130 Abstract: Carbonaceous particles account for 10% of the particulate ma… read moreAbstract: Carbonaceous particles account for 10% of the particulate matter in the atmosphere. Atmospheric oxidation and aging of soot modulates its ice nucleation ability. It has been suggested that an increase in the ice nucleation ability of aged soot results from an increase in the hydrophilicity of the surfaces upon oxidation. Oxidation, however, also impacts the nanostructure of soot, making it difficult to assess the separate effects of soot nanostructure and hydrophilicity in experiments. Here we use molecular dynamics simulations to investigate the effect of changes in hydrophilicity of model graphitic surfaces on the freezing temperature of ice. Our results indicate that the hydrophilicity of the surface is not in general a good predictor of ice nucleation ability. We find a correlation between the ability of a surface to promote nucleation of ice and the layering of liquid water at the surface. The results of this work suggest that ordering of liquid water in contact with the surface plays an important role in the heterogeneous ice nucleation mechanism. read less NOT USED (high confidence) E. Lascaris, M. Hemmati, S. Buldyrev, H. Stanley, and C. Angell, “Search for a liquid-liquid critical point in models of silica.,” The Journal of chemical physics. 2014. link Times cited: 58 Abstract: Previous research has indicated the possible existence of a … read moreAbstract: Previous research has indicated the possible existence of a liquid-liquid critical point (LLCP) in models of silica at high pressure. To clarify this interesting question we run extended molecular dynamics simulations of two different silica models (WAC and BKS) and perform a detailed analysis of the liquid at temperatures much lower than those previously simulated. We find no LLCP in either model within the accessible temperature range, although it is closely approached in the case of the WAC potential near 4000 K and 5 GPa. Comparing our results with those obtained for other tetrahedral liquids, and relating the average Si-O-Si bond angle and liquid density at the model glass temperature to those of the ice-like β-cristobalite structure, we conclude that the absence of a critical point can be attributed to insufficient "stiffness" in the bond angle. We hypothesize that a modification of the potential to mildly favor larger average bond angles will generate a LLCP in a temperature range that is accessible to simulation. The tendency to crystallize in these models is extremely weak in the pressure range studied, although this tendency will undoubtedly increase with increasing stiffness. read less NOT USED (high confidence) L. Lupi, A. Hudait, and V. Molinero, “Heterogeneous nucleation of ice on carbon surfaces.,” Journal of the American Chemical Society. 2014. link Times cited: 234 Abstract: Atmospheric aerosols can promote the heterogeneous nucleatio… read moreAbstract: Atmospheric aerosols can promote the heterogeneous nucleation of ice, impacting the radiative properties of clouds and Earth's climate. The experimental investigation of heterogeneous freezing of water droplets by carbonaceous particles reveals widespread ice freezing temperatures. It is not known which structural and chemical characteristics of soot account for the variability in ice nucleation efficiency. Here we use molecular dynamics simulations to investigate the nucleation of ice from liquid water in contact with graphitic surfaces. We find that atomically flat carbon surfaces promote heterogeneous nucleation of ice, while molecularly rough surfaces with the same hydrophobicity do not. Graphitic surfaces and other surfaces that promote ice nucleation induce layering in the interfacial water, suggesting that the order imposed by the surface on liquid water may play an important role in the heterogeneous nucleation mechanism. We investigate a large set of graphitic surfaces of various dimensions and radii of curvature and find that variations in nanostructures alone could account for the spread in the freezing temperatures of ice on soot in experiments. We conclude that a characterization of the nanostructure of soot is needed to predict its ice nucleation efficiency. read less NOT USED (high confidence) K. Garcez and A. Antonelli, “Pressure-induced Transformations In Amorphous Silicon: A Computational Study,” Journal of Applied Physics. 2014. link Times cited: 2 Abstract: We study the transformations between amorphous phases of Si … read moreAbstract: We study the transformations between amorphous phases of Si through molecular simulations using the environment dependent interatomic potential (EDIP) for Si. Our results show that upon pressure, the material undergoes a transformation from the low density amorphous (LDA) Si to the high density amorphous (HDA) Si. This transformation can be reversed by decompressing the material. This process, however, exhibits clear hysteresis, suggesting that the transformation LDA ↔ HDA is first-order like. The HDA phase is predominantly five-fold coordinated, whereas the LDA phase is the normal tetrahedrally bonded amorphous Si. The HDA phase at 400 K and 20 GPa was submitted to an isobaric annealing up to 800 K, resulting in a denser amorphous phase, which is structurally distinct from the HDA phase. Our results also show that the atomic volume and structure of this new amorphous phase are identical to those of the glass obtained by an isobaric quenching of the liquid in equilibrium at 2000 K and 20 GPa down to 400 K... read less NOT USED (high confidence) J. Ding, M. Xu, P. Guan, S. Deng, Y. Cheng, and E. Ma, “Temperature effects on atomic pair distribution functions of melts.,” The Journal of chemical physics. 2014. link Times cited: 42 Abstract: Using molecular dynamics simulations, we investigate the tem… read moreAbstract: Using molecular dynamics simulations, we investigate the temperature-dependent evolution of the first peak position/shape in pair distribution functions of liquids. For metallic liquids, the peak skews towards the left (shorter distance side) with increasing temperature, similar to the previously reported anomalous peak shift. Making use of constant-volume simulations in the absence of thermal expansion and change in inherent structure, we demonstrate that the apparent shift of the peak maximum can be a result of the asymmetric shape of the peak, as the asymmetry increases with temperature-induced spreading of neighboring atoms to shorter and longer distances due to the anharmonic nature of the interatomic interaction potential. These findings shed light on the first-shell expansion/contraction paradox for metallic liquids, aside from possible changes in local topological or chemical short-range ordering. The melts of covalent materials are found to exhibit an opposite trend of peak shift, which is attributed to an effect of the directionality of the interatomic bonds. read less NOT USED (high confidence) J. R. Bordin, L. B. Krott, and M. Barbosa, “Surface Phase Transition in Anomalous Fluid in Nanoconfinement,” arXiv: Soft Condensed Matter. 2014. link Times cited: 30 Abstract: We explore by molecular dynamic simulations the thermodynami… read moreAbstract: We explore by molecular dynamic simulations the thermodynamical behavior of an anomalous fluid confined inside rigid and flexible nanopores. The fluid is modeled by a two length scale potential. In the bulk this system exhibits the density and diffusion anomalous behavior observed in liquid water. We show that the anomalous fluid confined inside rigid and flexible nanopores forms layers. As the volume of the nanopore is decreased the rigid surface exhibits three consecutive first order phase transitions associated with the change in the number of layers. These phase transitions are not present for flexible confinement. Our results indicate that the nature of confinement is relevant for the properties of the confined liquid what suggests that confinement in carbon nanotubes should be quite different from confinement in biological channels. read less NOT USED (high confidence) X. A. Deng, Y. Song, J. Li, and Y. Pu, “Parametrization of the Stillinger-Weber potential for Si/N/H system and its application to simulations of silicon nitride film deposition with SiH4/NH3,” Journal of Applied Physics. 2014. link Times cited: 1 Abstract: We determined the Stillinger-Weber interatomic potential par… read moreAbstract: We determined the Stillinger-Weber interatomic potential parameters for Si/N/H system based on first principles density functional calculations. This new potential can be used to perform classical molecular dynamics simulation for silicon nitride deposition on Si substrate. During the first principles calculations, cluster models have been carefully and systematically chosen to make sampling of the interatomic potential supersurface more thoroughly. Global optimization method was used to fit the ab initio data into Stillinger-Weber form. We used a recursive method to perform the classical molecular dynamics simulations for silicon nitride (SiN) film growth on Si substrate with SiH4/NH3 gas mixtures. During the simulation, we could clearly observe the silicon nitride film growth progress. In this paper, we present the details of potential derivation and simulation results with different SiH4:NH3 ratios. It is demonstrated that this new potential is suitable to describe the surface reactions of the Si/N/H s... read less NOT USED (high confidence) Y. Shi, J. Luo, F. Yuan, and L. Huang, “Intrinsic ductility of glassy solids,” Journal of Applied Physics. 2014. link Times cited: 68 Abstract: Glasses are usually brittle, seriously limiting their practi… read moreAbstract: Glasses are usually brittle, seriously limiting their practical usage. Recently, the intrinsic ductility of glass was found to increase with the Poisson's ratio (v), with a sharp brittle-to-ductile (BTD) transition at vBTD = 0.31-0.32. Such a correlation between far-from-equilibrium fracture and near-equilibrium elasticity is unexpected and not understood. Molecular dynamics simulations, on three families of glasses (metallic glasses, amorphous silicon, and silica) with controlled bonding, processing, and testing conditions, show that glasses with low covalency and high structural disorder have high v and ductility, and vice versa. The BTD transitions triggered by the aforementioned causes in each system correspond to a unified vBTD value, which increases with its average coordination number (CN). The vBTD-CN relation can be comprehended by recognizing v as a measure of covalency and disorder, and the BTD transition as a competition between shear and cleavage. Our results provide guidelines for developing... read less NOT USED (high confidence) S. Sengupta, V. V. Vasisht, and S. Sastry, “Diffusivity anomaly in modified Stillinger-Weber liquids.,” The Journal of chemical physics. 2014. link Times cited: 10 Abstract: By modifying the tetrahedrality (the strength of the three b… read moreAbstract: By modifying the tetrahedrality (the strength of the three body interactions) in the well-known Stillinger-Weber model for silicon, we study the diffusivity of a series of model liquids as a function of tetrahedrality and temperature at fixed pressure. Previous work has shown that at constant temperature, the diffusivity exhibits a maximum as a function of tetrahedrality, which we refer to as the diffusivity anomaly, in analogy with the well-known anomaly in water upon variation of pressure at constant temperature. We explore to what extent the structural and thermodynamic changes accompanying changes in the interaction potential can help rationalize the diffusivity anomaly, by employing the Rosenfeld relation between diffusivity and the excess entropy (over the ideal gas reference value), and the pair correlation entropy, which provides an approximation to the excess entropy in terms of the pair correlation function. We find that in the modified Stillinger-Weber liquids, the Rosenfeld relation works well above the melting temperatures but exhibits deviations below, with the deviations becoming smaller for smaller tetrahedrality. Further we find that both the excess entropy and the pair correlation entropy at constant temperature go through maxima as a function of the tetrahedrality, thus demonstrating the close relationship between structural, thermodynamic, and dynamical anomalies in the modified Stillinger-Weber liquids. read less NOT USED (high confidence) T. Hofer, “Perspectives for hybrid ab initio/molecular mechanical simulations of solutions: from complex chemistry to proton-transfer reactions and interfaces,” Pure and Applied Chemistry. 2014. link Times cited: 29 Abstract: As a consequence of the ongoing development of enhanced comp… read moreAbstract: As a consequence of the ongoing development of enhanced computational resources, theoretical chemistry has become an increasingly valuable field for the investigation of a variety of chemical systems. Simulations employing a hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) technique have been shown to be a particularly promising approach, whenever ultrafast (i.e., picosecond) dynamical properties are to be studied, which are in many cases difficult to access via experimental techniques. Details of the quantum mechanical charge field (QMCF) ansatz, an advanced QM/MM protocol, are discussed and simulation results for various systems ranging from simple ionic hydrates to solvated organic molecules and coordination complexes in solution are presented. A particularly challenging application is the description of proton-transfer reactions in chemical simulations, which is a prerequisite to study acidified and basic systems. The methodical requirements for a combination of the QMCF methodology with a dissociative potential model for the description of the solvent are discussed. Furthermore, the possible extension of QM/MM approaches to solid/liquid interfaces is outlined. read less NOT USED (high confidence) A. Pham, M. Barisik, and B. H. Kim, “Pressure dependence of Kapitza resistance at gold/water and silicon/water interfaces.,” The Journal of chemical physics. 2013. link Times cited: 64 Abstract: We conducted non-equilibrium molecular dynamics simulations … read moreAbstract: We conducted non-equilibrium molecular dynamics simulations to investigate Kapitza length at solid/liquid interfaces under the effects of bulk liquid pressures. Gold and silicon were utilized as hydrophilic and hydrophobic solid walls with different wetting surface behaviors, while the number of confined liquid water molecules was adjusted to obtain different pressures inside the channels. The interactions of solid/liquid couples were reparameterized accurately by measuring the water contact angle of solid substrates. In this paper, we present a thorough analysis of the structure, normal stress, and temperature distribution of liquid water to elucidate thermal energy transport across interfaces. Our results demonstrate excellent agreement between the pressures of liquid water in nano-channels and published thermodynamics data. The pressures measured as normal stress components were characterized using a long cut-off distance reinforced by a long-range van der Waals tail correction term. To clarify the effects of bulk liquid pressures on water structure at hydrophilic and hydrophobic solid surfaces, we defined solid/liquid interface spacing as the distance between the surface and the peak value of the first water density layer. Near the gold surface, we found that interface spacing and peak value of first water density layer were constant and did not depend on bulk liquid pressure; near the silicon surface, those values depended directly upon bulk liquid. Our results reveal that the pressure dependence of Kapitza length strongly depends on the wettability of the solid surface. In the case of the hydrophilic gold surface, Kapitza length was stable despite increasing bulk liquid pressure, while it varied significantly at the hydrophobic silicon surface. read less NOT USED (high confidence) C. Ricolleau, Y. Bouar, H. Amara, O. Landon-Cardinal, and D. Alloyeau, “Random vs realistic amorphous carbon models for high resolution microscopy and electron diffraction,” Journal of Applied Physics. 2013. link Times cited: 21 Abstract: Amorphous carbon and amorphous materials in general are of p… read moreAbstract: Amorphous carbon and amorphous materials in general are of particular importance for high resolution electron microscopy, either for bulk materials, generally covered with an amorphous layer when prepared by ion milling techniques, or for nanoscale objects deposited on amorphous substrates. In order to quantify the information of the high resolution images at the atomic scale, a structural modeling of the sample is necessary prior to the calculation of the electron wave function propagation. It is thus essential to be able to reproduce the carbon structure as close as possible to the real one. The approach we propose here is to simulate a realistic carbon from an energetic model based on the tight-binding approximation in order to reproduce the important structural properties of amorphous carbon. At first, we compare this carbon with the carbon obtained by randomly generating the carbon atom positions. In both cases, we discuss the limit thickness of the phase object approximation. In a second step, we show the influence of both carbons models on (i) the contrast of Cu, Ag, and Au single atoms deposited on carbon and (ii) the determination of the long-range order parameter in CoPt bimetallic nanoalloys. read less NOT USED (high confidence) C. Becker, F. Tavazza, Z. Trautt, and R. B. D. Macedo, “Considerations for choosing and using force fields and interatomic potentials in materials science and engineering,” Current Opinion in Solid State & Materials Science. 2013. link Times cited: 196 NOT USED (high confidence) V. Kazimirov, A. Yakovenko, A. Muratov, A. Roik, and V. Sokol’skii, “X-ray diffraction study of Al-Si melts,” Journal of Structural Chemistry. 2013. link Times cited: 6 NOT USED (high confidence) D. Belashchenko, “Computer simulation of liquid metals,” Physics—Uspekhi. 2013. link Times cited: 84 Abstract: Methods for and the results of the computer simulation of li… read moreAbstract: Methods for and the results of the computer simulation of liquid metals are reviewed. Two basic methods, classical molecular dynamics with known interparticle potentials and the ab initio method, are considered. Most attention is given to the simulated results obtained using the embedded atom model (EAM). The thermodynamic, structural, and diffusion properties of liquid metal models under normal and extreme (shock) pressure conditions are considered. Liquid-metal simulated results for the Groups I–IV elements, a number of transition metals, and some binary systems (Fe–C, Fe–S) are examined. Possibilities for the simulation to account for the thermal contribution of delocalized electrons to energy and pressure are considered. Solidification features of supercooled metals are also discussed. read less NOT USED (high confidence) K. Raleva and D. Vasileska, “The importance of thermal conductivity modeling for simulations of self-heating effects in FD SOI devices,” Journal of Computational Electronics. 2013. link Times cited: 5 NOT USED (high confidence) K. Raleva and D. Vasileska, “The importance of thermal conductivity modeling for simulations of self-heating effects in FD SOI devices,” Journal of Computational Electronics. 2013. link Times cited: 0 NOT USED (high confidence) C. D. Cruz, N. A. Katcho, N. Mingo, and R. Veiga, “Thermal conductivity of nanocrystalline SiGe alloys using molecular dynamics simulations,” Journal of Applied Physics. 2013. link Times cited: 14 Abstract: We have studied the effect of nanocrystalline microstructure… read moreAbstract: We have studied the effect of nanocrystalline microstructure on the thermal conductivity of SiGe alloys using molecular dynamics simulations. Nanograins are modeled using both the coincidence site lattice and the Voronoi tessellation methods, and the thermal conductivity is computed using the Green-Kubo formalism. We analyze the dependence of the thermal conductivity with temperature, grain size L, and misorientation angle. We find a power dependence of L1/4 of the thermal conductivity with the grain size, instead of the linear dependence shown by non-alloyed nanograined systems. This dependence can be derived analytically underlines the important role that disorder scattering plays even when the grains are of the order of a few nm. This is in contrast to non-alloyed systems, where phonon transport is governed mainly by the boundary scattering. The temperature dependence is weak, in agreement with experimental measurements. The effect of angle misorientation is also small, which stresses the main role pla... read less NOT USED (high confidence) U. Monteverde, M. Migliorato, J. Pal, and D. Powell, “Elastic and vibrational properties of group IV semiconductors in empirical potential modelling,” Journal of Physics: Condensed Matter. 2013. link Times cited: 8 Abstract: We have developed an interatomic potential that with a singl… read moreAbstract: We have developed an interatomic potential that with a single set of parameters is able to accurately describe at the same time the elastic, vibrational and thermodynamics properties of semiconductors. The simultaneous inclusion of radial and angular forces of the interacting atom pairs (short range) together with the influence of the broken crystal symmetry when the atomic arrangement is out of equilibrium (long range) results in correct predictions of all of the phonon dispersion spectrum and mode-Grüneisen parameters of silicon and germanium. The long range interactions are taken into account up to the second nearest neighbours, to correctly influence the elastic and vibrational properties, and therefore represent only a marginal computational cost compared to the full treatment of other proposed potentials. Results of molecular dynamics simulations are compared with those of ab initio calculations, showing that when our proposed potential is used to perform the initial stages of the structural relaxation, a significant reduction of the computational time needed during the geometry optimization of density functional theory simulations is observed. read less NOT USED (high confidence) Y. Jing, M. Hu, and L. Guo, “Thermal conductivity of hybrid graphene/silicon heterostructures,” Journal of Applied Physics. 2013. link Times cited: 23 Abstract: The success of fabricating single layer graphene and silicon… read moreAbstract: The success of fabricating single layer graphene and silicon nanofilm (could be as thin as single layer so far) has triggered enormous interest in exploring their unique physics and novel applications. An intuitive idea is to investigate what happens if we construct a heterostructure composed of these two sheets. In this paper, we perform nonequilibrium molecular dynamics simulations to systematically investigate the in-plane thermal transport in graphene/silicon/graphene (Gr/Si/Gr) heterostructures. The effects of Si film thickness, interfacial interaction strength, and length on the thermal conductivity of the Gr/Si/Gr heterostructures are explicitly considered. Our simulations identify a unified scaling law for thickness dependence of thermal conductivity of the Gr/Si/Gr heterostructures, despite different interfacial interaction forms are used (weak van der Waals interaction and strong covalent bonding). By quantifying relative contribution from phonon polarizations and defining heat flux onto single ... read less NOT USED (high confidence) C. Várnai, N. Bernstein, L. Mones, and G. Csányi, “Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.,” The journal of physical chemistry. B. 2013. link Times cited: 21 Abstract: We present reaction free energy calculations using the adapt… read moreAbstract: We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions. read less NOT USED (high confidence) A. Soper, “Radical re-appraisal of water structure in hydrophilic confinement☆,” Chemical Physics Letters. 2013. link Times cited: 39 NOT USED (high confidence) V. Bocchetti, H. Diep, H. Enriquez, H. Oughaddou, and A. Kara, “Thermal stability of standalone silicene sheet,” Journal of Physics: Conference Series. 2013. link Times cited: 14 Abstract: Extensive Monte Carlo simulations are carried out to study t… read moreAbstract: Extensive Monte Carlo simulations are carried out to study thermal stability of an infinite standalone silicon sheet. We used the Tersoff potential that has been used with success for silicon at low temperatures. However, the melting temperature Tm calculated with the original parameters provided by Tersoff is too high with respect to the experimental one. Agrawal, Raff and Komanduri have proposed a modified set of parameters to reduce Tm. For comparison, we have used these two sets of parameters to study the stability and the melting of a standalone 2D sheet of silicon called "silicene", by analogy with graphene for the carbon sheet. We find that 2D crystalline silicene is stable up to a high temperature unlike in 2D systems with isotropic potentials such as Lennard-Jones. The differences in the obtained results using two sets of parameters are striking. read less NOT USED (high confidence) J. Kermode, L. Ben-Bashat, F. Atrash, J. Cilliers, D. Sherman, and A. D. Vita, “Macroscopic scattering of cracks initiated at single impurity atoms,” Nature Communications. 2013. link Times cited: 49 NOT USED (high confidence) T. Aoki, “Molecular dynamics simulations of cluster impacts on solid targets: implantation, surface modification, and sputtering,” Journal of Computational Electronics. 2013. link Times cited: 31 NOT USED (high confidence) I. Saika-Voivod, F. Smallenburg, and F. Sciortino, “Understanding tetrahedral liquids through patchy colloids.,” The Journal of chemical physics. 2013. link Times cited: 37 Abstract: We investigate the structural properties of a simple model f… read moreAbstract: We investigate the structural properties of a simple model for tetrahedral patchy colloids in which the patch width and the patch range can be tuned independently. For wide bond angles, a fully bonded network can be generated by standard Monte Carlo or molecular dynamics simulations of the model, providing a good method for generating defect-free random tetrahedral networks. This offers the possibility of focusing on the role of the patch angular width on the structure of the fully bonded network. The analysis of the fully bonded configurations as a function of the bonding angle shows how the bonding angle controls the system compressibility, the strength of the pre-peak in the structure factor, and ring size distribution. Comparison with models of liquid water and silica allows us to find the best mapping between these continuous potentials and the colloidal one. Building on previous studies focused on the connection between angular range and crystallization, the mapping makes it possible to shed new light on the glass-forming ability of network-forming tetrahedral liquids. read less NOT USED (high confidence) F. Zipoli, T. Laino, S. Stolz, E. Martin, C. Winkelmann, and A. Curioni, “Improved coarse-grained model for molecular-dynamics simulations of water nucleation.,” The Journal of chemical physics. 2013. link Times cited: 14 Abstract: We developed a new coarse-grained (CG) model for water to st… read moreAbstract: We developed a new coarse-grained (CG) model for water to study nucleation of droplets from the vapor phase. The resulting potential has a more flexible functional form and a longer range cutoff compared to other CG potentials available for water. This allowed us to extend the range of applicability of coarse-grained techniques to nucleation phenomena. By improving the description of the interactions between water molecules in the gas phase, we obtained CG model that gives similar results than the all-atom (AA) TIP4P model but at a lower computational cost. In this work we present the validation of the potential and its application to the study of nucleation of water droplets from the supersaturated vapor phase via molecular-dynamics simulations. The computed nucleation rates at T = 320 K and 350 K at different supersaturations, ranging from 5 to 15, compare very well with AA TIP4P simulations and show the right dependence on the temperature compared with available experimental data. To help comparison with the experiments, we explored in detail the different ways to control the temperature and the effects on nucleation. read less NOT USED (high confidence) Z. Li, N. Mathew, and R. C. Picu, “Dependence of Peierls stress on lattice strains in silicon,” Computational Materials Science. 2013. link Times cited: 7 NOT USED (high confidence) P. Käshammer and T. Sinno, “Interactions of twin boundaries with intrinsic point defects and carbon in silicon,” Journal of Applied Physics. 2013. link Times cited: 22 Abstract: Although multicrystalline silicon (mc-Si) is currently the m… read moreAbstract: Although multicrystalline silicon (mc-Si) is currently the most widely used material for fabricating photovoltaic cells, its electrical properties remain limited by several types of defects, which interact in complex ways that are not yet fully understood. A particularly important phenomenon is the interaction between grain boundaries and intrinsic point defects or impurity atoms, such as carbon, oxygen, nitrogen, and various types of metals. Here, we use empirical molecular dynamics to study the interactions of Σ3{111}, Σ9{221}, and Σ27{552} twin boundaries, which account for over 50% of all grain boundaries in mc-Si, with self-interstitials, vacancies, and substitutional carbon atoms. It is shown that twin boundary-point defect interaction energies increase with twinning order and that they are predominantly attractive. We also find that twin boundary interactions with substitutional carbon are highly spatially heterogeneous, exhibiting alternating repulsive-attractive regions that correlate strongly wi... read less NOT USED (high confidence) B. Song and V. Molinero, “Thermodynamic and structural signatures of water-driven methane-methane attraction in coarse-grained mW water.,” The Journal of chemical physics. 2013. link Times cited: 49 Abstract: Hydrophobic interactions are responsible for water-driven pr… read moreAbstract: Hydrophobic interactions are responsible for water-driven processes such as protein folding and self-assembly of biomolecules. Microscopic theories and molecular simulations have been used to study association of a pair of methanes in water, the paradigmatic example of hydrophobic attraction, and determined that entropy is the driving force for the association of the methane pair, while the enthalpy disfavors it. An open question is to which extent coarse-grained water models can still produce correct thermodynamic and structural signatures of hydrophobic interaction. In this work, we investigate the hydrophobic interaction between a methane pair in water at temperatures from 260 to 340 K through molecular dynamics simulations with the coarse-grained monatomic water model mW. We find that the coarse-grained model correctly represents the free energy of association of the methane pair, the temperature dependence of free energy, and the positive change in entropy and enthalpy upon association. We investigate the relationship between thermodynamic signatures and structural order of water through the analysis of the spatial distribution of the density, energy, and tetrahedral order parameter Qt of water. The simulations reveal an enhancement of tetrahedral order in the region between the first and second hydration shells of the methane molecules. The increase in tetrahedral order, however, is far from what would be expected for a clathrate-like or ice-like shell around the solutes. This work shows that the mW water model reproduces the key signatures of hydrophobic interaction without long ranged electrostatics or the need to be re-parameterized for different thermodynamic states. These characteristics, and its hundred-fold increase in efficiency with respect to atomistic models, make mW a promising water model for studying water-driven hydrophobic processes in more complex systems. read less NOT USED (high confidence) M. I. Español, D. Kochmann, S. Conti, and M. Ortiz, “A Γ-Convergence Analysis of the Quasicontinuum Method,” Multiscale Model. Simul. 2013. link Times cited: 14 Abstract: We present a $\Gamma$-convergence analysis of the quasiconti… read moreAbstract: We present a $\Gamma$-convergence analysis of the quasicontinuum method focused on the behavior of the approximate energy functionals in the continuum limit of a harmonic and defect-free crystal. The analysis shows that, under general conditions of stability and boundedness of the energy, the continuum limit is attained provided that the continuum---e.g., finite-element---approximation spaces are strongly dense in an appropriate topology and provided that the lattice size converges to zero more rapidly than the mesh size. The equicoercivity of the quasicontinuum energy functionals is likewise established with broad generality, which, in conjunction with $\Gamma$-convergence, ensures the convergence of the minimizers. We also show under rather general conditions that, for interatomic energies having a clusterwise additive structure, summation or quadrature rules that suitably approximate the local element energies do not affect the continuum limit. Finally, we propose a discrete patch test that provides a ... read less NOT USED (high confidence) U. Monteverde, M. Migliorato, and D. Powell, “Atomistic modelling of elasticity and phonons in diamond and graphene,” 2013 13th International Conference on Numerical Simulation of Optoelectronic Devices (NUSOD). 2013. link Times cited: 0 Abstract: We present an atomistic interatomic potential that with a si… read moreAbstract: We present an atomistic interatomic potential that with a single set of parameters is able to accurately describe at the same time the elastic, vibrational and thermodynamics properties of semiconductors. We also show that the correct inclusion in the potential of short and long range interactions provides a model for the force field that accurately performs Static Dynamics and Molecular Dynamics. read less NOT USED (high confidence) D. Spiteri, J. Pomeroy, and M. Kuball, “Influence of microstructural defects on the thermal conductivity of GaN: A molecular dynamics study,” physica status solidi (b). 2013. link Times cited: 14 Abstract: The lattice thermal conductivity is known to depend on cryst… read moreAbstract: The lattice thermal conductivity is known to depend on crystal quality, but the reduction in thermal conductivity due to specific defects is presently unclear. Molecular dynamics simulations were used to investigate the impact of microstructural defects on the thermal conductivity of gallium nitride. The conductivity of a finite crystal was reduced to (39 ± 4)% by a screw dislocation density of 2.0 × 1013 cm−2 and to (51 ± 4)% by an edge dislocation of similar density, illustrating that the type of dislocation is important for thermal conductivity. The effect of stacking faults on thermal conductivity was also investigated. read less NOT USED (high confidence) E. Lampin, P. Palla, P. A. Francioso, and F. Cleri, “Thermal conductivity from approach-to-equilibrium molecular dynamics,” Journal of Applied Physics. 2013. link Times cited: 81 Abstract: We use molecular dynamics simulations to study the thermal t… read moreAbstract: We use molecular dynamics simulations to study the thermal transport properties of a range of poor to good thermal conductors by a method in which two portions are delimited and heated at two different temperatures before the approach-to-equilibrium in the whole structure is monitored. The numerical results are compared to the corresponding solution of the heat equation. Based on this comparison, the observed exponential decay of the temperature difference is interpreted and used to extract the thermal conductivity of homogeneous materials. The method is first applied to bulk silicon and an excellent agreement with previous calculations is obtained. Finally, we predict the thermal conductivity of germanium and α-quartz. read less NOT USED (high confidence) J. Welker, A. J. Weymouth, and F. Giessibl, “The influence of chemical bonding configuration on atomic identification by force spectroscopy.,” ACS nano. 2013. link Times cited: 31 Abstract: The force between two atoms depends not only on their chemic… read moreAbstract: The force between two atoms depends not only on their chemical species and distance, but also on the configuration of their chemical bonds to other atoms. This strongly affects atomic force spectroscopy, in which the force between the tip of an atomic force microscope and a sample is measured as a function of distance. We show that the short-range forces between tip and sample atoms depend strongly on the configuration of the tip, to the point of preventing atom identification with a poorly defined tip. Our solution is to control the tip apex before using it for spectroscopy. We demonstrate a method by which a CO molecule on Cu can be used to characterize the tip. In combination with gentle pokes, this can be used to engineer a specific tip apex. This CO Front atom Identification (COFI) method allows us to use a well-defined tip to conduct force spectroscopy. read less NOT USED (high confidence) G. Norman and V. Stegailov, “Stochastic theory of the classical molecular dynamics method,” Mathematical Models and Computer Simulations. 2013. link Times cited: 137 NOT USED (high confidence) J. Larkin and A. McGaughey, “Predicting alloy vibrational mode properties using lattice dynamics calculations, molecular dynamics simulations, and the virtual crystal approximation,” Journal of Applied Physics. 2013. link Times cited: 62 Abstract: The virtual crystal (VC) approximation for mass disorder is … read moreAbstract: The virtual crystal (VC) approximation for mass disorder is evaluated by examining two model alloy systems: Lennard-Jones argon and Stillinger-Weber silicon. In both material systems, the perfect crystal is alloyed with a heavier mass species up to equal concentration. The analysis is performed using molecular dynamics simulations and lattice dynamics calculations. Mode frequencies and lifetimes are first calculated by treating the disorder explicitly and under the VC approximation, with differences found in the high-concentration alloys at high frequencies. Notably, the lifetimes of high-frequency modes are underpredicted using the VC approximation, a result we attribute to the neglect of higher-order terms in the model used to include point-defect scattering. The mode properties are then used to predict thermal conductivity under the VC approximation. For the Lennard-Jones alloys, where high-frequency modes make a significant contribution to thermal conductivity, the high-frequency lifetime underprediction leads to an underprediction of thermal conductivity compared to predictions from the Green-Kubo method, where no assumptions about the thermal transport are required. Based on observations of a minimum mode diffusivity, we propose a correction that brings the VC approximation thermal conductivities into better agreement with the Green-Kubo values. For the Stillinger-Weber alloys, where the thermal conductivity is dominated by low-frequency modes, the high-frequency lifetime underprediction does not affect the thermal conductivity prediction and reasonable agreement is found with the Green-Kubo values. read less NOT USED (high confidence) A. N. Karpov, E. M. Trukhanov, and N. Shwartz, “Modeling of misft dislocation creation at Ge island — Si(111) substrate interface,” 2013 14th International Conference of Young Specialists on Micro/Nanotechnologies and Electron Devices. 2013. link Times cited: 0 Abstract: The sizes of Ge island on Si(111) surface corresponding to i… read moreAbstract: The sizes of Ge island on Si(111) surface corresponding to introduction of misft dislocation were determined by modeling. The critical thickness of pseudomorphic Ge layer was demonstrated to be 2 bilayers with lateral island size exceeded 60 nm when creation of misft dislocations became energy-favorable. read less NOT USED (high confidence) B. H. Kim, “Interface thermal resistance modeling of the silicon-argon interface,” International Journal of Precision Engineering and Manufacturing. 2013. link Times cited: 12 NOT USED (high confidence) M. Hejna, P. Steinhardt, and S. Torquato, “Nearly hyperuniform network models of amorphous silicon,” Physical Review B. 2013. link Times cited: 48 Abstract: We introduce the concept of nearly hyperuniform network (NHN… read moreAbstract: We introduce the concept of nearly hyperuniform network (NHN) structures as alternatives to the conventional continuous random network (CRN) models for amorphous tetrahedrally coordinated solids, such as amorphous silicon (a-Si). A hyperuniform solid has a structure factor $S(k)$ that approaches zero as the wavenumber $k\ensuremath{\rightarrow}0$. We define a NHN as an amorphous network whose structure factor $S(k\ensuremath{\rightarrow}0)$ is smaller than the liquid value at the melting temperature. Using a novel implementation of the Stillinger-Weber potential for the interatomic interactions, we show that the energy landscape for a spectrum of NHNs includes a sequence of local minima with an increasing degree of hyperuniformity [smaller $S(k\ensuremath{\rightarrow}0)$] that is significantly below the frozen-liquid value and that correlates with other measurable features in $S(k)$ at intermediate and large $k$ and with the width of the electronic band gap. read less NOT USED (high confidence) J. R. Srour and J. W. Palko, “Displacement Damage Effects in Irradiated Semiconductor Devices,” IEEE Transactions on Nuclear Science. 2013. link Times cited: 154 Abstract: A review of radiation-induced displacement damage effects in… read moreAbstract: A review of radiation-induced displacement damage effects in semiconductor devices is presented, with emphasis placed on silicon technology. The history of displacement damage studies is summarized, and damage production mechanisms are discussed. Properties of defect clusters and isolated defects are addressed. Displacement damage effects in materials and devices are considered, including effects produced in silicon particle detectors, visible imaging arrays, and solar cells. Additional topics examined include NIEL scaling, carrier concentration changes, random telegraph signals, radiation hardness assurance, and simulation methods for displacement damage. Areas needing further study are noted. read less NOT USED (high confidence) Q. Lu, J. Meng, W. Song, Y. Mu, and J. Wan, “Stuffing Enhances the Stability of Medium-Sized (GaAs)n Clusters,” Journal of Physical Chemistry C. 2013. link Times cited: 7 Abstract: The structure and properties of medium-sized (GaAs)n cluster… read moreAbstract: The structure and properties of medium-sized (GaAs)n clusters (n = 18–36) were investigated using density functional theory with the generalized gradient approximation. In general, stuffed topologies are the lowest energy states. Tubular and other cage-like structures are less energetically preferable. Structural transition from cages to stuffed topologies occurred at an approximate size of n = 20. In addition, the binding energy per unit, the highest occupied molecular orbital and the lowest unoccupied molecular orbital gaps, the density of states, and infrared spectra were investigated. read less NOT USED (high confidence) J. Solomon, P. Chung, D. Srivastava, and E. F. Darve, “Method and Advantages of Genetic Algorithms in Parameterization of Interatomic Potentials: Metal-Oxides,” arXiv: Materials Science. 2013. link Times cited: 14 NOT USED (high confidence) T. Zohdi, “Electromagnetically-Induced Vibration in Particulate-Functionalized Materials,” Journal of Vibration and Acoustics. 2013. link Times cited: 7 Abstract: In many small-scale devices, the materials employed are func… read moreAbstract: In many small-scale devices, the materials employed are functionalized (doped) withmicroscale and/or nanoscale particles, in order to deliver desired overall dielectric prop-erties. In this work, we develop a reduced-order lumped-mass model to characterize thedynamic response of a material possessing a microstructure that is comprised of anelectromagnetically-neutral binder with embedded electromagnetically-sensitive(charged) particles. In certain industrial applications, such materials may encounterexternal electrical loading that can be highly oscillatory. Therefore, it is possible for theforcing frequencies to activate the inherent resonant frequencies of these micro- andnanostructures. In order to extract qualitative information, this paper first analyticallyinvestigates the mechanical and electromagnetic (cyclotronic) contributions to thedynamic response for a single particle, and then quantitatively investigates the responseof a model problem consisting of a coupled multiparticle periodic array, via numericalsimulation, using an implicit temporally-adaptive trapezoidal time-stepping scheme. Forthe model problem, numerical studies are conducted to observe the cyclotronically-dominated resonant frequency and associated beat phenomena, which arises due to thepresence of mechanical and electromagnetic harmonics in the material system.[DOI: 10.1115/1.4023251]Keywords: particulate composites, electromagnetics, vibration read less NOT USED (high confidence) B. H. Kim, “Interface thermal resistance modeling of the silicon-argon interface,” International Journal of Precision Engineering and Manufacturing. 2013. link Times cited: 0 NOT USED (high confidence) J. J. Möller, A. Prakash, and E. Bitzek, “FE2AT—finite element informed atomistic simulations,” Modelling and Simulation in Materials Science and Engineering. 2013. link Times cited: 17 Abstract: Atomistic simulations play an important role in advancing ou… read moreAbstract: Atomistic simulations play an important role in advancing our understanding of the mechanical properties of materials. Currently, most atomistic simulations are performed using relatively simple geometries under homogeneous loading conditions, and a significant part of the computer time is spent calculating the elastic response of the material, while the focus of the studies lies usually on the mechanisms of plastic deformation and failure. Here we present a simple but versatile approach called FE2AT to use finite element calculations to provide appropriate initial and boundary conditions for atomistic simulations. FE2AT allows us to forgo the simulation of large parts of the elastic loading process, even in the case of complex sample geometries and loading conditions. FE2AT is open source and can be used in combination with different atomistic simulation codes and methods. Its application is demonstrated using the bending of a nano-beam and the determination of the displacement field around a crack tip as examples. read less NOT USED (high confidence) A. Matsuda, Y. Nakakubo, Y. Takao, K. Eriguchi, and K. Ono, “Atomistic simulations of plasma process-induced Si substrate damage - Effects of substrate bias-power frequency,” Proceedings of 2013 International Conference on IC Design & Technology (ICICDT). 2013. link Times cited: 9 Abstract: Plasma-induced defect generation process in crystalline Si s… read moreAbstract: Plasma-induced defect generation process in crystalline Si structure was simulated by classical molecular dynamics simulations. Energy distribution functions of Ar and Cl ions incident on the Si surface (IEDF) were implemented to predict the impacts on the defect generation processes in present-day plasma process equipments. The damaged-layer thickness was confirmed to be a weak function of IEDF, which are consistent with a binary-collision-based range model and experimental results. In the case of “fin-gate structure”, the simulation results predict that the sidewall may be damaged not by the incident angular distribution of ions but by the straggling of high-energy ions near the reaction surface, which leads to an on-current degradation of FinFETs. read less NOT USED (high confidence) T. Hori, T. Shiga, and J. Shiomi, “Phonon transport analysis of silicon germanium alloys using molecular dynamics simulations,” Journal of Applied Physics. 2013. link Times cited: 25 Abstract: The phonon transport properties and the lattice thermal cond… read moreAbstract: The phonon transport properties and the lattice thermal conductivity of silicon germanium alloy crystals have been investigated based on phonon gas model by using classical molecular dynamics simulations. The attenuation of the mode-dependent phonon relaxation time due to alloying and its dependence on the alloy fraction were quantified by projecting the molecular dynamics phase space trajectory onto the normal mode of the alloyed crystal. By empirically approximating the group velocities from the extended dispersion relations, the lattice thermal conductivity was calculated based on the phonon gas model under relaxation time approximation. The obtained reduction in the lattice thermal conductivity caused by alloying agrees well with that of the experiment and direct non-equilibrium molecular dynamics calculations. The phonon-mean-free-path dependent contribution to thermal conductivity suggests that the effect of nanostructuring can have non-monotonic dependence on the alloy fraction. read less NOT USED (high confidence) A. H. Nguyen and V. Molinero, “Stability and metastability of bromine clathrate polymorphs.,” The journal of physical chemistry. B. 2013. link Times cited: 23 Abstract: Clathrate hydrates are crystals in which water forms a netwo… read moreAbstract: Clathrate hydrates are crystals in which water forms a network of fully hydrogen-bonded polyhedral cages that contain small guests. Clathrate hydrates occur mostly in two cubic crystal polymorphs, sI and sII. Bromine is one of two guests that yield a hydrate with the tetragonal structure (TS), the topological dual of the Frank-Kasper σ phase. There has been a long-standing disagreement on whether bromine hydrate also forms metastable sI and sII crystals. To date there are no data on the thermodynamic range of stability (e.g., the melting temperatures) of the metastable polymorphs. Here we use molecular dynamics simulations with the coarse-grained model of water mW to (i) investigate the thermodynamic stability of the empty and guest-filled the sI, sII, TS, and HS-I hydrate polymorphs, (ii) develop a coarse-grained model of bromine compatible with mW water, and (iii) evaluate the stability of the bromine hydrate polymorphs. The mW model predicts the same relative energy of the empty clathrate polymorphs and the same phase diagram as a function of water-guest interaction than the fully atomistic TIP4P water model. There is a narrow region in water-guest parameter space for which TS is marginally more stable than sI or sII. We parametrize a coarse-grained model of bromine compatible with mW water and use it to determine the order of stability of the bromine hydrate polymorphs. The melting temperatures of the bromine hydrate polymorphs predicted by the coarse-grained model are 281 ± 1 K for TS, 279 ± 1 K for sII, and 276 ± 1 K for sI. The closeness of the melting temperatures supports the plausibility of formation of metastable sII and sI bromine hydrates. read less NOT USED (high confidence) J. C. Castro-Palacio, L. Velazquez-Abad, M. Fernández, and J. Q. Cuador-Gil, “Molecular dynamics study of one dimensional nanoscale Si/SiO2 interfaces,” The European Physical Journal D. 2013. link Times cited: 1 NOT USED (high confidence) D. T. Limmer and D. Chandler, “Corresponding states for mesostructure and dynamics of supercooled water.,” Faraday discussions. 2013. link Times cited: 36 Abstract: Water famously expands upon freezing, foreshadowed by a nega… read moreAbstract: Water famously expands upon freezing, foreshadowed by a negative coefficient of expansion of the liquid at temperatures close to its freezing temperature. These behaviors, and many others, reflect the energetic preference for local tetrahedral arrangements of water molecules and entropic effects that oppose it. Here, we provide theoretical analysis of mesoscopic implications of this competition, both equilibrium and non-equilibrium, including mediation by interfaces. With general scaling arguments bolstered by simulation results, and with reduced units that elucidate corresponding states, we derive a phase diagram for bulk and confined water and water-like materials. For water itself, the corresponding states cover the temperature range of 150 K to 300 K and the pressure range of 1 bar to 2 kbar. In this regime, there are two reversible condensed phases - ice and liquid. Out of equilibrium, there is irreversible polyamorphism, i.e., more than one glass phase, reflecting dynamical arrest of coarsening ice. Temperature-time plots are derived to characterize time scales of the different phases and explain contrasting dynamical behaviors of different water-like systems. read less NOT USED (high confidence) Z. Zhu, D. A. Romero, D. Sellan, A. Nabovati, and C. Amon, “Assessment of the Holland model for silicon phonon-phonon relaxation times using lattice dynamics calculations,” Journal of Applied Physics. 2013. link Times cited: 10 Abstract: We assess the ability of the Holland model to accurately pre… read moreAbstract: We assess the ability of the Holland model to accurately predict phonon-phonon relaxation times from bulk thermal conductivity values. First, lattice dynamics calculations are used to obtain phonon-phonon relaxation times and thermal conductivities for temperatures ranging from 10 K to 1000 K for Stillinger-Weber silicon. The Holland model is then fitted to these thermal conductivities and used to predict relaxation times, which are compared to the relaxation times obtained by lattice dynamics calculations. We find that fitting the Holland model to both total and mode-dependent thermal conductivities does not result in accurate mode-dependent phonon-phonon relaxation times. Introduction of Umklapp scattering for longitudinal modes resulted in improved prediction of mode-dependent relative contributions to thermal conductivity, especially at high temperatures. However, assumptions made by Holland regarding the frequency-dependence of phonon scattering mechanisms are found to be inconsistent with lattice dynamics data. Instead, we introduce a simple method based on using cumulative thermal conductivity functions to obtain better predictions of the frequency-dependence of relaxation times.We assess the ability of the Holland model to accurately predict phonon-phonon relaxation times from bulk thermal conductivity values. First, lattice dynamics calculations are used to obtain phonon-phonon relaxation times and thermal conductivities for temperatures ranging from 10 K to 1000 K for Stillinger-Weber silicon. The Holland model is then fitted to these thermal conductivities and used to predict relaxation times, which are compared to the relaxation times obtained by lattice dynamics calculations. We find that fitting the Holland model to both total and mode-dependent thermal conductivities does not result in accurate mode-dependent phonon-phonon relaxation times. Introduction of Umklapp scattering for longitudinal modes resulted in improved prediction of mode-dependent relative contributions to thermal conductivity, especially at high temperatures. However, assumptions made by Holland regarding the frequency-dependence of phonon scattering mechanisms are found to be inconsistent with lattice dy... read less NOT USED (high confidence) G. K. Lockwood and S. Garofalini, “Lifetimes of excess protons in water using a dissociative water potential.,” The journal of physical chemistry. B. 2013. link Times cited: 33 Abstract: Molecular dynamics simulations using a dissociative water po… read moreAbstract: Molecular dynamics simulations using a dissociative water potential were applied to study transport of excess protons in water and determine the applicability of this potential to describe such behavior. While originally developed for gas-phase molecules and bulk liquid water, the potential is transferrable to nanoconfinement and interface scenarios. Applied here, it shows proton behavior consistent with ab initio calculations and empirical models specifically designed to describe proton transport. Both Eigen and Zundel complexes are observed in the simulations showing the Eigen-Zundel-Eigen-type mechanism. In addition to reproducing the short-time rattling of the excess proton between the two oxygens of Zundel complexes, a picosecond-scale lifetime was also found. These longer-lived H3O(+) ions are caused by the rapid conversion of the local solvation structure around the transferring proton from a Zundel-like form to an Eigen-like form following the transfer, effectively severing the path along which the proton can rattle. The migration of H(+) over long times (>100 ps) deviates from the conventional short-time multiexponentially decaying lifetime autocorrelation model and follows the t(-3/2) power-law behavior. The potential function employed here matches many of the features of proton transport observed in ab initio molecular dynamics simulations as well as the highly developed empirical valence bond models, yet is computationally very efficient, enabling longer time and larger systems to be studied. read less NOT USED (high confidence) Z. Li and R. C. Picu, “Shuffle-glide dislocation transformation in Si,” Journal of Applied Physics. 2013. link Times cited: 23 Abstract: The transformation of dislocation cores from the shuffle to … read moreAbstract: The transformation of dislocation cores from the shuffle to the glide set of {111} glide planes in Si is examined in this work. The transformation is thermally activated and is favored by a resolved shear stress which applies no force on the original perfect shuffle dislocation. A resolved shear stress driving dislocation motion in the glide plane is not observed to promote the transition. The stress-dependent activation energy for the described shuffle-glide transformation mechanism is evaluated using a statistical analysis. It is observed that the transformation is not associated with an intermediate metastable state, as has been previously suggested in the literature. read less NOT USED (high confidence) G. Xie et al., “Ultralow thermal conductivity in Si/GexSi1−x core-shell nanowires,” Journal of Applied Physics. 2013. link Times cited: 12 Abstract: By applying non-equilibrium molecular dynamics simulation, i… read moreAbstract: By applying non-equilibrium molecular dynamics simulation, it is demonstrated that the thermal conductivity of the reported Si/Ge core-shell nanowires (NWs) can be further reduced by shell doping. The thermal conductivity of Si/Ge0.6Si0.4 core-shell NWs is only about 66% of that of Si/Ge core-shell NWs. By analyzing the participation ratios of eigenmodes, it is revealed that the large reduction in the thermal conductivity of Si/Ge0.6Si0.4 core-shell NWs stems from the strong localization of the phonon modes from 1.0 THz to 2.0 THz and the modes from 9.0 THz to 16.0 THz due to both impurity scattering and interface scattering associated with peculiar structure of shell doped silicon NWs. read less NOT USED (high confidence) S. Ju and X.-gang Liang, “Investigation on interfacial thermal resistance and phonon scattering at twist boundary of silicon,” Journal of Applied Physics. 2013. link Times cited: 29 Abstract: Grain interfaces in nanocrystalline materials play a critica… read moreAbstract: Grain interfaces in nanocrystalline materials play a critical role in thermal transport. A series of twist boundary thermal resistances in silicon is investigated by the nonequilibrium molecular dynamics simulation so as to find the relationship between the boundary resistance, the twist angle, the boundary energy and temperature. The results indicate that the magnitude of the twist grain boundary (GB) thermal resistance is on the order of 10−9 m2 KW−1, and the GB thermal resistance becomes larger with increasing GB energy at most twist angles, and it drops obviously with increasing temperature. The phonon wave packet dynamic simulation shows that the transmission coefficient of the low frequency phonons with long wavelength is close to 100% at the boundary with different twist angles. The transmission coefficient of the longitudinal phonon wave packet decreases with increasing frequency and transverse phonons are produced due to the scattering. In most cases, higher grain boundary energy corresponds to lower transmission coefficient, leading to larger GB thermal resistance. read less NOT USED (high confidence) A. Weiss and T. Hofer, “Exploiting the capabilities of quantum chemical simulations to characterise the hydration of molecular compounds,” RSC Advances. 2013. link Times cited: 46 Abstract: Solvation phenomena have been the focus of experimental and … read moreAbstract: Solvation phenomena have been the focus of experimental and theoretical research for many decades. While the determination of solvation properties of mono-atomic, ionic species is already a challenging task, the associated difficulties are amplified in the case of molecular compounds. Theoretical approaches have the ability to yield manifold information of the investigated systems, providing that a reliable description of the interatomic energies and forces is employed. Hybrid quantum mechanical/molecular mechanical simulations constitute a particularly successful approach for the study of solvation phenomena, and have been employed in investigations of a variety of molecular compounds in aqueous solution. While an accurate description of these systems depends on the application of reliable, theoretical approaches, the analysis of the resulting dataset is a challenge of its own. It is outlined that standard means of analysis via pair correlation functions may yield an unspecific picture of hydration phenomena, and in some cases wrong conclusions on the hydration may be drawn. More advanced means of structural analysis are thus required as they yield manifold information on solvation phenomena since pair correlations are not sufficiently responsive in such cases. The theoretical approaches required to obtain a reliable description of the investigated systems as well as increasingly complex means of structural analysis ranging from two- and three-body correlations via angular-radial distributions and two-dimensional particle mapping to the so-called SLICE projections are discussed. The application of these analysis schemes is demonstrated for a variety of systems including mono- and polyatomic ionic solutes as well as molecular organic compounds, highlighting various aspects of the hydration of these species. read less NOT USED (high confidence) J. Schall and J. Harrison, “Reactive Bond-Order Potential for Si-, C-, and H-Containing Materials,” Journal of Physical Chemistry C. 2013. link Times cited: 8 Abstract: A new bond-order potential for modeling systems containing s… read moreAbstract: A new bond-order potential for modeling systems containing silicon, carbon, and hydrogen, such as organosilicon molecules (CxSiyHz), solid silicon, solid carbon, and alloys of silicon and carbon, is presented. This reactive potential utilizes the formalism of the second-generation reactive empirical bond-order potential (REBO) [Brenner et al. J. Phys.: Condens. Matter 2002, 14, 783] for hydrocarbons and the REBO parameters for silicon [Schall, Gao, Harrison. Phys. Rev. B 2008, 77, 115209]. Modifications to the hydrocarbon REBO potential were made to improve the description of three-atom type systems. The widespread use of Brenner’s REBO potential, its ability to model a wide range of hydrocarbon materials, and the existence of parameters for several atom types are some of the motivating factors for obtaining this Si–C–H (2B-SiCH) parametrization. The usefulness and flexibility of this potential is demonstrated by examining the properties of organosilicon molecules, the bulk, surface, and defect properties... read less NOT USED (high confidence) L. Pizzagalli et al., “A new parametrization of the Stillinger–Weber potential for an improved description of defects and plasticity of silicon,” Journal of Physics: Condensed Matter. 2013. link Times cited: 66 Abstract: A new parametrization of the widely used Stillinger–Weber po… read moreAbstract: A new parametrization of the widely used Stillinger–Weber potential is proposed for silicon, allowing for an improved modelling of defects and plasticity-related properties. The performance of the new potential is compared to the original version, as well as to another parametrization (Vink et al 2001 J. Non-Cryst. Solids, 282 248), in the case of several situations: point defects and dislocation core stability, threshold displacement energies, bulk shear, generalized stacking fault energy surfaces, fracture, melting temperature, amorphous structure, and crystalline phase stability. A significant improvement is obtained in the case of dislocation cores, bulk behaviour under high shear stress, the amorphous structure, and computation of threshold displacement energies, while most of the features of the original version (elastic constants, point defects) are retained. However, despite a slight improvement, a complex process like fracture remains difficult to model. read less NOT USED (high confidence) D. Ward, X. W. Zhou, B. M. Wong, F. Doty, and J. Zimmerman, “Analytical bond-order potential for the Cd-Zn-Te ternary system,” Physical Review B. 2012. link Times cited: 32 Abstract: CdTe/CdSe core/shell structured quantum dots do not suffer f… read moreAbstract: CdTe/CdSe core/shell structured quantum dots do not suffer from the defects typically seen in lattice-mismatched films and can therefore lead to improved solid-state lighting devices as compared to the multilayered structures (e.g., InxGa1–xN/GaN). To achieve these devices, however, the quantum dots must be optimized with respect to the structural details at an atomistic level. Molecular dynamics simulations are effective for exploring nano structures at a resolution unattainable by experimental techniques. To enable accurate molecular dynamics simulations of CdTe/CdSe core/shell structures, we have developed a full Cd–Te–Se ternary bond-order potential based on the analytical formalisms derived from quantum mechanical theories by Pettifor et al. A variety of elemental and compound configurations (with coordination varying from 1 to 12) including small clusters, bulk lattices, defects, and surfaces are explicitly considered during potential parametrization. More importantly, enormous iterations are perfor... read less NOT USED (high confidence) K. Fujiwara, K. Maeda, H. Koizumi, J. Nozawa, and S. Uda, “Effect of silicon/crucible interfacial energy on orientation of multicrystalline silicon ingot in unidirectional growth,” Journal of Applied Physics. 2012. link Times cited: 10 Abstract: We investigated the effects of the Si crystal/crucible and S… read moreAbstract: We investigated the effects of the Si crystal/crucible and Si melt/crucible interfacial energies on the orientation of the nucleus of multicrystalline Si during unidirectional growth. We calculated the Gibbs free energy upon nucleation on the crucible by considering the shape of the nucleus of the Si crystal and found that the nucleus with the 〈111〉 or 〈100〉 upper direction is stable. It was experimentally shown that {111} planes are dominant at the bottom of a multicrystalline Si ingot grown at a low rate, which was explained by the difference between the Si crystal/crucible and Si melt/crucible interfacial energies at nucleation. read less NOT USED (high confidence) P. Howell, “Comparison of molecular dynamics methods and interatomic potentials for calculating the thermal conductivity of silicon.,” The Journal of chemical physics. 2012. link Times cited: 74 Abstract: We compare the molecular dynamics Green-Kubo and direct meth… read moreAbstract: We compare the molecular dynamics Green-Kubo and direct methods for calculating thermal conductivity κ, using as a test case crystalline silicon at temperatures T in the range 500-1000 K (classical regime). We pay careful attention to the convergence with respect to simulation size and duration and to the procedures used to fit the simulation data. We show that in the Green-Kubo method the heat current autocorrelation function is characterized by three decay processes, of which the slowest lasts several tens of picoseconds so that convergence requires several tens of nanoseconds of data. Using the Stillinger-Weber potential we find excellent agreement between the two methods. We also use the direct method to calculate κ(T) for the Tersoff potential and find that the magnitude and the temperature-dependence are different for the two potentials and that neither potential agrees with experimental data. We argue that this implies that using the Stillinger-Weber or Tersoff potentials to predict trends in kappa as some system parameter is varied may yield results which are specific to the potential but not intrinsic to Si. read less NOT USED (high confidence) T. Zhu, J. Li, and S. Yip, “Atomistic Reaction Pathway Sampling: The Nudged Elastic Band Method and Nanomechanics Applications.” 2012. link Times cited: 15 Abstract: Two of the central recurring themes in nanomechanics are str… read moreAbstract: Two of the central recurring themes in nanomechanics are strength and plasticity [1–3]. They are naturally coupled because plastic deformation is a major strength-determining mechanism and understanding the resistance to deformation (strength) is a principal motivation for studying plasticity. Many phenomena of interest in mechanics can be discussed in the framework of microstructural evolution of a system where defects like cracks and dislocations are formed and evolve interactively. Microstructure evolution at the nanoscale is particularly relevant from the standpoint of probing unit processes of deformation, such as advancement of a crack front by a lattice unit or propagation of a dislocation core by a Burgers vector. These atomic-level details can reveal the mechanisms of deformation, which are the essential inputs to describing microstructure evolution at the mesoscale − the next length and time scales. This hierarchical relation is the essence of multiscale modeling and simulation paradigm [4–6]. The purpose of this chapter is to discuss the atomistic approach to describe the evolution of crystalline defects [1–3,6]. We focus on a method, which is becoming widely used, that allows one to track the microstructure evolution through the sampling of a read less NOT USED (high confidence) P. Moseley, J. Oswald, and T. Belytschko, “Adaptive atomistic‐to‐continuum modeling of propagating defects,” International Journal for Numerical Methods in Engineering. 2012. link Times cited: 25 Abstract: An adaptive atomistic‐to‐continuum method is presented for m… read moreAbstract: An adaptive atomistic‐to‐continuum method is presented for modeling the propagation of material defects. This method extends the bridging domain method to allow the atomic domain to dynamically conform to the evolving defect regions during a simulation, without introducing spurious oscillations and without requiring mesh refinement. The atomic domain expands as defects approach the bridging domain method coupling domain by fine graining nearby finite elements into equivalent atomistic subdomains. Additional algorithms coarse grain portions of the atomic domain to the continuum scale, reducing the degrees of freedom, when the atomic displacements in a subdomain can be approximated by FEM or extended FEM elements to within a certain homogeneity tolerance. The extended FEM approximations are created by fitting the broken inter‐atomic bonds of fractured surfaces and dislocation slip planes. Because atomic degrees of freedom are maintained only where needed for each timestep, the solution retains the advantages of multiscale modeling, with a reduced computational cost compared with other multiscale methods. Copyright © 2012 John Wiley & Sons, Ltd. read less NOT USED (high confidence) A. Kumar, M. Wilson, M. Thorpe, and M. Thorpe, “Amorphous graphene: a realization of Zachariasen’s glass,” Journal of Physics: Condensed Matter. 2012. link Times cited: 49 Abstract: Amorphous graphene is a realization of a two-dimensional Zac… read moreAbstract: Amorphous graphene is a realization of a two-dimensional Zachariasen glass as first proposed 80 years ago. Planar continuous random networks of this archetypal two-dimensional network are generated by two complementary simulation methods. In the first, a Monte Carlo bond switching algorithm is employed to systematically amorphize a crystalline graphene sheet. In the second, molecular dynamics simulations are utilized to quench from the high temperature liquid state. The two approaches lead to similar results as detailed here, through the pair distribution function and the associated diffraction pattern. Details of the structure, including ring statistics and angular distortions, are shown to be sensitive to preparation conditions, and await experimental confirmation. read less NOT USED (high confidence) Y. He, I. Savić, D. Donadio, and G. Galli, “Lattice thermal conductivity of semiconducting bulk materials: atomistic simulations.,” Physical chemistry chemical physics : PCCP. 2012. link Times cited: 105 Abstract: This paper presents a theoretical investigation of the micro… read moreAbstract: This paper presents a theoretical investigation of the microscopic mechanisms responsible for heat transport in bulk Si, Ge and SiGe alloys, with the goal of providing insight into design rules for efficient Si-based nanostructured thermoelectric semiconductors. We carried out a detailed atomistic study of the thermal conductivity, using molecular dynamics and the Boltzmann transport equation. We investigated in detail the effects of the physical approximations underlying each approach, as well as the effect of the numerical approximations involved in the implementation of the two different methods. Our findings permitted us to understand and reconcile apparently conflicting results reported in the literature. read less NOT USED (high confidence) T. Frolov and M. Asta, “Step free energies at faceted solid-liquid interfaces from equilibrium molecular dynamics simulations.,” The Journal of chemical physics. 2012. link Times cited: 15 Abstract: In this work a method is proposed for computing step free en… read moreAbstract: In this work a method is proposed for computing step free energies for faceted solid-liquid interfaces based on atomistic simulations. The method is demonstrated in an application to (111) interfaces in elemental Si, modeled with the classical Stillinger-Weber potential. The approach makes use of an adiabatic trapping procedure, and involves simulations of systems with coexisting solid and liquid phases separated by faceted interfaces containing islands with different sizes, for which the corresponding equilibrium temperatures are computed. We demonstrate that the calculated coexistence temperature is strongly affected by the geometry of the interface. We find that island radius is inversely proportional to superheating, allowing us to compute the step free energy by fitting simulation data within the formalism of classical nucleation theory. The step free energy value is computed to be γ(st) = 0.103 ± 0.005 × 10(-10) J/m. The approach outlined in this work paves the way to the calculation of step free energies relevant to the solidification of faceted crystals from liquid mixtures, as encountered in nanowire growth by the vapor-liquid-solid mechanism and in alloy casting. The present work also shows that at low undercoolings the Stillinger-Weber interatomic potential for Si tends to crystallize in the wurtzite, rather than the diamond-cubic structure. read less NOT USED (high confidence) A. Gothandaraman, T. Nason, and G. L. Warren, “Poster: A Disc-Based Decomposition Alogrithm with Optimal Load Balancing for N-Body Simulations,” 2012 SC Companion: High Performance Computing, Networking Storage and Analysis. 2012. link Times cited: 0 Abstract: We propose a novel disc-based data decomposition algorithm f… read moreAbstract: We propose a novel disc-based data decomposition algorithm for N-body simulations and compare its performance against a cyclic decomposition algorithm. We implement the data decomposition algorithms towards the calculation of three-body interactions in the Stillinger-Weber potential for a system of water molecules. The performance is studied in terms of load balance behavior and speedup from the MPI implementations of the two algorithms. We are also currently working on a performance study of the disc-based decomposition algorithm on graphics processing units (GPUs). read less NOT USED (high confidence) C. Henager, F. Gao, S. Hu, G. Lin, E. Bylaska, and N. Zabaras, “Simulating Interface Growth and Defect Generation in CZT – Simulation State of the Art and Known Gaps.” 2012. link Times cited: 1 Abstract: This one-year, study topic project will survey and investiga… read moreAbstract: This one-year, study topic project will survey and investigate the known state-of-the-art of modeling and simulation methods suitable for performing fine-scale, fully 3-D modeling, of the growth of CZT crystals at the melt-solid interface, and correlating physical growth and post-growth conditions with generation and incorporation of defects into the solid CZT crystal. In the course of this study, this project will also identify the critical gaps in our knowledge of modeling and simulation techniques in terms of what would be needed to be developed in order to perform accurate physical simulations of defect generation in melt-grown CZT. The transformational nature of this study will be, for the first time, an investigation of modeling and simulation methods for describing microstructural evolution during crystal growth and the identification of the critical gaps in our knowledge of such methods, which is recognized as having tremendous scientific impacts for future model developments in a wide variety of materials science areas. read less NOT USED (high confidence) H. Gong, W. Lu, L. Wang, and G. Li, “Cluster size and substrate temperature affecting thin film formation during copper cluster deposition on a Si (001) surface,” Chinese Physics B. 2012. link Times cited: 4 Abstract: The soft deposition of Cu clusters on a Si (001) surface was… read moreAbstract: The soft deposition of Cu clusters on a Si (001) surface was studied by molecular dynamics simulations. The embedded atom method, the Stillinger—Weber and the Lennar—Jones potentials were used to describe the interactions between the cluster atoms, between the substrate atoms, and between the cluster and the substrate atoms, respectively. The Cu13, Cu55, and Cu147 clusters were investigated at different substrate temperatures. We found that the substrate temperature had a significant effect on the Cu147 cluster. For smaller Cu13 and Cu55 clusters, the substrate temperature in the range of study appeared to have little effect on the mean center-of-mass height. The clusters showed better degrees of epitaxy at 800 K. With the same substrate temperature, the Cu55 cluster demonstrated the highest degree of epitaxy, followed by Cu147 and then Cu13 clusters. In addition, the Cu55 cluster showed the lowest mean center-of-mass height. These results suggested that the Cu55 cluster is a better choice for the thin-film formation among the clusters considered. Our studies may provide insight into the formation of desired Cu thin films on a Si substrate. read less NOT USED (high confidence) C. Lo, P. Somasundaran, and J. W. Lee, “Quick Assessment of Potential Hydrate Promoters for Rapid Formation.” 2012. link Times cited: 12 Abstract: Hydrate technology has advanced to greater proportions: impl… read moreAbstract: Hydrate technology has advanced to greater proportions: implementing the high latent heats as refrigerant, safe carbon capture as carbon sequestration in hydrates, purifying rare gases in hydrates, and safe efficient transport of energy using rapid hydrate formation. These account for only a small amount of the fundamental understanding of gas hydrates and the use of such a novel technology. A quick and broad analysis of novel hydrate promoters is needed to assess the potential of other promoter agents. This will improve the understanding of rapid hydrate formation and fundamental ideas related to the kinetics and formation of hydrates. There are still hundreds of other surfactants that have not been identified for rapid formation. The insurmountable endeavor deters many from trying as it can be like finding a needle in a hay stack. This almost futile endeavor of correctly identifying a surfactant as a promoter agent without doing a formation test can be accomplished with recent techniques. Using Raman and a liquid hydrocarbon (Cyclo-pentane), surfactants may shift the sample’s peak towards the hydrate peak (890 cm–1), thereby identifying it as a choice surfactant for rapid formation of hydrates. With a broad survey of surfactants, understanding fundamental science and engineering kinetics for hydrates will be easily achieved. Finding more effective and novel surfactants for hydrate formations will broaden the field of hydrates and self-assembling crystallization. As hydrate technology broadens, interdisciplinary fields can contribute expertise from surface science to spectroscopy leading to geological formations and engineering kinetics. read less NOT USED (high confidence) J. Lan and G. Li, “A multiscale component mode synthesis approach for dynamic analysis of nanostructures,” International Journal for Numerical Methods in Engineering. 2012. link Times cited: 3 Abstract: A component mode synthesis‐based multiscale approach is deve… read moreAbstract: A component mode synthesis‐based multiscale approach is developed for dynamic analysis of nanostructures. The multiscale approach decomposes a nanostructure into atomistic and continuum regions and employs vibrational modes to connect the regions of different scales, enabling a reflectionless atomistic‐to‐continuum coupling. Dynamic response of the coupled atomistic and continuum regions is computed concurrently using a common time scale. Numerical results indicate that the multiscale approach has significant condensation and scaling advantages, and it is well suited for modeling and simulation of large and complex systems. Copyright © 2012 John Wiley & Sons, Ltd. read less NOT USED (high confidence) V. Bocchetti and H. Diep, “Melting of rare-gas crystals: Monte Carlo simulation versus experiments.,” The Journal of chemical physics. 2012. link Times cited: 7 Abstract: We study the melting transition in crystals of rare gas Ar, … read moreAbstract: We study the melting transition in crystals of rare gas Ar, Xe, and Kr by the use of extensive Monte Carlo simulations with the Lennard-Jones potential. The parameters of this potential have been deduced by Bernardes in 1958 from experiments of rare gas in the gaseous phase. It is amazing that the parameters of such a popular potential were not fully tested so far. Using the Bernardes parameters, we find that the melting temperature of several rare gas is from 13% to 20% higher than that obtained from experiments. We have throughout studied the case of Ar by examining both finite-size and cutoff-distance effects. In order to get a good agreement with the experimental melting temperature, we propose a modification of these parameters to describe better the melting of rare-gas crystals. read less NOT USED (high confidence) C. Yang, Y. Wang, and X. Xu, “Molecular dynamics studies of ultrafast laser-induced phase and structural change in crystalline silicon,” International Journal of Heat and Mass Transfer. 2012. link Times cited: 17 NOT USED (high confidence) P. A. Apte and A. Gautam, “Nonmonotonic Dependence of the Absolute Entropy on Temperature in Supercooled Stillinger-Weber Silicon,” Journal of Statistical Physics. 2012. link Times cited: 0 NOT USED (high confidence) S. Ju and X.-gang Liang, “Thermal conductivity of nanocrystalline silicon by direct molecular dynamics simulation,” Journal of Applied Physics. 2012. link Times cited: 38 Abstract: The thermal conductivity simulation of nanocrystalline silic… read moreAbstract: The thermal conductivity simulation of nanocrystalline silicon is conducted on a three-dimensional configuration of nanocrystalline silicon with random grain shape for molecular dynamics simulation. The configuration is formed by the Voronoi tessellation method and the thermal conductivity is calculated by the Green-Kubo method. The effects of random grain distribution, periodic boundary, and the simulation system size are examined. Their effects on the simulation results can be neglected. The conductivity at temperature range from 300 K to 1100 K is obtained. The results indicate that the nanocrystalline thermal conductivity of silicon is far below the bulk single crystal and increases quickly with increasing grain size. The average grain boundary thermal resistance varies from 1.0 × 10−9 m2 KW−1 to 1.16 × 10−9 m2 KW−1. The restrain of the phonon mean free path by the nano-grain boundary is responsible for the sharp decrease in thermal conductivity. The effective phonon mean free path plays an important ... read less NOT USED (high confidence) A. H. Nguyen, L. C. Jacobson, and V. Molinero, “Structure of the clathrate/solution interface and mechanism of cross-nucleation of clathrate hydrates,” Journal of Physical Chemistry C. 2012. link Times cited: 63 Abstract: Clathrate hydrates mostly occur in two cubic crystal structu… read moreAbstract: Clathrate hydrates mostly occur in two cubic crystal structures, sI and sII. Cross-nucleation between these clathrate crystals has been observed in simulations and may be relevant to the transformation between clathrate polymorphs reported in experiments. Nevertheless, the mechanism by which clathrate crystals cross-nucleate and the structure of the interface between the distinct crystals have not yet been fully characterized. In this work, we use extensive molecular dynamics simulations to investigate the structure of the clathrate/solution interface for sI and sII guest-free and methane-filled hydrates at different degrees of supercooling and the mechanism of cross-nucleation between clathrate polymorphs. We find that 51263 water cages, which are not native to the sI or sII crystals, occur assiduously in their interfaces with the solution and play a central role in the mechanism of cross-nucleation of clathrate hydrates: cross-nucleation between sI and sII requires the formation of an interfacial layer ... read less NOT USED (high confidence) Y. Gao, Y. Jing, Q. Meng, L. Zhang, J. Liu, and X. Qin, “Investigation of the thermal‐transport properties for silicon nanofilm covered with graphene via nonequilibrium molecular dynamics,” physica status solidi (b). 2012. link Times cited: 7 Abstract: Nonequilibrium molecular dynamics (NEMD) is used to investig… read moreAbstract: Nonequilibrium molecular dynamics (NEMD) is used to investigate the thermal‐transport properties of a silicon nanofilm covered with graphene (Gr/Si/Gr nanofilm). The investigation results demonstrate that graphene can enhance the thermal‐transport properties and weaken the ballistic characteristics of silicon nanofilm. Under the action of a small strain, the thermal conductivity decreases with the growth of tensile and compressive strain, respectively. In addition, the higher‐frequency phonons in graphene give more contributions to the variation of thermal conductivity of Gr/Si/Gr nanofilm under strain. The thermal conductivity of Gr/Si/Gr nanofilm increases linearly with the increase of temperature in the lower‐temperature regime due to the quantum effect, and begins to clearly decrease when the temperature exceeds a definite value. read less NOT USED (high confidence) M. Wilson, “Model investigations of network-forming materials.,” Physical chemistry chemical physics : PCCP. 2012. link Times cited: 16 Abstract: Recent advances in the study of network-forming materials ar… read moreAbstract: Recent advances in the study of network-forming materials are described for systems dominated both by ionic and covalent interatomic interactions. Modelling strategies are described which focus both on describing specific systems of interest and on modelling the systematic evolution of network topology. The effect of network topology on the presence of ordering both on intermediate- and extended-length-scales is discussed. The effect of the topology on the mechanical rigidity is also described and analysed in terms of a mean coordination model. In addition, the isomorphology between amorphous silicon and the silicon sub-lattice in SiO(2) is described. Polyamorphism in Si and ZnCl(2) is analysed and discussed. Finally, the study of reduced (two) dimensional systems is discussed for carbon, silicon and germanium. read less NOT USED (high confidence) V. Dozhdikov, A. Basharin, and P. Levashov, “Two-phase simulation of the crystalline silicon melting line at pressures from -1 to 3 GPa.,” The Journal of chemical physics. 2012. link Times cited: 32 Abstract: Results of a numerical investigation of crystalline silicon … read moreAbstract: Results of a numerical investigation of crystalline silicon melting line within the range of pressures from -1 to 3 GPa are presented. A two-phase molecular dynamics method is applied to obtain temperature, pressure, and densities of solid and liquid phases on the melting line. Using a special procedure we ensure the strict control of the two-phase equilibrium in the simulation cell. To describe the interaction between the atoms four classic potentials have been chosen: the Stillinger-Weber one and three modified variants of the Tersoff potential. For the Stillinger-Weber and Tersoff potentials in the modification by Kumagai-Izumi-Hara-Sakai a good coincidence with experimental data on crystalline Si melting temperature is obtained within the range of pressure from 0 to 3 GPa. Calculations of the solid and liquid phase densities on the silicon melting line for the Stillinger-Weber potential are also in close agreement with experiments. read less NOT USED (high confidence) H. Gong, W. Lu, L. Wang, G. Li, and S. Zhang, “The effects of substrate size and temperature on the deposition of Cu clusters on a Si substrate,” Journal of Applied Physics. 2012. link Times cited: 8 Abstract: The deposition of a Cu13 cluster on a Si (001) surface was s… read moreAbstract: The deposition of a Cu13 cluster on a Si (001) surface was studied by molecular dynamics simulations. Embedded atom method, Stillinger-Weber, and Lennar-Jones potentials were used to describe the interaction between cluster atoms, substrate atoms, and the cluster-substrate interaction. Quantitative characteristic parameters, such as kinetic energy of the cluster and the substrate, the degree of epitaxy, and the mean height of mass center of the cluster, were calculated to study the effect of substrate size and substrate temperature on cluster deposition. The substrate temperature was found to affect the degree of epitaxy at different substrate sizes. When the size ratio of the substrate and cluster is relatively small or large, the epitaxial degree was higher at 800 K than at 300 K. If the size of the substrate matches that of the cluster, the substrate temperature appeared to have minimum effect. For a given temperature, the substrate size was found to have no obvious effect on the degree of epitaxy or t... read less NOT USED (high confidence) Y. Zou, X. Huai, F. Xin, and Z. Guo, “Molecular Dynamics Simulation of Heat Conduction in Si Thin Films Induced by Ultrafast Laser Heating.” 2012. link Times cited: 0 Abstract: article i nfo Molecular dynamics simulations are carried out… read moreAbstract: article i nfo Molecular dynamics simulations are carried out to study the thermal and mechanical phenomena of heat conduction induced by ultrafast laser heating of nanoscale Si films. A distribution of internal heat source obeying Beer-Lambdalawisappliedtomodelthelaserenergydepositioninthe filmandtocalculate theinducedtemper- ature and stress distributions. Thermal waves are observed from the local temperature temporal variations and spatial distributions. The developments of averaged static pressure and local displacement in the film show a consistent periodicity. The time evolutions of both the local pressure and net heat flux fluctuate strongly, but show similar trends between these two local physical quantities, demonstrating a close relationship between the stress and the net heat flow. read less NOT USED (high confidence) T. D. Shepherd, M. Koc, and V. Molinero, “The Quasi-Liquid Layer of Ice under Conditions of Methane Clathrate Formation,” Journal of Physical Chemistry C. 2012. link Times cited: 58 Abstract: A premelted layer of water wets the surface of ice at temper… read moreAbstract: A premelted layer of water wets the surface of ice at temperatures below the melting temperature. Experiments suggest that this quasi-liquid layer may play an important role in the nucleation of clathrate hydrates from ice. Nevertheless, the structure of the quasi-liquid layer of ice in the presence of methane or other clathrate-forming gases has not yet been elucidated. In this work, we perform large-scale molecular dynamic simulations with a coarse-grained molecular model to investigate the properties of the quasi-liquid layer of ice in the presence of methane gas under pressure. We characterize the structure and thickness of the ice/methane and ice/vacuum interfaces, and the solubility of methane in the premelted layer as a function of temperature. We find that the width of the quasi-liquid layer fluctuates between 5 and 45 A in the presence of a methane-like solute at temperatures within 1 K of the melting point. The width of the quasi-liquid layer of ice at temperatures lower than 270 K is less than ... read less NOT USED (high confidence) A. Das and H. C. Andersen, “The multiscale coarse-graining method. IX. A general method for construction of three body coarse-grained force fields.,” The Journal of chemical physics. 2012. link Times cited: 54 Abstract: The multiscale coarse-graining (MS-CG) method is a method fo… read moreAbstract: The multiscale coarse-graining (MS-CG) method is a method for constructing a coarse-grained (CG) model of a system using data obtained from molecular dynamics simulations of the corresponding atomically detailed model. The formal statistical mechanical derivation of the method shows that the potential energy function extracted from an MS-CG calculation is a variational approximation for the true potential of mean force of the CG sites, one that becomes exact in the limit that a complete basis set is used in the variational calculation if enough data are obtained from the atomistic simulations. Most applications of the MS-CG method have employed a representation for the nonbonded part of the CG potential that is a sum of all possible pair interactions. This approach, despite being quite successful for some CG models, is inadequate for some others. Here we propose a systematic method for including three body terms as well as two body terms in the nonbonded part of the CG potential energy. The current method is more general than a previous version presented in a recent paper of this series [L. Larini, L. Lu, and G. A. Voth, J. Chem. Phys. 132, 164107 (2010)], in the sense that it does not make any restrictive choices for the functional form of the three body potential. We use hierarchical multiresolution functions that are similar to wavelets to develop very flexible basis function expansions with both two and three body basis functions. The variational problem is solved by a numerical technique that is capable of automatically selecting an appropriate subset of basis functions from a large initial set. We apply the method to two very different coarse-grained models: a solvent free model of a two component solution made of identical Lennard-Jones particles and a one site model of SPC/E water where a site is placed at the center of mass of each water molecule. These calculations show that the inclusion of three body terms in the nonbonded CG potential can lead to significant improvement in the accuracy of CG potentials and hence of CG simulations. read less NOT USED (high confidence) K. Jose, N. Artrith, and J. Behler, “Construction of high-dimensional neural network potentials using environment-dependent atom pairs.,” The Journal of chemical physics. 2012. link Times cited: 109 Abstract: An accurate determination of the potential energy is the cru… read moreAbstract: An accurate determination of the potential energy is the crucial step in computer simulations of chemical processes, but using electronic structure methods on-the-fly in molecular dynamics (MD) is computationally too demanding for many systems. Constructing more efficient interatomic potentials becomes intricate with increasing dimensionality of the potential-energy surface (PES), and for numerous systems the accuracy that can be achieved is still not satisfying and far from the reliability of first-principles calculations. Feed-forward neural networks (NNs) have a very flexible functional form, and in recent years they have been shown to be an accurate tool to construct efficient PESs. High-dimensional NN potentials based on environment-dependent atomic energy contributions have been presented for a number of materials. Still, these potentials may be improved by a more detailed structural description, e.g., in form of atom pairs, which directly reflect the atomic interactions and take the chemical environment into account. We present an implementation of an NN method based on atom pairs, and its accuracy and performance are compared to the atom-based NN approach using two very different systems, the methanol molecule and metallic copper. We find that both types of NN potentials provide an excellent description of both PESs, with the pair-based method yielding a slightly higher accuracy making it a competitive alternative for addressing complex systems in MD simulations. read less NOT USED (high confidence) J. Carrete, N. Mingo, G. Tian, H. Ågren, A. Baev, and P. Prasad, “Thermoelectric Properties of Hybrid Organic-Inorganic Superlattices,” Journal of Physical Chemistry C. 2012. link Times cited: 22 Abstract: We theoretically evaluate the thermoelectric transport coeff… read moreAbstract: We theoretically evaluate the thermoelectric transport coefficients of hybrid thiophene/SiGe superlattices and the effect of their chemical tuning via phenyl groups. Owing to the interplay between alloy scattering and phonon transmission at the molecular layers, very low thermal conductivities under 1 W/(m K) and values of ZT more than twice as large as those of bulk SiGe can be attained. These results highlight exciting possibilities of organic–inorganic hybrid systems, as compared to traditional inorganic thermoelectrics. read less NOT USED (high confidence) J. Chen, G. Zhang, and B. Li, “Impacts of atomistic coating on thermal conductivity of germanium nanowires.,” Nano letters. 2012. link Times cited: 88 Abstract: By using nonequilibrium molecular dynamics simulations, we d… read moreAbstract: By using nonequilibrium molecular dynamics simulations, we demonstrated that thermal conductivity of germanium nanowires can be reduced more than 25% at room temperature by atomistic coating. There is a critical coating thickness beyond which thermal conductivity of the coated nanowire is larger than that of the host nanowire. The diameter-dependent critical coating thickness and minimum thermal conductivity are explored. Moreover, we found that interface roughness can induce further reduction of thermal conductivity in coated nanowires. From the vibrational eigenmode analysis, it is found that coating induces localization for low-frequency phonons, while interface roughness localizes the high-frequency phonons. Our results provide an available approach to tune thermal conductivity of nanowires by atomic layer coating. read less NOT USED (high confidence) Y. Shin et al., “Variable charge many-body interatomic potentials,” MRS Bulletin. 2012. link Times cited: 56 Abstract: Recent developments in reactive potentials for the simulatio… read moreAbstract: Recent developments in reactive potentials for the simulation of complex bonding and complex chemistry are reviewed. In particular, the reactive force field and charged optimized many-body methods are two paradigms that enable atoms to autonomously determine their charge state and the nature of their local bonding environments. The capabilities of these methods are illustrated by examples involving ionic-covalent systems, a metal-covalent system, a high- k dielectric gate stack, and the interaction of water with an oxide. Prospects for future development and applications are also discussed. read less NOT USED (high confidence) X.-J. Yuan, N. Chen, and J. Shen, “Construction of embedded-atom-method interatomic potentials for alkaline metals (Li, Na, and K) by lattice inversion,” Chinese Physics B. 2012. link Times cited: 1 Abstract: The lattice-inversion embedded-atom-method interatomic poten… read moreAbstract: The lattice-inversion embedded-atom-method interatomic potential developed previously by us is extended to alkaline metals including Li, Na, and K. It is found that considering interatomic interactions between neighboring atoms of an appropriate distance is a matter of great significance in constructing accurate embedded-atom-method interatomic potentials, especially for the prediction of surface energy. The lattice-inversion embedded-atom-method interatomic potentials for Li, Na, and K are successfully constructed by taking the fourth-neighbor atoms into consideration. These angular-independent potentials markedly promote the accuracy of predicted surface energies, which agree well with experimental results. In addition, the predicted structural stability, elastic constants, formation and migration energies of vacancy, and activation energy of vacancy diffusion are in good agreement with available experimental data and first-principles calculations, and the equilibrium condition is satisfied. read less NOT USED (high confidence) M. T. Knippenberg, P. Mikulski, K. E. Ryan, S. Stuart, G. Gao, and J. Harrison, “Bond-order potentials with split-charge equilibration: application to C-, H-, and O-containing systems.,” The Journal of chemical physics. 2012. link Times cited: 25 Abstract: A method for extending charge transfer to bond-order potenti… read moreAbstract: A method for extending charge transfer to bond-order potentials, known as the bond-order potential/split-charge equilibration (BOP/SQE) method [P. T. Mikulski, M. T. Knippenberg, and J. A. Harrison, J. Chem. Phys. 131, 241105 (2009)], is integrated into a new bond-order potential for interactions between oxygen, carbon, and hydrogen. This reactive potential utilizes the formalism of the adaptive intermolecular reactive empirical bond-order potential [S. J. Stuart, A. B. Tutein, and J. A. Harrison, J. Chem. Phys. 112, 6472 (2000)] with additional terms for oxygen and charge interactions. This implementation of the reactive potential is able to model chemical reactions where partial charges change in gas- and condensed-phase systems containing oxygen, carbon, and hydrogen. The BOP/SQE method prevents the unrestricted growth of charges, often observed in charge equilibration methods, without adding significant computational time, because it makes use of a quantity which is calculated as part of the underlying covalent portion of the potential, namely, the bond order. The implementation of this method with the qAIREBO potential is designed to provide a tool that can be used to model dynamics in a wide range of systems without significant computational cost. To demonstrate the usefulness and flexibility of this potential, heats of formation for isolated molecules, radial distribution functions of liquids, and energies of oxygenated diamond surfaces are calculated. read less NOT USED (high confidence) R. Jones and K. Mandadapu, “Adaptive Green-Kubo estimates of transport coefficients from molecular dynamics based on robust error analysis.,” The Journal of chemical physics. 2012. link Times cited: 42 Abstract: We present a rigorous Green-Kubo methodology for calculating… read moreAbstract: We present a rigorous Green-Kubo methodology for calculating transport coefficients based on on-the-fly estimates of: (a) statistical stationarity of the relevant process, and (b) error in the resulting coefficient. The methodology uses time samples efficiently across an ensemble of parallel replicas to yield accurate estimates, which is particularly useful for estimating the thermal conductivity of semi-conductors near their Debye temperatures where the characteristic decay times of the heat flux correlation functions are large. Employing and extending the error analysis of Zwanzig and Ailawadi [Phys. Rev. 182, 280 (1969)] and Frenkel [in Proceedings of the International School of Physics "Enrico Fermi", Course LXXV (North-Holland Publishing Company, Amsterdam, 1980)] to the integral of correlation, we are able to provide tight theoretical bounds for the error in the estimate of the transport coefficient. To demonstrate the performance of the method, four test cases of increasing computational cost and complexity are presented: the viscosity of Ar and water, and the thermal conductivity of Si and GaN. In addition to producing accurate estimates of the transport coefficients for these materials, this work demonstrates precise agreement of the computed variances in the estimates of the correlation and the transport coefficient with the extended theory based on the assumption that fluctuations follow a Gaussian process. The proposed algorithm in conjunction with the extended theory enables the calculation of transport coefficients with the Green-Kubo method accurately and efficiently. read less NOT USED (high confidence) K. Farah, F. Müller-Plathe, and M. Böhm, “Classical reactive molecular dynamics implementations: state of the art.,” Chemphyschem : a European journal of chemical physics and physical chemistry. 2012. link Times cited: 71 Abstract: Reactive molecular dynamics (RMD) implementations equipped w… read moreAbstract: Reactive molecular dynamics (RMD) implementations equipped with force field approaches to simulate both the time evolution as well as chemical reactions of a broad class of materials are reviewed herein. We subdivide the RMD approaches developed during the last decade as well as older ones already reviewed in 1995 by Srivastava and Garrison and in 2000 by Brenner into two classes. The methods in the first RMD class rely on the use of a reaction cutoff distance and employ a sudden transition from the educts to the products. Due to their simplicity these methods are well suited to generate equilibrated atomistic or material-specific coarse-grained polymer structures. In connection with generic models they offer useful qualitative insight into polymerization reactions. The methods in the second RMD class are based on empirical reactive force fields and implement a smooth and continuous transition from the educts to the products. In this RMD class, the reactive potentials are based on many-body or bond-order force fields as well as on empirical standard force fields, such as CHARMM, AMBER or MM3 that are modified to become reactive. The aim with the more sophisticated implementations of the second RMD class is the investigation of the reaction kinetics and mechanisms as well as the evaluation of transition state geometries. Pure or hybrid ab initio, density functional, semi-empirical, molecular mechanics, and Monte Carlo methods for which no time evolution of the chemical systems is achieved are excluded from the present review. So are molecular dynamics techniques coupled with quantum chemical methods for the treatment of the reactive regions, such as Car-Parinello molecular dynamics. read less NOT USED (high confidence) K. Termentzidis and S. Merabia, “Molecular Dynamics Simulations and Thermal Transport at the Nano-Scale.” 2012. link Times cited: 14 Abstract: This chapter presents an overview of the Molecular Dynamics … read moreAbstract: This chapter presents an overview of the Molecular Dynamics (MD) simulation technique to predict thermal transport properties of nanostructured materials. This covers systems having characteristic lengths of the order of a few nanometers like carbon nanotubes, nanowires and also superlattices, i.e. composite materials made of submicronic thickness of solid layers. The common features of these systems is the small ratio between their characteristic system size and the phonon mean free path, which leads to ballistic heat transport and deviations from the classical Fourier law. Also when the density of interfaces gets large, the energy transport properties of the materials can not longer be described solely by the thermal conductivities of the constituents of the material, but depend also on the thermal boundary resistance which measures the transmission of phonons across an interface. In this context, molecular dynamics was proven to be a very useful technique to study heat transport in nanostructured materials. The main reasons are; the length scale probed by the method is in the nanometer range, and it does not make any assumption on the phonons dynamics except their classical nature. read less NOT USED (high confidence) E. Pastukhov, N. I. Sidorov, A. A. Vostrjakov, and V. Chentsov, “Molecular Dynamic Simulation of Short Order and Hydrogen Diffusion in the Disordered Metal Systems.” 2012. link Times cited: 0 Abstract: Main concepts of Hydrogen permeability (HP) mechanism for th… read moreAbstract: Main concepts of Hydrogen permeability (HP) mechanism for the pure crystal metals are already stated. There are well-founded theoretical models and numerous experimental researches. As far as disordered systems (in which Hydrogen solubility is much more, than in crystal samples) are concerned, such works appear to be comparatively recent and rare. Particularly, they are devoted to Hydrogen interaction of with amorphous structures. Deficiency of similar researches is caused by thermo-temporal instability of amorphous materials structure and properties. read less NOT USED (high confidence) A. Dongare, B. Lamattina, D. Irving, A. Rajendran, M. Zikry, and D. Brenner, “An angular-dependent embedded atom method (A-EAM) interatomic potential to model thermodynamic and mechanical behavior of Al/Si composite materials,” Modelling and Simulation in Materials Science and Engineering. 2012. link Times cited: 23 Abstract: A new interatomic potential is developed for the Al/Si syste… read moreAbstract: A new interatomic potential is developed for the Al/Si system in the formulation of the recently developed angular-dependent embedded atom method (A-EAM). The A-EAM is formulated by combining the embedded atom method potential for Al with the Stillinger–Weber potential for Si. The parameters of the Al/Si cross-interactions are fitted to reproduce the structural energetics of Al/Si bulk alloys determined based on the results of density functional theory calculations and the experimentally observed mixing behavior of the AlSi liquid alloy at high temperatures. The ability to investigate the thermodynamic properties of the Al/Si system is demonstrated by computing the binary phase diagram of the Al–Si system as predicted by the A-EAM potential and comparing with that obtained using experiments. The ability to study the mechanical behavior of the Al/Si composite systems is demonstrated by investigating the micromechanisms related to dynamic failure of the Al/Si nanocomposites using MD simulations. read less NOT USED (high confidence) D. Mathieu, “Formation Enthalpies Derived from Pairwise Interactions: A Step toward More Transferable Reactive Potentials for Organic Compounds.,” Journal of chemical theory and computation. 2012. link Times cited: 4 Abstract: A new approach to the development and parametrization of rea… read moreAbstract: A new approach to the development and parametrization of reactive potentials for organic compounds is put forward. As a byproduct of preliminary efforts in this direction, the performance of a simple representation of the energy of equilibrium structures in term of pairwise atom-atom and bond-bond contributions is investigated. For now, each contribution is assumed constant, given the multiplicity of covalent bonds, rather than computed on-the-fly from geometries and bond orders. In spite of this rough approximation, the approach performs remarkably well by comparison with semiempirical quantum chemical methods. Nevertheless, further refinement proves necessary for some unstable species involved in chemical reactions. As it stands, the present model appears as a promising basis in view of less empirical and more versatile alternatives to group contribution methods for the fast prediction of heats of formation, although much work remains to be done to demonstrate its value as a starting point toward better reactive potentials. read less NOT USED (high confidence) Y. Lee and G. Hwang, “Force-matching-based parameterization of the Stillinger-Weber potential for thermal conduction in silicon,” Physical Review B. 2012. link Times cited: 38 NOT USED (high confidence) K. V. Shanavas, K. Pandey, N. Garg, and S. M. Sharma, “Computer simulations of crystallization kinetics in amorphous silicon under pressure,” Journal of Applied Physics. 2012. link Times cited: 9 Abstract: With the help of computer simulations we have studied the cr… read moreAbstract: With the help of computer simulations we have studied the crystallization kinetics of amorphous silicon in solid phase epitaxial (SPE) and random nucleation growth processes. Our simulations employing classical molecular dynamics and first principles methods suggest qualitatively similar behavior in both processes. Pressure is found to reduce the difference in molar volumes and coordination numbers between the amorphous and crystalline phases, which in turn lowers the energy barrier of crystallization. The activation energy for the SPE growth of four coordinated diamond phase is found to reach a minimum (a maximum in growth rates) close to 10 GPa when its density becomes equal to that of the amorphous phase. The crystallization temperatures of successive high pressure phases of silicon are found to decrease, offering a possible explanation for the pressure induced crystallization reported in this material. read less NOT USED (high confidence) E. B. Moore, J. Allen, and V. Molinero, “Liquid-ice coexistence below the melting temperature for water confined in hydrophilic and hydrophobic nanopores,” Journal of Physical Chemistry C. 2012. link Times cited: 95 Abstract: We use molecular dynamics simulations to investigate the coe… read moreAbstract: We use molecular dynamics simulations to investigate the coexistence between confined ice and liquid water as a function of temperature for a series of cylindrical nanopores with water–wall interactions ranging from strongly hydrophilic to very hydrophobic. In agreement with previous results from experiments, we find that the ice formed in the nanopores is a hybrid ice I with stacks of cubic and hexagonal layers and that the melting temperature of the nanoconfined ice is strongly dependent on the radius of the pore but rather insensitive to the hydrophilicity of the pore surface. We find a premelted liquid layer in coexistence with the confined ice down to the lowest temperatures of this study, 50 K below the melting temperatures of the confined ices. The fraction of water in the premelted liquid layer decreases with increasing hydrophobicity of the pore wall, but it does not vanish even for the most hydrophobic nanopores. The simulations suggest that the decrease in the fraction of water in the liquid la... read less NOT USED (high confidence) D. Ward, X. W. Zhou, B. M. Wong, J. Zimmerman, and F. Doty, “Analytical bond-order potential for the cadmium telluride binary system.” 2012. link Times cited: 69 Abstract: CdTe and Cd${}_{1\ensuremath{-}x}$Zn${}_{x}$Te are the leadi… read moreAbstract: CdTe and Cd${}_{1\ensuremath{-}x}$Zn${}_{x}$Te are the leading semiconductor compounds for both photovoltaic and radiation detection applications. The performance of these materials is sensitive to the presence of atomic-scale defects in the structures. To enable accurate studies of these defects using modern atomistic simulation technologies, we have developed a high-fidelity analytical bond-order potential for the CdTe system. This potential incorporates primary ($\ensuremath{\sigma}$) and secondary ($\ensuremath{\pi}$) bonding and the valence dependence of the heteroatom interactions. The functional forms of the potential are directly derived from quantum-mechanical tight-binding theory under the condition that the first two and first four levels of the expanded Green's function for the $\ensuremath{\sigma}$- and $\ensuremath{\pi}$-bond orders, respectively, are retained. The potential parameters are optimized using iteration cycles that include first-fitting properties of a variety of elemental and compound configurations (with coordination varying from 1 to 12) including small clusters, bulk lattices, defects, and surfaces, and then checking crystalline growth through vapor deposition simulations. It is demonstrated that this CdTe bond-order potential gives structural and property trends close to those seen in experiments and quantum-mechanical calculations and provides a good description of melting temperature, defect characteristics, and surface reconstructions of the CdTe compound. Most importantly, this potential captures the crystalline growth of the ground-state structures for Cd, Te, and CdTe phases in vapor deposition simulations. read less NOT USED (high confidence) A. A. Selezenev, A. Aleinikov, P. V. Ermakov, N. S. Ganchuk, S. Ganchuk, and R. Jones, “Molecular-dynamics calculation of the thermal conductivity coefficient of the germanium single crystal,” Physics of the Solid State. 2012. link Times cited: 7 NOT USED (high confidence) L. Hale et al., “Dislocation morphology and nucleation within compressed Si nanospheres: A molecular dynamics study,” Computational Materials Science. 2012. link Times cited: 24 NOT USED (high confidence) A. Danescu and G. Grenet, “Continuum strain-gradient elasticity from discrete valence force field model for diamond-like crystals,” International Journal of Fracture. 2012. link Times cited: 7 NOT USED (high confidence) P. López, L. Pelaz, I. Santos, L. Marqués, and M. Aboy, “Molecular dynamics simulations of damage production by thermal spikes in Ge,” Journal of Applied Physics. 2012. link Times cited: 20 Abstract: Molecular dynamics simulation techniques are used to analyze… read moreAbstract: Molecular dynamics simulation techniques are used to analyze damage production in Ge by the thermal spike process and to compare the results to those obtained for Si. As simulation results are sensitive to the choice of the inter-atomic potential, several potentials are compared in terms of material properties relevant for damage generation, and the most suitable potentials for this kind of analysis are identified. A simplified simulation scheme is used to characterize, in a controlled way, the damage generation through the local melting of regions in which energy is deposited. Our results show the outstanding role of thermal spikes in Ge, since the lower melting temperature and thermal conductivity of Ge make this process much more efficient in terms of damage generation than in Si. The study is extended to the modeling of full implant cascades, in which both collision events and thermal spikes coexist. Our simulations reveal the existence of bigger damaged or amorphous regions in Ge than in Si, which ma... read less NOT USED (high confidence) A. Butenuth et al., “Ab initio derived force‐field parameters for molecular dynamics simulations of deprotonated amorphous‐SiO2/water interfaces,” physica status solidi (b). 2012. link Times cited: 71 Abstract: We present a set of Coulomb point charges and van der Waals … read moreAbstract: We present a set of Coulomb point charges and van der Waals parameters for molecular dynamics simulations of interfaces between natively deprotonated amorphous SiO2 surfaces and liquid water, to be used in combination with standard biomolecular force fields. We pay particular attention to the extent of negative charge delocalisation in the solid that follows the deprotonation of terminal silanol groups, as revealed by extensive Bader analysis of electronic densities computed by density functional theory (DFT). The absolute charge values in our force field are determined from best‐fitting to the electrostatic potential computed ab initio (ESP charges). Our proposed parameter set is found to reproduce the energy landscape of single water molecules over neutral and deprotonated amorphous SiO2 surfaces and, after a minor adjustment, over thin oxide films on Si. Our analysis reveals a certain degree of arbitrariness in the choice of the DFT scheme used as the reference for the force‐field optimisation procedure, highlighting its intrinsic limits. read less NOT USED (high confidence) N. Fazouan, E. Atmani, F. E. Kasri, M. Rouhani, and A. Estève, “Interface structure of deposited GaSb on GaAs (001): Monte Carlo simulation and experimental study,” Journal of Materials Science. 2012. link Times cited: 4 NOT USED (high confidence) J. Carrete et al., “Thermal Conductivity of Ionic Liquids: A Pseudolattice Approach,” Journal of Physical Chemistry C. 2012. link Times cited: 18 Abstract: In this paper, we present a model for the thermal conductivi… read moreAbstract: In this paper, we present a model for the thermal conductivity of ionic liquids and their mixtures with solvents based on the pseudolattice framework developed by Bahe and Varela. To this end, we first discuss the possible interpretation of some of the fundamental elements of lattice dynamics in the context of a liquid and show computational results that point to the existence of a well-defined vibrational spectrum in these systems. By adapting the idea of phonon hopping (a heat transfer mechanism with its roots in the theory of amorphous solids) we then arrive at a set of analytic expressions whose results are compared to our own experimental measurements of the temperature behavior of the thermal conductivity of pure ionic liquids and its dependence on concentration in mixtures with water and ethanol. read less NOT USED (high confidence) E. D. L. Llave, V. Molinero, and D. Scherlis, “Role of Confinement and Surface Affinity on Filling Mechanisms and Sorption Hysteresis of Water in Nanopores,” Journal of Physical Chemistry C. 2012. link Times cited: 30 Abstract: The liquid–vapor transition in cylindrical pores is studied … read moreAbstract: The liquid–vapor transition in cylindrical pores is studied as a function of pore size and hydrophilicity through molecular dynamics simulations with the mW coarse-grained model of water. We identify two distinct filling mechanisms, depending on whether the water–pore interaction is smaller or larger than the water–water interaction. In the former case (that we term hydrophobic pore), the formation of the condensed phase proceeds gradually with filling, through the nucleation of a water cluster which grows toward the center of the cavity. In hydrophilic pores, instead, the condensed phase develops in conditions of supersaturation, which in principle become more extreme with increasing pore radius and surface affinity. For highly hydrophilic interfaces (those with adsorption energy for water above 10 kcal/mol), the equilibrium and dynamical properties of water in confinement turn out to be practically independent of water affinity. read less NOT USED (high confidence) C. Hou and W. Ge, “GPU-accelerated molecular dynamics simulation of solid covalent crystals,” Molecular Simulation. 2012. link Times cited: 17 Abstract: Graphics processing unit (GPU) is becoming a powerful comput… read moreAbstract: Graphics processing unit (GPU) is becoming a powerful computational tool in science and engineering. In this paper, different from previous molecular dynamics (MD) simulation with pair potentials and many-body potentials, two MD simulation algorithms implemented on a single GPU are presented to describe a special category of many-body potentials – bond order potentials used frequently in solid covalent materials, such as the Tersoff potentials for silicon crystals. The simulation results reveal that the performance of GPU implementations is apparently superior to their CPU counterpart. Furthermore, the proposed algorithms are generalised, transferable and scalable, and can be extended to the simulations with general many-body interactions such as Stillinger–Weber potential and so on. read less NOT USED (high confidence) S. Kraeusel and B. Hourahine, “Global search for stable screw dislocation cores in III‐N semiconductors,” physica status solidi (a). 2012. link Times cited: 2 Abstract: The promise of the broad range of direct band gaps of the {A… read moreAbstract: The promise of the broad range of direct band gaps of the {Al, Ga, In}N system is limited by the crystal quality of current material. As grown defect densities of InN, when compared with the more mature GaN, are extremely high and InN is strongly influenced by these defects. This is particularly important due to the unusual position of the charge neutrality level of InN, leading to both the well‐known surface charge accumulation and difficulties in p‐type doping. While impurities and native defects clearly impact on the bulk carrier density in InN, the effects of threading dislocations on the electrical properties are still in dispute. Issues such as whether the dislocation line is charged or contains dangling bonds remain open. We present the results of a global search for possible dislocation core reconstructions for a range of screw dislocations in wurtzite III‐N material, utilizing empirical Stillinger–Weber inter‐atomic potentials. In addition, we investigate a wide range of non‐stoichiometric core structures. read less NOT USED (high confidence) V. Hùng, L. D. Thanh, and N. T. Huong, “Study of Elastic Moduli of Semiconductors with Defects by the Statistical Moment Method,” E-journal of Surface Science and Nanotechnology. 2011. link Times cited: 2 Abstract: The elastic moduli of semiconductors at finite temperatures … read moreAbstract: The elastic moduli of semiconductors at finite temperatures have been studied using the statistical moment method. The Young, bulk and shear moduli of the semiconductor with point defects like Si crystal are calculated as a function of the temperature. We discuss the temperature dependence of the elastic moduli of Si crystal with defects and compare the calculated elastic moduli with the experimental results. [DOI: 10.1380/ejssnt.2011.499] read less NOT USED (high confidence) J. Chen, G. Zhang, and B. Li, “A universal gauge for thermal conductivity of silicon nanowires with different cross sectional geometries.,” The Journal of chemical physics. 2011. link Times cited: 51 Abstract: By using molecular dynamics simulations, we study thermal co… read moreAbstract: By using molecular dynamics simulations, we study thermal conductivity of silicon nanowires (SiNWs) with different cross sectional geometries. It is found that thermal conductivity decreases monotonically with the increase of surface-to-volume ratio (SVR). More interestingly, a simple universal linear dependence of thermal conductivity on SVR is observed for SiNWs with modest cross sectional area (larger than 20 nm(2)), regardless of the cross sectional geometry. As a result, among different shaped SiNWs with the same cross sectional area, the one with triangular cross section has the lowest thermal conductivity. Our study provides not only a universal gauge for thermal conductivity among different cross sectional geometries, but also a designing guidance to tune thermal conductivity by geometry. read less NOT USED (high confidence) T. Li, D. Donadio, G. Russo, and G. Galli, “Homogeneous ice nucleation from supercooled water.,” Physical chemistry chemical physics : PCCP. 2011. link Times cited: 212 Abstract: Homogeneous ice nucleation from supercooled water was studie… read moreAbstract: Homogeneous ice nucleation from supercooled water was studied in the temperature range of 220-240 K through combining the forward flux sampling method (Allen et al., J. Chem. Phys., 2006, 124, 024102) with molecular dynamics simulations (FFS/MD), based on a recently developed coarse-grained water model (mW) (Molinero et al., J. Phys. Chem. B, 2009, 113, 4008). The calculated ice nucleation rates display a strong temperature dependence, ranging from 2.148 ± 0.635 × 10(25) m(-3) s(-1) at 220 K to 1.672 ± 0.970 × 10(-7) m(-3) s(-1) at 240 K. These rates can be fitted according to the classical nucleation theory, yielding an estimate of the effective ice-water interface energy γ(ls) of 31.01 ± 0.21 mJ m(-2) for the mW water model. Compared to experiments, our calculation underestimates the homogeneous ice nucleation rate by a few orders of magnitude. Possible reasons for the discrepancy are discussed. The nucleating ice embryo contains both cubic ice Ic and hexagonal ice Ih, with the fraction of each structure being roughly 50% when the critical size is reached. In particular, a novel defect structure containing nearly five-fold twin boundaries is identified in the ice clusters formed during nucleation. The way such defect structure is formed is found to be different from mechanisms proposed for the formation of the same defect in metallic nanoparticles and thin film. The quasi five-fold twin boundary structure found here is expected to occur in the crystallization of a wide range of materials with the diamond cubic structure, including ice. read less NOT USED (high confidence) M. Friák et al., “Methodological challenges in combining quantum-mechanical and continuum approaches for materials science applications,” The European Physical Journal Plus. 2011. link Times cited: 26 NOT USED (high confidence) J. Y. Abraham, S. Buldyrev, and N. Giovambattista, “Liquid and glass polymorphism in a monatomic system with isotropic, smooth pair interactions.,” The journal of physical chemistry. B. 2011. link Times cited: 33 Abstract: Systems of particles with interactions given by the Jagla co… read moreAbstract: Systems of particles with interactions given by the Jagla core-softened pair potential are known to exhibit water-like thermodynamic anomalies and a liquid-liquid phase transition. The drawback of the Jagla potential is that it is characterized by discontinuous forces acting between particles and thus is not suitable for standard molecular dynamics (MD) simulations. Here we introduce a smooth version of the Jagla potential based on two Fermi distributions and study the properties of a system of particles interacting via this new "Fermi-Jagla" pair potential by using standard MD simulations. We find that the liquid based on the Fermi-Jagla potential retains most of the properties of the liquid based on the original Jagla potential. Namely, it exhibits the following water-like anomalies: (i) decrease of density, (ii) increase of compressibility, κ(T)(T,P), and (iii) increase of isobaric specific heat, C(P)(T,P), upon isobaric cooling, and (iv) increase of diffusivity upon isothermal compression. The Fermi-Jagla potential also exhibits (i') density minima, (ii') compressibility minima, (iii') isobaric specific heat minima upon isobaric cooling, and (iv') diffusivity minima upon isothermal compression. As in the Jagla model case, we find a liquid-liquid phase transition (LLPT) and a liquid-liquid critical point in the equilibrium liquid. Contrary to the case of the original Jagla model liquid, the LLPT line for the Fermi-Jagla potential has a negative slope in the P-T plane that extends well above the crystallization temperature. This feature makes the Fermi-Jagla potential a better candidate to reproduce the behavior of tetrahedral liquids including water, for which the LLPT line observed in simulations has also negative slope. In the glass state, the Fermi-Jagla pair potential results in reversible polyamorphism between low- and high-density amorphous solids (LDA and HDA, respectively). We also find that HDA results from pressure-induced amorphization of the model's low pressure crystal, as observed in water and other materials. The Fermi-Jagla pair potential, being a smooth function of the interparticle separation, can be easily implemented in standard MD simulation codes. Moreover, since spontaneous crystallization for the Fermi-Jagla potential can be avoided by fast cooling, it can be used to study the phenomenology of glasses. read less NOT USED (high confidence) H. Minari, T. Zushi, T. Watanabe, Y. Kamakura, and N. Mori, “Effects of atomic disorder on carrier transport in Si nanowire transistors,” 2011 International Conference on Simulation of Semiconductor Processes and Devices. 2011. link Times cited: 0 Abstract: Effects of oxidation-process-induced atomic disorder on exte… read moreAbstract: Effects of oxidation-process-induced atomic disorder on extended electronic states in the channel region of narrow Si nanowire (NW) field-effect-transistors (FETs) are theoretically investigated by using the molecular dynamics, empirical tight-binding, and non-equilibrium Green's function methods. Simulation results show that the injection velocity in n-type Si NW FETs is less affected by the disorder compared to p-type devices, which can be attributed to differences in the in-plane carrier profile. read less NOT USED (high confidence) C. Wilcox, M. Strout, and J. Bieman, “Tool support for software lookup table optimization,” Scientific programming. 2011. link Times cited: 8 Abstract: A number of scientific applications are performance-limited … read moreAbstract: A number of scientific applications are performance-limited by expressions that repeatedly call costly elementary functions. Lookup table (LUT) optimization accelerates the evaluation of such functions by reusing previously computed results. LUT methods can speed up applications that tolerate an approximation of function results, thereby achieving a high level of fuzzy reuse. One problem with LUT optimization is the difficulty of controlling the tradeoff between performance and accuracy. The current practice of manual LUT optimization adds programming effort by requiring extensive experimentation to make this tradeoff, and such hand tuning can obfuscate algorithms. In this paper we describe a methodology and tool implementation to improve the application of software LUT optimization. Our Mesa tool implements source-to-source transformations for C or C++ code to automate the tedious and error-prone aspects of LUT generation such as domain profiling, error analysis, and code generation. We evaluate Mesa with five scientific applications. Our results show a performance improvement of 3.0 × and 6.9 × for two molecular biology algorithms, 1.4 × for a molecular dynamics program, 2.1 × to 2.8 × for a neural network application, and 4.6 × for a hydrology calculation. We find that Mesa enables LUT optimization with more control over accuracy and less effort than manual approaches. read less NOT USED (high confidence) T. Coquil, J. Fang, and L. Pilon, “Molecular dynamics study of the thermal conductivity of amorphous nanoporous silica,” International Journal of Heat and Mass Transfer. 2011. link Times cited: 65 NOT USED (high confidence) A. Reinhardt and J. Doye, “Free energy landscapes for homogeneous nucleation of ice for a monatomic water model.,” The Journal of chemical physics. 2011. link Times cited: 90 Abstract: We simulate the homogeneous nucleation of ice from supercool… read moreAbstract: We simulate the homogeneous nucleation of ice from supercooled liquid water at 220 K in the isobaric-isothermal ensemble using the MW monatomic water potential. Monte Carlo simulations using umbrella sampling are performed in order to determine the nucleation free energy barrier. We find the Gibbs energy profile to be relatively consistent with that predicted by classical nucleation theory; the free energy barrier to nucleation was determined to be ~18 k(B)T and the critical nucleus comprised ~85 ice particles. Growth from the supercooled liquid gives clusters that are predominantly cubic, whilst starting with a pre-formed subcritical nucleus of cubic or hexagonal ice results in the growth of predominantly that phase of ice only. read less NOT USED (high confidence) S. Ju, X.-gang Liang, and X. Xu, “Out-of-plane thermal conductivity of polycrystalline silicon nanofilm by molecular dynamics simulation,” Journal of Applied Physics. 2011. link Times cited: 24 Abstract: The out-of-plane thermal conductivity of polycrystalline sil… read moreAbstract: The out-of-plane thermal conductivity of polycrystalline silicon nanofilm is investigated by molecular dynamics simulation. The polycrystalline silicon nanofilm with a random shape of grains is generated by the three-dimensional Voronoi tessellation method. The out-of-plane thermal conductivity of polycrystalline silicon nanofilm at different temperature, film thickness, and average grain size is calculated by the Muller-Plathe method. The results indicate that the polycrystalline thermal conductivity is lower than that of the bulk single crystal and the single crystal nanofilm of silicon. The out-of-plane thermal conductivity of polycrystalline silicon nanofilm is insensitive to temperature and film thickness that is apparently larger than grain size, but mainly depends on the grain size. read less NOT USED (high confidence) J. P. Lewis et al., “Advances and applications in the FIREBALL ab initio tight‐binding molecular‐dynamics formalism,” physica status solidi (b). 2011. link Times cited: 177 Abstract: One of the outstanding advancements in electronic‐structure … read moreAbstract: One of the outstanding advancements in electronic‐structure density‐functional methods is the Sankey–Niklewski (SN) approach [Sankey and Niklewski, Phys. Rev. B 40, 3979 (1989)]; a method for computing total energies and forces, within an ab initio tight‐binding formalism. Over the past two decades, several improvements to the method have been proposed and utilized to calculate materials ranging from biomolecules to semiconductors. In particular, the improved method (called FIREBALL) uses separable pseudopotentials and goes beyond the minimal sp3 basis set of the SN method, allowing for double numerical (DN) basis sets with the addition of polarization orbitals and d‐orbitals to the basis set. Herein, we report a review of the method, some improved theoretical developments, and some recent application to a variety of systems. read less NOT USED (high confidence) S. Hoilijoki, E. Holmström, and K. Nordlund, “Enhancement of irradiation-induced defect production in Si nanowires,” Journal of Applied Physics. 2011. link Times cited: 18 Abstract: We performed classical molecular dynamics simulations of def… read moreAbstract: We performed classical molecular dynamics simulations of defect production in small-diameter hexagonal Si nanowires under Ar ion irradiation. Using irradiation energies of 30 eV to 10 keV, we find that for low energies the defect production in the nanowires may be enhanced by as much as a factor of 3 in comparison to bulk Si due to the large surface-to-volume ratio of the systems. Conversely, at higher energies the increased transmission of ions causes a significant decrease in defect production. read less NOT USED (high confidence) F. Zirkelbach, B. Stritzker, K. Nordlund, J. Lindner, W. Schmidt, and E. Rauls, “Combined ab initio and classical potential simulation study on silicon carbide precipitation in silicon,” Physical Review B. 2011. link Times cited: 22 Abstract: Atomistic simulations on the silicon carbide precipitation i… read moreAbstract: Atomistic simulations on the silicon carbide precipitation in bulk silicon employing both, classical potential and first-principles methods are presented. The calculations aim at a comprehensive, microscopic understanding of the precipitation mechanism in the context of controversial discussions in the literature. For the quantum-mechanical treatment, basic processes assumed in the precipitation process are calculated in feasible systems of small size. The migration mechanism of a carbon 〈1 0 0〉 interstitial and silicon 〈11 0〉 self-interstitial in otherwise defect-free silicon are investigated using density functional theory calculations. The influence of a nearby vacancy, another carbon interstitial and a substitutional defect as well as a silicon self-interstitial has been investigated systematically. Interactions of various combinations of defects have been characterized including a couple of selected migration pathways within these configurations. Most of the investigated pairs of defects tend to agglomerate allowing for a reduction in strain. The formation of structures involving strong carbon–carbon bonds turns out to be very unlikely. In contrast, substitutional carbon occurs in all probability. A long range capture radius has been observed for pairs of interstitial carbon as well as interstitial carbon and vacancies. A rather small capture radius is predicted for substitutional carbon and silicon self-interstitials. Initial assumptions regarding the precipitation mechanism of silicon carbide in bulk silicon are established and conformability to experimental findings is discussed. Furthermore, results of the accurate first-principles calculations on defects and carbon diffusion in silicon are compared to results of classical potential simulations revealing significant limitations of the latter method. An approach to work around this problem is proposed. Finally, results of the classical potential molecular dynamics simulations of large systems are examined, which reinforce previous assumptions and give further insight into basic processes involved in the silicon carbide transition. read less NOT USED (high confidence) D. Daisenberger et al., “Polyamorphic amorphous silicon at high pressure: raman and spatially resolved X-ray scattering and molecular dynamics studies.,” The journal of physical chemistry. B. 2011. link Times cited: 34 Abstract: We studied the low-frequency Raman and X-ray scattering beha… read moreAbstract: We studied the low-frequency Raman and X-ray scattering behavior of amorphous silicon (a-Si) at high pressure throughout the range where the density-driven polyamorphic transformation between the low-density amorphous (LDA) semiconductor and a novel metallic high-density amorphous (HDA) polyamorph occurs. The experimental data were analyzed with the aid of molecular dynamics (MD) simulations using the Stillinger-Weber potential. The heat capacity of a-Si obtained from the low pressure Raman data exhibits non Debye-like behavior, but the effect is small, and our data support the conclusion that no boson peak is present. The high-pressure Raman data show the presence of a distinct low frequency band for the HDA polyamorph in agreement with ab initio MD simulations. Spatially resolved synchrotron X-ray diffraction was used to study the high pressure behavior of the a-Si sample throughout the LDA-HDA transition range without interference by crystallization events. The X-ray data were analyzed using an iterative refinement strategy to extract real-space structural information. The appearance of the first diffraction peak (FDP) in the scattering function S(Q) is discussed in terms of the void structure determined from Voronoi analysis of the MD simulation data. read less NOT USED (high confidence) P. A. Apte and A. Gautam, “Nonmonotonic Dependence of the Absolute Entropy on Temperature in Supercooled Stillinger-Weber Silicon,” Journal of Statistical Physics. 2011. link Times cited: 6 NOT USED (high confidence) C. D. Cruz, K. Termentzidis, P. Chantrenne, and X. Kleber, “Molecular dynamics simulations for the prediction of thermal conductivity of bulk silicon and silicon nanowires: Influence of interatomic potentials and boundary conditions,” Journal of Applied Physics. 2011. link Times cited: 62 Abstract: The reliability of molecular dynamics (MD) results depends s… read moreAbstract: The reliability of molecular dynamics (MD) results depends strongly on the choice of interatomic potentials and simulation conditions. Five interatomic potentials have been evaluated for heat transfer MD simulations of silicon, based on the description of the harmonic (dispersion curves) and anharmonic (linear thermal expansion) properties. The best interatomic potential is the second nearest-neighbor modified embedded atom method potential followed by the Stillinger-Weber, and then the Tersoff III. However, the prediction of the bulk silicon thermal conductivity leads to the conclusion that the Tersoff III potential gives the best results for isotopically pure silicon at high temperatures. The thermal conductivity of silicon nanowires as a function of cross-section and length is calculated, and the influence of the boundary conditions is studied for those five potentials. read less NOT USED (high confidence) J. Los, C. Bichara, and R. Pellenq, “Tight binding within the fourth moment approximation: Efficient implementation and application to liquid Ni droplet diffusion on graphene.” 2011. link Times cited: 9 Abstract: (Received 8 February 2011; revised manuscript received 13 Ma… read moreAbstract: (Received 8 February 2011; revised manuscript received 13 May 2011; published 31 August 2011)Application of the fourth moment approximation (FMA) to the local density of states within a tight bindingdescription to build a reactive, interatomic interaction potential for use in large scale molecular simulations,is a logical and significant step forward to improve the second moment approximation, standing at the basisof several, widely used (semi-)empirical interatomic interaction models. In this paper we present a sufficientlydetailed description of the FMA and its technical implications, containing the essential elements for an efficientimplementationinasimulationcode.Usingarecent,existingFMA-basedmodelforC-Nisystems,weinvestigatedthesizedependenceofthediffusionofaliquidNiclusteronagraphenesheetandfindapowerlawdependenceofthediffusionconstantontheclustersize(numberofclusteratoms)withanexponentverycloseto−2 read less NOT USED (high confidence) L.-M. Wang and X. Zeng, “Molecular dynamics simulations of femtosecond laser ablation of silicon,” Proceedings of 2011 International Conference on Electronics and Optoelectronics. 2011. link Times cited: 1 Abstract: Molecular dynamics simulations were carried out to investiga… read moreAbstract: Molecular dynamics simulations were carried out to investigate the ablation process of silicon under irradiation of 266nm femtosecond laser. Evolutions of macro-variables were studied and final Profile and movement traces of atoms were obtained in Si(100) with laser intensity of 400GW/cm2. Characteristics of ablation processes of Si(100) and Si(111) were compared. The amount of removal atoms and ablation depths were analyzed quantitatively in the two bulks with laser intensity of 400GW/cm2. Propagations of stress wave in the two bulks were also investigated. read less NOT USED (high confidence) W. Hujo, B. S. Jabes, V. K. Rana, C. Chakravarty, and V. Molinero, “The Rise and Fall of Anomalies in Tetrahedral Liquids,” Journal of Statistical Physics. 2011. link Times cited: 64 NOT USED (high confidence) A. Dongare and B. Lamattina, “Deformation and Failure Mechanisms in Ceramic-Reinforced Metal-Matrix Composites at Atomic Scales.” 2011. link Times cited: 1 NOT USED (high confidence) K. Esfarjani, G. Chen, and H. Stokes, “Heat transport in silicon from first-principles calculations,” Physical Review B. 2011. link Times cited: 577 Abstract: Using harmonic and anharmonic force constants extracted from… read moreAbstract: Using harmonic and anharmonic force constants extracted from density functional calculations within a supercell, we have developed a relatively simple but general method to compute thermodynamic and thermal properties of any crystal. First, from the harmonic, cubic, and quartic force constants, we construct a force field for molecular dynamics. It is exact in the limit of small atomic displacements and thus does not suffer from inaccuracies inherent in semiempirical potentials such as Stillinger-Weber's. By using the Green-Kubo formula and molecular dynamics simulations, we extract the bulk thermal conductivity. This method is accurate at high temperatures where three-phonon processes need to be included to higher orders, but may suffer from size scaling issues. Next, we use perturbation theory (Fermi golden rule) to extract the phonon lifetimes and compute the thermal conductivity $\ensuremath{\kappa}$ from the relaxation-time approximation. This method is valid at most temperatures, but will overestimate $\ensuremath{\kappa}$ at very high temperatures, where higher-order processes neglected in our calculations also contribute. As a test, these methods are applied to bulk crystalline silicon, and the results are compared and differences are discussed in more detail. The presented methodology paves the way for a systematic approach to model heat transport in solids using multiscale modeling, in which the relaxation time due to anharmonic three-phonon processes is calculated quantitatively, in addition to the usual harmonic properties such as phonon frequencies and group velocities. It also allows the construction of an accurate bulk interatomic potentials database. read less NOT USED (high confidence) I. Saika-Voivod, H. King, P. Tartaglia, F. Sciortino, and E. Zaccarelli, “Silica through the eyes of colloidal models—when glass is a gel,” Journal of Physics: Condensed Matter. 2011. link Times cited: 11 Abstract: We perform molecular dynamics simulations of ‘floating bond’… read moreAbstract: We perform molecular dynamics simulations of ‘floating bond’ (FB) models of network-forming liquids and compare the structure and dynamics against the BKS model of silica (van Beest et al 1990 Phys. Rev. Lett. 64 1955), with the aim of gaining a better understanding of glassy silica in terms of the variety of non-ergodic states seen in colloids. At low densities, all the models form tetrahedral networks. At higher densities, tailoring the FB model to allow a higher number of bonds does not capture the structure seen in BKS. Upon rescaling the time and length in order to compare mean squared displacements between models, we find that there are significant differences in the temperature dependence of the diffusion coefficient at high density. Additionally, the FB models show a greater range in variability in the behavior of the non-ergodicity parameter and caging length, quantities used to distinguish colloidal gels and glasses. Hence, we find that the glassy behavior of BKS silica can be interpreted as a ‘gel’ at low densities, with only a marginal gel-to-glass crossover at higher densities. read less NOT USED (high confidence) S. Mahajan, G. Subbarayan, and B. Sammakia, “Estimating Kapitza Resistance Between \rm Si\hbox-\rm SiO_2 Interface Using Molecular Dynamics Simulations,” IEEE Transactions on Components, Packaging and Manufacturing Technology. 2011. link Times cited: 20 Abstract: The interface between nano-scale films is of relevance in ma… read moreAbstract: The interface between nano-scale films is of relevance in many critical applications. Specifically, recent technological advances in semiconductor industry that utilize silicon-on-insulator devices have given importance to the understanding of thermal transport across ${\rm Si}{\hbox{-}}{\rm SiO}_{2}$ interface. Estimates of interfacial (Kapitza) resistance to the thermal transport across ${\rm Si}{\hbox{-}}{\rm SiO}_{2}$ films do not appear to exist at the present time. In this paper, we develop and carryout reverse non-equilibrium molecular dynamics simulations by imposing known heat flux to determine the Kapitza resistance between ${\rm Si}{\hbox{-}}{\rm SiO}_{2}$ thin films. For the ${\rm Si}{\hbox{-}}{\rm SiO}_{2}$ interface, the average Kapitza resistance for a ${\sim}{8}~{\rm\AA}$ thick oxide layer system was 0.503 ${\times}10^{-9}~{\rm m}^{2}{\rm K}/{\rm W}$ and for a ${\sim}{\rm 11.5}~{\rm\AA}$ thick oxide layer system was 0.518 $\,\times 10^{-9}~{\rm m}^{2}{\rm K}/{\rm W}$. These values were of the same order of magnitude as the Kapitza resistance values determined from the acoustic mismatch model and the diffuse mismatch model for the ${\rm Si}\hbox{-}{\rm SiO}_{2}$ interface. read less NOT USED (high confidence) C. Krzeminski, Q. Brulin, V. Cuny, E. Lecat, E. Lampin, and F. Cleri, “Molecular dynamics simulation of the recrystallization of amorphous Si layers: Comprehensive study of the dependence of the recrystallization velocity on the interatomic potential,” arXiv: Computational Physics. 2011. link Times cited: 37 Abstract: The molecular dynamics method is applied to simulate the rec… read moreAbstract: The molecular dynamics method is applied to simulate the recrystallization of an amorphous/crystalline silicon interface. The atomic structure of the amorphous material is constructed with the method of Wooten, Winer, and Weaire. The amorphous on crystalline stack is annealed afterward on a wide range of temperature and time using five different interatomic potentials: Stillinger-Weber, Tersoff, EDIP, SW115, and Lenosky. The simulations are exploited to systematically extract the recrystallization velocity. A strong dependency of the results on the interatomic potential is evidenced and explained by the capability of some potentials (Tersoff and SW115) to correctly handle the amorphous structure, while other potentials (Stillinger-Weber, EDIP, and Lenosky) lead to the melting of the amorphous. Consequently, the interatomic potentials are classified according to their ability to simulate the solid or the liquid phase epitaxy. read less NOT USED (high confidence) M. Tungare, Y. Shi, N. Tripathi, P. Suvarna, and F. Shahedipour-Sandvik, “A Tersoff‐based interatomic potential for wurtzite AlN,” physica status solidi (a). 2011. link Times cited: 41 Abstract: Aluminum nitride (AlN) is a popular buffer layer and interla… read moreAbstract: Aluminum nitride (AlN) is a popular buffer layer and interlayer. The understanding of how AlN serves as a wetting and fracture‐mitigating layer relies on molecular pictures of the AlN layer and the interfaces. However, molecular dynamics (MD) simulation studies on AlN system, particularly on its wurtzite phase, have been limited. This is because most existing interatomic force fields of AlN target the less common zinc blende phase. Here, we report a new Tersoff‐based AlN force field for its wurtzite structure. This potential has been extensively tested in terms of lattice parameters, bulk modulus, cohesive energy, and heat capacity. In addition, thermal expansion coefficient (TEC) of wurtzite AlN, a key property to precisely model heterostructures, has been calculated using MD method. The value of 2.66 × 10−6 K−1 calculated at 300 K for TEC is in excellent agreement with the reported experimental value. read less NOT USED (high confidence) A. Soper, “Water: two liquids divided by a common hydrogen bond.,” The journal of physical chemistry. B. 2011. link Times cited: 33 Abstract: The structure of water is the subject of a long and ongoing … read moreAbstract: The structure of water is the subject of a long and ongoing controversy. Unlike simpler liquids, where atomic interactions are dominated by strong repulsive forces at short distances and weaker attractive (van der Waals) forces at longer distances, giving rise to local atomic coordination numbers of order 12, water has pronounced and directional hydrogen bonds which cause the dense liquid close-packed structure to open out into a disordered and dynamic network, with coordination number 4-5. Here I show that water structure can be accurately represented as a mixture of two identical, interpenetrating, molecular species separated by common hydrogen bonds. Molecules of one type can form hydrogen bonds with molecules of the other type but cannot form hydrogen bonds with molecules of the same type. These hydrogen bonds are strong along the bond but weak with respect to changes in the angle between neighboring bonds. The observed pressure and temperature dependence of water structure and thermodynamic properties follow naturally from this choice of water model, and it also gives a simple explanation of the enduring claims based on spectroscopic evidence that water is a mixture of two components. read less NOT USED (high confidence) D. Ward, X. W. Zhou, B. M. Wong, F. Doty, and J. Zimmerman, “Accuracy of existing atomic potentials for the CdTe semiconductor compound.,” The Journal of chemical physics. 2011. link Times cited: 35 Abstract: CdTe and CdTe-based Cd(1-x)Zn(x)Te (CZT) alloys are importan… read moreAbstract: CdTe and CdTe-based Cd(1-x)Zn(x)Te (CZT) alloys are important semiconductor compounds that are used in a variety of technologies including solar cells, radiation detectors, and medical imaging devices. Performance of such systems, however, is limited due to the propensity of nano- and micro-scale defects that form during crystal growth and manufacturing processes. Molecular dynamics simulations offer an effective approach to study the formation and interaction of atomic scale defects in these crystals, and provide insight on how to minimize their concentrations. The success of such a modeling effort relies on the accuracy and transferability of the underlying interatomic potential used in simulations. Such a potential must not only predict a correct trend of structures and energies of a variety of elemental and compound lattices, defects, and surfaces but also capture correct melting behavior and should be capable of simulating crystalline growth during vapor deposition as these processes sample a variety of local configurations. In this paper, we perform a detailed evaluation of the performance of two literature potentials for CdTe, one having the Stillinger-Weber form and the other possessing the Tersoff form. We examine simulations of structures and the corresponding energies of a variety of elemental and compound lattices, defects, and surfaces compared to those obtained from ab initio calculations and experiments. We also perform melting temperature calculations and vapor deposition simulations. Our calculations show that the Stillinger-Weber parameterization produces the correct lowest energy structure. This potential, however, is not sufficiently transferrable for defect studies. Origins of the problems of these potentials are discussed and insights leading to the development of a more transferrable potential suitable for molecular dynamics simulations of defects in CdTe crystals are provided. read less NOT USED (high confidence) L. T. Le and V. Molinero, “Nanophase segregation in supercooled aqueous solutions and their glasses driven by the polyamorphism of water.,” The journal of physical chemistry. A. 2011. link Times cited: 78 Abstract: We use large-scale molecular dynamics simulations to investi… read moreAbstract: We use large-scale molecular dynamics simulations to investigate the phase transformation of aqueous solutions of electrolytes cooled at the critical rate to avoid the crystallization of ice. Homogeneous liquid solutions with up to 20% moles of ions demix on cooling producing nanophase segregated glasses with characteristic dimensions of phase segregation of about 5 nm. The immiscibility is driven by the transformation of water to form a four-coordinated low-density liquid (LDL) as it crosses the liquid-liquid transformation temperature T(LL) of the solution. The ions cannot be incorporated into the tetrahedral LDL network and are expelled to form a solute-rich water nanophase. The simulations quantitatively reproduce the relative amounts of low and high-density liquid water as a function of solute content in LiCl glasses [Suzuki and Mishima, Phys. Rev. Lett. 2000, 85, 1322-1325] and provide direct evidence of segregation in aqueous glasses and their dimensions of phase segregation. read less NOT USED (high confidence) K. Sasikumar and P. Keblinski, “Effect of chain conformation in the phonon transport across a Si-polyethylene single-molecule covalent junction,” Journal of Applied Physics. 2011. link Times cited: 35 Abstract: We use nonequilibrium molecular dynamics simulations to stud… read moreAbstract: We use nonequilibrium molecular dynamics simulations to study heat transfer across molecular junctions formed by alkane chains covalently bonded to crystalline silicon leads. We focus our studies on the role of chain conformation on phonon transport across junctions and along the chain. We find that in the case of straight chains, all trans conformations, the silicon-polyethylene junction conductance is 180 pW/K, and heat flows ballistically, i.e. with no resistance, along the chain. The introduction of gauche conformations (kinks) leads to a nonzero thermal resistance of the chain and also reduces the junction conductance to 100 pW/K. The chain thermal resistance is proportional to the number of gauche conformations indicating that they act as strong and independent phonon scattering centers. We attribute the 80% enhancement in junction conductance during extension from coiled to straight chain conformation to ballistic (coherent) phonon transport along a straight chain. read less NOT USED (high confidence) T. Watanabe, “Dynamic bond-order force field,” Journal of Computational Electronics. 2011. link Times cited: 8 NOT USED (high confidence) P. Han and G. Bester, “Interatomic potentials for the vibrational properties of III-V semiconductor nanostructures,” Physical Review B. 2011. link Times cited: 22 Abstract: We derive interatomic potentials for zinc blende InAs, InP, … read moreAbstract: We derive interatomic potentials for zinc blende InAs, InP, GaAs and GaP semiconductors with possible applications in the realm of nanostructures. The potentials include bond stretching interaction between the nearest and next-nearest neighbors, a three body term and a long-range Coulomb interaction. The optimized potential parameters are obtained by (i) fitting to bulk phonon dispersions and elastic properties and (ii) constraining the parameter space to deliver well behaved potentials for the structural relaxation and vibrational properties of nanostructure clusters. The targets are thereby calculated by density functional theory for clusters of up to 633 atoms. We illustrate the new capability by the calculation Kleinman and Gr\"uneisen parameters and of the vibrational properties of nanostructures with 3 to 5.5 nm diameter. read less NOT USED (high confidence) K. Fichthorn, Y. Tiwary, T. Hammerschmidt, P. Kratzer, and M. Scheffler, “Analytic many-body potential for GaAs(001) homoepitaxy: Bulk and surface properties,” Physical Review B. 2011. link Times cited: 14 Abstract: We employ atomic-scale simulation methods to investigate bul… read moreAbstract: We employ atomic-scale simulation methods to investigate bulk and surface properties of an analytic TersoffAbell type potential for describing interatomic interactions in GaAs. The potential is a modified form of that proposed by Albe and colleagues [Phys. Rev. B 66, 035205 (2002)] in which the cut-off parameters for the As-As interaction have been shortened. With this modification, many bulk properties predicted by the potential for solid GaAs are the same as those in the original potential, but properties of the GaAs(001) surface better match results from first-principles calculations with density-functional theory (DFT). We tested the ability of the potential to reproduce the phonon dispersion and heat capacity of bulk solid GaAs by comparing it to experiment and the overall agreement is good. In the modified potential, the GaAs(001) β2(2 × 4) reconstruction is favored under As-rich growth conditions in agreement with DFT calculations. Additionally, the binding energies and diffusion barriers for a Ga adatom on the β2(2 × 4) reconstruction generally match results from DFT calculations. These studies indicate that the potential is suitable for investigating aspects of GaAs(001) homoepitaxy. read less NOT USED (high confidence) S. Zhang et al., “Voronoi Structural Evolution of Bulk Silicon upon Melting,” Chinese Physics Letters. 2011. link Times cited: 2 Abstract: The Voronoi structural evolution of silicon upon melting is … read moreAbstract: The Voronoi structural evolution of silicon upon melting is investigated using a molecular dynamics simulation. At temperatures below the melting point, the solid state system is identified to have a four-fold coordination structure 〈4,0,0,0〉. As the temperature increases, the five-fold coordination 〈2,3,0,0〉 and six-fold coordination structures 〈2,2,2,0〉 and 〈0,6,0,0〉 are observed. This is explained in terms of increasing atomic displacement due to thermal motion and the trapping of the moving atoms by others. At temperatures above the melting point, nearly all of the four-fold coordination structures grows into multiple-fold coordination ones. read less NOT USED (high confidence) S. Zhao, R. Ramírez, R. Vuilleumier, and D. Borgis, “Molecular density functional theory of solvation: from polar solvents to water.,” The Journal of chemical physics. 2011. link Times cited: 95 Abstract: A classical density functional theory approach to solvation … read moreAbstract: A classical density functional theory approach to solvation in molecular solvent is presented. The solvation properties of an arbitrary solute in a given solvent, both described by a molecular force field, can be obtained by minimization of a position and orientation-dependent free-energy density functional. In the homogeneous reference fluid approximation, limited to two-body correlations, the unknown excess term of the functional approximated by the angular-dependent direct correlation function of the pure solvent. We show that this function can be extracted from a preliminary MD simulation of the pure solvent by computing the angular-dependent pair distribution function and solving subsequently the molecular Ornstein-Zernike equation using a discrete angular representation. The corresponding functional can then be minimized in the presence of an arbitrary solute on a three-dimensional cubic grid for positions and Gauss-Legendre angular grid for orientations to provide the solvation structure and free-energy. This two-step procedure is proved to be much more efficient than direct molecular dynamics simulations combined to thermodynamic integration schemes. The approach is shown to be relevant and accurate for prototype polar solvents such as the Stockmayer solvent or acetonitrile. For water, although correct for neutral or moderately charged solute, it tends to underestimate the tetrahedral solvation structure around H-bonded solutes, such as spherical ions. This can be corrected by introducing suitable three-body correlation terms that restore both an accurate hydration structure and a satisfactory energetics. read less NOT USED (high confidence) J. Carrete, R. Longo, and L. J. Gallego, “Prediction of phonon thermal transport in thin GaAs, InAs and InP nanowires by molecular dynamics simulations: influence of the interatomic potential,” Nanotechnology. 2011. link Times cited: 12 Abstract: A number of different potentials are currently being used in… read moreAbstract: A number of different potentials are currently being used in molecular dynamics simulations of semiconductor nanostructures. Confusion can arise if an inappropriate potential is used. To illustrate this point, we performed direct molecular dynamics simulations to predict the room temperature lattice thermal conductivity λ of thin GaAs, InAs and InP nanowires. In each case, simulations performed using the classical Harrison potential afforded values of λ about an order of magnitude smaller than those obtained using more elaborate potentials (an Abell–Tersoff, as parameterized by Hammerschmidt et al for GaAs and InAs, and a potential of Vashishta type for InP). These results will be a warning to those wishing to use computer simulations to orient the development of quasi-one-dimensional systems as heat sinks or thermoelectric devices. read less NOT USED (high confidence) L. Shokeen and P. Schelling, “Thermodynamics and kinetics of silicon under conditions of strong electronic excitation,” Journal of Applied Physics. 2011. link Times cited: 28 Abstract: We present a detailed analysis of a recently-developed empir… read moreAbstract: We present a detailed analysis of a recently-developed empirical potential to describe silicon under conditions of strong electronic excitation. The parameters of the potential are given as smooth functions of the electronic temperature Te, with the dependence determined by fitting to finite-temperature density-functional theory calculations. We analyze the thermodynamics of this potential as a function of the electronic temperature Te and lattice temperature Tion. The potential predicts phonon spectra in good agreement with finite-temperature density-functional theory, including the previously predicted lattice instability. We predict that the melting temperature Tm decreases strongly as a function of Te. Electronic excitation has a strong effect on the rate of crystallization from the melt. In particular, high Te results in very slow kinetics for growing crystal from the melt, due mainly to the fact that diamond becomes much less stable as Te increases. Finally, we explore annealing amorphous Si (a-Si) ... read less NOT USED (high confidence) S. Huang and T. Zhu, “Atomistic mechanisms of lithium insertion in amorphous silicon,” The Lancet. 2011. link Times cited: 113 NOT USED (high confidence) N. Zhang et al., “Deformation mechanisms in silicon nanoparticles,” Journal of Applied Physics. 2011. link Times cited: 65 Abstract: We report here on the observation of dislocation nucleation … read moreAbstract: We report here on the observation of dislocation nucleation and glide in silicon nanoparticles, after phase transformation from diamond cubic to β-tin crystal structure, within the formed β-tin metallic phase region in atomistic simulations of indentation. The simulation results provide an explanation of the super-high hardness of silicon nanoparticles measured in experiments. By comparing the simulation results with experimental measurement of hardness, we are able to evaluate the performance of two widely used interatomic potential functions: Stillinger–Weber and Tersoff potentials. Through simulations, we have found a critical size of silicon nanoparticles where there is a change in deformation mechanisms, strength, and hardness. The effect of the applied strain rate on simulation results is also investigated. read less NOT USED (high confidence) R. Bonner et al., “Die level thermal storage for improved cooling of pulsed devices,” 2011 27th Annual IEEE Semiconductor Thermal Measurement and Management Symposium. 2011. link Times cited: 13 Abstract: In many communications applications semiconductor devices op… read moreAbstract: In many communications applications semiconductor devices operate in a pulsed mode, where rapid temperature transients are continuously experienced within the die. We proposed a novel junction-level cooling technology where a metallic phase change material (PCM) was embedded in close proximity to the active transistor channels without interfering with the device's electrical response. Here we present multiscale simulations that were performed to determine the thermal performance improvement and electrical performance impact under pulsed operating conditions. The modeling effort was focused on Gallium Nitride (GaN) on Silicon (Si) chips with Indium (In) as the PCM. To accurately capture the microscale transient melting process, a hierarchical multiscale model was developed that includes linking of atomistic-level molecular dynamics simulations and macroscale finite element analysis simulations. Macroscale physics, including the melting process, were captured with a transient two-dimensional finite element analysis (FEA) model. The FEA model also includes interfacial and contact resistances between the semiconductor materials and PCM. Non-equilibrium Molecular Dynamic (MD) simulations were performed to estimate the value of the interfacial resistances between the Si substrate and the In PCM, which included a new interatomic potential between In and Si that was developed from experimental scattering results available in the literature. The thermal modeling results indicate 26% more heat can be dissipated through the PCM enhanced transistor while maintain a safe operating temperature. A separate electrical modeling effort showed that the metallic PCM layer did not create appreciable parasitic capacitances as long as the PCM was farther than 1μm from the active channel. The lower, more constant temperatures achieved by this technology can help improve the reliability and performance of future communication devices. read less NOT USED (high confidence) J. Carrete, L. J. Gallego, L. M. Varela, and N. Mingo, “Surface roughness and thermal conductivity of semiconductor nanowires: Going below the Casimir limit,” Physical Review B. 2011. link Times cited: 69 Abstract: By explicitly considering surface roughness at the atomic le… read moreAbstract: By explicitly considering surface roughness at the atomic level, we quantitatively show that the thermal conductivity of Si nanowires can be lower than Casimir's classical limit. However, this violation only occurs for deep surface degradation. For shallow surface roughness, the Casimir formula is shown to yield a good approximation to the phonon mean free paths and conductivity, even for nanowire diameters as thin as 2.22 nm. Our exact treatment of roughness scattering is in stark contrast with a previously proposed perturbative approach, which is found to overpredict scattering rates by an order of magnitude. The obtained results suggest that a complete theoretical understanding of some previously published experimental results is still lacking. read less NOT USED (high confidence) V. V. Vasisht, S. Saw, and S. Sastry, “Liquid–liquid critical point in supercooled silicon,” Nature Physics. 2011. link Times cited: 135 NOT USED (high confidence) P. Alfaro, R. Cisneros, M. Bizarro, M. Cruz‐Irisson, and C. Wang, “Raman scattering by confined optical phonons in Si and Ge nanostructures.,” Nanoscale. 2011. link Times cited: 25 Abstract: A microscopic theory of the Raman scattering based on the lo… read moreAbstract: A microscopic theory of the Raman scattering based on the local bond-polarizability model is presented and applied to the analysis of phonon confinement in porous silicon and porous germanium, as well as nanowire structures. Within the linear response approximation, the Raman shift intensity is calculated by means of the displacement-displacement Green's function and the Born model, including central and non-central interatomic forces. For the porous case, the supercell method is used and ordered pores are produced by removing columns of Si or Ge atoms from their crystalline structures. This microscopic theory predicts a remarkable shift of the highest-frequency of first-order Raman peaks towards lower energies, in comparison with the crystalline case. This shift is discussed within the quantum confinement framework and quantitatively compared with the experimental results obtained from porous silicon samples, which were produced by anodizing p--type (001)-oriented crystalline Si wafers in a hydrofluoric acid bath. read less NOT USED (high confidence) A. Mokshin, S. O. Zabegaev, and R. Khusnutdinoff, “Dynamic heterogeneity of a colloidal solution near the sol-gel transition,” Physics of the Solid State. 2011. link Times cited: 12 NOT USED (high confidence) T. Zohdi, “Dynamics of clusters of charged particulates in electromagnetic fields,” International Journal for Numerical Methods in Engineering. 2011. link Times cited: 16 Abstract: The dynamics of rigid clusters of charged particulates is th… read moreAbstract: The dynamics of rigid clusters of charged particulates is the subject of this work. The work ascertains what properties of the cluster control its dynamic response to an external electromagnetic field. A primary focus is on the role of the distribution of the charges within the cluster and the effects of the Lorentz force on the overall body's linear and angular momentum. The presentation contains a derivation of the equations governing a charged cluster's dynamics and development of corresponding numerical methods for the simulation. Numerical examples are presented, along with comparisons to qualitative analytical results, where possible. Copyright © 2010 John Wiley & Sons, Ltd. read less NOT USED (high confidence) A. Beaber et al., “Smaller is tougher,” Philosophical Magazine. 2011. link Times cited: 33 Abstract: “Smaller is stronger” is now a tenet generally consistent wi… read moreAbstract: “Smaller is stronger” is now a tenet generally consistent with the predominance of evidence. An equally accepted tenet is that fracture toughness almost always decreases with increasing yield strength. Can “smaller is tougher” then be consistent with these two tenets? It is taught in undergraduate engineering courses that one design parameter that allows for both increased strength and fracture toughness is reduced grain size. The present study on the very brittle semiconductor silicon proves this exception to the rule and demonstrates that smaller can be both stronger and tougher. Three nanostructures are considered theoretically and experimentally: thin films, nanospheres, and nanopillars. Using a simple work per unit fracture area approach, it is shown at small scale that toughness is inversely proportional to the square root of size. This is supported by experimental evidence from in situ electron microscopy nanoindentation at length scales of less than a micron. It is further suggested that dislocation shielding can explain both strength and toughness increases at the small scales. read less NOT USED (high confidence) R. A. Bernal et al., “Effect of growth orientation and diameter on the elasticity of GaN nanowires. A combined in situ TEM and atomistic modeling investigation.,” Nano letters. 2011. link Times cited: 88 Abstract: We characterized the elastic properties of GaN nanowires gro… read moreAbstract: We characterized the elastic properties of GaN nanowires grown along different crystallographic orientations. In situ transmission electron microscopy tensile tests were conducted using a MEMS-based nanoscale testing system. Complementary atomistic simulations were performed using density functional theory and molecular dynamics. Our work establishes that elasticity size dependence is limited to nanowires with diameters smaller than 20 nm. For larger diameters, the elastic modulus converges to the bulk values of 300 GPa for c-axis and 267 GPa for a- and m-axis. read less NOT USED (high confidence) C. Ribeiro-Silva, J. Rino, L. G. Gonçalves, and A. Picinin, “An effective interaction potential for gallium phosphide,” Journal of Physics: Condensed Matter. 2011. link Times cited: 14 Abstract: An effective interatomic potential consisting of two- and th… read moreAbstract: An effective interatomic potential consisting of two- and three-body covalent interactions is used here to study the properties of gallium phosphide by molecular dynamics simulations. The many-body interatomic potential accounts for the energy scale, length scale and mechanical properties of GaP. At atmospheric pressure, the calculated melting temperature, linear thermal expansion, vibrational density of states and specific heat are in excellent agreement with experimental results. The structural phase transition induced by hydrostatic pressure at 27 GPa is also in quite good agreement with experimental findings. We also studied the energy of vacancy formation in the GaP lattice and the surface energy, which is in reasonable agreement with experimental data. read less NOT USED (high confidence) L. Xiong, G. Tucker, D. McDowell, and Y. Chen, “Coarse-grained atomistic simulation of dislocations,” Journal of The Mechanics and Physics of Solids. 2011. link Times cited: 93 NOT USED (high confidence) Z. Zhang, A. Chatterjee, C. Grein, A. Ciani, and P. Chung, “Molecular Dynamics Simulation of MBE Growth
of CdTe/ZnTe/Si,” Journal of Electronic Materials. 2011. link Times cited: 6 NOT USED (high confidence) T. Luo and J. Lloyd, “Molecular dynamics study of thermal transport in GaAs-self-assembly monolayer-GaAs junctions with ab initio characterization of thiol-GaAs bonds,” Journal of Applied Physics. 2011. link Times cited: 33 Abstract: Thermal dissipation in molecular electronic devices is a cri… read moreAbstract: Thermal dissipation in molecular electronic devices is a critical issue for the proper functioning of such devices. In this work, molecular dynamics (MD) simulations were carried out to study the thermal energy transport in GaAs-SAM (self-assembly monolayer)-GaAs junctions, with alkanedithiols being the SAM molecules. In order to characterize the molecule-GaAs interface, ab initio density functional theory (DFT) was used to study the structural and binding properties of alkanethiolates on GaAs(001) surfaces. Parameters of classical potentials, which were used to model the molecule-GaAs interactions, were obtained by fitting to the results from the DFT calculations. Then, nonequilibrium MD (NEMD) simulations were performed to reveal the GaAs-SAM interfacial thermal conductance at different temperatures. The results from this work showed that the GaAs-SAM interfaces are the major sources of thermal resistance in the GaAs-SAM-GaAs junctions. The delocalized phonon modes carry thermal energy efficiently insid... read less NOT USED (high confidence) X. W. Zhou and R. Jones, “Effects of cutoff functions of Tersoff potentials on molecular dynamics simulations of thermal transport,” Modelling and Simulation in Materials Science and Engineering. 2011. link Times cited: 19 Abstract: Past molecular dynamics studies of thermal transport have pr… read moreAbstract: Past molecular dynamics studies of thermal transport have predominantly used Stillinger–Weber potentials. As materials continuously shrink, their properties increasingly depend on defect and surface effects. Unfortunately, Stillinger–Weber potentials are best used for diamond-cubic-like bulk crystals. They cannot represent the energies of many metastable phases, nor can they accurately predict the energetics of defective and surface regions. To study nanostructured materials, where these regions can dominate thermal transport, the accuracy of Tersoff potentials in representing these structures is more desirable. Based upon an analysis of thermal transport in a GaN system, we demonstrate that the cutoff function of the existing Tersoff potentials may lead to problems in determining the thermal conductivity. To remedy this issue, improved cutoff schemes are proposed and evaluated. read less NOT USED (high confidence) S. Saw, N. Ellegaard, W. Kob, and S. Sastry, “Computer simulation study of the phase behavior and structural relaxation in a gel-former modeled by three-body interactions.,” The Journal of chemical physics. 2011. link Times cited: 20 Abstract: We report a computer simulation study of a model gel-former … read moreAbstract: We report a computer simulation study of a model gel-former obtained by modifying the three-body interactions of the Stillinger-Weber potential for silicon. This modification reduces the average coordination number and consequently shifts the liquid-gas phase coexistence curve to low densities, thus facilitating the formation of gels without phase separation. At low temperatures and densities, the structure of the system is characterized by the presence of long linear chains interconnected by a small number of three coordinated junctions at random locations. At small wave vectors the static structure factor shows a nonmonotonic dependence on temperature, a behavior which is due to the competition between the percolation transition of the particles and the stiffening of the formed chains. We compare in detail the relaxation dynamics of the system as obtained from molecular dynamics with the one obtained from Monte Carlo dynamics. We find that the bond correlation function displays stretched exponential behavior at moderately low temperatures and densities, but exponential relaxation at low temperatures. The bond lifetime shows an Arrhenius behavior, independent of the microscopic dynamics. For the molecular dynamics at low temperatures, the mean squared displacement and the (coherent and incoherent) intermediate scattering function display at intermediate times a dynamics with ballistic character and we show that this leads to compressed exponential relaxation. For the Monte Carlo dynamics we always find an exponential or stretched exponential relaxation. Thus we conclude that the compressed exponential relaxation observed in experiments is due to the out-of-equilibrium dynamics. read less NOT USED (high confidence) C. Tomaras, B. Schmid, and W. Schirmacher, “Replica field theory for anharmonic sound attenuation in glasses,” Journal of Non-crystalline Solids. 2011. link Times cited: 1 NOT USED (high confidence) J. Goicochea, B. Michel, and C. Amon, “Molecular dynamics simulations of oblique phonon scattering at semiconductor interfaces,” 2010 3rd International Conference on Thermal Issues in Emerging Technologies Theory and Applications. 2010. link Times cited: 0 Abstract: Equilibrium molecular dynamics simulations are used to deter… read moreAbstract: Equilibrium molecular dynamics simulations are used to determine the transmission probability of oblique phonons scattering on flat and rough surfaces. The transmission is determined from the total energy change of the materials comprising the interface. We consider semiconductor films of silicon (Si) and germanium (Ge) as interfacing materials. A symmetric sawtooth (triangular) structure of varying height (similar to that analyzed in Appl. Phys. Lett., 93(8), 2008) is used to introduce surface roughness. We have found that the transmission is a strong function of the phonon incident angle, frequency, mass ratio of the comprising semiconductors and roughness height. An interesting behavior in the transmission probability is observed with the introduction of controlled surface roughness. Low frequency phonons can have transmission values higher than those predicted in the acoustic limit. Conversely, they decrease significantly for high frequency phonons. Maximum and minimum values in the transmission probability are found for surface roughness of 4.34 nm height. read less NOT USED (high confidence) Y. Zhao, C.-yu Wang, Q. Peng, and G. Lu, “Error analysis and applications of a general QM/MM approach,” Computational Materials Science. 2010. link Times cited: 10 NOT USED (high confidence) H. Lei, J. Chen, and P. Ruterana, “Influences of the biaxial strain and c-screw dislocation on the clustering in InGaN alloys,” Journal of Applied Physics. 2010. link Times cited: 20 Abstract: Using the molecular dynamics simulation based on Stillinger–… read moreAbstract: Using the molecular dynamics simulation based on Stillinger–Weber potentials, the roles of lattice mismatch and threading dislocations (c-screw type) on phase segregation in InGaN alloys have been explored. The thermodynamic stability and structural deformation of the InGaN alloys with In-rich clusters are analyzed when biaxial stress and c-screw dislocations act on the systems. The results show that the formation of In-rich clusters is suppressed in the case of lattice mismatch, whereas it takes place in the presence of c-screw dislocations independent of the strain condition of InGaN alloys. read less NOT USED (high confidence) T. Zushi, I. Ohdomari, T. Watanabe, Y. Kamakura, and K. Taniguchi, “Molecular dynamics simulation on LO phonon mode decay in Si nano-structure covered with oxide films,” 2010 International Conference on Simulation of Semiconductor Processes and Devices. 2010. link Times cited: 1 Abstract: A series of molecular dynamics (MD) simulations is conducted… read moreAbstract: A series of molecular dynamics (MD) simulations is conducted to investigate the dynamics of longitudinal optical (LO) phonon in Si nano-structure confined with oxide films. This work is motivated by heat issues in nanoscopic devices; it is considered that the LO phonons with low group velocity are accumulated in the nanoscopic device and the electric property deteriorates. We estimate the relaxation time of the LO phonon and investigate its dependency on the oxide thickness. The calculation results show that the LO phonon decays faster as the oxide thickness increases and turns into acoustic phonon. The result indicates that the presence of SiO2 films promotes the scattering of the phonon and this is effective to diminish the optical phonon. read less NOT USED (high confidence) V. Favre-Nicolin, J. Coraux, M. Richard, and H. Renevier, “Fast computation of scattering maps of nanostructures using graphical processing units,” Journal of Applied Crystallography. 2010. link Times cited: 31 Abstract: Scattering maps from strained or disordered nanostructures a… read moreAbstract: Scattering maps from strained or disordered nanostructures around a Bragg reflection can be either computed quickly using approximations and a (fast) Fourier transform or obtained using individual atomic positions. In this article, it is shown that it is possible to compute up to 4 × 1010 reflections atoms s−1 using a single graphics card, and the manner in which this speed depends on the number of atoms and points in reciprocal space is evaluated. An open-source software library (PyNX) allowing easy scattering computations (including grazing-incidence conditions) in the Python language is described, with examples of scattering from non-ideal nanostructures. read less NOT USED (high confidence) F. Zirkelbach, B. Stritzker, K. Nordlund, J. Lindner, W. Schmidt, and E. Rauls, “Defects in carbon implanted silicon calculated by classical potentials and first-principles methods,” Physical Review B. 2010. link Times cited: 7 Abstract: A comparative theoretical investigation of carbon interstiti… read moreAbstract: A comparative theoretical investigation of carbon interstitials in silicon is presented. Calculations using classical potentials are compared to first-principles density-functional theory calculations of the geometries, formation, and activation energies of the carbon dumbbell interstitial, showing the importance of a quantummechanical description of this system. In contrast to previous studies, the present first-principles calculations of the interstitial carbon migration path yield an activation energy that excellently matches the experiment. The bond-centered interstitial configuration shows a net magnetization of two electrons, illustrating the need for spin-polarized calculations. read less NOT USED (high confidence) M. Oliver, G. Dubois, M. Sherwood, D. M. Gage, and R. Dauskardt, “Molecular Origins of the Mechanical Behavior of Hybrid Glasses,” Advanced Functional Materials. 2010. link Times cited: 68 Abstract: Hybrid organic‐inorganic glasses exhibit unique electro‐opti… read moreAbstract: Hybrid organic‐inorganic glasses exhibit unique electro‐optical properties along with excellent thermal stability. Their inherently mechanically fragile nature, however, which derives from the oxide component of the hybrid glass network together with the presence of terminal groups that reduce network connectivity, remains a fundamental challenge for their integration in nanoscience and energy technologies. We report on a combined synthesis and computational strategy to elucidate the effect of molecular structure on mechanical properties of hybrid glass films. We first demonstrate the importance of rigidity percolation to elastic behavior. Secondly, using a novel application of graph theory, we reveal the complex 3‐D fracture path at the molecular scale and show that fracture energy in brittle hybrid glasses is fundamentally governed by the bond percolation properties of the network. The computational tools and scaling laws presented provide a robust predictive capability for guiding precursor selection and molecular network design of advanced hybrid organic‐inorganic materials. read less NOT USED (high confidence) K. Kang and W. Cai, “Size and temperature effects on the fracture mechanisms of silicon nanowires: Molecular dynamics simulations,” International Journal of Plasticity. 2010. link Times cited: 136 NOT USED (high confidence) A. Kerrache, N. Mousseau, and L. J. Lewis, “Amorphous silicon under mechanical shear deformations: Shear velocity and temperature effects,” Physical Review B. 2010. link Times cited: 8 Abstract: Mechanical shear deformations lead, in some cases, to effect… read moreAbstract: Mechanical shear deformations lead, in some cases, to effects similar to those resulting from ion irradiation. Here we characterize the effects of shear velocity and temperature on amorphous silicon (\aSi) modelled using classical molecular dynamics simulations based on the empirical Environment Dependent Inter-atomic Potential (EDIP). With increasing shear velocity at low temperature, we find a systematic increase in the internal strain leading to the rapid appearance of structural defects (5-fold coordinated atoms). The impacts of externally applied strain can be almost fully compensated by increasing the temperature, allowing the system to respond more rapidly to the deformation. In particular, we find opposite power-law relations between the temperature and the shear velocity and the deformation energy. The spatial distribution of defects is also found to strongly depend on temperature and strain velocity. For low temperature or high shear velocity, defects are concentrated in a few atomic layers near the center of the cell while, with increasing temperature or decreasing shear velocity, they spread slowly throughout the full simulation cell. This complex behavior can be related to the structure of the energy landscape and the existence of a continuous energy-barrier distribution. read less NOT USED (high confidence) R. Pottathuparambil and R. Sass, “FPGA-based three-body molecular dynamics simulator,” 2010 International Conference on High Performance Computing & Simulation. 2010. link Times cited: 1 Abstract: The computer simulation of three-body potentials using the S… read moreAbstract: The computer simulation of three-body potentials using the Stillinger-Weber method has been extensively used in the study of three-body molecular forces between partially rigid molecules such as silicon. The Stillinger-Weber method of computing three-body interactions is generally computationally intense. This paper presents a FPGA-based framework that is designed and implemented on a Virtex 4 that can be used to compute Stillinger-Weber potential. This framework extends the PowerPC instruction set to include vector operations and a custom datapath. Design details of the framework along with initial performance results with two well-known data sets are also presented. The results show that FPGA design is competitive with current microprocessors on small problems sizes and with only half of the algorithm implemented. As the problem size increases, the results suggest the FPGA-based design will gain a significant performance advantage. Coding the second half of the algorithm will increase the on-chip parallelism as well. read less NOT USED (high confidence) E. Holmström, L. Toikka, A. Krasheninnikov, and K. Nordlund, “Response of mechanically strained nanomaterials to irradiation: Insight from atomistic simulations,” Physical Review B. 2010. link Times cited: 29 Abstract: By combining analytical molecular-dynamics with density-func… read moreAbstract: By combining analytical molecular-dynamics with density-functional theory simulations, we study the radiation hardness of mechanically strained low-dimensional nanosystems such as carbon nanotubes, graphene, and Si nanowires. We show that the radiation hardness of all these structures decreases with strain but the effect is most pronounced in nanowire due to the bulk structure of its core in contrast with the planar structure of nanotubes and graphene. Our results not only elucidate the microscopic mechanism of irradiation-induced defect production in strained nanomaterials but also provide quantitative information required for assessing the stability of nanocomponents in composite materials subjected to mechanical strain and irradiation, e.g., in space applications. read less NOT USED (high confidence) V. Kuzkin, “Interatomic force in systems with multibody interactions.,” Physical review. E, Statistical, nonlinear, and soft matter physics. 2010. link Times cited: 10 Abstract: The system of particles (atoms) interacting via multibody in… read moreAbstract: The system of particles (atoms) interacting via multibody interatomic potential of general form is considered. Possible variants of partition for the total force acting on a single particle into pair contributions are discussed. Two definitions for the force acting between a pair of particles are compared. The forces coincide only if the particles interact via pair or embedded-atom potentials. However in literature both definitions are used in order to determine Cauchy stress tensor. A simplest example of pure shear for perfect square lattice is analyzed. Two methods for stress calculation are considered. It is observed that, at least in the particular case, stresses calculated using classical continuum mechanics definition do not depend on the way of partition for the total force. In contrast, Hardy's definition gives different results depending on the radius of localization function. The differences strongly depend on the way of the partition. read less NOT USED (high confidence) M. Aboy, L. Pelaz, P. López, E. Bruno, and S. Mirabella, “Atomistic analysis of B clustering and mobility degradation in highly B-doped junctions.” 2010. link Times cited: 1 Abstract: In this paper we discuss from an atomistic point of view som… read moreAbstract: In this paper we discuss from an atomistic point of view some of the issues involved in the modeling of electrical characteristics evolution in silicon devices as a result of ion implantation and annealing processes in silicon. In particular, evolution of electrically active dose, sheet resistance and hole mobility has been investigated for high B concentration profiles in pre-amorphized Si. For this purpose, Hall measurements combined with atomistic kinetic Monte Carlo atomistic simulations have been performed. An apparent anomalous behavior has been observed for the evolution of the active dose and the sheet resistance, in contrast to opposite trend evolutions reported previously. Our results indicate that this anomalous behavior is due to large variations in hole mobility with active dopant concentration, much larger than that associated to the classical dependence of hole mobility with carrier concentration. Simulations suggest that hole mobility is significantly degraded by the presence of a large concentration of boron-interstitial clusters, indicating the existence of an additional scattering mechanism. Copyright © 2009 John Wiley & Sons, Ltd. read less NOT USED (high confidence) K. Eriguchi, Y. Nakakubo, A. Matsuda, Y. Takao, and K. Ono, “Model for Bias Frequency Effects on Plasma-Damaged Layer Formation in Si Substrates,” Japanese Journal of Applied Physics. 2010. link Times cited: 42 Abstract: Bias frequency effects on damaged-layer formation during pla… read moreAbstract: Bias frequency effects on damaged-layer formation during plasma processing were investigated. High-energy ion bombardment on Si substrates and subsequent damaged-layer formation are modeled on the basis of range theory. We propose a simplified model introducing a stopping power Sd(Eion) with a power-law dependence on the energy of incident ions (Eion). We applied this model to damaged-layer formation in plasma with an rf bias, where various energies of incident ions are expected. The ion energy distribution function (IEDF) was considered, and the distribution profile of defect sites was estimated. We found that, owing to the characteristic ion-energy-dependent stopping power Sd(Eion) and the straggling, the bias frequency effect was subject to suppression, i.e., the thickness of the damaged layer is a weak function of bias frequency. These predicted features were compared with experimental data on the damage created using an inductively coupled plasma reactor with two different bias frequencies; 13.56 MHz and 400 kHz. The model prediction showed good agreement with experimental observations of the samples exposed to plasmas with various bias configurations. read less NOT USED (high confidence) M. Yu, H. Ji, J. Wang, Y. Jin, R. Huang, and X. Zhang, “Simulation on Boron Concentration Profile in Silicon Introduced by Plasma Doping,” IEEE Transactions on Plasma Science. 2010. link Times cited: 5 Abstract: Plasma doping (PD) is a potential shallow junction technolog… read moreAbstract: Plasma doping (PD) is a potential shallow junction technology for advanced integrated circuits manufacturing. Accurate simulation on PD is thus needed. The simulation on PD induced B concentration profile in Si is presented in this paper. A computational efficiency Molecular Dynamics (MD) method is applied. The plasma potential, the deviation of ion energy, and the injection angle are considered. The effect of physical models, including different ion species, threshold energy of displacement, energy variation model, electronic stopping model, is investigated. It is demonstrated that the proper agreement between simulation results and experimental data can be achieved for PD. read less NOT USED (high confidence) J. Chen, G. Zhang, and B. Li, “How to improve the accuracy of equilibrium molecular dynamics for computation of thermal conductivity,” Physics Letters A. 2010. link Times cited: 67 NOT USED (high confidence) A. Mavromaras et al., “Computational materials engineering: Capabilities of atomic-scale prediction of mechanical, thermal, and electrical properties of microelectronic materials,” 2010 11th International Thermal, Mechanical & Multi-Physics Simulation, and Experiments in Microelectronics and Microsystems (EuroSimE). 2010. link Times cited: 3 Abstract: Atomic-scale computational materials engineering offers an e… read moreAbstract: Atomic-scale computational materials engineering offers an exciting complement to experimental observations, revealing critical materials property data, and providing understanding which can form the basis for innovation. This contribution reviews the current state of atomic-scale simulations and their capabilities to predict mechanical, thermal, and electric properties of microelectronics materials. Specific examples are the elastic moduli of compounds such as aluminum oxide, the strength of an aluminum/silicon nitride interface, the first-principles prediction of coefficients of thermal expansion of bulk aluminum and silicon nitride, thermal conductivity of polyethylene, the prediction of the diffusion coefficient of hydrogen in metallic nickel, the calculation of dielectric properties of zinc oxide and optical properties of silicon carbide. The final example illustrates the control of the work function in the HfO2/TiN interface of a CMOS gate stack. For an increasing number of materials properties, computed values possess accuracies similar to measured data. Such accuracy has become possible due to advances in theoretical approaches and numerical algorithms combined with the astounding increase in compute power. read less NOT USED (high confidence) L. Larini, L. Lu, and G. Voth, “The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials.,” The Journal of chemical physics. 2010. link Times cited: 111 Abstract: Many methodologies have been proposed to build reliable and … read moreAbstract: Many methodologies have been proposed to build reliable and computationally fast coarse-grained potentials. Typically, these force fields rely on the assumption that the relevant properties of the system under examination can be reproduced using a pairwise decomposition of the effective coarse-grained forces. In this work it is shown that an extension of the multiscale coarse-graining technique can be employed to parameterize a certain class of two-body and three-body force fields from atomistic configurations. The use of explicit three-body potentials greatly improves the results over the more commonly used two-body approximation. The method proposed here is applied to develop accurate one-site coarse-grained water models. read less NOT USED (high confidence) T. Zushi, Y. Kamakura, K. Taniguchi, I. Ohdomari, and T. Watanabe, “Molecular Dynamics Simulation of Heat Transport in Silicon Nano-structures Covered with Oxide Films,” Japanese Journal of Applied Physics. 2010. link Times cited: 7 Abstract: We perform a series of molecular dynamics (MD) simulations t… read moreAbstract: We perform a series of molecular dynamics (MD) simulations to investigate the heat transport in Si nano-structures, while explicitly including oxide cover layers in the simulation system for the first time. The dependences of thermal diffusion velocity on the thicknesses of the SiO2 film and Si lattice are investigated. The results show that thermal diffusion velocity decreases with Si lattice thickness and does not depend on SiO2 film thickness. read less NOT USED (high confidence) V. Samvedi and V. Tomar, “The role of straining and morphology in thermal conductivity of a set of Si–Ge superlattices and biomimetic Si–Ge nanocomposites,” Journal of Physics D: Applied Physics. 2010. link Times cited: 32 Abstract: The ability to alter the thermal and mechanical properties o… read moreAbstract: The ability to alter the thermal and mechanical properties of nanostructures by tailoring nanoscale morphology has led to vast activity in applications such as high figure of merit (ZT) thermoelectric, microelectronic and optoelectronic devices. Two types of nanostructures that have gained significant attention are Si–Ge superlattices and Si–Ge biomimetic nanocomposites, in which one phase is distributed in the other phase in a staggered biomimetic manner similar to biological materials. A systematic comparison of the atomistic factors that affect their thermal behaviour under different extents of straining at a range of temperatures remains to be performed. In this investigation, such analyses are performed for a set of Si–Ge superlattices and Si–Ge biomimetic nanocomposites using non-equilibrium molecular dynamics (NEMD) simulations at three different temperatures (400, 600 and 800 K) and at strain levels varying between −10% and 10%. Analyses indicate that the nanoscale morphology differences between the superlattices and the nanocomposites lead to a striking contrast in the phonon spectral density, interfacial thermal boundary resistance and thermal conductivity. In the case of the nanocomposites, morphology variation at the nanoscale and the tensile or compressive straining at temperatures from 400 to 800 K do not have a significant effect on the changes in thermal conductivity values. Such factors, however, strongly influence the thermal conductivity of superlattices. The thickness of the nanocomposites, however, is found to influence the thermal conductivity values significantly under straining, with the effect of straining increasing with increasing nanocomposite thickness. A relation based on the effective medium approach is shown to fit the NEMD calculated nanocomposite thermal conductivity values. read less NOT USED (high confidence) W. Miller, “Numerical simulations of bulk crystal growth on different scales: silicon and GeSi,” physica status solidi (b). 2010. link Times cited: 11 Abstract: Numerical modelling has become an important tool for improvi… read moreAbstract: Numerical modelling has become an important tool for improving or introducing new processes in bulk crystal growth. For a complete description, scales ranging from atomistic ones up to those of industrial furnaces have to be considered. This article presents methods used on different scales for the Czochralski growth of silicon as well as of Ge1–xSix alloys and for ingot casting of silicon. It shows the recent developments for the different scales and the attempts at coupling the approaches. read less NOT USED (high confidence) T. Zohdi, “On the Dynamics of Charged Electromagnetic Particulate Jets,” Archives of Computational Methods in Engineering. 2010. link Times cited: 64 NOT USED (high confidence) A. Galashev, “Simulation of silicon nanoparticles stabilized by hydrogen at high temperatures,” Journal of Nanoparticle Research. 2010. link Times cited: 4 NOT USED (high confidence) L. Hale, X. W. Zhou, J. Zimmerman, N. Moody, R. Ballarini, and W. Gerberich, “Phase transformations, dislocations and hardening behavior in uniaxially compressed silicon nanospheres,” Computational Materials Science. 2010. link Times cited: 26 NOT USED (high confidence) R. Choudhury, C. Gattinoni, G. Makov, and A. D. Vita, “Molecular dynamics studies of the dissociated screw dislocation in silicon,” Journal of Physics: Condensed Matter. 2010. link Times cited: 6 Abstract: Characterizing the motion of dislocations through covalent, … read moreAbstract: Characterizing the motion of dislocations through covalent, high Peierls barrier materials is a key problem in materials science, while despite the progress in experimental studies the actual observation of the atomistic behaviour involved in core migration remains limited. We have applied a hybrid embedding scheme to investigate the dissociated screw dislocation in silicon, consisting of two 30° partials separated by a stacking fault ribbon, under the influence of a constant external strain. Our ‘learn on the fly’ hybrid technique allows us to calculate the forces on atoms in the vicinity of the core region using the tight binding Kwon potential, whilst the remainder of the bulk matrix is treated within a classical approximation. Applying a 5% strain to the dissociated screw dislocation, for a simulation time of 100 ps at a temperature of 600 K, we observe movement of the partials through two different mechanisms: double kink formation and square ring diffusion at the core. Our results suggest that in these conditions, the role of solitons or anti-phase defects in seeding kink formation and subsequent migration is an important one, which should be taken into account in future studies. read less NOT USED (high confidence) S. Ryu and W. Cai, “A gold–silicon potential fitted to the binary phase diagram,” Journal of Physics: Condensed Matter. 2010. link Times cited: 30 Abstract: We develop an empirical interatomic potential model for the … read moreAbstract: We develop an empirical interatomic potential model for the gold–silicon binary system that is fitted to the experimental phase diagram. The model is constructed on the basis of the modified embedded-atom-method formalism and its binary phase diagram is computed by efficient free energy methods. The eutectic temperature and eutectic composition of the model match well with the experimental values. We expect the model to be useful for atomistic simulations of gold-catalyzed growth of silicon nanowires. read less NOT USED (high confidence) C.-J. Huang, C.-J. Wu, H. Teng, and K. Chiang, “Determination of mechanical property of nanostructure using nano-macro equivalent mechanics method,” 2010 International Conference on Nanoscience and Nanotechnology. 2010. link Times cited: 0 Abstract: The importance of research in nanoscale structure grew in th… read moreAbstract: The importance of research in nanoscale structure grew in the last two decades. However, the experimental method in this research field is not yet sufficiently advanced to provide people with a reliable and suitable mechanical property. The aim of this paper was to determine the utility of the equivalent method for establishing a mechanical property definition. In this method, equivalent atomistic-continuum elements replaced an originally discrete atomic structure. The method was based on the semi-empirical potential function and the finite element method. This study utilized a spring network model to describe interaction force of bi-atoms, and to investigate the Young's modulus of silicon/germanium, carbon nanotube, and copper in a nanostructure. The Young's moduli of these materials were confirmed by literature. Results indicated that the equivalent mechanics method may provide the basis for a useful and convenient process. read less NOT USED (high confidence) Y. Mishin, M. Asta, and J. Li, “Atomistic modeling of interfaces and their impact on microstructure and properties,” Acta Materialia. 2010. link Times cited: 418 NOT USED (high confidence) R. Soulairol and F. Cleri, “Interface structure of silicon nanocrystals embedded in an amorphous silica matrix,” Solid State Sciences. 2010. link Times cited: 17 NOT USED (high confidence) G. Lucas, M. Bertolus, and L. Pizzagalli, “An environment-dependent interatomic potential for silicon carbide: calculation of bulk properties, high-pressure phases, point and extended defects, and amorphous structures,” Journal of Physics: Condensed Matter. 2010. link Times cited: 41 Abstract: An interatomic potential has been developed to describe inte… read moreAbstract: An interatomic potential has been developed to describe interactions in silicon, carbon and silicon carbide, based on the environment-dependent interatomic potential (EDIP) (Bazant et al 1997 Phys. Rev. B 56 8542). The functional form of the original EDIP has been generalized and two sets of parameters have been proposed. Tests with these two potentials have been performed for many properties of SiC, including bulk properties, high-pressure phases, point and extended defects, and amorphous structures. One parameter set allows us to keep the original EDIP formulation for silicon, and is shown to be well suited for modelling irradiation-induced effects in silicon carbide, with a very good description of point defects and of the disordered phase. The other set, including a new parametrization for silicon, has been shown to be efficient for modelling point and extended defects, as well as high-pressure phases. read less NOT USED (high confidence) W. M. Brown, A. Thompson, and P. Schultz, “Efficient hybrid evolutionary optimization of interatomic potential models.,” The Journal of chemical physics. 2010. link Times cited: 19 Abstract: The lack of adequately predictive atomistic empirical models… read moreAbstract: The lack of adequately predictive atomistic empirical models precludes meaningful simulations for many materials systems. We describe advances in the development of a hybrid, population based optimization strategy intended for the automated development of material specific interatomic potentials. We compare two strategies for parallel genetic programming and show that the Hierarchical Fair Competition algorithm produces better results in terms of transferability, despite a lower training set accuracy. We evaluate the use of hybrid local search and several fitness models using system energies and/or particle forces. We demonstrate a drastic reduction in the computation time with the use of a correlation-based fitness statistic. We show that the problem difficulty increases with the number of atoms present in the systems used for model development and demonstrate that vectorization can help to address this issue. Finally, we show that with the use of this method, we are able to "rediscover" the exact model for simple known two- and three-body interatomic potentials using only the system energies and particle forces from the supplied atomic configurations. read less NOT USED (high confidence) A. Galashev, “Molecular dynamics study of hydrogenated silicon clusters at high temperatures,” Molecular Physics. 2009. link Times cited: 5 Abstract: This paper reports on a study of the stability of silicon cl… read moreAbstract: This paper reports on a study of the stability of silicon clusters of intermediate size at a high temperature. The temperature dependence of the physicochemical properties of 60- and 73-atom silicon nanoparticles are investigated using the molecular dynamics method. The 73-atom particles have a crystal structure, a random atomic packing, and a packing formed by inserting a 13-atom icosahedron into a 60-atom fullerene. They are surrounded by a ‘coat’ from 60 atoms of hydrogen. The nanoassembled particle at the presence of a hydrogen ‘coat’ has the most stable number (close to four) of Si–Si bonds per atom. The structure and kinetic properties of a hollow single-layer fullerene-structured Si60 cluster are considered in the temperature range 10 K ≤ T ≤ 1760 K. Five series of calculations are conducted, with a simulation of several media inside and outside the Si60 cluster, specifically, the vacuum and interior spaces filled with 30 and 60 hydrogen atoms with and without the exterior hydrogen environment of 60 atoms. Fullerene surrounded by a hydrogen ‘coat’ and containing 60 hydrogen atoms in the interior space has a higher stability. Such clusters have smaller self-diffusion coefficients at high temperatures. The fullerene stabilized with hydrogen is stable to the formation of linear atomic chains up to the temperatures 270–280 K. read less NOT USED (high confidence) K. Albe, J. Nord, and K. Nordlund, “Dynamic charge-transfer bond-order potential for gallium nitride,” Philosophical Magazine. 2009. link Times cited: 10 Abstract: We present an analytical interatomic potential for gallium n… read moreAbstract: We present an analytical interatomic potential for gallium nitride which is based on a new environment-dependent dynamic charge-transfer model. The model consists of a short-ranged bond-order potential that accounts for covalent/metallic interactions and an ionic Coulomb potential with effective point charges that are dynamically adjusted. In contrast to established models, these point charges are distance-dependent and vary with the number and type of nearest neighbour atoms. The basic concepts stem from the idea of bond charges. We assume pairwise symmetric charge transfer between atoms of different type forming a bond. Charge contributions of all bonds to an atomic site are weighted and added, yielding the effective charge per atom. Mulliken charges, as obtained from density-functional theory calculations within the local-density approximation, are used for adjusting the parameters and functional form of the potential. The short-range contributions are chosen as angular-dependent many-body bond-order potentials, which can be understood as an extension of a Finnis–Sinclair type potential. read less NOT USED (high confidence) A. M. Ukpong, “Studies of the electronic and vibrational signatures of the unusual bonding geometries in melt-quenched amorphous silicon,” Molecular Physics. 2009. link Times cited: 2 Abstract: Tight-binding molecular dynamics simulations have been perfo… read moreAbstract: Tight-binding molecular dynamics simulations have been performed to investigate the effect of quenching rate of the Si melt on the resulting local structure of amorphous silicon. Different quenching rates were used to cool liquid silicon in the simulations to demonstrate that the choice of quenching rates significantly influences the resulting local structure. The calculated pair correlation functions show that the local structure is sensitive to the thermal processing of the liquid silicon melt. The use of cooling rates higher than 10−13 K s−1 appears to prevent the activation of the required structural re-arrangements necessary to stabilise the networks, causing unexpected bonding geometries to develop. The electronic signatures of the defects show that only the triangular defect structure contributes resonance states to the conduction band tail. Also, the vibrational signature of the triangular structure shows a high energy transverse optical mode at 95 meV, indicating that the defect is likely to be unstable at 300 K, although both defects contribute minimal states to the mid-gap level. read less NOT USED (high confidence) J. Végh and D. Graves, “A molecular dynamics study of H radical bombardment of CH3 : Si(1 0 0)— comparison of simulation and experiment,” Journal of Physics D: Applied Physics. 2009. link Times cited: 2 Abstract: Molecular dynamics (MD) simulations have been carried out to… read moreAbstract: Molecular dynamics (MD) simulations have been carried out to examine the bombardment of a methylated Si(1 0 0) surface with thermal (300 K) and elevated energy (1 and 5 eV) H radicals. The simulations are based on a reactive empirical bond order (REBO) potential energy function (PEF) for Si–C–H interactions. The observed product distributions and etch mechanisms for the removal of the CH3 from the surface are consistent with experimental observations in the literature. All of the CH3 groups are removed as SixCyHz species, with SiCH6 being the predominant etch product. No formation of CH4 is seen. Additionally, the accuracy of the REBO PEF for thermal processes is examined and the pertinent limitations are discussed as the basis for future development of simulations of plasma–surface interactions. read less NOT USED (high confidence) R. Cabriolu, M. G. D. Pópolo, and P. Ballone, “Melting of a tetrahedral network model of silica.,” Physical chemistry chemical physics : PCCP. 2009. link Times cited: 4 Abstract: Thermal properties of an idealised tetrahedral network model… read moreAbstract: Thermal properties of an idealised tetrahedral network model of silica are investigated by Monte Carlo simulations. The interatomic potential consists of anharmonic stretching and bending terms, plus a short range repulsion. The model includes a bond interchange rule similar to the well known Wooten, Winer and Weaire (WWW) algorithm (see Phys. Rev. Lett., 1985, 54, 1392). Simulations reveal an apparent first order melting transition at T = 2200 K. The computed changes in the local coordination upon melting are consistent with experimental and ab initio data. read less NOT USED (high confidence) H. Tsuda, K. Eriguchi, K. Ono, and H. Ohta, “Molecular-Dynamics-Based Profile Evolution Simulation for Sub-10-nm Si Processing Technology,” Applied Physics Express. 2009. link Times cited: 7 Abstract: Fully atomistic profile evolution simulations in dry etching… read moreAbstract: Fully atomistic profile evolution simulations in dry etching processes have been demonstrated by classical molecular dynamics (MD) simulations. In our first attempt, this technique was applied to 5 nm Si trench etching by halogen (F, Cl, and Br) mono-energetic beams. The trench profile evolutions were dynamically reproduced on the atomic scale and qualitatively agreed with our common view based on the chemical properties of the injected species. This MD-based ab-initio approach is not only a baseline to verify the existing continuum-model-based simulation but a tool to estimate electrical performance including the effects of damaging layers and process margins/yields in the sub-10-nm processing rules. read less NOT USED (high confidence) Z. Chen, Z. Yu, P. Lu, and Y. Liu, “Point defects in relaxed and strained Si studied by molecular dynamics method,” 2009 Asia Communications and Photonics conference and Exhibition (ACP). 2009. link Times cited: 0 Abstract: Molecular dynamics simulations using the Tersoff potential h… read moreAbstract: Molecular dynamics simulations using the Tersoff potential have been performed to investigate the perturbation effects caused by different kinds of the point defects (vacancies and substitutional impurities) on the strained and relaxed Si matrices. Lattice distortion, mean square displacement, pair correlation function and vibrational spectra are studied. It is found that Ge substitution lead to little distortion of the Si matrix. However, vacancy and C substitution lead to more distortion. Diffusion directions of Si atoms around different kinds of point defects are different. When C substitution is introduced in the relaxed Si matrices or Ge substitution is introduced in the strained Si matrices, the system needs longer time to reach equilibrium. The crystallinity and symmetry degree of relaxed Si matrices are more satisfying than those of strained Si matrices after relaxation. Changes of the vibrational spectra caused by vacancy and C substitution are obvious. All above have a great effect on the photoelectric properties of the materials. read less NOT USED (high confidence) E. Bouchbinder, J. Fineberg, and M. P. Marder, “Dynamics of Simple Cracks,” Annual Review of Condensed Matter Physics. 2009. link Times cited: 70 Abstract: Cracks are the major vehicle for material failure and often … read moreAbstract: Cracks are the major vehicle for material failure and often exhibit rather complex dynamics. The laws that govern their motion have remained an object of constant study for nearly a century. The simplest kind of dynamic crack is a single crack that moves along a straight line. We first briefly review the current understanding of this “simple” object. We then critically examine the assumptions of the classic, scale-free theory of dynamic fracture and note when it works and how it may fail if certain assumptions are relaxed. Several examples are provided in which the introduction of physical scales into this scale-free theory profoundly affects both a crack’s structure and the resulting dynamics. read less NOT USED (high confidence) L. Lymperakis, M. Friák, and J. Neugebauer, “Atomistic calculations on interfaces: Bridging the length and time scales,” The European Physical Journal Special Topics. 2009. link Times cited: 8 NOT USED (high confidence) J. Zimmerman, B. M. Wong, R. Jones, J. Templeton, and J. W. Lee, “Enhanced molecular dynamics for simulating porous interphase layers in batteries.” 2009. link Times cited: 0 Abstract: Understanding charge transport processes at a molecular leve… read moreAbstract: Understanding charge transport processes at a molecular level using computational techniques is currently hindered by a lack of appropriate models for incorporating anistropic electric fields in molecular dynamics (MD) simulations. An important technological example is ion transport through solid-electrolyte interphase (SEI) layers that form in many common types of batteries. These layers regulate the rate at which electro-chemical reactions occur, affecting power, safety, and reliability. In this work, we develop a model for incorporating electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. In this application, the electric potential is represented on a FE mesh and is calculated from a Poisson equation with source terms determined by the distribution of the atomic charges. Boundary conditions can be imposed naturally using the FE description of the potential, which then propagates to each atom through modified forces. The method is verified using simulations where analytical or theoretical solutions are known. Calculations of salt water solutions in complex domains are performed to understand how ions are attracted to charged surfaces in the presence of electric fields and interfering media. read less NOT USED (high confidence) S. Ryu, C. Weinberger, M. Baskes, and W. Cai, “Improved modified embedded-atom method potentials for gold and silicon,” Modelling and Simulation in Materials Science and Engineering. 2009. link Times cited: 47 Abstract: The modified embedded-atom method interatomic potentials for… read moreAbstract: The modified embedded-atom method interatomic potentials for pure gold and pure silicon are improved in their melting point and latent heat predictions, by modifying the multi-body screening function and the equation of state function. The fitting of the new parameters requires rapid calculations of melting point and latent heat, which are enabled by efficient free-energy methods. The results provide the basis for constructing a cross-potential that will be fitted to the binary gold–silicon phase diagram. read less NOT USED (high confidence) V. Samvedi and V. Tomar, “The role of interface thermal boundary resistance in the overall thermal conductivity of Si–Ge multilayered structures,” Nanotechnology. 2009. link Times cited: 74 Abstract: Nanoscale engineered materials with tailored thermal propert… read moreAbstract: Nanoscale engineered materials with tailored thermal properties are desirable for applications such as highly efficient thermoelectric, microelectronic and optoelectronic devices. It has been shown earlier that by judiciously varying the interface thermal boundary resistance (TBR), thermal conductivity in nanostructures can be controlled. In the presented investigation, the role of TBR in controlling thermal conductivity at the nanoscale is analyzed by performing non-equilibrium molecular dynamics (NEMD) simulations to calculate thermal conductivity of a range of Si–Ge multilayered structures with 1–3 periods, and with four different layer thicknesses. The analyses are performed at three different temperatures (400, 600 and 800 K). As expected, the thermal conductivity of all layered structures increases with the increase in the number of periods as well as with the increase in the monolayer thickness. Invariably, we find that the TBR offered by the interface nearest to the hot reservoir is the highest. This effect is in contrast to the usual notion that each interface contributes equally to the heat transfer resistance in a layered structure. Findings also suggest that for high period structures the average TBR offered by the interfaces is not equal. Findings are used to derive an analytical expression that describes period-length-dependent thermal conductivity of multilayered structures. read less NOT USED (high confidence) H.-jun Shen, “Thermal and tensile properties of Si/Ge core-shell and superlattice nanowires,” Frontiers of Materials Science in China. 2009. link Times cited: 0 NOT USED (high confidence) A. Dongare, L. Zhigilei, A. Rajendran, and B. Lamattina, “Interatomic potentials for atomic scale modeling of metal–matrix ceramic particle reinforced nanocomposites,” Composites Part B-engineering. 2009. link Times cited: 15 NOT USED (high confidence) H. Wei and Y. Xiang, “A generalized Peierls–Nabarro model for kinked dislocations,” Philosophical Magazine. 2009. link Times cited: 9 Abstract: We present a generalized Peierls–Nabarro model for curved di… read moreAbstract: We present a generalized Peierls–Nabarro model for curved dislocations incorporating directly the Peierls energies for both straight dislocations and dislocation kinks. In our model, the anisotropic elastic energy is calculated efficiently using the discrete Fourier transform on the discrete lattice sites of the slip plane, and the discreteness in both the elastic energy and the misfit energy is included. We have used our model to calculate the kink migration and nucleation energies of the 30° dislocations in silicon. The results agree well with those obtained using atomistic potentials and first principles calculations, and the experimental results. read less NOT USED (high confidence) J. Chen, G. Zhang, and B. Li, “Tunable thermal conductivity of Si1−xGex nanowires,” Applied Physics Letters. 2009. link Times cited: 115 Abstract: By using molecular dynamics simulation, we demonstrate that … read moreAbstract: By using molecular dynamics simulation, we demonstrate that the thermal conductivity of silicon-germanium nanowires (Si1−xGex NWs) depends on the composition remarkably. The thermal conductivity reaches the minimum, which is about 18% of that of pure Si NW, when Ge content is 50%. More interesting, with only 5% Ge atoms (Si0.95Ge0.05 NW), SiNW’s thermal conductivity is reduced to 50%. The reduction of thermal conductivity mainly comes from the localization of phonon modes due to random scattering. Our results demonstrate that Si1−xGex NW might have promising application in thermoelectrics. read less NOT USED (high confidence) Y. Park, H. M. Atkulga, A. Grama, and A. Strachan, “Strain relaxation in Si/Ge/Si nanoscale bars from molecular dynamics simulations,” Journal of Applied Physics. 2009. link Times cited: 16 Abstract: We use molecular dynamics (MD) with the reactive interatomic… read moreAbstract: We use molecular dynamics (MD) with the reactive interatomic potential ReaxFF to characterize the local strains of epitaxial Si/Ge/Si nanoscale bars as a function of their width and height. While the longitudinal strain (along the bars length) is independent of geometry, surface relaxation leads to transverse strain relaxation in the Ge section. This strain relaxation increases with increasing height of the Ge section and reduction in its width and is complete (i.e., zero transverse strain) for roughly square cross sections of Ge leading to a uniaxial strain state. Such strain state is desirable in some microelectronics applications. From the MD results, which are in excellent agreement with experiments, we derive a simple model to predict lateral strain as a function of geometry for this class of nanobars. read less NOT USED (high confidence) J. Godet, P. Hirel, S. Brochard, and L. Pizzagalli, “Dislocation nucleation from surface step in silicon: The glide set versus the shuffle set,” physica status solidi (a). 2009. link Times cited: 19 Abstract: We have studied the mechanisms of dislocation nucleation fro… read moreAbstract: We have studied the mechanisms of dislocation nucleation from surface defects in silicon submitted to various stresses and temperatures. Molecular dynamics simulations with three classical potentials have shown the existence of two different plastic modes in silicon which can be activated from surfaces. At high temperatures and low stresses dislocations nucleation occurs in the {111} glide set planes, while at low temperatures and large stresses it occurs in the {111} shuffle set planes. The analysis of dislocation cores and kinks shows structures like those well known in bulk silicon. This study supports the idea that plasticity in crystalline Si structures could be governed by dislocation nucleation from surfaces. read less NOT USED (high confidence) J. Kioseoglou, P. Komninou, and T. Karakostas, “Core models of a‐edge threading dislocations in wurtzite III(Al,Ga,In)‐nitrides,” physica status solidi (a). 2009. link Times cited: 14 Abstract: An empirical bond‐order many body interatomic Tersoff potent… read moreAbstract: An empirical bond‐order many body interatomic Tersoff potential is used for atomistic calculations of the multiple atomic configurations (5/7, 8 and 4) of the a‐edge threading dislocations in III(Al,Ga,In)‐N compound semiconductors. Structural‐ and energy‐related conclusions are drawn which are attributed to the complexity of the III–III metal type and N–N interactions (bondGa–Ga < bondAl–Al < bondIn–In) in connection with the difference of the lattice parameters (aAlN < aGaN < aInN) and the elastic constants. The 5/7‐atomic core configuration is calculated as the most energetically and structurally favourable in all the three compounds. Taking the 5/7‐atom model as a reference, the 8‐atom core model becomes the next favourable one when the lattice parameter increases (aInN) while the 4‐atom core model is the second energetically favourable when the lattice parameter decreases (aAlN). read less NOT USED (high confidence) R. DeMille and V. Molinero, “Coarse-grained ions without charges: reproducing the solvation structure of NaCl in water using short-ranged potentials.,” The Journal of chemical physics. 2009. link Times cited: 72 Abstract: A coarse-grained model of NaCl in water is presented where t… read moreAbstract: A coarse-grained model of NaCl in water is presented where the ions are modeled without charge to avoid computationally challenging electrostatics. A monatomic model of water [V. Molinero and E. B. Moore, J. Phys. Chem. B 113, 4008 (2009)] is used as the basis for this coarse-grain approach. The ability of Na(+) to disrupt the native tetrahedral arrangement of water molecules, and of Cl(-) to integrate within this organization, is preserved in this mW-ion model through parametrization focused on water's solvation of these ions. This model successfully reproduces the structural effect of ions on water, referenced to observations from experiments and atomistic molecular dynamics simulations, while using extremely short-ranged potentials. Without Coulomb interactions the model replicates details of the ion-water structure such as distinguishing contact and solvent-separated ion pairs and the free energy barriers between them. The approach of mimicking ionic effects with short-ranged interactions results in performance gains of two orders of magnitude compared to Ewald methods. Explored over a broad range of salt concentration, the model reproduces the solvation structure and trends of diffusion relative to atomistic simulations and experimental results. The functional form of the mW-ion model can be parametrized to represent other electrolytes. With increased computational efficiency and reliable structural fidelity, this model promises to be an asset for accessing significantly longer simulation time scales with an explicit solvent in a coarse-grained system involving, for example, polyelectrolytes such as proteins, nucleic acids, and fuel-cell membranes. read less NOT USED (high confidence) S. Nangia and B. Garrison, “Advanced Monte Carlo approach to study evolution of quartz surface during the dissolution process.,” Journal of the American Chemical Society. 2009. link Times cited: 28 Abstract: A newly developed Monte Carlo (MC) algorithm designed to stu… read moreAbstract: A newly developed Monte Carlo (MC) algorithm designed to study the complex interplay of dissolution and precipitation reactions on mineral surface is presented. This algorithm utilizes existing advanced reactive and configurational-biased MC techniques with new protocols specific for mineral-water interfaces. This time-independent methodology is especially advantageous for studying the kinetically slow quartz-water dissolution process. The aim is to use this method to understand the role of the local arrangement of reactive sites and surface topography in the surface evolution during dissolution. The simulations were performed in neutral pH medium, and two possible dissolution mechanisms were tested. The results indicate that out of the direct and stepwise mechanisms, the direct mechanism leads to complete dissolution that is not experimentally observed in the natural environment. On the other hand, the stepwise dissolution is more realistic, as it resembles the experimentally observed steady-state dissolution of the quartz-water system. These simulations identify the least coordinated surface sites (Q(1)) as the primary reactive site for hydrolysis and precipitation. Other surface sites (Q(2) and Q(3)) also undergo hydrolysis, but they are sterically hindered and are turned passive by precipitating Q(1) groups. The conclusions from the simulations are dominated by the surface topology of quartz; thus, we believe that the results are applicable for other polymorphs of silica and other protonation conditions. read less NOT USED (high confidence) T. Loerting, V. Brazhkin, and T. Morishita, “Multiple Amorphous–Amorphous Transitions.” 2009. link Times cited: 29 NOT USED (high confidence) L. C. Jacobson, W. Hujo, and V. Molinero, “Thermodynamic stability and growth of guest-free clathrate hydrates: a low-density crystal phase of water.,” The journal of physical chemistry. B. 2009. link Times cited: 246 Abstract: We use molecular dynamics simulations with the monatomic wat… read moreAbstract: We use molecular dynamics simulations with the monatomic water (mW) model to investigate the phase diagram, metastability, and growth of guest-free water clathrates of structure sI and sII. At 1 atm pressure, the simulated guest-free water clathrates are metastable with respect to ice and stable with respect to the liquid up to their melting temperatures, 245+/-2 and 252+/-2 K for sI and sII, respectively. We characterize the growth of the sI and sII water crystals from supercooled water and find that the clathrates are unable to nucleate ice, the stable crystal. We computed the phase relations of ice, guest-free sII clathrate, and liquid water from -1500 to 500 atm. The resulting phase diagram indicates that empty sII may be the stable phase of water at pressures lower than approximately -1300 atm and temperatures lower than 275 K. The simulations show that, even in the region of stability of the empty clathrates, supercooled liquid water crystallizes to ice. This suggests that the barrier for nucleation of ice is lower than that for clathrates. We find no evidence for the existence of the characteristic polyhedral clathrate cages in supercooled extended water. Our results show that clathrates do not need the presence of a guest molecule to grow, but they need the guest to nucleate from liquid water. We conclude that nucleation of empty clathrates from supercooled liquid water would be extremely challenging if not impossible to attain in experiments. We propose two strategies to produce empty water clathrates in laboratory experiments at low positive pressures. read less NOT USED (high confidence) C. Qin, W. Hengan, W. Yu, and W. Xiu-xi, “Orientation and Rate Dependence of Wave Propagation in Shocked Beta-SiC from Atomistic Simulations,” Chinese Physics Letters. 2009. link Times cited: 1 Abstract: The orientation dependence of planar wave propagation in bet… read moreAbstract: The orientation dependence of planar wave propagation in beta-SiC is studied via the molecular dynamics (MD) method. Simulations are implemented under impact loadings in four main crystal directions, i.e., (100), (110), (111), and (112). The dispersion of stress states in different directions increases with rising impact velocity, which implies the anisotropic characteristic of shock wave propagation for beta-SiC materials. We also obtain the Hugoniot relations between the shock wave velocity and the impact velocity, and find that the shock velocity falls into a plateau above a threshold of impact velocity. The shock velocity of the plateaux is dependent on the shock directions, while (111) and (112) can be regarded as equivalent directions as they almost reach the same plateau. A comparison between the atomic stress from MD and the stress from Rankine–Hugoniot jump conditions is also made, and it is found that they agree with each other very well. read less NOT USED (high confidence) E. B. Moore and V. Molinero, “Growing correlation length in supercooled water.,” The Journal of chemical physics. 2009. link Times cited: 157 Abstract: The evolution of the structure of water from the stable high… read moreAbstract: The evolution of the structure of water from the stable high temperature liquid to its glass, low-density amorphous ice (LDA), is studied through large-scale molecular dynamics simulations with the mW model [J. Phys. Chem. B 113, 4008 (2009)]. We characterize the density, translational, and orientational ordering of liquid water from the high temperature stable liquid to the low-density glass LDA at the critical cooling rate for vitrification. A continuous transition to a tetrahedrally ordered low-density liquid is observed at 50 K below the temperature of maximum density and 25 K above a temperature of minimum density. The structures of the low-density liquid and glass are consistent with that of a continuous random tetrahedral network. The liquid-liquid transformation temperature T(LL), defined by the maximum isobaric expansivity, coincides with the maximum rate of change in the local structure of water. Long-range structural fluctuations of patches of four-coordinated molecules form in the liquid. The correlation length of the four-coordinated patches in the liquid increases according to a power law in the range 300 K to T(LL)+10 K; a maximum is predicted at T(LL). To the best of our knowledge this is the first direct estimation of the Widom line of supercooled water through the analysis of structural correlations. read less NOT USED (high confidence) H. Zhao, N. Chen, and Y. Long, “Interfacial potentials for Al/SiC(111),” Journal of Physics: Condensed Matter. 2009. link Times cited: 18 Abstract: To study the metal/semiconductor interface by means of atomi… read moreAbstract: To study the metal/semiconductor interface by means of atomistic simulation, an effective interfacial potential is an important issue. In this work, ab initio adhesive energies are used to derive interfacial potentials for the Al/SiC(111) interface. In order to describe the directional covalent bonds at the interface, we suggest a potential model comprising both two-body and three-body terms. The former is a parameter-free potential obtained by a lattice inversion method and the latter is assigned in modified Stillinger–Weber potential form. The obtained potentials are used to study the position of misfit dislocations in the Al/SiC(111) interface. There is a coherent Al interlayer on the interface plane and the dislocation appears on the Al side. read less NOT USED (high confidence) J. Yuhang, M. Qingyuan, and Z. Wei, “Atomistic simulations of the tensile and melting behavior of silicon nanowires,” Journal of Semiconductors. 2009. link Times cited: 5 Abstract: Molecular dynamics simulations with Stillinger–Weber potenti… read moreAbstract: Molecular dynamics simulations with Stillinger–Weber potential are used to study the tensile and melting behavior of single-crystalline silicon nanowires (SiNWs). The tensile tests show that the tensile behavior of the SiNWs is strongly dependent on the simulation temperature, the strain rate, and the diameter of the nanowires. For a given diameter, the critical load significantly decreases as the temperature increases and also as the strain rate decreases. Additionally, the critical load increases as the diameter increases. Moreover, the melting tests demonstrate that both melting temperature and melting heat of the SiNWs decrease with decreasing diameter and length, due to the increase in surface energy. The melting process of SiNWs with increasing temperature is also investigated. read less NOT USED (high confidence) K. Mandadapu, R. Jones, and P. Papadopoulos, “A homogeneous nonequilibrium molecular dynamics method for calculating thermal conductivity with a three-body potential.,” The Journal of chemical physics. 2009. link Times cited: 39 Abstract: In this work, Evans' homogeneous nonequilibrium molecul… read moreAbstract: In this work, Evans' homogeneous nonequilibrium molecular dynamics method for estimating thermal conductivity is extended to systems employing three-body potentials. This extension is put on a firm theoretical basis and applied to a silicon lattice modeled by the Stillinger-Weber potential. Two new methods are suggested for estimating the thermal conductivity based on a range of values of the fictitious force. Also, kinetic theory is used to estimate the linear range of the fictitious force necessary to bias the heat flow, thereby potentially reducing the number of simulations needed to estimate thermal conductivity. read less NOT USED (high confidence) M. Yu et al., “Simulation on Low Energy Ion Implantation into Ge and SiGe With Molecular Dynamics Method,” 2009 13th International Workshop on Computational Electronics. 2009. link Times cited: 0 Abstract: Using binomial distribution, we have created a structure to … read moreAbstract: Using binomial distribution, we have created a structure to describe Si 1-x Ge x substrate, so ion implantation into Ge and Si 1-x Ge x can be simulated based on Molecular dynamics method. ZBL potential is applied to describe interaction between implanted ion and target atoms. David Cai's electronic stopping power model is applied to calculate collision between implanted ion and electronics. The results of boron implantation into pure Ge and Si 1-x Ge x are compared with SIMS data. The phenomenon of fluence loss due to surface sputtering and backscattering is investigated. Factors affecting range profile and fluence loss including Ge fraction and implant tilt is also presented in this paper.This electronic document is a "live" template. The various components of your paper [title, text, heads, etc.] are already defined on the style sheet, as illustrated by the portions given in this document. read less NOT USED (high confidence) H. Zhao and N. Aluru, “Size and surface orientation effects on thermal expansion coefficient of one-dimensional silicon nanostructures,” Journal of Applied Physics. 2009. link Times cited: 13 Abstract: We perform classical molecular dynamics simulations based on… read moreAbstract: We perform classical molecular dynamics simulations based on the Tersoff interatomic potential to investigate the size and surface orientation dependence of lattice constant and thermal expansion coefficient of one-dimensional silicon nanostructures. Three different surface orientations of silicon are considered, i.e., Si(110), Si(111), and Si(100) with 2×1 reconstruction. For each surface orientation, we investigate nanostructures with thicknesses ranging from 0.3 to 5.0 nm. We compute the vibrational amplitude of surface atoms, lattice constant, and thermal expansion coefficient as a function of size and temperature, and compare them for different surface orientations. An analytical expression is developed to compute the variation of the thermal expansion coefficient with size of the nanostructure. read less NOT USED (high confidence) J. Végh and D. Graves, “Molecular Dynamics Simulations of Ar+–Organic Polymer Interactions,” Plasma Processes and Polymers. 2009. link Times cited: 16 Abstract: MD simulations of ion―organic styrene-containing polymer int… read moreAbstract: MD simulations of ion―organic styrene-containing polymer interactions are reviewed and compared to experiment. We report results for argon ion bombardment of PS, PαMS and P4MS. All three polymers exhibit the formation of a similar, highly cross-linking, dehydrogenated near-surface damaged layer at steady state, but small changes in the structure of the polymer (P4MS and PαMS are isomers) can lead to drastic changes in the initial transient sputtering of the material. We correlate this behavior to differences in radiation chemistry (P4MS and PS are cross-linking while PaMS is a chain scission polymer), and examine how the behavior in MD may relate to larger-scale experimental results, such as roughness formation. read less NOT USED (high confidence) B. Gillespie and H. Wadley, “Atomistic examinations of the solid-phase epitaxial growth of silicon,” Journal of Crystal Growth. 2009. link Times cited: 14 NOT USED (high confidence) X. Huang, X. Huai, S. Liang, and X. Wang, “Thermal transport in Si/Ge nanocomposites,” Journal of Physics D: Applied Physics. 2009. link Times cited: 30 Abstract: In this paper, a systematic study is carried out to investig… read moreAbstract: In this paper, a systematic study is carried out to investigate the thermal transport in Si/Ge nanocomposites by using molecular dynamics simulation. Emphasis is placed on the effect of nanowire size, heat flux, Si/Ge interface, atomic ratio and defects (voids). The results show that the thermal conductivity of nanowire composites is much lower than that of alloy, which accounts mainly for ZT enhancement and owes a great deal to the effect of interface thermal resistance. A ‘reflecting effect’ in temperature distribution is observed at the Si/Ge interface, which is largely due to the lack of right quantum temperature correction in the region adjacent to the interface. The thermal conductivity of the nanocomposite is found to have weak dependence on the bulk temperature (200–900 K) and the heat flux in the range (0.5–3.5) × 1010 W m−2. Simulation results reveal that for a constant Si wire dimension, the thermal conductivity of the Si1−xGex nanocomposites increases with x. Our study on the influence of the defects (voids) has the same order of relative thermal conductivity reduction with increasing void density in comparison with the experimental data. Due to the small size (10 nm) of Si nanowires in our nanocomposites, the voids show less effect on thermal conductivity reduction in comparison with the experimental data with 100 nm Si wires. read less NOT USED (high confidence) X. Li, R. Latour, and S. Stuart, “TIGER2: an improved algorithm for temperature intervals with global exchange of replicas.,” The Journal of chemical physics. 2009. link Times cited: 40 Abstract: An empirical sampling method for molecular simulation based … read moreAbstract: An empirical sampling method for molecular simulation based on "temperature intervals with global exchange of replicas" (TIGER2) has been developed to reduce the high demand for computational resources and the low computational efficiency of the conventional replica-exchange molecular dynamics (REMD) method. This new method overcomes the limitation of its previous version, called TIGER, which requires the assumption of constant heat capacity during quenching of replicas from elevated temperatures to the baseline temperature. The robustness of the TIGER2 method is examined by comparing it against a Metropolis Monte Carlo simulation for sampling the conformational distribution of a single butane molecule in vacuum, a REMD simulation for sampling the behavior of alanine dipeptide in explicit solvent, and REMD simulations for sampling the folding behavior of two peptides, (AAQAA)(3) and chignolin, in implicit solvent. The agreement between the results from these conventional sampling methods and the TIGER2 simulations indicates that the TIGER2 algorithm is able to closely approximate a Boltzmann-weighted ensemble of states for these systems but without the limiting assumptions that were required for the original TIGER algorithm. TIGER2 is an efficient replica-exchange sampling method that enables the number of replicas that are used for a replica-exchange simulation to be substantially reduced compared to the conventional REMD method. read less NOT USED (high confidence) T. Zohdi, “Mechanistic modeling of swarms,” Computer Methods in Applied Mechanics and Engineering. 2009. link Times cited: 37 NOT USED (high confidence) S. Huang, S. Zhang, T. Belytschko, S. S. Terdalkar, and T. Zhu, “Mechanics of nanocrack: Fracture, dislocation emission, and amorphization,” Journal of The Mechanics and Physics of Solids. 2009. link Times cited: 77 NOT USED (high confidence) M. Z. Hossain, J. Freund, and H. Johnson, “Improved calculation of Si sputter yield via first principles derived interatomic potential,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2009. link Times cited: 5 NOT USED (high confidence) Q. Tang, “Effect Of Water On Brittle Fracture Of Sio2 By Molecular Dynamics Study,” Computational Materials Science. 2009. link Times cited: 5 NOT USED (high confidence) H. Jeschke, M. Diakhate, and M. E. Garcia, “Molecular dynamics simulations of laser-induced damage of nanostructures and solids,” Applied Physics A. 2009. link Times cited: 25 NOT USED (high confidence) T. Itina, “Molecular dynamics study of the role of material properties on nanoparticles formed by rapid expansion of a heated target,” Applied Surface Science. 2009. link Times cited: 10 NOT USED (high confidence) C.-ying Wang and Q. Meng, “Atomic simulation of the 30° partial dislocation interaction with divacancy in silicon,” physica status solidi (RRL) – Rapid Research Letters. 2009. link Times cited: 5 Abstract: The interactions of the 30° partial dislocation with a divac… read moreAbstract: The interactions of the 30° partial dislocation with a divacancy (V2) in silicon are investigated by the molecular dynamics simulation method. The results under different temperature and shear stress conditions show that the 30° partial dislocation is pinned when the dislocation encounters V2. When the shear stress approaches a critical value τc, the dislocation can overcome the pin. As the temperature increases, τc decreases approximately as a linear function. Moreover, it is found that τc is mainly determined by the migration barrier of the corresponding kink. Finally, V2 can make the 30° partial dislocation move faster once the dislocation overcomes the pin. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) read less NOT USED (high confidence) E. Landry and A. McGaughey, “Effect of interfacial species mixing on phonon transport in semiconductor superlattices,” Physical Review B. 2009. link Times cited: 111 Abstract: Molecular dynamics simulations are used to examine the effec… read moreAbstract: Molecular dynamics simulations are used to examine the effect of interfacial species mixing on the thermal conductivity of Stillinger-Weber $\text{Si}/{\text{Si}}_{0.7}{\text{Ge}}_{0.3}$ and Si/Ge superlattices at a temperature of 500 K. The thermal conductivity of $\text{Si}/{\text{Si}}_{0.7}{\text{Ge}}_{0.3}$ superlattices is predicted to not depend on the interfacial species mixing and to increase with increasing period length. This period length dependence is indicative of incoherent phonon transport and related to decreasing interface density. The thermal conductivity of Si/Ge superlattices is predicted to depend strongly on the interface quality. For Si/Ge superlattices with perfect interfaces, the predicted thermal conductivity decreases with increasing period length before reaching a constant value, a trend indicative of coherent phonon transport. When interfacial species mixing is added to the model, however, the thermal conductivity is predicted to increase with increasing period length, indicating incoherent phonon transport. These results suggest that the assumption of coherent phonon transport made in lattice dynamics--based models may not be justified. read less NOT USED (high confidence) D. Graves and P. Brault, “Molecular dynamics for low temperature plasma–surface interaction studies,” Journal of Physics D: Applied Physics. 2009. link Times cited: 112 Abstract: The mechanisms of physical and chemical interactions of low … read moreAbstract: The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms through integration of atomic equations of motion, using inter-atomic potentials that can account for bond breaking and formation that result when energetic species from the plasma impact surfaces. This paper summarizes the current status of the technique for various applications of low temperature plasmas to material processing technologies. The method is reviewed, and commonly used inter-atomic potentials are described. Special attention is paid to the use of MD in understanding various representative applications, including tetrahedral amorphous carbon film deposition from energetic carbon ions, the interactions of radical species with amorphous hydrogenated silicon films, silicon nanoparticles in plasmas, and plasma etching. read less NOT USED (high confidence) H. Ohta, T. Nagaoka, K. Eriguchi, and K. Ono, “An Improvement of Stillinger–Weber Interatomic Potential Model for Reactive Ion Etching Simulations,” Japanese Journal of Applied Physics. 2009. link Times cited: 13 Abstract: An approach to improve the interatomic potential model by St… read moreAbstract: An approach to improve the interatomic potential model by Stillinger and Weber (SW), which has been frequently utilized for molecular dynamics simulations of energetic-particle-induced surface reactions, was proposed. It was found that this well-known model for Si/halogen systems had a flaw in its three-body potential form if it was applied to reactive ion etching simulations. The repulsive interaction is overestimated owing to the simple summation form ∑i, j,khjik when a halogen atom is surrounded by more than three atoms. This situation always occurs when a high-energy halogen penetrates a Si lattice and, in this case, the penetration energy into the lattice is overestimated. The test simulations using our model showed that the surface structures predicted were markedly different from those using the original model. This improved model has a profound effect on the prediction of surface structures. read less NOT USED (high confidence) Y. Niquet, D. Rideau, C. Tavernier, H. Jaouen, and X. Blase, “Onsite matrix elements of the tight-binding Hamiltonian of a strained crystal: Application to silicon, germanium, and their alloys,” Physical Review B. 2009. link Times cited: 140 Abstract: We discuss a model for the onsite matrix elements of the sp3… read moreAbstract: We discuss a model for the onsite matrix elements of the sp3d5s tight-binding Hamiltonian of a strained diamond or zinc-blende crystal or nanostructure. This model features onsite, off-diagonal couplings among the s, p, and d orbitals and is able to reproduce the effects of arbitrary strains on the band energies and effective masses in the full Brillouin zone. It introduces only a few additional parameters and is free from any ambiguities that might arise from the definition of the macroscopic strains as a function of the atomic positions. We apply this model to silicon, germanium, and their alloys as an illustration. In particular, we make a detailed comparison of tight-binding and ab initio data on strained Si, Ge, and SiGe. read less NOT USED (high confidence) N. Bernstein, J. Kermode, and G. Csányi, “Hybrid atomistic simulation methods for materials systems,” Reports on Progress in Physics. 2009. link Times cited: 148 Abstract: We review recent progress in the methodology of hybrid quant… read moreAbstract: We review recent progress in the methodology of hybrid quantum/classical (QM/MM) atomistic simulations for solid-state systems, from the earliest reports in 1993 up to the latest results. A unified terminology is defined into which the various and disparate schemes fit, based on whether the information from the QM and MM calculations is combined at the level of energies or forces. We discuss the pertinent issues for achieving ‘seamless’ coupling, the advantages and disadvantages of the proposed schemes and summarize the applications and scientific results that have been obtained to date. read less NOT USED (high confidence) P. S. Branicio, J. Rino, C. Gan, and H. Tsuzuki, “Interaction potential for indium phosphide: a molecular dynamics and first-principles study of the elastic constants, generalized stacking fault and surface energies,” Journal of Physics: Condensed Matter. 2009. link Times cited: 31 Abstract: Indium phosphide is investigated using molecular dynamics (M… read moreAbstract: Indium phosphide is investigated using molecular dynamics (MD) simulations and density-functional theory calculations. MD simulations use a proposed effective interaction potential for InP fitted to a selected experimental dataset of properties. The potential consists of two- and three-body terms that represent atomic-size effects, charge–charge, charge–dipole and dipole–dipole interactions as well as covalent bond bending and stretching. Predictions are made for the elastic constants as a function of density and temperature, the generalized stacking fault energy and the low-index surface energies. read less NOT USED (high confidence) S. Maruyama, “Molecular Dynamics Method for Micro/Nano Systems.” 2009. link Times cited: 13 Abstract: Molecular dynamics simulations are becoming more important a… read moreAbstract: Molecular dynamics simulations are becoming more important and more practical for microscale and nanoscale heat transfer problems. For example, studies of basic mechanisms of heat transfer such as phase change demand the understanding of microscopic liquid-solid contact phenomena. The efficient heat transfer at a three-phase interface (evaporation and condensation of liquid on a solid surface) becomes the singular problem in the macroscopic treatment. The nucleation theory of liquid droplets in vapor or of vapor bubbles in liquid sometimes needs to take account of nuclei of the size of molecular clusters. The effect of the surfactant on the heat and mass transfer through liquid-vapor interface is also an example of the direct effect of molecular scale phenomena on the macroscopic heat and mass transfer. Even though there has been much effort of extending our macroscopic analysis to extremely microscopic conditions in space (micrometer and nanometer scales), time (microseconds, nanoseconds and picoseconds), and rate (extremely high heat flux), there are certain limitations in the extrapolations. Hence, the bottom-up approach from molecular level is strongly anticipated. On the other hand, recent advances in microscale and nanoscale heat transfer and in nanotechnology require the detailed understandings of phase change and heat and mass transfer in nanometer and micrometer scale regimes. The chemical engineering processes to generate nanoscale structures such as carbon nanotubes or mesoporous silica structures are examples. The wetting of liquid or absorption is also important since the adhesive force is extremely important for micro/nano system and the creation of extremely large surface area is possible with nanoscale structures. The use of molecular dynamics simulations is straightforward for such a nanoscale system. Here, again, it is important to compare such nanoscale phenomena with macroscopic phenomena, because an analogy to the macroscopic system is often an important strategy in understanding a nanoscale phenomenon. Important physics intrinsic to a nanoscale system is usually found through the rational comparison 4 with a macroscopic system. In this chapter, one of the promising numerical techniques, the classical molecular dynamics method, is overviewed with a special emphasis on applications to inter-phase and heat transfer problems. The molecular dynamics methods have long been used and are well developed as a tool in statistical mechanics and physical chemistry [1, 2]. However, it is a new challenge to extend the method to the spatial and temporal scales of macroscopic heat transfer phenomena [3-6]. On the other hand, the thin film technology related … read less NOT USED (high confidence) T. Nagaoka, K. Eriguchi, K. Ono, and H. Ohta, “Classical interatomic potential model for Si/H/Br systems and its application to atomistic Si etching simulation by HBr+,” Journal of Applied Physics. 2009. link Times cited: 18 Abstract: An interatomic potential model for Si/H/Br systems has been … read moreAbstract: An interatomic potential model for Si/H/Br systems has been developed for performing classical molecular dynamics simulations of Si etching processes by HBr plasmas. The potential form used here is the improved Stillinger–Weber potential function involving a correction term in order to predict the reaction dynamics more accurately. Parameters were determined based on ab initio data obtained from previous works on Si/Br systems by [Ohta et al. J. Appl. Phys. 104, 073302 (2008)]. By using this model, we performed Si etching simulations by monoenergetic HBr+ and Br+ beams. H atom has about 1% of the translational energy of cluster ions due to the small H/Br mass ratio (=1.0/79.9); therefore, H atoms in HBr+ behave like H radicals. This results in higher etch yields by HBr+ than those by Br+ in the low-energy region (less than 100 eV). This can be attributed to the chemical enhancement induced by the formation of Si–H bonds. On the other hand, yields by HBr+ and Br+ were almost the same in the high-energy reg... read less NOT USED (high confidence) C. Ciobanu, C. Wang, and K. Ho, “Global Optimization of 2-Dimensional Nanoscale Structures: A Brief Review,” Materials and Manufacturing Processes. 2009. link Times cited: 11 Abstract: In the cluster structure community, global optimization meth… read moreAbstract: In the cluster structure community, global optimization methods are common tools for arriving at the atomic structure of molecular and atomic clusters. The large number of local minima of the potential energy surface (PES) of these clusters, and the fact that these local minima proliferate exponentially with the number of atoms in the cluster simply demands the use of fast stochastic methods to find the optimum atomic configuration. Therefore, most of the development work has come from (and mostly stayed within) the cluster structure community. Partly due to wide availability and landmark successes of scanning tunneling microscopy (STM) and other high resolution microscopy techniques, finding the structure of periodically reconstructed semiconductor surfaces was not posed as a problem of stochastic optimization until recently, when it was shown that high-index semiconductor surfaces can posses a rather large number of local minima with such low surface energies that the identification of the global minimum becomes problematic. We have therefore set out to develop global optimization methods for systems other than clusters, focusing on periodic systems in two dimensions (2-D) as such systems currently occupy a central place in the field of nanoscience. In this article, we review some of our recent theoretical work on finding the atomic structure of surfaces, with emphasis the global optimization methods. While focused mainly on atomic structure, our account will show examples of how these development efforts contributed to elucidating several physical problems, and we will attempt to make a case for widespread use of these methods for structural problems in one and two dimensions. read less NOT USED (high confidence) V. Samvedi and V. Tomar, “Role of heat flow direction, monolayer film thickness, and periodicity in controlling thermal conductivity of a Si–Ge superlattice system,” Journal of Applied Physics. 2009. link Times cited: 30 Abstract: Superlattices are considered one of the most promising mater… read moreAbstract: Superlattices are considered one of the most promising material systems for nanotechnological applications in fields such as high figure of merit (ZT) thermoelectrics, microelectronics, and optoelectronics owing to the possibility that these materials could be tailored to obtain desired thermal properties. Factors that could be adjusted for tailoring the thermal conductivity of the superlattices include the monolayer film thickness, periodicity, heat flow direction, straining, and temperature of operation. In the presented study, nonequilibrium molecular dynamics (NEMD) simulations are performed to obtain an understanding of the effect of such factors on the thermal conductivity of Si–Ge superlattices at three different temperatures (400, 600, and 800 K). The NEMD simulations are performed using Tersoff bond-order potential. The thermal conductivity is found to increase with an increase in the number of periods as well as with the increase in the period thickness. The dependence of thermal conductivity on... read less NOT USED (high confidence) J. Behler, R. Martoňák, D. Donadio, and M. Parrinello, “Pressure‐induced phase transitions in silicon studied by neural network‐based metadynamics simulations,” physica status solidi (b). 2008. link Times cited: 59 Abstract: We present a combination of the metadynamics method for the … read moreAbstract: We present a combination of the metadynamics method for the investigation of pressure‐induced phase transitions in solids with a neural network representation of high‐dimensional density‐functional theory (DFT) potential‐energy surfaces. In a recent illustration of the method for the complex high‐pressure phase diagram of silicon [Behler et al., Phys. Rev. Lett. 100, 185501 (2008)] we have shown that the full sequence of phases can be reconstructed by a series of subsequent simulations. In the present paper we give a detailed account of the underlying methodology and discuss the scope and limitations of the approach, which promises to be a valuable tool for the investigation of a variety of inorganic materials. The method is several orders of magnitude faster than a direct coupling of metadynamics with electronic structure calculations, while the accuracy is essentially maintained, thus providing access to extended simulations of large systems. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) read less NOT USED (high confidence) V. Kharlamov, Y. Trushin, E. E. Zhurkin, M. Lubov, and J. Pezoldt, “Study of Si and C adatoms and SiC clusters on the silicon surface by the molecular dynamics method,” Technical Physics. 2008. link Times cited: 7 NOT USED (high confidence) S. Ryu and W. Cai, “Comparison of thermal properties predicted by interatomic potential models,” Modelling and Simulation in Materials Science and Engineering. 2008. link Times cited: 54 Abstract: We report melting points and other thermal properties of sev… read moreAbstract: We report melting points and other thermal properties of several semiconducting and metallic elements as they are modeled by different empirical interatomic potential models, including the Stillinger–Weber, the embedded-atom method, the Finnis–Sinclair and the modified-embedded-atom method. The state-of-the-art free energy methods are used to determine the melting points of these models within a very small error bar, so that they can be cross-compared with each other. The comparison reveals several systematic trends among elements with the same crystal structure. It identifies areas that require caution in the application of these models and suggests directions for their future improvement. read less NOT USED (high confidence) T. Hawa and M. Zachariah, “Understanding the Effect of Hydrogen Surface Passivation and Etching on the Shape of Silicon Nanocrystals,” Journal of Physical Chemistry C. 2008. link Times cited: 15 Abstract: One of the significant challenges in the use of nanocrystals… read moreAbstract: One of the significant challenges in the use of nanocrystals, is the control of crystal shape when grown from the gas-phase. Recently, the Kortshagen group has succeeded in generating cubic Si nanocrystals in a nonequilibrium plasma. In this paper we consider the energetics of various shaped Si nanocrystals, and the role that hydrogen surface termination plays. We consider cube, truncated octahedron, icosahedron, and spherical shapes for both bare and hydrogen coated silicon nanocrystals for sizes between 2 and 10 nm. From our molecular dynamics (MD) simulations, show that for bare Si crystals, icosahedron crystals are the most energetically stable, and cubic the least. On the other hand, when hydrogenated, the cubic structure comes about because 1) the cubic structure is energetically favored when hydrogen terminated and 2) the plasma that operates with hydrogen also provides a steady source of hydrogen atoms for etching. read less NOT USED (high confidence) Z. Wang, X. Zu, L. Yang, F. Gao, and W. J. Weber, “Orientation and temperature dependence of the tensile behavior of GaN nanowires: an atomistic study,” Journal of Materials Science: Materials in Electronics. 2008. link Times cited: 5 NOT USED (high confidence) J. Hui-hui, Y. Min, R. Li-Ming, Z. Xing, H. Ru, and Z. You-guang, “Simulation of plasma doping process by using the localized molecular dynamics method,” Chinese Physics B. 2008. link Times cited: 1 Abstract: Plasma doping is the candidate for semiconductor doping. Acc… read moreAbstract: Plasma doping is the candidate for semiconductor doping. Accurate simulation of the doping technology is needed for the advanced integrated circuit manufacturing. In this paper, the plasma doping process simulation is performed by using the localized molecular dynamics method. Models that involve the statistics of the implanted compositions, angles and energies are developed. The effect of the model on simulation results is studied. The simulation results about the doping concentration profile are supported by experimental data. read less NOT USED (high confidence) A. Heuer, “Exploring the potential energy landscape of glass-forming systems: from inherent structures via metabasins to macroscopic transport,” Journal of Physics: Condensed Matter. 2008. link Times cited: 322 Abstract: In this review a systematic analysis of the potential energy… read moreAbstract: In this review a systematic analysis of the potential energy landscape (PEL) of glass-forming systems is presented. Starting from the thermodynamics, the route towards the dynamics is elucidated. A key step in this endeavor is the concept of metabasins. The relevant energy scales of the PEL can be characterized. Based on the simulation results for some glass-forming systems one can formulate a relevant model system (ideal Gaussian glass-former) which can be treated analytically. The macroscopic transport can be related to the microscopic hopping processes, using either the strong relation between energy (thermodynamics) and waiting times (dynamics) or, alternatively, the concepts of the continuous-time random walk. The relation to the geometric properties of the PEL is stressed. The emergence of length scales within the PEL approach as well as the nature of finite-size effects is discussed. Furthermore, the PEL view is compared to other approaches describing the glass transition. read less NOT USED (high confidence) A. Iwakawa, H. Ohta, K. Eriguchi, and K. Ono, “Numerical Investigation on Origin of Microscopic Surface Roughness during Si Etching by Chemically Reactive Plasmas,” Japanese Journal of Applied Physics. 2008. link Times cited: 13 Abstract: A key factor for the formation of nanoscale surface roughnes… read moreAbstract: A key factor for the formation of nanoscale surface roughness during chemically reactive plasma and beam etchings has been distinguished by classical molecular dynamics (MD) simulations using well-known Stillinger–Weber potential models. In this study, MD simulations of Si(100) etching using monoenergetic (=100 eV) Cl+ and Br+ beams were performed. On the basis of analyses of surface structures and ion trajectories, it was concluded that the penetration of impinging species into the Si surface and residual halogens inside the Si lattice is a crucial factor for enhancing the surface roughness. The accurate estimation of potential energies for the penetration into interstitial sites is essential for further qualitative improvement of etching simulations. read less NOT USED (high confidence) J. Zimmerman, R. Jones, and J. Templeton, “A material frame approach for evaluating continuum variables in atomistic simulations,” J. Comput. Phys. 2008. link Times cited: 71 NOT USED (high confidence) E. Sanville, A. Bholoa, R. Smith, and S. Kenny, “Silicon potentials investigated using density functional theory fitted neural networks,” Journal of Physics: Condensed Matter. 2008. link Times cited: 34 Abstract: We present a method for fitting neural networks to geometric… read moreAbstract: We present a method for fitting neural networks to geometric and energetic data sets. We then apply this method by fitting a neural network to a set of data generated using the local density approximation for systems composed entirely of silicon. In order to generate atomic potential energy data, we use the Bader analysis scheme to partition the total system energy among the constituent atoms. We then demonstrate the transferability of the neural network potential by fitting to various bulk, surface, and cluster systems. read less NOT USED (high confidence) Z.-H. Hong, S. Hwang, and T. Fang, “Effect of substrate temperature and deposition rate on alloyzation for Co or Fe onto Cu(001) substrate,” Journal of Applied Physics. 2008. link Times cited: 12 Abstract: The mixing situation of Fe or Co atoms implanting onto Cu(00… read moreAbstract: The mixing situation of Fe or Co atoms implanting onto Cu(001) substrate is investigated with regard to substrate temperature and deposition rate by molecular dynamics. The tight-binding-second-momentum-approach many-body potential is used to model the atomic interaction. The results indicate that the morphology of the layer is under epitaxial growth as the substrate temperature is 700 or 1000 K, while it is not epitaxial at the substrate temperature of 300 or 450 K. The quality of epitaxial film is better when the substrate temperature is increased. The intermixing at the deposited layers becomes clear as the substrate temperature increases. It also indicates that there are more Co atoms penetrating into the substrate than the Fe atoms, regardless of the substrate temperature. Hence, one could say that the interface mixing of Co and Cu atoms is better than that of Fe and Cu atoms. When the deposition rate is raised from 5 to 10 atoms/ps, there is no increase in the interface mixing at both systems except... read less NOT USED (high confidence) E. Moore, “Computational modelling of inorganic solids.” 2008. link Times cited: 10 Abstract: This report covers papers published in 2011 dealing with the… read moreAbstract: This report covers papers published in 2011 dealing with the application of computational techniques to inorganic solids. It deals mainly with continuous solids that are ionic in nature; work on metals and MOFs is excluded. Special attention is given to solids used in solid oxide fuel cells, iron-based superconductors, zeolites and systems of interest to the life and earth sciences. Relevant advances in computational methods are also covered. read less NOT USED (high confidence) A. Skye and P. Schelling, “Thermal resistivity of Si–Ge alloys by molecular-dynamics simulation,” Journal of Applied Physics. 2008. link Times cited: 51 Abstract: We explore the ability of molecular-dynamics simulation to e… read moreAbstract: We explore the ability of molecular-dynamics simulation to elucidate thermal transport in Si–Ge alloys. Simulations using Stillinger–Weber potentials yield values for the thermal resistivity significantly higher than experimental measurements. In agreement with experiment and theoretical predictions, we find that scattering from mass disorder is dominant, with bond disorder and strain effects playing a very minor role. To explore the origins of the large discrepancies with experiment, we use theoretical methods suitable for the limit where point-defect scattering dominates the resistivity. We find that point-defect scattering models based on a Debye spectrum cannot be used to fit our simulations, indicating that high-frequency modes may play an important role in the simulation. The results have important implications for using classical molecular-dynamics simulation to predict properties of alloy materials near and below the Debye temperature. read less NOT USED (high confidence) M. Talati, T. Albaret, and A. Tanguy, “Atomistic simulations of elastic and plastic properties in amorphous silicon,” EPL (Europhysics Letters). 2008. link Times cited: 19 Abstract: We present here potential-dependent mechanical properties of… read moreAbstract: We present here potential-dependent mechanical properties of amorphous silicon studied through molecular dynamics (MD) at low temperature. On average, the localization of elementary plastic events and the co-ordination defect sites appears to be correlated. For Tersoff potential and SW potential the plastic events centered on defect sites prefer 5-fold defect sites, while for modified Stillinger-Weber potential such plastic events choose 3-fold defect sites. We also analyze the non-affine displacement field in amorphous silicon obtained for different shear regime. The non-affine displacement field localizes when plastic events occur and shows elementary shear band formation at higher shear strains. read less NOT USED (high confidence) Z. Insepov, M. Terasawa, and K. Takayama, “Surface erosion and modification by highly charged ions,” Physical Review A. 2008. link Times cited: 12 Abstract: Analyses were conducted of various models and mechanisms of … read moreAbstract: Analyses were conducted of various models and mechanisms of highly charged ion (HCI) and swift-heavy ion energy transfer into a solid target, such as hollow atom formation, charge screening, neutralization, shock wave generation, crater formation, and sputtering. A plasma model of space charge neutralization based on impact ionization of semiconductors at high electric fields was developed and applied to analyze HCI impacts on Si and W. Surface erosions of semiconductor and metal surfaces caused by HCI bombardments were studied by using a molecular dynamics simulation method, and the results were compared with experimental sputtering data. read less NOT USED (high confidence) J. Kioseoglou, P. Komninou, and T. Karakostas, “Interatomic potential calculations of III(Al, In)–N planar defects with a III‐species environment approach,” physica status solidi (b). 2008. link Times cited: 22 Abstract: III–N compound semiconductors are nowadays widely used in el… read moreAbstract: III–N compound semiconductors are nowadays widely used in electronic device technology. Due to the complexity of their structures planar and linear defects may have various atomic configurations. Since in the wurtzite structure of AlN and InN the second‐neighbor distance is very close to the stable “metallic” Al–Al and In–In distances respectively, a III‐species environment approach based on a Tersoff empirical bond order interatomic potential is developed in which the cut‐off distance for Al–Al and In–In interactions is tuned. In particular, the work is focused on two issues: the development of an approach for the calculation of defected structures in III‐nitrides and the application of this method on a series of planar defects in wurtzite structure. Various structural and energy‐related conclusions are drawn that are attributed to the complexity of the III–III metal type and N–N interactions in connection with the difference of the lattice parameters and the elastic constants. Molecular dynamic simulations are led to the conclusion that structural transformations may also occur. The Austerman–Gehman and Holt models for the inversion domain boundary (IDB) on the (10$ \bar 1 $0) plane are higher in energy than the IDB* model of Northrup, Neugebauer, and Romano. The model of Blank et al. for the translation domain boundary (TDB) on the {1$ \bar 2 $10} plane is unstable with respect to Drum's model. The Austerman model for the IDB on the {1$ \bar 2 $10} plane is unstable with respect to the IDB* model appropriate for this plane. The Austerman {10$ \bar 1 $0} IDB model is recognized as a strong candidate, among the IDB atomic configurations. Moreover, models for IDBs on {10$ \bar 1 $0} planes in which the boundary plane intersects two bonds (type‐2 models) are less stable than models in which the boundary plane intersects one bond (type‐1 models), in all cases considered. It is confirmed that the III‐species environment approach describes the “wrong”‐bonded defect local configuration structures more realistically with respect to the standard approach. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) read less NOT USED (high confidence) J. Goicochea, M. Madrid, and C. Amon, “Hierarchical modeling of heat transfer in silicon-based electronic devices,” 2008 11th Intersociety Conference on Thermal and Thermomechanical Phenomena in Electronic Systems. 2008. link Times cited: 15 Abstract: Heat transfer modeling in electronic devices has gained impo… read moreAbstract: Heat transfer modeling in electronic devices has gained importance over the last decade in the design of better performing devices. The trend towards miniaturization of these devices has led to components that operate in the micro and nano-meter and in the micro and pico-second ranges. When the characteristic dimensions of the electronic components are comparable to or smaller than the mean free path of the energy carriers (in this case phonons), the thermal conductivity, which affects their performance and reliability, reduces due to the scattering of the energy carriers with the boundaries. Several modeling approaches have been proposed in the literature to describe sub-continuum heat transport; however, the hierarchical modeling of heat transfer in electronic devices has been limited. This has precluded, at the industry level, the analysis of how changes at sub-continuum level impact the overall performance and reliability of these devices. There are numerous devices and applications whose design, performance and reliability are suitable for optimization if a hierarchical model was available. In this work, we present a hierarchical model capable of integrating the scales involved in the thermal analysis of electronic components. The integration of participating scales is achieved in three steps. First, we use molecular dynamics simulations to estimate the thermal properties (i.e. phonon relaxation times, dispersion relations and group velocities, among others), required to solve the Boltzmann transport equation (BTE). Then we apply quantum corrections (QCs) to the MD results to make them suitable for BTE, and lastly, we solve the BTE on various domains, subject to different boundary and initial conditions. Our hierarchical model is applied to silicon-based devices. read less NOT USED (high confidence) S. Mahajan, G. Subbarayan, and B. Sammakia, “Estimating Kapitza resistance between Si-SiO2 interface using molecular dynamics simulations,” 2008 11th Intersociety Conference on Thermal and Thermomechanical Phenomena in Electronic Systems. 2008. link Times cited: 13 Abstract: The interface between nano-scale films is of relevance in ma… read moreAbstract: The interface between nano-scale films is of relevance in many critical applications. Specifically, recent technological advances in semiconductor industry that utilize Silicon-on-Insulator (SOI) devices have given urgency to understanding thermal transport across Si-SiO2 interface. Estimates of interfacial (Kapitza) resistance to thermal transport across Si-SiO2 films do not appear to exist at the present time. In this paper, we develop and carryout reverse non-equilibrium molecular dynamics (NEMD) simulations by imposing known heat flux to determine the Kapitza resistance between Si-SiO2 thin films. For the Si-SiO2 interface, the average Kapitza resistance for a ~8 Aring thick oxide layer system was 0.503 times 10-9 m K/W and for a ~11.5 Aring thick oxide layer system was 0.518 times 10-9 m K/W. These values were of the same order of magnitude as the Kapitza resistance values determined from the acoustic mismatch model (AMM) and the diffuse mismatch model (DMM) for the Si-SiO2 interface. read less NOT USED (high confidence) M. Yu, H. Ji, M. Li, R. Huang, and X. Zhang, “Simulation on plasma doping for shallow junction formation,” Extended Abstracts - 2008 8th International Workshop on Junction Technology (IWJT ’08). 2008. link Times cited: 1 Abstract: Plasma doping (PD) is a potential shallow junction technolog… read moreAbstract: Plasma doping (PD) is a potential shallow junction technology. Accurate simulation on PD is needed for further development and application. The simulation on PD with localized molecular method is presented in this paper. The verification of simulation results on dopant concentration profile by experimental data is shown. Simulation on FinFET doping is illustrated. The efficiency of side doping on fin structure is investigated. read less NOT USED (high confidence) Z. Insepov, J. Norem, D. Swenson, and A. Hassanein, “Surface erosion and modification by energetic ions.,” Vacuum. 2008. link Times cited: 6 NOT USED (high confidence) C. Angell, “Glass-Formers and Viscous Liquid Slowdown since David Turnbull: Enduring Puzzles and New Twists,” MRS Bulletin. 2008. link Times cited: 117 Abstract: To Turnbull’s study of the kinetic problem of nucleation and… read moreAbstract: To Turnbull’s study of the kinetic problem of nucleation and growth of crystals, we add the further enquiry into what lies behind the slow nucleation kinetics of glass-formers. Our answer to this question leads to the proposal of conditions in which a pure liquid metal, monatomic and elemental, can be vitrified. Using the case of high-pressure liquid germanium, we give electron microscope evidence for the validity of our thinking. On the question of how liquids behave when crystals do not form, Turnbull pioneered the study of glass transitions in metallic alloys, measuring the heat capacity change at the glass transition T _g for the first time, and developing with Cohen the free volume model for the temperature dependence of liquid transport properties approaching T _g. We extend the phenomenological picture to include networks where free volume does not play a role and reveal a pattern of behavior that provides for a classification of glass-formers (from “strong” to “fragile”). Where Turnbull studied supercooled liquid metals and P_4 to the homogeneous nucleation limit using small droplets, we studied supercooled water in capillaries and emulsions to the homogeneous nucleation limit near −40°C. We discuss the puzzling divergences observed that are now seen as part of a cooperative transition that leads to very untypical glass-transition behavior at lower temperatures (when crystallization is bypassed by hyperquenching). Finally, we show how our interpretation of water behavior can be seen as a bridge between the behavior of the “strong” (network) liquids of classical glass science (e.g., SiO_2) and the “fragile” behavior of typical molecular glass-formers. The link is made using a “Gaussian excitations” model by Matyushov and the author in which the spike in heat capacity for water is pushed by cooperativity (disorder stabilization of excitations) into a first-order transition to the ground state, at a temperature typically below T _g. In exceptional cases like triphenyl phosphite, this liquid-to-glass first-order transition lies above T _g and can be studied in detail. read less NOT USED (high confidence) G. Li, “A multilevel component mode synthesis approach for the calculation of the phonon density of states of nanocomposite structures,” Computational Mechanics. 2008. link Times cited: 6 NOT USED (high confidence) S. Murad and I. Puri, “Thermal transport across nanoscale solid-fluid interfaces,” Applied Physics Letters. 2008. link Times cited: 79 Abstract: An explanation for the effective thermal resistance RK can b… read moreAbstract: An explanation for the effective thermal resistance RK can be based on the impedance to the passage of thermal phonons across an interface. We conjecture that (1) increasing the fluid pressure, and (2) making an interface more hydrophilic should facilitate better acoustic matching and thus lower RK. Our molecular dynamics simulations confirm this. Overall, RK decreases with increasing temperature and is inversely proportional to the heat flux. read less NOT USED (high confidence) A. M. Ukpong, M. Härting, and D. Britton, “Theoretical study of strain fields and local order in hydrogenated amorphous silicon,” Philosophical Magazine Letters. 2008. link Times cited: 5 Abstract: This paper presents the results of a tight-binding molecular… read moreAbstract: This paper presents the results of a tight-binding molecular-dynamics simulation which demonstrates that the local order and intrinsic stress in hydrogenated amorphous silicon are influenced by the hydrogen concentration. Snapshots of the atomic-level stresses in the simulated structures show that amorphous silicon exhibits a broad distribution in the magnitude of the local stress, rather than a uniform stress field over the whole simulated structure. The corresponding spatial and temporal correlations of the stress fields are interpreted to provide information on the effects of hydrogen on the short- and medium-range order. read less NOT USED (high confidence) S. Yoo, N. Shao, and X. Zeng, “Structures and relative stability of medium- and large-sized silicon clusters. VI. Fullerene cage motifs for low-lying clusters Si(39), Si(40), Si(50), Si(60), Si(70), and Si(80).,” The Journal of chemical physics. 2008. link Times cited: 31 Abstract: We performed a constrained search, combined with density-fun… read moreAbstract: We performed a constrained search, combined with density-functional theory optimization, of low-energy geometric structures of silicon clusters Si(39), Si(40), Si(50), Si(60), Si(70), and Si(80). We used fullerene cages as structural motifs to construct initial configurations of endohedral fullerene structures. For Si(39), we examined six endohedral fullerene structures using all six homolog C(34) fullerene isomers as cage motifs. We found that the Si(39) constructed based on the C(34)(C(s):2) cage motif results in a new leading candidate for the lowest-energy structure whose energy is appreciably lower than that of the previously reported leading candidate obtained based on unbiased searches (combined with tight-binding optimization). The C(34)(C(s):2) cage motif also leads to a new candidate for the lowest-energy structure of Si(40) whose energy is notably lower than that of the previously reported leading candidate with outer cage homolog to the C(34)(C(1):1). Low-lying structures of larger silicon clusters Si(50) and Si(60) are also obtained on the basis of preconstructed endohedral fullerene structures. For Si(50), Si(60), and Si(80), the obtained low-energy structures are all notably lower in energy than the lowest-energy silicon structures obtained based on an unbiased search with the empirical Stillinger-Weber potential of silicon. Additionally, we found that the binding energy per atom (or cohesive energy) increases typically >10 meV with addition of every ten Si atoms. This result may be used as an empirical criterion (or the minimal requirement) to identify low-lying silicon clusters with size larger than Si(50). read less NOT USED (high confidence) J. Kermode, “Multiscale hybrid simulation of brittle fracture.” 2008. link Times cited: 5 NOT USED (high confidence) Z. Wang, X. Zu, F. Gao, and W. J. Weber, “Atomistic level studies on the tensile behavior of GaN nanotubes under uniaxial tension,” The European Physical Journal B. 2008. link Times cited: 7 NOT USED (high confidence) J. Jia, G. Chen, D. Shi, and B. Wang, “Structural and electronic properties of Bin (n = 2-14) clusters from density-functional calculations,” The European Physical Journal D. 2008. link Times cited: 22 NOT USED (high confidence) D.-B. Zhang, M. Hua, and T. Dumitricǎ, “Stability of polycrystalline and wurtzite Si nanowires via symmetry-adapted tight-binding objective molecular dynamics.,” The Journal of chemical physics. 2008. link Times cited: 45 Abstract: The stability of the most promising ground state candidate S… read moreAbstract: The stability of the most promising ground state candidate Si nanowires with less than 10 nm in diameter is comparatively studied with objective molecular dynamics coupled with nonorthogonal tight-binding and classical potential models. The computationally expensive tight-binding treatment becomes tractable due to the substantial simplifications introduced by the presented symmetry-adapted scheme. It indicates that the achiral polycrystalline of fivefold symmetry and the wurtzite wires of threefold symmetry are the most favorable quasi-one-dimensional Si arrangements. Quantitative differences with the classical model description are noted over the whole diameter range. Using a Wulff energy decomposition approach it is revealed that these differences are caused by the inability of the classical potential to accurately describe the interaction of Si atoms on surfaces and strained morphologies. read less NOT USED (high confidence) B. Puchala, M. Falk, and K. Garikipati, “Elastic effects on relaxation volume tensor calculations,” Physical Review B. 2008. link Times cited: 16 Abstract: Relaxation volume tensors quantify the effect of stress on d… read moreAbstract: Relaxation volume tensors quantify the effect of stress on diffusion of crystal defects. Continuum linear elasticity predicts that calculations of these parameters using periodic boundary conditions do not suffer from systematic deviations due to elastic image effects and should be independent of the supercell size or symmetry. In practice, however, calculations of formation volume tensors of the $⟨110⟩$ interstitial in Stillinger--Weber silicon demonstrate that changes in bonding at the defect affect the elastic moduli and result in system-size dependent relaxation volumes. These vary with the inverse of the system size. Knowing the rate of convergence permits accurate estimates of these quantities from modestly sized calculations. Furthermore, within the continuum linear elasticity assumptions, the average stress can be used to estimate the relaxation volume tensor from constant volume calculations. read less NOT USED (high confidence) F. Ramirez, P. Heyliger, A. Rappé, and R. G. Leisure, “Vibrational modes of free nanoparticles: from atomic to continuum scales.,” The Journal of the Acoustical Society of America. 2008. link Times cited: 10 Abstract: Vibration analysis of free standing silicon nanoparticles, w… read moreAbstract: Vibration analysis of free standing silicon nanoparticles, with sizes ranging from 0.732 to 4.223 nm, are calculated using two different methods: molecular mechanics and classical continuum elasticity. Three different geometries are studied: cubes, spheres, and tetrahedrons. Continuum mechanics methods provide good estimates of the lowest natural frequency of particles having at least 836 (R>1.5 nm) and 800 (R>1.28 nm) atoms for cube- and tetrahedron-shaped nanostructures, respectively. Equations for vibrational frequencies of smaller particles as a function of size are proposed. The vibrational modes obtained from both methods were practically the same for the sphere- and tetrahedron-shaped particles with a large number of atoms. However, for the cube geometry only the shape of the modes corresponding to the lowest couple of frequencies occur in the same order. In general, vibrational modes shapes obtained using both methods are the same although the order in which they appear may be shifted. read less NOT USED (high confidence) J. Samela and K. Nordlund, “Emergence of non-linear effects in nanocluster collision cascades in amorphous silicon,” New Journal of Physics. 2008. link Times cited: 11 Abstract: Cluster ion beams create considerably more damage in silicon… read moreAbstract: Cluster ion beams create considerably more damage in silicon and other substrates and eject more material than single ions that deposit at the same kinetic energy on the substrate. The mechanisms that causes the non-linear growth of damage and sputtering are interesting from the point of view of both basic materials research and industrial applications. Using classical molecular dynamics, we analyse the dynamics of collision cascades that are induced in amorphous silicon by small noble gas nanoclusters. We show that the sputtering and other non-linear effects emerge due to the high-energy density induced in a relatively small region in the substrate during the cluster stopping phase and because of the timing of consequent events that dissipate the energy over a larger volume of the substrate. read less NOT USED (high confidence) K. Raleva, D. Vasileska, S. Goodnick, and T. Dzekov, “Modeling thermal effects in nano-devices,” Journal of Computational Electronics. 2008. link Times cited: 114 NOT USED (high confidence) D. Torii, T. Nakano, and T. Ohara, “Contribution of inter- and intramolecular energy transfers to heat conduction in liquids.,” The Journal of chemical physics. 2008. link Times cited: 69 Abstract: The molecular dynamics expression of heat flux, originally d… read moreAbstract: The molecular dynamics expression of heat flux, originally derived by Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] for pairwise potentials, is generalized in this paper for systems with many-body potentials. The original formula consists of a kinetic part and a potential part, and the latter term is found in the present study to be expressible as a summation of contributions from all the many-body potentials defined in the system. The energy transfer among a set of sites for which a many-body potential is defined is discussed and evaluated by the rate of increase in the kinetic energy of each site due to the potential, and its accumulation over all the potentials in the system is shown to make up the potential part of the generalized expression. A molecular dynamics simulation for liquid n-octane was performed to demonstrate the applicability of the new expression obtained in this study to measure the heat flux and to elucidate the contributions of inter- and intramolecular potentials to heat conduction. read less NOT USED (high confidence) C. Fulk, W. Walkosz, A. Chatterjee, S. Ogut, C. Grein, and P. Chung, “First principles calculation of Stillinger-Weber potential parameters for InN,” Journal of Vacuum Science and Technology. 2008. link Times cited: 3 Abstract: The compliance coefficients and Stillinger-Weber interatomic… read moreAbstract: The compliance coefficients and Stillinger-Weber interatomic potential parameters of wurtzite InN were determined by first principles methods. The structural parameters of InN were calculated within the local density approximation of Ceperley-Alder and the generalized gradient approximation of Perdew-Wang exchange-correlation functionals. It was found that the shallow 4d electrons were required as part of the valence shell to obtain accurate results due to the large difference in electronegativity between In and N. The calculated compliance parameters were in good agreement with previously reported theoretical values and in fair agreement with the scattered experimental values. The ab initio results were then fitted to Stillinger-Weber potential forms. read less NOT USED (high confidence) R. E. Rudd and B. L. Lawrence, “Mechanics of silicon nanowires: size-dependent elasticity from first principles,” Molecular Simulation. 2008. link Times cited: 38 Abstract: We discuss size-dependent elastic properties in the context … read moreAbstract: We discuss size-dependent elastic properties in the context of our recent work on the mechanics of silicon nanowires. The results are based on first-principles density functional theory calculations. We focus especially on the size dependence of the Young's modulus, but also comment on the size dependence of the residual stress and the equilibrium length of the hydrogen-passivated Si nanowires. We compare these results to prior results from classical molecular dynamics based on empirical potentials. read less NOT USED (high confidence) Y. Yang, X. Liu, and J. P. Yang, “Nonequilibrium molecular dynamics simulation for size effects on thermal conductivity of Si nanostructures,” Molecular Simulation. 2008. link Times cited: 19 Abstract: The thermal conductivity of Si nanostructres is investigated… read moreAbstract: The thermal conductivity of Si nanostructres is investigated using nonequilibrium molecular dynamics (NEMD) simulation based on the Tersoff III inter-atomic potential. A reliable range of heat flux for the calculation of thermal conductivity is determined by the comparative study of NEMD simulations with different heat fluxes. The remarkable dependence of thermal conductivity on the length of nanostructures is observed. It is also found that the thermal conductivity is less sensitive to the cross-section area perpendicular to the heat flux than to the length of Si nanostructures. Based on the relationship between the thermal conductivity and the nanostructure length, the thermal conductivity and the phonon mean-free path of the infinite bulk Si system are extrapolated. read less NOT USED (high confidence) C. Angell, “Glass formation and glass transition in supercooled liquids, with insights from study of related phenomena in crystals,” Journal of Non-crystalline Solids. 2007. link Times cited: 64 NOT USED (high confidence) J. Dolado, M. Griebel, and J. Hamaekers, “A Molecular Dynamic Study of Cementitious Calcium Silicate Hydrate (C–S–H) Gels,” Journal of the American Ceramic Society. 2007. link Times cited: 138 Abstract: In this article, we study the polymerization of silicic acid… read moreAbstract: In this article, we study the polymerization of silicic acids (Si(OH) 4 ) in the presence of calcium ions by molecular dynamics simulations. We focus on the formation and structure of cementitious calcium silicate hydrate (C-S-H) gels. Our simulations confirm that, in accordance with experiments, a larger content of calcium ions slows down the polymerization of the cementitious silicate chains and prevents them from forming rings and three-dimensional structures. Furthermore, by an analysis of the connectivity of our simulated silicate chains and by a count of the number of Ca-OH and Si-OH bonds formed, the relationship with commonly used structural models of C-S-H gels, such as 1.4 nm tobermorite and jennite, is discussed. read less NOT USED (high confidence) Q. Tang, “Md Simulation Of Dislocation Mobility During Cutting With Diamond Tip On Silicon,” Materials Science in Semiconductor Processing. 2007. link Times cited: 14 NOT USED (high confidence) V. Kapko, D. Matyushov, and A. Angell, “Thermodynamics and dynamics of a monoatomic glass former. Constant pressure and constant volume behavior.,” The Journal of chemical physics. 2007. link Times cited: 3 Abstract: We report constant-volume and constant-pressure simulations … read moreAbstract: We report constant-volume and constant-pressure simulations of the thermodynamic and dynamic properties of the low-temperature liquid and crystalline phases of the modified Stillinger-Weber (SW) model. We have found an approximately linear temperature increase of the effective Gaussian width of the distribution of inherent structures. This effect comes from non-Gaussianity of the landscape and is consistent with the predictions of the Gaussian excitations model representing the thermodynamics of the configurational manifold as an ensemble of excitations, each carrying an excitation entropy. The SW model provides us with both the configurational and excess entropies, with the difference mostly attributed to vibrational anharmonicity. We therefore can address the distinction between the excess thermodynamic quantities, often used to interpret experiments, and configurational thermodynamics used to describe the dynamics in the Adam-Gibbs (AG) equation. However we are limited computationally to work at temperatures above the "crossover" temperature at which the breakdown in the Adam-Gibbs relation has been identified in laboratory studies. We find a new break in the slope of the constant pressure AG plot (in the same sense but at much higher temperature than with laboratory data) when the excess entropy is used in the AG equation. This break, which we associate with anharmonic vibrational effects, is not seen when the configurational entropy is used. The simulation diffusivity data are equally well fitted by the AG equation and by a new equation, derived within the Gaussian excitations model, that emphasizes enthalpy over entropy as the thermodynamic control variable for transport in viscous liquids. We show that the modified SW model has close links to the behavior observed for bulk metallic glasses, both in its diffusional and in its thermodynamic properties. read less NOT USED (high confidence) D. Cole, M. Payne, G. Csányi, S. Spearing, and L. C. Ciacchi, “Development of a classical force field for the oxidized Si surface: application to hydrophilic wafer bonding.,” The Journal of chemical physics. 2007. link Times cited: 72 Abstract: We have developed a classical two- and three-body interactio… read moreAbstract: We have developed a classical two- and three-body interaction potential to simulate the hydroxylated, natively oxidized Si surface in contact with water solutions, based on the combination and extension of the Stillinger-Weber potential and of a potential originally developed to simulate SiO(2) polymorphs. The potential parameters are chosen to reproduce the structure, charge distribution, tensile surface stress, and interactions with single water molecules of a natively oxidized Si surface model previously obtained by means of accurate density functional theory simulations. We have applied the potential to the case of hydrophilic silicon wafer bonding at room temperature, revealing maximum room temperature work of adhesion values for natively oxidized and amorphous silica surfaces of 97 and 90 mJm(2), respectively, at a water adsorption coverage of approximately 1 ML. The difference arises from the stronger interaction of the natively oxidized surface with liquid water, resulting in a higher heat of immersion (203 vs 166 mJm(2)), and may be explained in terms of the more pronounced water structuring close to the surface in alternating layers of larger and smaller densities with respect to the liquid bulk. The computed force-displacement bonding curves may be a useful input for cohesive zone models where both the topographic details of the surfaces and the dependence of the attractive force on the initial surface separation and wetting can be taken into account. read less NOT USED (high confidence) N. Combe, J. Huntzinger, and A. Mlayah, “Vibrations of quantum dots and light scattering properties: Atomistic versus continuous models,” Physical Review B. 2007. link Times cited: 28 Abstract: The resonant inelastic light scattering by acoustic vibratio… read moreAbstract: The resonant inelastic light scattering by acoustic vibration modes in spherical germanium nanocrystals is studied theoretically. The Raman-Brillouin efficiency is calculated using quantum perturbation theory and assuming deformation-potential interaction between the confined electronic states and the nanocrystal vibration modes. The electronic states are described using the effective mass approximation. The vibration modes are calculated, on one hand, using an atomistic approach based on the Stillinger-Weber interaction potential and, on the other hand, using elasticity theory Lamb’s model. Both models are compared depending on the nanocrystal size and on the surface boundary conditions. By projecting the Stillinger-Weber vibration modes on Lamb’s modes, we are able to discuss the validity of the elasticity theory and to determine the origin of the low-frequency Raman-Brillouin scattering. read less NOT USED (high confidence) W. Zhang, N. Mingo, and T. Fisher, “Simulation of phonon transport across a non-polar nanowire junction using an atomistic Green’s function method,” Physical Review B. 2007. link Times cited: 57 Abstract: Phonon transport across a non-polar nanowire situated betwee… read moreAbstract: Phonon transport across a non-polar nanowire situated between two semi-infinite contacts is simulated in this paper using the atomistic Green's function method. Abrupt geometric changes between the nanowire and bulk contacts are handled by self-energy matrices obtained from bare surface Green's functions. Transport properties such as phonon transmission functions and thermal conductances are calculated, and their dependencies on the interatomic potential, length, diameter, shape, and lattice orientation are investigated. The results reveal that the overall thermal conductance of the nanowire\char21{}bulk-contact structure increases with nanowire diameter while the normalized thermal conductance approaches an asymptotic value. Thermal conductance decreases significantly with increasing nanowire length and converges to that of the single-contact case. This method can be generalized to study phonon transport through a variety of nanostructures between bulk contacts. read less NOT USED (high confidence) X. Li et al., “An improved replica-exchange sampling method: temperature intervals with global energy reassignment.,” The Journal of chemical physics. 2007. link Times cited: 34 Abstract: In a molecular dynamics (MD) simulation, representative samp… read moreAbstract: In a molecular dynamics (MD) simulation, representative sampling over the entire phase space is desired to obtain an accurate canonical distribution at a given temperature. For large molecules, such as proteins, this is problematic because systems tend to become trapped in local energy minima. The extensively used replica-exchange molecular dynamics (REMD) simulation technique overcomes this kinetic-trapping problem by allowing Boltzmann-weighted configuration exchange processes to occur between numerous thermally adjacent and compositionally identical simulations that are thermostated at sequentially higher temperatures. While the REMD method provides much better sampling than conventional MD, there are two substantial difficulties that are inherent in its application: (1) the large number of replicas that must be used to span a designated temperature range and (2) the subsequent long time required for configurations sampled at high temperatures to exchange down for potential inclusion within the low-temperature ensemble of interest. In this work, a new method based on temperature intervals with global energy reassignment (TIGER) is presented that overcomes both of these problems. A TIGER simulation is conducted as a series of short heating-sampling-quenching cycles. At the end of each cycle, the potential energies of all replicas are simultaneously compared at the same temperature using a Metropolis sampling method and then globally reassigned to the designated temperature levels. TIGER is compared with regular MD and REMD methods for the alanine dipeptide in water. The results indicate that TIGER increases sampling efficiency while substantially reducing the number of central processing units required for a comparable conventional REMD simulation. read less NOT USED (high confidence) M. Matsumoto, A. Baba, and I. Ohmine, “Topological building blocks of hydrogen bond network in water.,” The Journal of chemical physics. 2007. link Times cited: 90 Abstract: Basic three-dimensional units of the network, called fragmen… read moreAbstract: Basic three-dimensional units of the network, called fragments, are introduced to characterize the hydrogen bond (HB) network structure of water. Topological differences among normal liquid water, water at low temperature, and water under high pressure are elucidated by their fragment statistics. Water at low temperature has almost defect-free network and is filled with stable fragments with small distortion. It is found that there exists a certain way on how fragments mutually aggregate. Well-formed aggregates heterogeneously constitute very stable network structures. HB network rearrangements occur scarcely inside these aggregated domains but take place in their surface areas. The heterogeneity of HB structure and rearrangement in water is thus explained in terms of the fragment structure and its rearrangements. The fragment analysis thus elucidates the intermediate-range order in water HB network. read less NOT USED (high confidence) D. Swanson and H. Jiang, “Adaptive Load-Balancing for Force-Decomposition Based 3-Body Molecular Dynamics Simulations in A Heterogeneous Distributed Environment with Variable Number of Processors,” 2007 International Conference on Parallel Processing (ICPP 2007). 2007. link Times cited: 1 Abstract: Molecular dynamics (MD), a computationally intensive problem… read moreAbstract: Molecular dynamics (MD), a computationally intensive problem, is used by researchers in various fields. The computational parallelism inherent in this application can be exploited in parallel and distributed environments. However, in heterogeneous distributed environments such as the grid, the available resources, namely the network and computational power, are continually changing with respect to every available node. To optimally utilize these dynamic resources, a scheduler should be able to continually adapt to the changes and suitably vary the number of interactions scheduled to each node. We propose one such scheduling algorithm in this paper. MD simulations based on the spatial-decomposition (for short-range potentials) technique assuming heterogeneous compute power and homogeneous links exist in the literature. To the best of our knowledge, this paper is the first to perform a block-level decomposition of the force-matrix for three-body potentials in a distributed environment with heterogeneous compute power with heterogeneous network links while exploiting the symmetries that exist in a three-body force matrix. Our previous work [24] targeted MD simulations using the atom-decomposition method (slice level decomposition of the force-matrix) in a heterogeneous environment. The proposed scheduling algorithm builds and continually updates a model of the distributed system, which it then uses to make decisions about how to optimally redistribute the load in the system at every time step of the MD simulation. The scheduling algorithm can additionally handle dynamic changes in the number of nodes available for computation at runtime. We implement our algorithm and evaluate its effectiveness by measuring the idle fraction which is a measure of the idle time experienced by all compute clients at every time-step. This idle fraction is a load-balance optimality measure that indicates how close the load balancing is to the theoretical optimal of 0%. We find that under most typical conditions, it is roughly 6%. We also determine potential enhancements to improve the idle fraction further. read less NOT USED (high confidence) M. Demkowicz, A. Argon, D. Farkas, and M. Frary, “Simulation of plasticity in nanocrystalline silicon,” Philosophical Magazine. 2007. link Times cited: 46 Abstract: Molecular dynamics investigation of plasticity in a model na… read moreAbstract: Molecular dynamics investigation of plasticity in a model nanocrystalline silicon system demonstrates that inelastic deformation localizes in intergranular regions. The carriers of plasticity in these regions are atomic environments, which can be described as high-density liquid-like amorphous silicon. During fully developed flow, plasticity is confined to system-spanning intergranular zones of easy flow. As an active flow zone rotates out of the plane of maximum resolved shear stress during deformation to large strain, new zones of easy flow are formed. Compatibility of the microstructure is accommodated by processes such as grain rotation and formation of new grains. Nano-scale voids or cracks may form if stress concentrations emerge which cannot be relaxed by a mechanism that simultaneously preserves microstructural compatibility. read less NOT USED (high confidence) S. Srinivasan and R. S. Miller, “On Parallel Nonequilibrium Molecular Dynamics Simulations of Heat Conduction in Heterogeneous Materials with Three-Body Potentials: Si/Ge Superlattice,” Numerical Heat Transfer, Part B: Fundamentals. 2007. link Times cited: 15 Abstract: Parallelization strategies for nonequilibrium molecular dyna… read moreAbstract: Parallelization strategies for nonequilibrium molecular dynamics (NEMD) simulations of heat conduction in heterogeneous materials are presented. In particular, a previously published algorithm involving the pair decomposition of three-body potentials is extended for heterogeneous materials. In addition, a novel and linear scaling scheme, also based on pair decomposition of three-body terms, is introduced for the calculation of the heat flux. The distributed-computing-based implementation of this algorithm is outlined and its speed-up characteristics are demonstrated to be close to ideal. Example NEMD simulations using the new algorithm are performed for the Si/Ge superlattice based on the three-body Stillinger-Weber potential. read less NOT USED (high confidence) J. A. Pascual-Gutiérrez, J. Murthy, and R. Viskanta, “Limits of size confinement in silicon thin films and wires,” Journal of Applied Physics. 2007. link Times cited: 15 Abstract: Physically confined structures such as thin films and nanowi… read moreAbstract: Physically confined structures such as thin films and nanowires are becoming increasingly important in nanoscale energy conversion and nanoelectronics. The main focus of this work is to determine the size threshold below which the volumetric specific heat and group velocity of one- and two-dimensionally confined silicon nanostructures begin to differ significantly with respect to bulk silicon and to quantify these changes. The dynamical matrix approach subject to free-standing boundary conditions is employed to determine the phonon normal modes of vibration of the structures. The environment-dependent interatomic potential under the harmonic approximation is used to model interatomic forces. We find that above 10nm thickness, silicon [111]-films yield specific heats and group velocities which exhibit size-invariant behavior; for [111]-silicon nanowires, the limit is approximately 5nm. Moreover, we show that computed phonon group velocities using the dynamical matrix approach are affected by geometry-speci... read less NOT USED (high confidence) T. Hawa and M. Zachariah, “Development of a phenomenological scaling law for fractal aggregate sintering from molecular dynamics simulation,” Journal of Aerosol Science. 2007. link Times cited: 28 NOT USED (high confidence) T. Zohdi, “Computation of strongly coupled multifield interaction in particle–fluid systems,” Computer Methods in Applied Mechanics and Engineering. 2007. link Times cited: 84 NOT USED (high confidence) I. Szlufarska, R. Kalia, A. Nakano, and P. Vashishta, “A molecular dynamics study of nanoindentation of amorphous silicon carbide,” Journal of Applied Physics. 2007. link Times cited: 35 Abstract: Through molecular dynamics simulation of nanoindentation of … read moreAbstract: Through molecular dynamics simulation of nanoindentation of amorphous a‐SiC, we have found a correlation between its atomic structure and the load-displacement (P‐h) curve. We show that a density profile of a‐SiC exhibits oscillations normal to the surface, analogous to liquid metal surfaces. Short-range P‐h response of a‐SiC is similar to that of crystalline 3C‐SiC, e.g., it shows a series of load drops associated with local rearrangements of atoms. However, the load drops are less pronounced than in 3C‐SiC due to lower critical stress required for rearrangement of local clusters of atoms. The nanoindentation damage is less localized than in 3C‐SiC. The maximum pressure under the indenter is 60% lower than in 3C‐SiC with the same system geometry. The onset of plastic deformation occurs at the depth of 0.5A, which is ∼25% of the corresponding value in 3C‐SiC. a‐SiC exhibits lower damping as compared to 3C‐SiC, which is reflected in the longer relaxation time of transient forces after each discrete indenta... read less NOT USED (high confidence) L. Xiong, Y. Chen, and J. D. Lee, “Atomistic simulation of mechanical properties of diamond and silicon carbide by a field theory,” Modelling and Simulation in Materials Science and Engineering. 2007. link Times cited: 21 Abstract: This paper presents a multiscale field theory and its applic… read moreAbstract: This paper presents a multiscale field theory and its application in modelling and simulation of atomistic systems involving three-body interaction forces. Atomistic formulation of the multiscale field theory is introduced. Numerical simulations based on the field theory are performed to investigate the material behaviours of diamond and silicon carbide at the atomic scale. We have obtained the tensile strength and the elastic modulus that approach that obtained by first principles calculations for both diamond and silicon carbide. Their nanoscale deformation and failure mechanism are revealed. It is interesting to observe that under tensile loading, unlike silicon carbide, diamond has gone through a phase transformation as well as local amorphization before failure. The potential application of this atomic field theory is discussed. read less NOT USED (high confidence) B. Cox and J. M. Hill, “New Carbon Molecules in the Form of Elbow-Connected Nanotori,” Journal of Physical Chemistry C. 2007. link Times cited: 27 Abstract: Toroidal caged molecules of carbon have been investigated pr… read moreAbstract: Toroidal caged molecules of carbon have been investigated previously as constructed from elbows formed from armchair (5,5) and zigzag (9,0) nanotubes connected through a pentagonal and heptagonal defect at each bend site. In this paper, we consider these elbows, and we describe two new elbows constructed from (3,3)-(5,0) and (4,4)-(7,0) nanotubes. By assuming the constituent atoms remain in their ideal positions on the nanotube sections, we determine the bend angle and nanotube lengths that characterize each elbow in the unconstrained state and also when the elbow is constrained as when incorporated in a toroidal caged molecule. Using these results, we describe specific examples of new families of carbon caged molecules and the associated geometric parameters of these molecules. In order to properly prescribe the new molecules, we need to introduce a new nomenclature N(n1, m1)pM(n2, m2)q..., where (n1, m1) and (n2, m2) designate the component nanotubes, p, q, ... are the number of atoms in each nanotube s... read less NOT USED (high confidence) S. J. V, D. Swanson, and H. Jiang, “A symmetric transformation for 3-body potential molecular dynamics using force-decomposition in a heterogeneous distributed environment,” International Conference on Supercomputing. 2007. link Times cited: 7 Abstract: Evaluating the Force Matrix constitutes the most computation… read moreAbstract: Evaluating the Force Matrix constitutes the most computationally intensive part of a Classical Molecular Dynamics (MD) simulation. In three-body MD simulations, the total energy of the system is determined by the energy of every unique triple in the system and the force matrix is three-dimensional. The execution time of a three-body MD algorithm is thus proportional to the cube of the number of atoms in the system. Fortunately, there exist symmetries in the Force Matrix that can be exploited to improve the running time of the algorithm. While this optimization is straight forward to implement in the case of sequential code, it has proven to be nontrivial for parallel code even in a homogeneous environment.
In this paper, we present two force matrix transformations that are capable of exploiting the symmetries in a 3-body force matrix in both a homogeneous and a heterogeneous environment while balancing the load among all the participating processors. The first transformation distributes the number of interactions to be computed uniformly among all the slices of the force matrix along any of the axes. The transformed matrix can be scheduled using any well known heterogeneous slice-level scheduling technique. The second transformation distributes interactions to be computed uniformly over the entire volume of the force matrix allowing us to perform a block decomposition of the force matrix. The transformed force matrix can be scheduled by any block level scheduling algorithm. We also derive theoretical bounds for efficiency and load balance for our transformations and prove some interesting and useful properties of our transformations and evaluate their advantages and disadvantages. The performance of an MPI implementation of the transformations is studied in terms of the Step Time Variation Ratio (STVR) in a homogeneous and heterogeneous environment. read less NOT USED (high confidence) H. Zhao and N. Aluru, “A semi-local quasi-harmonic model to compute the thermodynamic and mechanical properties of silicon nanostructures,” Journal of Physics: Condensed Matter. 2007. link Times cited: 2 Abstract: This paper presents a semi-local quasi-harmonic model with l… read moreAbstract: This paper presents a semi-local quasi-harmonic model with local phonon density of states (LPDOS) to compute the thermodynamic and mechanical properties of silicon nanostructures at finite temperature. In contrast to an earlier approach (Tang and Aluru 2006 Phys. Rev. B 74 235441), where a quasi-harmonic model with LPDOS computed by a Green’s function technique (QHMG) was developed considering many layers of atoms, the semi-local approach considers only two layers of atoms to compute the LPDOS. We show that the semi-local approach combines the accuracy of the QHMG approach and the computational efficiency of the local quasi-harmonic model. We present results for several silicon nanostructures to address the accuracy and efficiency of the semi-local approach. read less NOT USED (high confidence) A. Galashev, I. A. Izmodenov, O. Novruzova, and A. N. Novruzov, “Computer study of the temperature dependence of physical properties of noncrystalline silicon nanoparticles,” Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques. 2007. link Times cited: 1 NOT USED (high confidence) K. Sastry, D. Goldberg, and D. D. Johnson, “Scalability of a Hybrid Extended Compact Genetic Algorithm for Ground State Optimization of Clusters,” Materials and Manufacturing Processes. 2007. link Times cited: 28 Abstract: We analyze the utility and scalability of extended compact g… read moreAbstract: We analyze the utility and scalability of extended compact genetic algorithm (eCGA)—a genetic algorithm (GA) that automatically and adaptively mines the regularities of the fitness landscape using machine learning methods and information theoretic measures—for ground state optimization of clusters. In order to reduce the computational time requirements while retaining the high reliability of predicting near-optimal structures, we employ two efficiency-enhancement techniques: (1) hybridizing eCGA with a local search method, and (2) seeding the initial population with lowest energy structures of a smaller cluster. The proposed method is exemplified by optimizing silicon clusters with 4–20 atoms. The results indicate that the population size required to obtain near-optimal solutions with 98% probability scales sub linearly (as Θ(n 0.83)) with the cluster size. The total number of function evaluations (cluster energy calculations) scales sub-cubically (as Θ(n 2.45)), which is a significant improvement over exponential scaling of poorly designed evolutionary algorithms. read less NOT USED (high confidence) Y. Zhao, S. Xiong, and N. Xu, “The Geometry Optimization of Argon Atom Clusters Using Differential Evolution Algorithm,” International Conference on Conceptual Structures. 2007. link Times cited: 3 NOT USED (high confidence) N. Bernstein, “Surface passivation for tight-binding calculations of covalent solids,” Journal of Physics: Condensed Matter. 2007. link Times cited: 0 Abstract: Simulation of a cluster representing a finite portion of a l… read moreAbstract: Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp3 hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system. read less NOT USED (high confidence) P. Vashishta, R. Kalia, A. Nakano, and J. Rino, “Interaction potential for silicon carbide: A molecular dynamics study of elastic constants and vibrational density of states for crystalline and amorphous silicon carbide,” Journal of Applied Physics. 2007. link Times cited: 279 Abstract: An effective interatomic interaction potential for SiC is pr… read moreAbstract: An effective interatomic interaction potential for SiC is proposed. The potential consists of two-body and three-body covalent interactions. The two-body potential includes steric repulsions due to atomic sizes, Coulomb interactions resulting from charge transfer between atoms, charge-induced dipole-interactions due to the electronic polarizability of ions, and induced dipole-dipole (van der Waals) interactions. The covalent characters of the Si–C–Si and C–Si–C bonds are described by the three-body potential. The proposed three-body interaction potential is a modification of the Stillinger-Weber form proposed to describe Si. Using the molecular dynamics method, the interaction potential is used to study structural, elastic, and dynamical properties of crystalline (3C), amorphous, and liquid states of SiC for several densities and temperatures. The structural energy for cubic (3C) structure has the lowest energy, followed by the wurtzite (2H) and rock-salt (RS) structures. The pressure for the structural t... read less NOT USED (high confidence) X. W. Zhou and H. Wadley, “A potential for simulating the atomic assembly of cubic AB compounds,” Computational Materials Science. 2007. link Times cited: 7 NOT USED (high confidence) S. Saha and L. Shi, “Molecular dynamics simulation of thermal transport at a nanometer scale constriction in silicon,” Journal of Applied Physics. 2007. link Times cited: 39 Abstract: To better understand thermal transport at nanoscale point co… read moreAbstract: To better understand thermal transport at nanoscale point contacts such as the tip-sample contact of a scanning probe microscope and at the contact between a nanotube and a planar surface, we have used a nonequilibrium molecular dynamics (MD) method to calculate the temperature distribution and thermal resistance of a nanometer scale constriction formed between two planar silicon substrates of different temperatures. Surface reconstruction was observed at the two free silicon surfaces and at the constriction. The radius of the heated zone in the cold substrate was found to approach a limit of about 20 times the average nearest-neighbor distance of boron doping atoms when the constriction radius (a) is reduced below the interdopant distance. The phonon mean free path at the constriction was found to be suppressed by diffuse phonon-surface scattering and phonon-impurity scattering. The MD thermal resistance is close to the ballistic resistance when a is larger than 1nm, suggesting that surface reconstructio... read less NOT USED (high confidence) A. Galashev, I. A. Izmodenov, O. Rakhmanova, and O. Novruzova, “Computer simulation of the tension of noncrystalline silicon nanoparticles,” Glass Physics and Chemistry. 2007. link Times cited: 2 NOT USED (high confidence) X. W. Zhou and H. Wadley, “A potential for simulating the atomic assembly of cubic elements,” Computational Materials Science. 2007. link Times cited: 10 NOT USED (high confidence) R. D. Menezes, J. F. Justo, and L. Assali, “Energetics of silicon nanowires: a molecular dynamics investigation,” physica status solidi (a). 2007. link Times cited: 4 Abstract: Silicon nanowires, with the 〈100〉 and 〈110〉 growth direction… read moreAbstract: Silicon nanowires, with the 〈100〉 and 〈110〉 growth directions and at several surface facet configurations, were investigated by molecular dynamics simulations. We considered three commonly used interatomic potentials for silicon, and tested the reliability of each model to describe silicon nanowires. We find that, for each growth direction, the facet family plays a central role on the nanowire energy, which follows a universal scaling law as a function of the nanowire perimeter. Those results were discussed in the context of recent experimental and ab initio data. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) read less NOT USED (high confidence) S. Meloni, M. Rosati, and L. Colombo, “Efficient particle labeling in atomistic simulations.,” The Journal of chemical physics. 2007. link Times cited: 47 Abstract: The authors develop an efficient particle labeling procedure… read moreAbstract: The authors develop an efficient particle labeling procedure based on a linked cell algorithm which is shown to reduce the computing time for a molecular dynamics simulation by a factor of 3. They prove that the improvement of performance is due to the efficient fulfillment of both spatial and temporal locality principles, as implemented by the contiguity of labels corresponding to interacting atoms. Finally, they show that the present label reordering procedure can be used to devise an efficient parallel one-dimensional domain decomposition molecular dynamics scheme. read less NOT USED (high confidence) H. Wang et al., “High-pressure structural behaviour of nanocrystalline Ge,” Journal of Physics: Condensed Matter. 2007. link Times cited: 20 Abstract: The equation of state and the pressure of the I–II transitio… read moreAbstract: The equation of state and the pressure of the I–II transition have been studied for nanocrystalline Ge using synchrotron x-ray diffraction. The bulk modulus and the transition pressure increase with decreasing particle size for both Ge-I and Ge-II, but the percentage volume collapse at the transition remains constant. Simplified models for the high-pressure structural behaviour are presented, based on the assumption that a large fraction of the atoms reside in grain boundary regions of the nanocrystalline material. The interface structure plays a significant role in affecting the transition pressure and the bulk modulus. read less NOT USED (high confidence) J. Li, G. Lykotrafitis, M. Dao, and S. Suresh, “Cytoskeletal dynamics of human erythrocyte,” Proceedings of the National Academy of Sciences. 2007. link Times cited: 248 Abstract: The human erythrocyte (red blood cell, RBC) demonstrates ext… read moreAbstract: The human erythrocyte (red blood cell, RBC) demonstrates extraordinary ability to undergo reversible large deformation and fluidity. Such mechanical response cannot be consistently rationalized on the basis of fixed connectivity of the cell cytoskeleton that comprises the spectrin molecular network tethered to phospholipid membrane. Active topological remodeling of spectrin network has been postulated, although detailed models of such dynamic reorganization are presently unavailable. Here we present a coarse-grained cytoskeletal dynamics simulation with breakable protein associations to elucidate the roles of shear stress, specific chemical agents, and thermal fluctuations in cytoskeleton remodeling. We demonstrate a clear solid-to-fluid transition depending on the metabolic energy influx. The solid network's plastic deformation also manifests creep and yield regimes depending on the strain rate. This cytoskeletal dynamics model offers a means to resolve long-standing questions regarding the reference state used in RBC elasticity theory for determining the equilibrium shape and deformation response. In addition, the simulations offer mechanistic insights into the onset of plasticity and void percolation in cytoskeleton. These phenomena may have implication for RBC membrane loss and shape change in the context of hereditary hemolytic disorders such as spherocytosis and elliptocytosis. read less NOT USED (high confidence) S. Nangia, N. Washton, K. Mueller, J. Kubicki, and B. Garrison, “Study of a Family of 40 Hydroxylated β-Cristobalite Surfaces Using Empirical Potential Energy Functions,” Journal of Physical Chemistry C. 2007. link Times cited: 25 Abstract: We present a study of a family of 40 unique hydroxylated β-c… read moreAbstract: We present a study of a family of 40 unique hydroxylated β-cristobalite surfaces generated by cleaving the β-cristobalite unit cell along crystallographic planes to include a combination of several low Miller index surfaces. The surface silicon atoms are quantified as percentages of Q 2 and Q 3 centers based on their polymeric state. We find that Q 3 centers are, on average, three times more abundant than Q 2 centers. To study the surface properties, we use two different empirical potential energy functions: the multibody potential proposed by Fueston and Garofalini (J. Phys. Chem. 1990, 94, 5351) and the newly developed CHARMM potential by Lopes et al. (J. Phys. Chem. B 2006, 110, 2782). Our results for the surface water interactions are in good agreement with previous ab initio theoretical studies by Yang et al. (Phys. Rev. B 2006, 73, 146102) for the (100) surface. We find that the most commonly studied family of {100} surfaces is unique and is the only surface with 100% abundance of Q 2 centers, whereas there are nine examples of surfaces with 100% Q 3 centers. The predominantly pure Q 3 surfaces show no hydrogen bonding with the neighboring surface hydroxyl groups and weakly adsorb water overlayers. This is markedly different from the {100} pure Q 2 surface that shows strong hydrogen bonding within the surface groups and with water. As compared to all the surfaces studied in this work, we find that the {100} surfaces are not true representations of the overall β-cristobalite surfaces and their properties. We find that the two main factors that characterize the physical properties of silica surfaces are the polymeric state of the silicon atom and surface topography. Two types of pure Q 3 crystallographic planes have been identified and are labeled as Q 3A and Q 3B based on the differences in their topological features. Using the {111} and {011} surfaces as examples, we show that the Q 3A surface adsorbs H 2 O that forms a stable monolayer, but the Q 3B surface fails to form a stable H 2 O overlayer. Other crystallographic planes with different ratios of Q 2 to Q 3 centers are contrasted by the differences in the hydrogen-bonding network and their ability to form ordered H 2 O overlayers. read less NOT USED (high confidence) I. Belabbas et al., “Atomistic modeling of the (a+c) -mixed dislocation core in wurtzite GaN,” Physical Review B. 2007. link Times cited: 39 Abstract: An atomistic simulation of the threading $(\mathbf{a}+\mathb… read moreAbstract: An atomistic simulation of the threading $(\mathbf{a}+\mathbf{c})$-mixed dislocation core in wurtzite GaN has been carried out. Starting from models generated in the framework of continuum elasticity theory, two core configurations are obtained independently by using an empirical potential and a tight-binding based ab initio method. The most energetically favorable core with a $5∕7$-atoms ring structure is fully coordinated without wrong bonds, whereas the other with a complex double $5∕6$-atoms ring structure contains two rows of dangling bonds. Both core configurations introduce empty states spread over the upper half of the band gap. read less NOT USED (high confidence) A. Chatterjee and D. Vlachos, “An overview of spatial microscopic and accelerated kinetic Monte Carlo methods,” Journal of Computer-Aided Materials Design. 2007. link Times cited: 400 NOT USED (high confidence) J. Mier, “Multi-scale interaction potentials (F − r) for describing fracture of brittle disordered materials like cement and concrete,” International Journal of Fracture. 2007. link Times cited: 40 NOT USED (high confidence) G. Malescio, “Complex phase behaviour from simple potentials,” Journal of Physics: Condensed Matter. 2007. link Times cited: 64 Abstract: Simple pair potentials, where the term ‘simple’ denotes pote… read moreAbstract: Simple pair potentials, where the term ‘simple’ denotes potentials that are isotropic and refer to one-component systems, can be used to describe effective interactions among substances with supramolecular architecture. By suitably choosing the functional dependence on the intermolecular distance, through such potentials it is possible to take into account, in an average way, the effect of the internal degrees of freedom of the macromolecules. This may give rise to phase phenomena that are radically different from those characterizing typical monoatomic systems. Here we review a number of simple model potentials presenting unusual, i.e. not argon-like, features and discuss the role of attraction and repulsion in determining their phase behaviour. read less NOT USED (high confidence) R. Drautz, X. W. Zhou, D. Murdick, B. Gillespie, H. Wadley, and D. Pettifor, “Analytic bond-order potentials for modelling the growth of semiconductor thin films,” Progress in Materials Science. 2007. link Times cited: 28 NOT USED (high confidence) A. Bholoa, S. Kenny, and R. Smith, “A new approach to potential fitting using neural networks,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2007. link Times cited: 30 NOT USED (high confidence) J. Samela, K. Nordlund, J. Keinonen, and V. Popok, “Comparison of silicon potentials for cluster bombardment simulations,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2007. link Times cited: 26 NOT USED (high confidence) A. Rappé et al., “APT a next generation QM-based reactive force field model,” Molecular Physics. 2007. link Times cited: 20 Abstract: Modelling reactivity at the nanoscale is a major computation… read moreAbstract: Modelling reactivity at the nanoscale is a major computational challenge. Both reactive force field and combined QM–MM methodologies have been and are being developed to study reactivity at this boundary between molecules and the solid state. There have been more than 1500 publications since the mid-1990s, on combined QM–MM methodologies. Limitations in current models include the distortional characteristics of force field potential terms, the smooth transit from one potential surface to another, rather than surface hopping, and the blending of electrostatics between QM and MM portions of a QM–MM model. Functional forms, potential surface coupling terms, and parameterization strategies for the Approximate Pair Theory (APT), a next generation reactive force field model, are described. The APT model has been developed to correct a number of limitations in current reactive force field models as well as providing a foundation for a next generation QM–MM model. Chemical bonding concepts are used to develop fully dissociative bond stretch, bend, torsion, and inversion valence terms. Quantum mechanics also provides functional forms for potential surface coupling terms that permit a general description of reactivity from hydrogen bonding, through non-classical carbocations and cracking, to olefin polymerization, oxidation, and metathesis. Van der Waals, electrostatic, and metallic bonding models also derive from quantum mechanical resonance. Finally, Pauli Principle-based orthogonality provides a way to electrostatically couple the QM and MM portions of a QM–MM model that will support arbitrarily large basis sets. read less NOT USED (high confidence) J. K. Christie, S. Taraskin, and S. Elliott, “Vibrational behavior of a realistic amorphous-silicon model,” Journal of Non-crystalline Solids. 2007. link Times cited: 9 NOT USED (high confidence) M. Taguchi and S. Hamaguchi, “Molecular dynamics study on Ar ion bombardment effects in amorphous SiO2 deposition processes,” Journal of Applied Physics. 2006. link Times cited: 16 Abstract: Argon ion bombardment effects on growing amorphous SiO2 film… read moreAbstract: Argon ion bombardment effects on growing amorphous SiO2 films during reactive sputtering deposition processes were examined based on molecular dynamics (MD) and Monte Carlo (MC) simulation techniques. The system we have considered here is a film that is subject to energetic Ar bombardment while it is formed by surface reactions of Si and O atoms separately supplied at low kinetic energies. It has been found that (1) Ar injections preferentially sputter O atoms from the surface over Si and (2) also have a compressing effect on the growing film during the deposition process. In other words, our MD/MC simulations have demonstrated at the atomic level that, with higher energy Ar injections, an amorphous SiO2 film grown in a reactive sputtering deposition process is denser and more Si rich. read less NOT USED (high confidence) A. Greenstein, S. Graham, Y. Hudiono, and S. Nair, “Thermal Properties and Lattice Dynamics of Polycrystalline MFI Zeolite Films,” Nanoscale and Microscale Thermophysical Engineering. 2006. link Times cited: 16 Abstract: A study of the thermal properties of the zeolite MFI by a co… read moreAbstract: A study of the thermal properties of the zeolite MFI by a combination of experimental measurements and lattice dynamical modeling is presented. Thermal conductivity data in the range of 150–400 K was obtained through 3ω measurements on polycrystalline zeolite films. While Debye theory is inadequate in predicting the zeolite thermal properties, a detailed calculation of the specific heat using a full set of dispersion relations obtained from atomistic simulations gives excellent agreement with experiments. In addition, the thermal conductivity is successfully reproduced by a phonon relaxation time–based model. The results indicate the possibility of developing a predictive model of the thermal properties of complex zeolite materials. read less NOT USED (high confidence) Q. Tang and Y. Yao, “The Kapitza Resistance Across Grain Boundary by Molecular Dynamics Simulation,” Nanoscale and Microscale Thermophysical Engineering. 2006. link Times cited: 6 Abstract: Nonequilibrium molecular dynamics (NEMD) simulations are per… read moreAbstract: Nonequilibrium molecular dynamics (NEMD) simulations are performed to calculate thermal boundary resistance that arises from heat flow across Si grain boundary. The environment-dependent interatomic potential (EDIP) on crystal silicon is adopted as a model system. The issues are related to nonlinear response, local thermal equilibrium, and statistical averaging. The tilt grain boundaries Σ5 and Σ13 are simulated, and the values of thermal boundary resistance by nonequilibrium molecular dynamics are compared with those by Maiti et al. (Solid State Communications, vol. 102, 1997). Using the disperse relation of EDIP potential, an average transmission coefficient of thermal conductivity across boundary is calculated. read less NOT USED (high confidence) Z. Tang and N. Aluru, “Calculation of thermodynamic and mechanical properties of silicon nanostructures using the local phonon density of states,” Physical Review B. 2006. link Times cited: 27 Abstract: We investigate thermodynamic and mechanical properties of si… read moreAbstract: We investigate thermodynamic and mechanical properties of silicon nanostructures at finite temperature. Thermodynamic properties for finite-temperature solid systems under isothermal conditions are characterized by the Helmholtz free energy density. The static part of the Helmholtz free energy is obtained directly from the interatomic potential, while the vibrational part is calculated by using the theory of local phonon density of states LPDOS . The LPDOS is calculated efficiently from the on-site phonon Green’s function by using a recursion technique based on a continued fraction representation. The Cauchy-Born hypothesis is employed to compute the mechanical properties. By considering ideal Si 001 , 2 1 reconstructed Si 001 , and monolayer-hydrogen-passivated 2 1 reconstructed Si 001 surfaces of a silicon nanowire, we calculate the local phonon structure and local thermodynamic and mechanical properties at finite temperature and observe that the surface effects on the local thermal and mechanical properties are localized to within one or two atomic layers of the silicon nanowire. read less NOT USED (high confidence) M. Buehler, “Mesoscale modeling of mechanics of carbon nanotubes: Self-assembly, self-folding, and fracture,” Journal of Materials Research. 2006. link Times cited: 184 Abstract: Using concepts of hierarchical multiscale modeling, we repor… read moreAbstract: Using concepts of hierarchical multiscale modeling, we report development of a mesoscopic model for single-wall carbon nanotubes with parameters completely derived from full atomistic simulations. The parameters in the mesoscopic model are fit to reproduce elastic, fracture, and adhesion properties of carbon nanotubes, in this article demonstrated for (5,5) carbon nanotubes. The mesoscale model enables modeling of the dynamics of systems with hundreds of ultralong carbon nanotubes over time scales approaching microseconds. We apply our mesoscopic model to study self-assembly processes, including self-folding, bundle formation, as well as the response of bundles of carbon nanotubes to severe mechanical stimulation under compression, bending, and tension. Our results with mesoscale modeling corroborate earlier results, suggesting a novel self-folding mechanism, leading to creation of racket-shaped carbon nanotube structures, provided that the aspect ratio of the carbon nanotube is sufficiently large. We find that the persistence length of the (5,5) carbon nanotube is on the order of a few micrometers in the temperature regime from 300 to 1000 K. read less NOT USED (high confidence) S. Alfthan, K. Kaski, and A. Sutton, “Order and structural units in simulations of twist grain boundaries in silicon at absolute zero,” Physical Review B. 2006. link Times cited: 29 NOT USED (high confidence) Z. Wang, X. Zu, F. Gao, and W. J. Weber, “Atomic-level study of melting behavior of GaN nanotubes,” Journal of Applied Physics. 2006. link Times cited: 25 Abstract: Molecular dynamics simulations with a Stillinger-Weber poten… read moreAbstract: Molecular dynamics simulations with a Stillinger-Weber potential have been used to investigate the melting behavior of wurtzite-type single-crystalline GaN nanotubes. The simulations show that the melting temperature of the GaN nanotubes increases with the thickness of the nanotubes to a saturation value, which is close to the melting temperature of a GaN slab. The results reveal that the nanotubes begin to melt at the surface, and then the melting rapidly extends to the interior of the nanotubes as the temperature increases. The melting temperature of a single-crystalline GaN nanotube with [100]-oriented lateral facets is higher than that with [110]-oriented lateral facets for the same thickness. read less NOT USED (high confidence) A. Argon and M. Demkowicz, “Atomistic simulation and analysis of plasticity in amorphous silicon,” Philosophical Magazine. 2006. link Times cited: 33 Abstract: The principal findings of a comprehensive computational simu… read moreAbstract: The principal findings of a comprehensive computational simulation of plastic flow in amorphous Si – presented elsewhere in detail – are summarized. The unit plastic events have been identified to consist of discrete shear transformations triggered at characteristic thresholds of stress that result in transformation shear strains of about 0.015. Based on these findings, a kinetic model of plastic flow is proposed that provides for the temperature dependence of the plastic flow resistance and explains the evolution of a unique flow state starting from different amorphous structures. It is proposed that these findings should be broadly applicable to other strongly bonded glassy covalent compounds. §Dedicated to F. R. N. Nabarro on the occasion of his 90th birthday, in recognition of six and a half decades of insightful contributions to materials science. read less NOT USED (high confidence) Z. Zhennan, G. Xiurun, and L. Yonghe, “A MULTISCALE MECHANICAL MODEL FOR MATERIALS BASED ON VIRTUAL INTERNAL BOND THEORY,” Acta Mechanica Solida Sinica. 2006. link Times cited: 15 NOT USED (high confidence) K.-C. Fang, C. Weng, and S. Ju, “An investigation into the structural features and thermal conductivity of silicon nanoparticles using molecular dynamics simulations,” Nanotechnology. 2006. link Times cited: 47 Abstract: The structural features and thermal conductivity of silicon … read moreAbstract: The structural features and thermal conductivity of silicon nanoparticles of diameter 2–12 nm are studied in a series of molecular dynamics simulations based on the Stilling–Weber (SW) potential model. The results show that the cohesive energy of the particles increases monotonically with an increasing particle size and is independent of the temperature. It is found that particles with a diameter of 2 nm have a heavily reconstructed geometry which generates lattice imperfections. The thermal conductivity of the nanoscale silicon particles increases linearly with their diameter and is two orders of magnitude lower than that of bulk silicon. The low thermal conductivity of the smallest nanoparticles is thought to be the result of particle boundary and lattice imperfections produced during fabrication, which reduce the phonon mean free path (MFP). Finally, it is found that the influence of the temperature on the thermal conductivity decreases significantly as the temperature increases. Again, this is thought to be the result of a reduced phonon MFP at elevated temperatures. read less NOT USED (high confidence) M. Gillan, D. Alfé, J. Brodholt, L. Vočadlo, and G. D. Price, “First-principles modelling of Earth and planetary materials at high pressures and temperatures,” Reports on Progress in Physics. 2006. link Times cited: 95 Abstract: Atomic-scale materials modelling based on first-principles q… read moreAbstract: Atomic-scale materials modelling based on first-principles quantum mechanics is playing an important role in the science of the Earth and the other planets. We outline the basic theory of this kind of modelling and explain how it can be applied in a variety of different ways to probe the thermodynamics, structure and transport properties of both solids and liquids under extreme conditions. After a summary of the density functional formulation of quantum mechanics and its practical implementation through pseudopotentials, we outline the simplest way of applying first-principles modelling, namely static zero-temperature calculations. We show how calculations of this kind can be compared with static compression experiments to demonstrate the accuracy of first-principles modelling at pressures reached in planetary interiors. Noting that virtually all problems concerning planetary interiors require an understanding of materials at high temperatures as well as high pressures, we then describe how first-principles lattice dynamics gives a powerful way of investigating solids at temperatures not too close to the melting line. We show how such calculations have contributed to important progress, including the recent discovery of the post-perovskite phase of MgSiO3 in the D′′ layer at the base of the Earth's mantle. A range of applications of first-principles molecular dynamics are then reviewed, including the properties of metallic hydrogen in Jupiter and Saturn, of water, ammonia and methane in Uranus and Neptune, and of oxides and silicates and solid and liquid iron and its alloys in the Earth's deep interior. Recognizing the importance of phase equilibria throughout the planetary sciences, we review recently developed techniques for the first-principles calculation of solid and liquid free energies, melting curves and chemical potentials of alloys. We show how such calculations have contributed to an improved understanding of the temperature distribution and the chemical composition throughout the Earth's interior. The review concludes with a summary of the present state of the field and with some ideas for future developments. read less NOT USED (high confidence) L. Pan, X. Wu, D. Xu, C. Lu, and H. P. Lee, “A new handshaking of Tight-Binding and Molecular Dynamics in multi-scale simulation,” The European Physical Journal B - Condensed Matter and Complex Systems. 2006. link Times cited: 0 NOT USED (high confidence) W. Chen and J. Fish, “A mathematical homogenization perspective of virial stress,” International Journal for Numerical Methods in Engineering. 2006. link Times cited: 35 Abstract: A continuum stress measure is derived from molecular dynamic… read moreAbstract: A continuum stress measure is derived from molecular dynamics equations using a generalized mathematical homogenization (GMH) theory. GMH consists of solving a coupled fine‐scale (atomistic unit cell) problem and a coarse‐scale (continuum) problem. The fine‐scale problem derived can be interpreted as a molecular statics (at 0 K) problem, where the coarse‐scale problem derived is a constitutive law‐free continuum equation, which calculates the Cauchy stress directly from atomistics. The continuum stress derived is compared to various versions of the virial stress formula. Copyright © 2005 John Wiley & Sons, Ltd. read less NOT USED (high confidence) W. Gerberich and M. Cordill, “Physics of adhesion,” Reports on Progress in Physics. 2006. link Times cited: 61 Abstract: Adhesion physics was relegated to the lowest echelons of aca… read moreAbstract: Adhesion physics was relegated to the lowest echelons of academic pursuit until the advent of three seemingly disconnected events. The first, atomic force microscopy (AFM), eventually allowed fine-scale measurement of adhesive point contacts. The second, large-scale computational materials science, now permits both hierarchical studies of a few thousand atoms from first principles or of billions of atoms with less precise interatomic potentials. The third is a microelectronics industry push towards the nanoscale which has provided the driving force for requiring a better understanding of adhesion physics. In the present contribution, an attempt is made at conjoining these separate events into an updating of how theoretical and experimental approaches are providing new understanding of adhesion physics. While all material couples are briefly considered, the emphasis is on metal/semiconductor and metal/ceramic interfaces. Here, adhesion energies typically range from 1 to 100 J m−2 where the larger value is considered a practical work of adhesion. Experimental emphasis is on thin-film de-adhesion for 10 to 1000 nm thick films. For comparison, theoretical approaches from first principles quantum mechanics to embedded atom methods used in multi-scale modelling are utilized. read less NOT USED (high confidence) T. Fujii and Y. Akiniwa, “Molecular dynamics analysis for fracture behaviour of single crystal silicon thin film with micro notch,” Modelling and Simulation in Materials Science and Engineering. 2006. link Times cited: 18 Abstract: Thin films of single crystal silicon are widely required in … read moreAbstract: Thin films of single crystal silicon are widely required in many applications of semiconductor devices and micro-electro-mechanical systems. In this study, molecular dynamics simulation is conducted to investigate the effect of notch depth on fracture strength. The specimen size is about 10 nm × 5 nm, and the periodic boundary condition is applied for thin films. The loading directions are [100], [110] and [111] direction. Brittle fracture occurs on the plane perpendicular to the loading direction. The stress intensity factor at the onset of the crack propagation increases with increasing notch depth. When the notch depth is longer than 2 nm, the stress intensity factor is nearly constant. At the onset of the crack propagation, the stress at the notch root becomes constant irrespective of the notch depth. read less NOT USED (high confidence) R. Zhu, E. Pan, P. W. Chung, X. Cai, K. M. Liew, and A. Buldum, “Atomistic calculation of elastic moduli in strained silicon,” Semiconductor Science and Technology. 2006. link Times cited: 113 Abstract: Strained silicon is becoming a new technology in silicon ind… read moreAbstract: Strained silicon is becoming a new technology in silicon industry where the novel strain-induced features are utilized. In this paper we present a molecular dynamic prediction for the elastic stiffnesses C11, C12 and C44 in strained silicon as functions of the volumetric strain level. Our approach combines basic continuum mechanics with the classical molecular dynamic approach, supplemented with the Stillinger–Weber potential. Using our approach, the bulk modulus, effective elastic stiffnesses C11, C12 and C44 of the strained silicon, including also the effective Young's modulus and Poisson's ratio, are all calculated and presented in terms of figures and formulae. In general, our simulation indicates that the bulk moduli, C11 and C12, increase with increasing volumetric strain whilst C44 is almost independent of the volumetric strain. The difference between strained moduli and those at zero strain can be very large, and therefore use of standard free-strained moduli should be cautious. read less NOT USED (high confidence) J. Kioseoglou, G. Dimitrakopulos, P. Komninou, T. Kehagias, and T. Karakostas, “Mixed partial dislocation core structure in GaN by high resolution electron microscopy,” physica status solidi (a). 2006. link Times cited: 7 Abstract: The core structures of a 1/6 [2$\bar 2$03] mixed partial dis… read moreAbstract: The core structures of a 1/6 [2$\bar 2$03] mixed partial dislocation in wurtzite GaN have been investigated using a combination of high resolution transmission electron microscopy, circuit mapping, and image simulation of relaxed models. HRTEM simulated images of relaxed atomic models, derived by energetic calculations with a modified Stillinger–Weber‐type empirical interatomic potential, were calculated and compared to the experimental images. Among twenty‐four stable core configurations the 12‐ and 10‐atom rings satisfied the experimental contrast. A pattern registration procedure was used for the matching of simulated and experimental HRTEM images. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) read less NOT USED (high confidence) P. Erhart, N. Juslin, O. Goy, K. Nordlund, R. Müller, and K. Albe, “Analytic bond-order potential for atomistic simulations of zinc oxide,” Journal of Physics: Condensed Matter. 2006. link Times cited: 75 Abstract: An interatomic potential for zinc oxide and its elemental co… read moreAbstract: An interatomic potential for zinc oxide and its elemental constituents is derived based on an analytical bond-order formalism. The model potential provides a good description of the bulk properties of various solid structures of zinc oxide including cohesive energies, lattice parameters, and elastic constants. For the pure elements zinc and oxygen the energetics and structural parameters of a variety of bulk phases and in the case of oxygen also molecular structures are reproduced. The dependence of thermal and point defect properties on the cutoff parameters is discussed. As exemplary applications the irradiation of bulk zinc oxide and the elastic response of individual nanorods are studied. read less NOT USED (high confidence) F. Cleri and P. Keblinski, “What’s so special about nanocrystalline semiconductors?,” Int. J. Comput. Sci. Eng. 2006. link Times cited: 2 Abstract: Nanocrystalline semiconductors display unique features compa… read moreAbstract: Nanocrystalline semiconductors display unique features compared to coarse-grained microstructures and even to their monocrystalline counterparts. We contend that such peculiarities are due to: (1) the extremely large fraction of atoms located at Grain Boundaries (GBs) and (2) the 'character distribution' of GBs, which are mostly high-energy, random interfaces. Initially, we study the structure of random GBs in nanocrystalline semiconductors by means of large-scale Molecular Dynamics (MD) simulations. Subsequently, the atomic structure and electronic properties of some typical high-energy GBs in Si- and C-based nanostructures are characterised by means of a semi-empirical tight-binding Hamiltonian. We show that relevant properties of nanocrystalline semiconductors containing a large fraction of high-energy GBs are quite distinct with respect to those of coarse-grained and bulk semiconductors. read less NOT USED (high confidence) C. N. Likos, “Soft matter with soft particles.,” Soft matter. 2006. link Times cited: 244 Abstract: In this review we present a summary of recent progress achie… read moreAbstract: In this review we present a summary of recent progress achieved in examining the equilibrium and dynamical properties of concentrated solutions of two novel kinds of soft matter systems: and starburst molecules known as . The two systems share a host of interesting properties. The both consist of highly branched polymers, they allow for tuning of their properties through modification of the macromolecular architecture and they are both representatives of a quite novel class of colloidal particles, termed . On the other hand there are also important differences, reflecting the fundamental difference in their architecture. It will be shown that a combination of scattering techniques and rheology with computer simulations and analytical methods from the realm of theoretical physics can shed light on the unusual properties of such systems. In this fashion, new ways appear for the manipulation of soft matter systems under external influences and promising perspectives for the fabrication of new materials are opened up and the versatility in manipulating soft matter is underlined. read less NOT USED (high confidence) B. Mouffok, H. Feraoun, and H. Aourag, “Two‐body potential of the Buckingham type for copper halides,” physica status solidi (b). 2006. link Times cited: 4 Abstract: The ground state, and elastic properties of copper halides i… read moreAbstract: The ground state, and elastic properties of copper halides in their zinc blende, NaCl and intermediate structures have been calculated using a two‐body potential of the Buckingham type coupled with a molecular dynamics simulation. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) read less NOT USED (high confidence) T. Akabane, Y. Sasajima, and J. Onuki, “Computer simulation of silicon nanoscratch test,” Materials Transactions. 2006. link Times cited: 4 Abstract: By the molecular dynamics method, a computer simulation of a… read moreAbstract: By the molecular dynamics method, a computer simulation of a scratch test with a nanometer scale was performed. The specimen was composed of 1008 silicon atoms with a diamond single-crystal structure. The indentor was assumed to be a perfect rigid body, and the Morse potential was utilized as the interaction between the indentor and a silicon atom. Two types of potential, i.e., Stillinger-Weber and Tersoff potentials, were examined as the interaction between silicon atoms. The present simulation clarified that the standard deviation of the friction constant increased with decreasing scratch depth and became maximum when the indentor just began to scratch the specimen surface at critical load. The friction coefficient, indentation hardness and scratch hardness at critical load were estimated to be 1.2–1.6, 80–90 GPa and 8.5– 9.4 GPa, respectively. read less NOT USED (high confidence) M. Heyde, M. Sterrer, H. Rust, and H.-J. Freund, “Frequency modulated atomic force microscopy on MgO(001) thin films: interpretation of atomic image resolution and distance dependence of tip–sample interaction,” Nanotechnology. 2006. link Times cited: 15 Abstract: Atomically resolved images on a MgO(001) thin film deposited… read moreAbstract: Atomically resolved images on a MgO(001) thin film deposited on Ag(001) obtained in ultrahigh vacuum by frequency modulated atomic force microscopy at low temperature are presented and analysed. Images obtained in the attractive regime show a different type of contrast formation from those acquired in the repulsive regime. For the interpretation of the image contrast we have investigated the tip–sample interaction. Force and energy were recovered from frequency shift versus distance curves. The derived force curves have been compared to the force laws of long-range, short-range and contact forces. In the attractive regime close to the minimum of the force–distance curve elastic deformations have been confirmed. The recovered energy curve has been scaled to the universal Rydberg model, yielding a decay length of l = 0.3 nm and ΔE = 4.2 aJ (26 eV) for the maximum adhesion energy. A universal binding-energy–distance relation is confirmed for the MgO(001) thin film. read less NOT USED (high confidence) P. Lorazo, L. J. Lewis, and M. Meunier, “Thermodynamic pathways to melting, ablation, and solidification in absorbing solids under pulsed laser irradiation,” Physical Review B. 2006. link Times cited: 293 Abstract: The thermodynamic pathways involved in laser irradiation of … read moreAbstract: The thermodynamic pathways involved in laser irradiation of absorbing solids are investigated in silicon for pulse durations of $500\phantom{\rule{0.3em}{0ex}}\mathrm{fs}$ and $100\phantom{\rule{0.3em}{0ex}}\mathrm{ps}$. This is achieved by accounting for carrier and atom dynamics within a combined Monte Carlo and molecular-dynamics scheme and simultaneously tracking the time evolution of the irradiated material in $\ensuremath{\rho}\text{\ensuremath{-}}T\text{\ensuremath{-}}P$ space. Our simulations reveal thermal changes in long-range order and state of aggregation driven, in most cases, by nonequilibrium states of rapidly heated or promptly cooled matter. Under femtosecond irradiation near the ablation threshold, the system is originally pulled to a near-critical state following rapid $(\ensuremath{\lesssim}{10}^{\ensuremath{-}12}\phantom{\rule{0.3em}{0ex}}\mathrm{s})$ disordering of the mechanically unstable crystal and isochoric heating of the resulting metallic liquid. The latter is then adiabatically cooled to the liquid-vapor regime where phase explosion of the subcritical, superheated melt is initiated by a direct conversion of translational, mechanical energy into surface energy on a $\ensuremath{\sim}{10}^{\ensuremath{-}12}--{10}^{\ensuremath{-}11}\phantom{\rule{0.3em}{0ex}}\mathrm{s}$ time scale. At higher fluences, matter removal involves, instead, the fragmentation of an initially homogeneous fluid subjected to large strain rates upon rapid, supercritical expansion in vacuum. Under picosecond irradiation, homogeneous and, at later times, heterogeneous melting of the superheated solid are followed by nonisochoric heating of the molten metal. In this case, the subcritical liquid material is subsequently cooled onto the binodal by thermal conduction and explosive boiling does not take place; as a result, ablation is associated with a ``trivial'' fragmentation process, i.e., the relatively slow expansion and dissociation into liquid droplets of supercritical matter near thermodynamic equilibrium. This implies a liquid-vapor equilibration time of $\ensuremath{\sim}{10}^{\ensuremath{-}11}--{10}^{\ensuremath{-}10}\phantom{\rule{0.3em}{0ex}}\mathrm{s}$ and heating along the binodal under nanosecond irradiation. Solidification of the nonablated, supercooled molten material is eventually observed on a $\ensuremath{\sim}{10}^{\ensuremath{-}11}--{10}^{\ensuremath{-}9}\phantom{\rule{0.3em}{0ex}}\mathrm{s}$ time scale, irrespective of the pulse duration. read less NOT USED (high confidence) L. Xu, I. Ehrenberg, S. Buldyrev, S. Buldyrev, and H. Stanley, “Relationship between the liquid–liquid phase transition and dynamic behaviour in the Jagla model,” Journal of Physics: Condensed Matter. 2006. link Times cited: 38 Abstract: Using molecular dynamics simulations, we study a spherically… read moreAbstract: Using molecular dynamics simulations, we study a spherically symmetric ‘two-scale’ Jagla potential with both repulsive and attractive ramps. This potential displays a liquid–liquid phase transition with a positively sloped coexistence line ending at a critical point well above the equilibrium melting line. We study the dynamic behaviour in the vicinity of this liquid–liquid critical point. Below the critical point, we find that the dynamics in the more ordered high density liquid (HDL) are much slower then the dynamics in the less ordered low density liquid (LDL). Moreover, the behaviour of the diffusion constant and relaxation time in the HDL phase follows approximately an Arrhenius law, while in the LDL phase the slope of the Arrhenius fit increases upon cooling. Above the critical pressure, as we cool the system at constant pressure, the behaviour of the dynamics smoothly changes with temperature. It resembles the behaviour of the LDL at high temperatures and resembles the behaviour of the HDL at low temperatures. This dynamic crossover happens in the vicinity of the Widom line (the extension of the coexistence line into the one-phase region) which also has a positive slope. Our work suggests a possible general relation between a liquid–liquid phase transition and the change in dynamics. read less NOT USED (high confidence) H. Zhao, Z. Tang, G. Li, and N. Aluru, “Quasiharmonic models for the calculation of thermodynamic properties of crystalline silicon under strain,” Journal of Applied Physics. 2006. link Times cited: 65 Abstract: Quasiharmonic models with Tersoff Phys. Rev. B 38, 9902 1988… read moreAbstract: Quasiharmonic models with Tersoff Phys. Rev. B 38, 9902 1988 interatomic potential are used to study the thermodynamic properties of crystalline silicon. It is shown that, compared to the molecular dynamics simulation data, the reciprocal space quasiharmonic model accurately predicts the thermal properties for temperatures up to 800 K. For higher temperatures, anharmonic effects become significant. With a significantly higher computational cost, the results from the real space quasiharmonic model approach the results from the reciprocal space quasiharmonic model as the number of atoms increases. The local quasiharmonic model does not accurately describe the thermal properties as it neglects the vibrational coupling of the atoms. We also investigate the effect of the strain on the thermodynamic properties. The variation of the thermodynamic properties with temperature under a tension, compression, and a shear deformation state is computed. © 2006 American Institute of Physics. DOI: 10.1063/1.2185834 I. INTRODUCTION Thermodynamic properties of crystalline silicon have long been a focus of interest because of their important role in elucidating the material behavior. Computational analysis is a powerful approach to investigate the thermodynamic properties of materials. First-principles quantum-mechanical methods are generally most accurate for predicting the material properties. Ab initio local density functional techniques have been used to determine the thermodynamic properties of silicon 1 and other materials. 2 However, due to the complexity of these methods and the need for large computational resources, ab initio calculations are limited to very small systems. Empirical and semi-empirical interatomic potentials 3‐5 have been developed to provide a simpler and yet a reasonably accurate description of materials. The various parameters in these potentials are determined by a weighted fitting of the material property databases obtained from experiments or ab initio calculations. Molecular dynamics MD and Monte Carlo MC simulations are the two popular methods that are based on interatomic potentials. In these methods, the thermal statistics are gathered to calculate the ensemble average of the thermal properties. MD calculations on the thermodynamic properties of crystalline silicon were carried out in Ref. 6, where the Tersoff potential 4 was read less NOT USED (high confidence) C.-T. Lin and K. Chiang, “Investigation of Nano-Scale Single Crystal Silicon Using the Atomistic-Continuum Mechanics with Stillinger-Weber Potential Function,” 2006 IEEE Conference on Emerging Technologies - Nanoelectronics. 2006. link Times cited: 1 Abstract: This research proposes a novel atomistic-continuum method (A… read moreAbstract: This research proposes a novel atomistic-continuum method (ACM) based on the finite element method (FEM) to investigation the mechanical behavior of nano-scale single crystal silicon under uniaxial tensile loading. The FEM is widely used to model and simulate the mechanical behaviors of solid structure, it is a mature technology after decades of development. The ACM could be reduced efficiently the computational time and maintained the simulation accuracy. Since, the ACM developed the bonding force between the two silicon atoms to the two kinds of the nonlinear spring element. Moreover, due to the FEM considered the minimization of the total potential energy, which includes strain energy and the potential energy possessed by applied loads of SCS, a robust FEM is applied to solve the numerical model based on ACM. Therefore, this study combines FEM and interatomic potential function to explore the mechanical properties of nano-scale single crystal silicon. A general form of Stillinger-Weber potential function was used for interaction between the silicon atoms in the simulations. Simulation results showed that the Young’s modulus of single crystal silicon were 121.8, 153 and 174.6 GPa along the read less NOT USED (high confidence) X. W. Zhou, D. Murdick, and H. Wadley, “An electron counting modification to potentials for covalently bonded surfaces,” Journal of Applied Physics. 2006. link Times cited: 4 Abstract: The surface structure of covalently bonded semiconductor mat… read moreAbstract: The surface structure of covalently bonded semiconductor materials undergoes reconstructions that are driven by electron redistribution between dangling and interatom bonds. Conventional interatomic potentials account for neither this electron redistribution nor its effects upon the atomic structure of surfaces. We have utilized an electron counting analysis to develop a surface interatomic potential that captures many of the effects of electron redistribution upon the surface structures of covalently bonded materials. The contributions from this potential decrease rapidly to zero beneath a surface. As a result, this surface potential can be added to many interatomic potentials for covalent materials without affecting its predictions of bulk properties such as cohesive energy, lattice parameters, and elastic constants. We demonstrate the approach by combining the surface potential with a recently proposed bond order potential and use it in a molecular statics simulation of the atomic reconstruction of a w... read less NOT USED (high confidence) A. Delisle, D. González, and M. J. Stott, “Pressure-induced structural and dynamical changes in liquid Si—an ab initio study,” Journal of Physics: Condensed Matter. 2006. link Times cited: 15 Abstract: The static and dynamic properties of liquid Si at high press… read moreAbstract: The static and dynamic properties of liquid Si at high pressure have been studied using the orbital-free ab initio molecular dynamics method. Four thermodynamic states at pressures of 4, 8, 14 and 24 GPa are considered, for which x-ray scattering data are available. The calculated static structure shows qualitative agreement with the available experimental data. We analyse the remarkable structural changes occurring between 8 and 14 GPa along with their effect on several dynamic properties. read less NOT USED (high confidence) M. Buehler, A. V. van Duin, and W. Goddard, “Multiparadigm modeling of dynamical crack propagation in silicon using a reactive force field.,” Physical review letters. 2006. link Times cited: 199 Abstract: We report a study of dynamic cracking in a silicon single cr… read moreAbstract: We report a study of dynamic cracking in a silicon single crystal in which the ReaxFF reactive force field is used for several thousand atoms near the crack tip, while more than 100,000 atoms are described with a nonreactive force field. ReaxFF is completely derived from quantum mechanical calculations of simple silicon systems without any empirical parameters. Our results reproduce experimental observations of fracture in silicon including changes in crack dynamics for different crack orientations. read less NOT USED (high confidence) H. Vach et al., “Growth dynamics of hydrogenated silicon nanoparticles under realistic conditions of a plasma reactor,” Computational Materials Science. 2006. link Times cited: 23 NOT USED (high confidence) S. Alfthan, P. D. Haynes, K. Kaski, and A. P. Sutton, “Are the structures of twist grain boundaries in silicon ordered at 0 K?,” Physical review letters. 2006. link Times cited: 90 Abstract: Contrary to previous simulation results on the existence of … read moreAbstract: Contrary to previous simulation results on the existence of amorphous intergranular films at high-angle twist grain boundaries (GBs) in elemental solids such as silicon, recent experimental results imply structural order in some high-angle boundaries. With a novel protocol for simulating twist GBs, which allows the number of atoms at the boundary to vary, we have found new low-energy ordered structures. We give a detailed exposition of the results for the simplest boundary. The validity of our results is confirmed by first-principles calculations. read less NOT USED (high confidence) G. Lulli, E. Albertazzi, S. Balboni, and L. Colombo, “Defect-induced homogeneous amorphization of silicon: the role of defect structure and population,” Journal of Physics: Condensed Matter. 2006. link Times cited: 7 Abstract: Molecular dynamics based on the environment-dependent intera… read moreAbstract: Molecular dynamics based on the environment-dependent interatomic potential is used to investigate the influence of the nature and distribution of defects on solid state, homogeneous amorphization of Si. To this end, different kinds of defects, including single interstitials and vacancies (both uncorrelated and correlated distributions), bond defects, and small interstitial and vacancy clusters, have been considered. It is shown that the threshold defect concentration for amorphization depends on the defect type, and, in the case of single defects, on the degree of correlation between interstitial and vacancy distributions. The threshold varies within the interval [0.18–0.28] atomic fraction, the upper value corresponding to the case of bond defects, the lower to the uncorrelated distributions of single split interstitials plus compensating vacancies. read less NOT USED (high confidence) I. Andrianov and P. Saalfrank, “Theoretical study of vibration-phonon coupling of H adsorbed on a Si(100) surface.,” The Journal of chemical physics. 2006. link Times cited: 50 Abstract: In this paper a perturbation-theory study of vibrational lif… read moreAbstract: In this paper a perturbation-theory study of vibrational lifetimes for the bending and stretching modes of hydrogen adsorbed on a Si(100) surface is presented. The hydrogen-silicon interaction is treated with a semiempirical bond-order potential. Calculations are performed for H-Si clusters of different sizes. The finite lifetime is due to vibration-phonon coupling, which is assumed to be linear or bilinear in the phonon and nonlinear in the H-Si stretching and bending modes. Lifetimes and vibrational transition rates are evaluated with one- and two-phonon processes taken into account. Temperature effects are also discussed. In agreement with the experiment and previous theoretical treatment it is found that the H-Si (upsilon(s) = 1) stretching vibration decays on a nanosecond timescale, whereas for the H-Si (upsilon(b) = 1) bending mode a picosecond decay is predicted. For higher-excited vibrations, simple scaling laws are found if the excitation energies are not too large. The relaxation mechanisms for the excited H-Si stretching and the H-Si bending modes are analyzed in detail. read less NOT USED (high confidence) V. Hùng, K. Masuda-Jindo, and P. Hanh, “Application of the statistical moment method to thermodynamic quantities of silicon,” Journal of Physics: Condensed Matter. 2006. link Times cited: 20 Abstract: The lattice constants, thermal expansion coefficients, speci… read moreAbstract: The lattice constants, thermal expansion coefficients, specific heats at constant volume and those at constant pressure, Cv and Cp, second cumulants, and Lindemann ratio are derived analytically for diamond cubic semiconductors, using the statistical moment method. The calculated thermodynamic quantities of the Si crystal are in good agreement with the experimental results. We also find the characteristic negative thermal expansion in the Si crystal at low temperatures. read less NOT USED (high confidence) V. Caciuc, H. Hölscher, S. Blügel, and H. Fuchs, “Atomic-scale sharpening of silicon tips in noncontact atomic force microscopy.,” Physical review letters. 2006. link Times cited: 14 Abstract: The atomic-scale stability of clean silicon tips used in non… read moreAbstract: The atomic-scale stability of clean silicon tips used in noncontact atomic force microscopy (NC-AFM) is simulated by ab initio calculations based on density functional theory. The tip structures are modeled by silicon clusters with and termination. For the often assumed Si(111)-type tip we observe the sharpening of the initially blunt tip via short-range chemical forces during the first approach and retraction cycle. The structural changes corresponding to this intrinsic process are irreversible and lead to stable NC-AFM imaging conditions. In opposition to the picture used in literature, the Si(001)-type tip does not exhibit the so-called "two-dangling bond" feature as a bulklike termination suggests. read less NOT USED (high confidence) D. Wales, “Energy landscapes: calculating pathways and rates,” International Reviews in Physical Chemistry. 2006. link Times cited: 161 Abstract: The stationary points of a potential energy surface provide … read moreAbstract: The stationary points of a potential energy surface provide a convenient framework for coarse-graining calculations of thermodynamics and kinetics. Thermodynamic properties can be extracted from a database of local minima using the superposition approach, where the total partition function is written as a sum over the contributions from each minimum. To analyse kinetics, we must also consider the transition states that link individual local minima, and evaluate rate constants for the corresponding elementary rearrangements. For small molecules the assignment of separate thermodynamic quantities, such as free energies, to individual isomers, and the notion of isomerisation rates between these structures, is usually straightforward. However, for larger systems the experimental states of interest generally correspond to sets of local minima with some common feature, such as a particular structural motif. This review focuses upon the discrete path sampling approach to obtaining phenomenological two-state rate constants between ensembles of local minima that are distinguished by suitable order parameters. Examples are discussed for atomic and molecular clusters, and for two peptides. Contents PAGE 1. Introduction 238 2. Discrete path sampling 240 2.1. Rate constant formulations 240 2.2. Building stationary point databases 246 2.3. Calculation of rate constants 248 3. Characterising stationary points and pathways 252 4. Disconnectivity graphs 255 5. Results 259 5.1. Lennard-Jones clusters 259 5.2. Water clusters 266 5.3. Peptides 270 References 277 read less NOT USED (high confidence) C. Abrams, “Concurrent dual-resolution Monte Carlo simulation of liquid methane.,” The Journal of chemical physics. 2005. link Times cited: 40 Abstract: We conduct molecular simulations of liquid methane in a syst… read moreAbstract: We conduct molecular simulations of liquid methane in a system where molecular resolution fluctuates between atomically explicit and spherically symmetric united atoms. An appropriate dual-resolution canonical ensemble is constructed using (a) effective united atom pair potentials and (b) resolution-control potentials that confine explicit and united atoms chiefly to different slabs in the simulation domain. A Monte Carlo simulation is developed to sample this ensemble. We show that compatibility of the united-atom potentials with the explicit potentials in a concurrent simulation can be tuned by adjusting the width of the interface between the two resolution regions and by direct modification of the united-atom pair potentials. Our results lay the groundwork for treatment of larger atomically specific molecules with similar concurrent multiresolution techniques. read less NOT USED (high confidence) L. Marqués, L. Pelaz, P. López, M. Aboy, I. Santos, and J. Barbolla, “Atomistic simulations in Si processing: Bridging the gap between atoms and experiments,” Materials Science and Engineering B-advanced Functional Solid-state Materials. 2005. link Times cited: 8 NOT USED (high confidence) S. Furukawa, T. Nishiumi, N. Aoyama, T. Nitta, and M. Nakano, “A Molecular Simulation Study on Adsorption of Acetone/Water in Mesoporous Silicas Modified by Pore Surface Silylation,” Journal of Chemical Engineering of Japan. 2005. link Times cited: 22 Abstract: Two types of molecular simulation techniques have been utili… read moreAbstract: Two types of molecular simulation techniques have been utilized to investigate surface modification effects on adsorption of acetone/water in mesoporous silicas with a hexagonal uniform pore structure: the NVT-ensemble Molecular Dynamics technique with the melt-quench algorithm for modeling a non-silylated mesoporous silica (an OH surface model) and a fully silylated mesoporous silica (an FS surface model), and the μVT-ensemble Orientational-Bias Monte Carlo method for calculating adsorption isotherms. A good agreement was obtained between simulations and experiments for adsorption of pure acetone and water at 298 K on non-silylated and silylated mesoporous silicas. Equilibrium adsorption densities of the equi-fugacity mixture of acetone and water are calculated for the OH and FS surface models, by specifying either the gas or the liquid phase for the mixture. A considerably large separation factor, 7300, was obtained for the adsorption from a liquid mixture in the FS surface model, though the adsorption amount was rather small, which explains why the pervaporation through highly silylated mesoporous silica membranes was effective for separation of organic/water mixtures. read less NOT USED (high confidence) A. Delisle, D. González, and M. J. Stott, “Structural and dynamical properties of liquid Si : An orbital-free molecular dynamics study,” Physical Review B. 2005. link Times cited: 24 Abstract: Several static and dynamic properties of liquid silicon near… read moreAbstract: Several static and dynamic properties of liquid silicon near melting have been determined from an orbital free {\em ab-initio} molecular dynamics simulation. The calculated static structure is in good agreement with the available X-ray and neutron diffraction data. The dynamical structure shows collective density excitations with an associated dispersion relation which closely follows recent experimental data. It is found that liquid silicon can not sustain the propagation of shear waves which can be related to the power spectrum of the velocity autocorrelation function. Accurate estimates have also been obtained for several transport coefficients. The overall picture is that the dynamic properties have many characteristics of the simple liquid metals although some conspicuous differences have been found. read less NOT USED (high confidence) D. Murdick, X. W. Zhou, H. Wadley, and D. Nguyen-Manh, “Predicting surface free energies with interatomic potentials and electron counting,” Journal of Physics: Condensed Matter. 2005. link Times cited: 15 Abstract: Current interatomic potentials for compound semiconductors, … read moreAbstract: Current interatomic potentials for compound semiconductors, such as GaAs, fail to correctly predict the ab initio calculated and experimentally observed surface reconstructions. These potentials do not address the electron occupancies of dangling bonds associated with surface atoms and their well established role in the formation of low-energy surfaces. The electron counting rule helps account for the electron distribution among covalent and dangling bonds, which, when applied to GaAs surfaces, requires the arsenic dangling bonds to be fully occupied and the gallium dangling bonds to be empty. A simple method for linking this electron counting constraint with interatomic potentials is proposed and used to investigate energetics of the atomic scale structures of the GaAs(001) surface using molecular statics methods. read less NOT USED (high confidence) M. P. Ariza and M. Ortiz, “Discrete Crystal Elasticity and Discrete Dislocations in Crystals,” Archive for Rational Mechanics and Analysis. 2005. link Times cited: 106 NOT USED (high confidence) Y. Nabetani, T. Matsumoto, G. Sasikala, and I. Suemune, “Theory of strain states in InAs quantum dots and dependence on their capping layers,” Journal of Applied Physics. 2005. link Times cited: 19 Abstract: The dependence of strain states in InAs self-assembled quant… read moreAbstract: The dependence of strain states in InAs self-assembled quantum dots (QDs) on their capping layers was investigated by valence-force field model calculations. An InAs QD on (001) GaAs and embedded in a GaNAs capping layer and the one with its dot surface terminated with nitrogen (N) and embedded in a GaAs capping layer show reduced compressive strain within the QDs in the (001) growth plane due to the lateral expansion of the QDs, while the one embedded in an InGaAs capping layer shows enhanced tensile strain along the [001] growth direction. The strain energies around the center of the InAs QDs with the GaNAs capping layer and with the N-surface termination are lowered compared with those for conventional GaAs capping layers. The burying conditions of InAs QDs also modify the sizes of QDs. The stress distributions obtained by strain energy mapping showed that In atoms around the top of QDs undergo inward stress. This inward stress prevents In segregation and explains the experimentally observed improved o... read less NOT USED (high confidence) M. Payne, G. Csányi, T. Albaret, and A. D. Vita, “A novel quantum/classical hybrid simulation technique.,” Chemphyschem : a European journal of chemical physics and physical chemistry. 2005. link Times cited: 3 Abstract: Natural phenomena occur on a variety of length scales. These… read moreAbstract: Natural phenomena occur on a variety of length scales. These lengthscales not only tend to define scientific disciplines (physics and chemistry for the very small, biology for intermediate, geology for very long times and large lengthscales, and cosmology for the largest) but can also delineate subfields within a given discipline due to the very different experimental methods and theoretical models that are applicable at each scale. In some cases, these models form a multiscale hierarchy in which the parameters used in the larger scale models can be measured or calculated using modelling carried out on a smaller scale. [1] However, in a large class of problems the length scales cannot be separated in this way because the coupling between them is strong, and “bidirectional”. This occurs, for instance, when microscopic phenomena are not only driven by macroscopic forces but also change these macroscopic forces. In this case, there is a feedback loop between the microscopic and macroscopic scales. Stress-induced defect processes in solids are a good example, and brittle fracture is the prototypical problem. If we wish to simulate such processes, we have to accurately simulate both length scales simultaneously. Crucially, one cannot use the smallest-scale model to simulate the entire system, because it would be too computationally demanding and it would also be hugely wasteful of resources. For instance, a typical quantum mechanical molecular dynamics simulation can deal with hundreds of atoms but the minimum system size that can capture the larger scale aspects of the problem, such as the long-range stress fields, could reach into hundreds of thousands of atoms or more. In the past decade there has been a growing effort to devise socalled hybrid simulation techniques, that seamlessly integrate a wide variety of different models, ranging from first-principles methods to finite elements techniques, into a concurrent simulation. [2, 3] A pioneering work in this field was the quasicontinuum method, [2] which successfully linked classical atomistic and read less NOT USED (high confidence) S. C. Costa, P. S. Pizani, J. Rino, and D. Borges, “Structural phase transition and dynamical properties of PbTiO3 simulated by molecular dynamics,” Journal of Physics: Condensed Matter. 2005. link Times cited: 25 Abstract: The temperature- and pressure-induced structural phase trans… read moreAbstract: The temperature- and pressure-induced structural phase transition in PbTiO3 is studied with the isoenthalpic–isobaric molecular-dynamics method, using an effective two-body interaction potential. The tetragonal to cubic transformation is successfully reproduced with both temperature and pressure. The behaviour of lattice parameters, vibrational density of states, and phonon anharmonicity with temperature and pressure are in very good agreement with experimental data. Two- and three-body correlations were analysed through pair distribution functions, coordination numbers and bond-angle distributions. read less NOT USED (high confidence) E. Ko, M. Alemany, J. Derby, and J. Chelikowsky, “Ab Initio simulations of nonstoichiometric Cd(x)Te(1-x) liquids.,” The Journal of chemical physics. 2005. link Times cited: 8 Abstract: We present ab initio molecular-dynamics simulations for Cd(x… read moreAbstract: We present ab initio molecular-dynamics simulations for Cd(x)Te(1-x) liquids where the composition is nonstoichiometric. The simulations are performed following Born-Oppenheimer molecular dynamics. The required forces are obtained from a solution of the Kohn-Sham equation using ab initio pseudopotentials. We consider stoichiometries of the form: Cd(x)Te(1-x), where x=0.2, 0.4, 0.6, and 0.8. For each composition of the melt, we consider a range of temperatures near the experimentally determined liquid temperatures. We examine the microstructural properties of the melt, the viscosity, and self-diffusion properties of the liquid as a function of the stoichiometry and temperature. We also perform an analysis of the distribution of the electronic density of states in these liquids. We find that structural changes in the local order, experimentally predicted to occur when the concentration of Cd is increased, are closely related to changes in the electronic properties of the melt. read less NOT USED (high confidence) K. Garikipati, M. Falk, M. Bouville, B. Puchala, and H. Narayanan, “The continuum elastic and atomistic viewpoints on the formation volume and strain energy of a point defect,” Journal of The Mechanics and Physics of Solids. 2005. link Times cited: 27 NOT USED (high confidence) H. Vocks, M. Chubynsky, G. Barkema, and N. Mousseau, “Activated sampling in complex materials at finite temperature: the properly obeying probability activation-relaxation technique.,” The Journal of chemical physics. 2005. link Times cited: 3 Abstract: While the dynamics of many complex systems is dominated by a… read moreAbstract: While the dynamics of many complex systems is dominated by activated events, there are very few simulation methods that take advantage of this fact. Most of these procedures are restricted to relatively simple systems or, as with the activation-relaxation technique (ART), sample the conformation space efficiently at the cost of a correct thermodynamical description. We present here an extension of ART, the properly obeying probability ART (POP-ART), that obeys detailed balance and samples correctly the thermodynamic ensemble. Testing POP-ART on two model systems, a vacancy and an interstitial in crystalline silicon, we show that this method recovers the proper thermodynamical weights associated with the various accessible states and is significantly faster than molecular dynamics in the simulations of a vacancy below 700 K. read less NOT USED (high confidence) X. W. Zhou, “Analytical and numerical calculations of interatomic forces and stresses,” Molecular Simulation. 2005. link Times cited: 0 Abstract: Atomistic simulation methods such as molecular dynamics requ… read moreAbstract: Atomistic simulation methods such as molecular dynamics require an efficient calculation of interatomic forces and stresses from pre–defined interatomic potentials. Both analytical and numerical approaches can be used to do this. Analytical approach directly calculates forces and stresses using analytical formulae, and can therefore yield accurate results. However, the force and stress expressions may become extremely complicated as the complexity level of the potential increases, resulting in a prolonged development cycle to implement new potentials. Numerical approach uses finite difference method to evaluate forces and stresses through simple calculation of energies at selected perturbations of crystal configurations. The method can be quickly implemented and tested for any potentials. However, it may result in significant numerical errors. We have compared analytical and numerical calculations of interatomic forces and stresses in molecular dynamics, and identified the conditions where numerical method can be successfully used without significant errors. read less NOT USED (high confidence) M. Blanchard, K. Wright, and J. Gale, “Atomistic simulation of Mg2SiO4 and Mg2GeO4 spinels: a new model,” Physics and Chemistry of Minerals. 2005. link Times cited: 19 NOT USED (high confidence) A. Horsfield, D. Bowler, A. Fisher, T. Todorov, and C. Sánchez, “Correlated electron–ion dynamics: the excitation of atomic motion by energetic electrons,” Journal of Physics: Condensed Matter. 2005. link Times cited: 56 Abstract: Correlated electron–ion dynamics (CEID) is an extension of m… read moreAbstract: Correlated electron–ion dynamics (CEID) is an extension of molecular dynamics that allows us to introduce in a correct manner the exchange of energy between electrons and ions. The formalism is based on a systematic approximation: small amplitude moment expansion. This formalism is extended here to include the explicit quantum spread of the ions and a generalization of the Hartree–Fock approximation for incoherent sums of Slater determinants. We demonstrate that the resultant dynamical equations reproduce analytically the selection rules for inelastic electron–phonon scattering from perturbation theory, which control the mutually driven excitations of the two interacting subsystems. We then use CEID to make direct numerical simulations of inelastic current–voltage spectroscopy in atomic wires, and to exhibit the crossover from ionic cooling to heating as a function of the relative degree of excitation of the electronic and ionic subsystems. read less NOT USED (high confidence) S. von Alfthan, A. Sutton, A. Kuronen, and K. Kaski, “Stability and crystallization of amorphous clusters in crystalline Si,” Journal of Physics: Condensed Matter. 2005. link Times cited: 4 Abstract: We have simulated using molecular dynamics the thermal stabi… read moreAbstract: We have simulated using molecular dynamics the thermal stability and crystallization kinetics of nanometre-sized clusters of amorphous Si embedded in crystalline Si, which are of interest for phase-change memory devices. We have calculated the interfacial and bulk excess energies of the amorphous clusters, and studied their crystallization kinetics at 700–1500 K. At temperatures below (above) 1150 K the activation energy is 0.73 ± 0.04 eV (1.52 ± 0.07 eV), indicating a change of mechanism at 1150 K. We predict the stability of much larger amorphous clusters by extrapolating our simulation data using an analytic model. read less NOT USED (high confidence) S. Meloni, M. Rosati, A. Federico, L. Ferraro, A. Mattoni, and L. Colombo, “Computational Materials Science application programming interface (CMSapi): a tool for developing applications for atomistic simulations,” Comput. Phys. Commun. 2005. link Times cited: 10 NOT USED (high confidence) R. Kalia, A. Nakano, and P. Vashishta, “Molecular Dynamics Simulations of Shock Propagation in High Strength Ceramics,” 2005 Users Group Conference (DOD-UGC’05). 2005. link Times cited: 0 Abstract: High-strength ceramics are being developed for light-weight … read moreAbstract: High-strength ceramics are being developed for light-weight armors. Atomistic simulations of shock damage are performed to determine modes of energy absorption and failure through cracking under hypervelocity impact. read less NOT USED (high confidence) T. Delph, “Conservation laws for multibody interatomic potentials,” Modelling and Simulation in Materials Science and Engineering. 2005. link Times cited: 30 Abstract: We consider here a formulation given by Hardy (1982 J. Chem.… read moreAbstract: We consider here a formulation given by Hardy (1982 J. Chem. Phys. 76 622–8) that relates the interatomic potential to the conservation equations for linear momentum and energy. Hardy's formulation was restricted to two-body interatomic potentials. We show that it can be extended to general multibody potentials. Of particular interest is a resulting general expression for the local Cauchy stress that results from the equation for conservation of linear momentum. read less NOT USED (high confidence) F. Baletto and R. Ferrando, “Structural properties of nanoclusters: Energetic, thermodynamic, and kinetic effects,” Reviews of Modern Physics. 2005. link Times cited: 1372 Abstract: The structural properties of free nanoclusters are reviewed.… read moreAbstract: The structural properties of free nanoclusters are reviewed. Special attention is paid to the interplay of energetic, thermodynamic, and kinetic factors in the explanation of cluster structures that are actually observed in experiments. The review starts with a brief summary of the experimental methods for the production of free nanoclusters and then considers theoretical and simulation issues, always discussed in close connection with the experimental results. The energetic properties are treated first, along with methods for modeling elementary constituent interactions and for global optimization on the cluster potential-energy surface. After that, a section on cluster thermodynamics follows. The discussion includes the analysis of solid-solid structural transitions and of melting, with its size dependence. The last section is devoted to the growth kinetics of free nanoclusters and treats the growth of isolated clusters and their coalescence. Several specific systems are analyzed. read less NOT USED (high confidence) S. Park, H. Kim, K. Kang, J. Lee, Y. Choi, and O. Kwon, “Experimental and molecular dynamics study on crystallization of amorphous silicon under external fields,” Journal of Physics D: Applied Physics. 2005. link Times cited: 17 Abstract: Solid-phase crystallization (SPC) of amorphous silicon (a-Si… read moreAbstract: Solid-phase crystallization (SPC) of amorphous silicon (a-Si) under an external force field is investigated experimentally and numerically. Experimental results show that the kinetics of crystallization can be greatly enhanced by applying induction fields without the heating problems of a-Si film and its substrate, since temperature rises during the crystallization process are negligibly small. To explore the underlying acceleration mechanisms for the SPC process under the external fields, molecular dynamics simulations are carried out using the Tersoff potential. The numerical amorphous structure is obtained by the liquid quenching method and is utilized to simulate the crystallization processes at various process temperatures with and without external force fields. While homogeneous crystallization of a-Si could not be achieved readily, it is shown that the heterogeneous crystallization can be significantly accelerated by external force fields. This enhancement is due to increased molecular jumping frequencies associated with the molecular potential energies being increased by external excitations, rather than due to thermal mechanisms dominant in conventional SPC processes. read less NOT USED (high confidence) P. Chantrenne, J. Barrat, X. Blase, and J. Gale, “An analytical model for the thermal conductivity of silicon nanostructures,” Journal of Applied Physics. 2005. link Times cited: 90 Abstract: A simple model of thermal conductivity, based on the harmoni… read moreAbstract: A simple model of thermal conductivity, based on the harmonic theory of solids, is used to study the heat transfer in nanostructures. The thermal conductivity is obtained by summing the contribution of all the vibration modes of the system. All the vibrational properties (dispersion curves and relaxation time) that are used in the model are obtained using the data for bulk samples. The size effect is taken into account through the sampling of the Brillouin zone and the distance that a wave vector can travel between two boundaries in the structure. The model is used to predict the thermal conductivity of silicon nanowires and nanofilms, and demonstrates a good agreement with experimental results. Finally, using this model, the quality of the silicon interatomic potential, used for molecular-dynamics simulations of heat transfer, is evaluated. read less NOT USED (high confidence) V. Samsonov, V. V. Dronnikov, M. Y. Pushkar,’ E. Nikiforova, A. Filippov, and S. D. Muravyev, “Molecular dynamics study of nanoscale structure formation in droplet spreading on solid surfaces,” Journal of Materials Science. 2005. link Times cited: 3 NOT USED (high confidence) F. Sciortino, “Potential energy landscape description of supercooled liquids and glasses,” Journal of Statistical Mechanics: Theory and Experiment. 2005. link Times cited: 179 Abstract: These notes review the potential energy landscape thermodyna… read moreAbstract: These notes review the potential energy landscape thermodynamic formalism and some of its recent applications to the study of supercooled glass forming liquids. They also review the techniques which have been recently developed to quantify the statistical properties of the landscape, i.e. the number and the distribution in energy of the local minima of the surface for bulk systems. A critical examination of the approximations involved in such a calculation and results for models of simple and molecular liquids are reported. Finally, these notes discuss how an equation of state, expressed only in terms of statistical properties of the landscape, can be derived and under which conditions such an equation of state can be generalized to describe out-of-equilibrium liquids. read less NOT USED (high confidence) H. Yamada and S. Hamaguchi, “Numerical analyses of surface interactions between radical beams and organic polymer surfaces,” Plasma Physics and Controlled Fusion. 2005. link Times cited: 14 Abstract: A classical interatomic potential model has been developed f… read moreAbstract: A classical interatomic potential model has been developed for systems consisting of hydrogen, carbon and nitrogen atoms. By using the new potential model, molecular dynamics simulations of low energy beam injections are carried out for an organic polymer substrate. Dose dependence of the net sputtering yields of a poly(1,4-phenylene) substrate by radical beam injections is obtained with the injection energy of 25 eV. Simulation results suggest that injected carbon or nitrogen atoms contribute to the formation of possible passivation layers. read less NOT USED (high confidence) M. Marder, “Supersonic rupture of rubber,” Journal of The Mechanics and Physics of Solids. 2005. link Times cited: 58 NOT USED (high confidence) K. Kakimoto, L. Liu, T. Kitashima, A. Murakawa, and Y. Hashimoto, “Silicon crystal growth from the melt: Analysis from atomic and macro scales,” Crystal Research and Technology. 2005. link Times cited: 0 Abstract: The effect of impurity concentration on thermal conductivity… read moreAbstract: The effect of impurity concentration on thermal conductivity of natural and isotope silicon by using equilibrium molecular dynamics simulation is investigated. It was found that the concentrations of the impurities such as boron, phosphor and arsene play an important role in the propagation of phonons in silicon crystals. It was also clarified that a mass difference of impurities and host crystals results in degradation of thermal conductivity of silicon. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) read less NOT USED (high confidence) N. Lorente, R. Rurali, and H. Tang, “Single-molecule manipulation and chemistry with the STM,” Journal of Physics: Condensed Matter. 2005. link Times cited: 59 Abstract: We review recent theoretical work on the manipulation of sin… read moreAbstract: We review recent theoretical work on the manipulation of single molecules with scanning probes, in particular the scanning tunnelling microscope (STM). The aim of theories and simulations is to account for the processes, ideally at a quantitative level, that permit the controlled manipulation of matter at the atomic scale in adsorbed molecular systems. In order to achieve this, simulations rely on total energy and electronic structure calculations where a trade-off is made between the size of the system and the accuracy of the calculation. This first stage of the calculation yields the basic quantities used for the second stage: the evaluation of the coupled electron–nuclear dynamics. This second stage is a formidable task and many approximations are involved. In this review, we will present some of the customary approximations regarding the theoretical study of mechanical and inelastic manipulations. Mechanical manipulations use the interaction between the acting probe (usually a metallic tip) and the targeted adsorbate. We review recent results in the field of adsorbate mechanical manipulations and explain how manipulations can be effected by using the interaction between the probe’s tip and certain molecular groups of complex chemisorbed molecular systems. On the other hand, inelastic manipulations use the tunnelling current to convey energy with sub-ångström precision. This current can excite localized vibrations that can induce measurable variations of the tunnelling conductance, hence providing a means of detecting single-molecule vibrations. This current can also inject energy in a few reaction coordinates. Recently, the possibility of vibrational selective manipulations of NH3/Cu(100) has been experimentally demonstrated. The theory presented here addresses the actual pathways accessed when the molecule is excited by the tunnelling current from an STM. read less NOT USED (high confidence) M. Kaczmarski, M. Kaczmarski, O. N. Bedoya‐Martínez, and E. Hernández, “Phase diagram of silicon from atomistic simulations.,” Physical review letters. 2005. link Times cited: 45 Abstract: In this Letter we present a calculation of the temperature-p… read moreAbstract: In this Letter we present a calculation of the temperature-pressure phase diagram of Si in a range of pressures covering from -5 to 20 GPa and temperatures up to the melting point. The phase boundaries and triple points between the diamond, liquid, beta-Sn, and Si34 clathrate phases are reported. We have employed efficient simulation techniques to calculate free energies and to numerically integrate the Clausius-Clapeyron equation, combined with a tight-binding model capable of an accuracy comparable to that of first-principles methods. The resulting phase diagram agrees well with the available experimental data. read less NOT USED (high confidence) T. Zohdi, “Charge‐induced clustering in multifield particulate flows,” International Journal for Numerical Methods in Engineering. 2005. link Times cited: 58 Abstract: The present work extends recent results in Zohdi (Int. J. So… read moreAbstract: The present work extends recent results in Zohdi (Int. J. Solids Struct., in press; Proc. Roy. Soc., in press) to develop models and robust solution strategies for the direct simulation of the dynamical flow of charged particles undergoing simultaneous contact, surface reactions and heat transfer. Emphasis is placed on the possibility of particle clustering which can lead to the formation of cluster‐structures within the particulate flow. A recursive ‘staggering’ solution scheme is developed, whereby the time‐steps are adaptively adjusted to control the rates of convergence within each time‐step, and hence, the error associated with the incomplete resolution of the coupled interaction between the various fields and associated constraints. Representative numerical simulations are provided in order to illustrate the character of the model and the solution strategy. Copyright © 2004 John Wiley & Sons, Ltd. read less NOT USED (high confidence) L. Marqués, L. Pelaz, P. Castrillo, and J. Barbolla, “Molecular dynamics study of the configurational and energetic properties of the silicon self-interstitial,” Physical Review B. 2005. link Times cited: 51 Abstract: We have carried out classical molecular dynamics simulations… read moreAbstract: We have carried out classical molecular dynamics simulations to study the configurational and energetic properties of the Si self-interstitial. We have shown that the Si self-interstitial can appear in four different configurations, characterized by different energetics. Along with the already known tetrahedral, dumbbell, and extended configurations, we have found a highly asymmetric configuration not previously reported in the literature. Using a data analysis technique based on time averages, we have extracted the formation enthalpies and the probability of finding the interstitial in a given configuration, both depending on temperature. By the use of thermodynamic integration techniques we have determined the Gibbs free energy and entropy of formation, and the relative concentration of each interstitial configuration as a function of temperature. We have demonstrated that the change of interstitial configuration is correlated with the diffusion process, and we have identified two different mechanisms for interstitial-mediated self-diffusion. In spite of the microscopic complexity of the interstitial-mediated diffusion process, our results predict a pure Arrhenius behavior with an activation energy of $4.60\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ in the temperature interval $900\char21{}1685\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, in good agreement with experiments. This energy is decomposed in an effective interstitial formation enthalpy of $3.83\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ and a migration barrier of $0.77\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$, which macroscopically represent the averaged behavior of the different interstitial configurations. read less NOT USED (high confidence) Y. Shin, V. Cooper, I. Grinberg, and A. Rappe, “Development of a bond-valence molecular-dynamics model for complex oxides,” Physical Review B. 2005. link Times cited: 68 Abstract: A simple ten-parameter interatomic potential model is descri… read moreAbstract: A simple ten-parameter interatomic potential model is described that is capable of accurately reproducing the static and dynamical properties of complex oxides. The accuracy of this model stems from the crystal-chemical bond-valence theory of ionic and covalent bonding. The development of a specific variant of this model for ferroelectric $\mathrm{Pb}\mathrm{Ti}{\mathrm{O}}_{3}$ (PT) is discussed in detail, and comparison of the model is made with density functional theory computations and with experimental data. Bond-valence molecular dynamics (BVMD) simulations for PT show a ferroelectric transition at $575\phantom{\rule{0.3em}{0ex}}\mathrm{K}$. The BVMD model correctly reproduces the mixed order-disorder and displacive phase transition character, the magnitudes of cation displacements in the ferroelectric and paraelectric phases, and the energy of 180\ifmmode^\circ\else\textdegree\fi{} domain walls. The success of this simple and physically motivated model makes the simulation of extended defects tractable in PT and other complex oxides. read less NOT USED (high confidence) J. Purton, M. Lavrentiev, and N. Allan, “Monte Carlo simulation of GaN/InN mixtures,” Journal of Materials Chemistry. 2005. link Times cited: 15 Abstract: Exchange Monte Carlo calculations in the semi-grand canonica… read moreAbstract: Exchange Monte Carlo calculations in the semi-grand canonical ensemble are used to determine the mixing properties of GaN and InN in both the wurtzite and zinc blende structures. Inter-atomic potentials are obtained via empirical fitting to the experimental, bulk properties of the end member materials. The difference in structure is reflected in the variation of the enthalpy of mixing with composition and phase diagrams for the hexagonal and cubic phases. The calculated consolute temperature is ≈1725 K, in line with previous calculations. The calculated phase diagrams for the two structures are markedly asymmetric with the maximum in the binodals lying markedly on the Ga rich side. Our results are compared with available experimental data. read less NOT USED (high confidence) P. Erhart and K. Albe, “Analytical potential for atomistic simulations of silicon, carbon, and silicon carbide,” Physical Review B. 2005. link Times cited: 462 Abstract: We present an analytical bond-order potential for silicon, c… read moreAbstract: We present an analytical bond-order potential for silicon, carbon, and silicon carbide that has been optimized by a systematic fitting scheme. The functional form is adopted from a preceding work {\}Phys. Rev. B 65, 195124 (2002) and is built on three independently fitted potentials for Si-Si, C-C, and Si-C interaction. For elemental silicon and carbon, the potential perfectly reproduces elastic properties and agrees very well with first-principles results for high-pressure phases. The formation enthalpies of point defects are reasonably reproduced. In the case of silicon stuctural features of the melt agree nicely with data taken from literature. For silicon carbide the dimer as well as the solid phases B1, B2, and B3 were considered. Again, elastic properties are very well reproduced including internal relaxations under shear. Comparison with first-principles data on point defect formation enthalpies shows fair agreement. The successful validation of the potentials for configurations ranging from the molecular to the bulk regime indicates the transferability of the potential model and makes it a good choice for atomistic simulations that sample a large configuration space. read less NOT USED (high confidence) E. J. Albenze and P. Clancy, “Interface Response Functions for Amorphous and Crystalline Si and the Implications for Explosive Crystallization,” Molecular Simulation. 2005. link Times cited: 12 Abstract: Interface response functions (IRFs) for amorphous and crysta… read moreAbstract: Interface response functions (IRFs) for amorphous and crystalline forms of Si have been determined for several empirical atomic-scale models using Molecular Dynamics and compared to available experimental results fitted to a Wilson-Frenkel equation form. Stillinger–Weber (SW), the environment-dependent intermolecular potential (EDIP), and a version of the modified embedded atom method (MEAM) models were found to produce unacceptable representations of the IRFs of both solid phases; they were either unable to predict the amorphous melting point and/or the maximum solidification velocity. The best of these models was judged to be the SW potential, known to produce a very accurate IRF for crystalline silicon. Increasing the strength of the three-body term by up to 25% above that of the original SW potential improves the prediction of the melting characteristics of the amorphous phase. Above this limit, liquid phase properties are impaired. The resultant IRFs provide an important backdrop to understand the kinetics of explosive crystallization (EC) processes, as we shall show in comparison to recent experimental data on the EC of amorphous Ge. [A. Chojnacka and M.O. Thompson, in Growth, Evolution and Properties of Surfaces, Thin Films and Self-Organized Structures, edited by S.C. Moss, D.B. Poker, D. Ila, (Mat. Res. Soc. Symp. Proc. 648, Warrendale, PA 2001) p. P11.12.1–8]. We also provide evidence that homogeneous melting within the bulk of the amorphous material competes with heterogeneous melting at the planar amorphous/liquid interface. read less NOT USED (high confidence) S. Izumi, S. Hara, T. Kumagai, and S. Sakai, “Molecular dynamics study of homogeneous crystal nucleation in amorphous silicon,” Journal of Crystal Growth. 2005. link Times cited: 23 NOT USED (high confidence) H. Zhao and J. Freund, “Lattice-dynamical calculation of phonon scattering at ideal Si–Ge interfaces,” Journal of Applied Physics. 2005. link Times cited: 96 Abstract: Detailed phonon scattering at an ideal Si–Ge interface is st… read moreAbstract: Detailed phonon scattering at an ideal Si–Ge interface is studied with a linear lattice dynamics model. Frequency dependent transmission coefficients indicate the significance of acoustic-optical phonon mode conversion at the interface. Applied to multiple interfaces, the method shows how the overall thermal resistance approaches a finite (Bloch mode) limit with the increasing number of interfaces in absence of other scattering mechanisms. The dependence of thermal resistance on the superlattice layer thickness is not significant even in the interface-scattering-only limit we study. We also assess errors incurred by the finite domain size and classical statistics in molecular dynamics simulations of interface thermal resistance. Results suggest that using 6×6 unit cells in the transverse directions, a tractable size for such simulations, will incur only a 5% error in the predicted thermal resistance. Similarly, the error due to the classical (Boltzmann) phonon distribution in molecular dynamics simulation... read less NOT USED (high confidence) D. Vvedensky, “Multiscale modelling of nanostructures,” Journal of Physics: Condensed Matter. 2004. link Times cited: 98 Abstract: Most materials phenomena are manifestations of processes tha… read moreAbstract: Most materials phenomena are manifestations of processes that are operative over a vast range of length and time scales. A complete understanding of the behaviour of materials thereby requires theoretical and computational tools that span the atomic-scale detail of first-principles methods and the more coarse-grained description provided by continuum equations. Recent efforts have focused on combining traditional methodologies—density functional theory, molecular dynamics, Monte Carlo methods and continuum descriptions—within a unified multiscale framework. This review covers the techniques that have been developed to model various aspects of materials behaviour with the ultimate aim of systematically coupling the atomistic to the continuum descriptions. The approaches described typically have been motivated by particular applications but can often be applied in wider contexts. The self-assembly of quantum dot ensembles will be used as a case study for the issues that arise and the methods used for all nanostructures. Although quantum dots can be obtained with all the standard growth methods and for a variety of material systems, their appearance is a quite selective process, involving the competition between equilibrium and kinetic effects, and the interplay between atomistic and long-range interactions. Most theoretical models have addressed particular aspects of the ordering kinetics of quantum dot ensembles, with far fewer attempts at a comprehensive synthesis of this inherently multiscale phenomenon. We conclude with an assessment of the current status of multiscale modelling strategies and highlight the main outstanding issues. read less NOT USED (high confidence) F. Chuang, C. Ciobanu, C. Predescu, C. Wang, and K. Ho, “Structure of Si(1 1 4) determined by global optimization methods,” Surface Science. 2004. link Times cited: 36 NOT USED (high confidence) R. Holenstein, S. Kirkwood, R. Fedosejevs, and Y. Tsui, “Simulation of femtosecond laser ablation of silicon,” Photonics North. 2004. link Times cited: 16 Abstract: Femtosecond laser ablation is an important process in microm… read moreAbstract: Femtosecond laser ablation is an important process in micromachining and nanomachining of microelectronic, optoelectronic, biophotonic and MEMS components. The process of laser ablation of silicon is being studied on an atomic level using molecular dynamics simulations. We investigate ablation thresholds for Gaussian laser pulses of 800 nm wavelength, in the range of a few hundred femtoseconds in duration. Absorption is modelled via linear and 2-photon absorption processes into a hot electron bath which then transfers energy into the crystal lattice. The simulation box is a narrow column approximately 5.4 nm x 5.4 nm x 81 nm with periodic boundaries in the x and y transverse directions and a 1-D heat flow model at the bottom coupled to a heat bath to simulate an infinite bulk medium corresponding to the solid bulk material. A modified Stillinger-Weber potential is used to model the silicon atoms. The calculated thresholds are compared to various reported experimental values for the ablation threshold of silicon. We provide an overview of the code and discuss the simulation techniques used. read less NOT USED (high confidence) T. Hawa and M. Zachariah, “Internal pressure and surface tension of bare and hydrogen coated silicon nanoparticles.,” The Journal of chemical physics. 2004. link Times cited: 62 Abstract: We present a study of internal pressure and surface tension … read moreAbstract: We present a study of internal pressure and surface tension of bare and hydrogen coated silicon nanoparticles of 2-10 nm diameter as a function of temperature, using molecular dynamics simulations employing a reparametrized Kohen-Tully-Stillinger interatomic potential. The internal pressure was found to increase with decreasing particle size but the density was found to be independent of the particle size. We showed that for covalent bond structures, changes in surface curvature and the associated surface forces were not sufficient to significantly change bond lengths and angles. Thus, the surface tension was also found to be independent of the particle size. Surface tension was found to decrease with increasing particle temperature while the internal pressure did not vary with temperature. The presence of hydrogen on the surface of a particle significantly reduces surface tension (e.g., drops from 0.83 J/m(2) to 0.42 J/m(2) at 1500 K). The computed pressure of bare and coated particles was found to follow the classical Laplace-Young equation. read less NOT USED (high confidence) C. L. Allred, X. Yuan, M. Bazant, and L. Hobbs, “Elastic constants of defected and amorphous silicon with the environment-dependent interatomic potential,” Physical Review B. 2004. link Times cited: 31 Abstract: The elastic constants of a wide range of models of defected … read moreAbstract: The elastic constants of a wide range of models of defected crystalline and amorphous silicon are calculated, using the environment-dependent interatomic potential (EDIP). The defected crystalline simulation cells contain randomly generated defect distributions. An extensive characterization of point defects is performed, including structure, energy and influence on elastic constants. Three important conclusions are drawn. (1) Defects have independent effects on the elastic constants of silicon up to (at least) a defect concentration of 0.3%. (2) The linear effect of Frenkel pairs on the Young's modulus of silicon is -1653 GPa per defect fraction. (3) 17 different point defect types cause a very similar decrease in the Young's modulus: -(0.28{+-}0.05)% when calculated in isolation using a 1728-atom cell. These principles will be very useful for predicting the effect of radiation damage on the elastic modulus of silicon in the typical case in which point-defect concentrations can be estimated, but the exact distribution and species of defects is unknown. We also study amorphous samples generated in quenching the liquid with EDIP, including an ideal structure of perfect fourfold coordination, samples with threefold and fivefold coordinated defects, one with a nanovoid, and one with an amorphous inclusion in a crystalline matrix.more » In the last case, a useful finding is that the change in the Young's modulus is simply related to the volume fraction of amorphous material, as has also been observed by experiment.« less read less NOT USED (high confidence) A. Lemaître and C. Maloney, “Sum Rules for the Quasi-Static and Visco-Elastic Response of Disordered Solids at Zero Temperature,” Journal of Statistical Physics. 2004. link Times cited: 134 NOT USED (high confidence) J. Feldman, N. Bernstein, D. Papaconstantopoulos, and M. Mehl, “Consequences of zero-point motion to the radial distribution function of amorphous silicon,” Journal of Physics: Condensed Matter. 2004. link Times cited: 6 Abstract: While there have been many studies based on models of amorph… read moreAbstract: While there have been many studies based on models of amorphous silicon, there have been surprisingly few (perhaps only one) that have seriously addressed the radial distribution function at low temperature. Our work is based in part on the so-called NRL tight binding method using parameters for silicon determined by Bernstein et al. As we have recently shown in the case of 216-atom models, upon including zero-point motion good agreement is obtained with very accurate low temperature x-ray diffraction measurements by Laaziri et al of the radial distribution function, although, as also found by Herrero who used the Stillinger–Weber potential, a slight asymmetry of the first peak in the RDF is predicted and this asymmetry has not been observed experimentally. Upon use of an estimate of zero-point broadening from our previous work we show here that 1000-atom models lead to good agreement with experiment for the RDF. Perhaps fortuitously, we obtain models that agree with the experimentally determined second peak in the RDF for both annealed and unannealed samples: our tight binding relaxed models based on topologies derived from the Wooten–Winer–Weaire method and the Barkema–Mousseau method yield unannealed-sample results, whereas our tight binding relaxed model based on an MD quench of the liquid using the semi-empirical interatomic potential, EDIP, of Kaxiras and coworkers yield the annealed-sample results. Finally, the significant effect of zero-point motion on the first peak in the radial distribution that we obtain in the case of amorphous silicon could also have implications for other amorphous materials, e.g. SiO2. read less NOT USED (high confidence) M. Makeev, W. Yu, and A. Madhukar, “Atomic scale stresses and strains in Ge/Si(001) nanopixels: An atomistic simulation study,” Journal of Applied Physics. 2004. link Times cited: 6 Abstract: Recent progress in the growth of nanostructures on nonplanar… read moreAbstract: Recent progress in the growth of nanostructures on nonplanar (patterned) substrates has brought to the forefront issues related to atomic-level surface and subsurface stress and strain field variations, as these govern the process of formation of such nanostructures and strongly affect their physical properties. In this work, we use atomistic simulations to study the atomically resolved displacements, stresses, strains, and the strain energy in laterally finite nanoscale Si(001) mesas, uncovered and covered with the lattice-mismatched Ge overlayers. The spatial variations of the stress are examined both across the surface profile of the mesas and in the direction down to the substrate. We find that the hydrostatic stress and strain at the Ge∕Si interface undergo rapid changes from tensile in the interior of the Si mesa to compressive in the Ge overlayer, with the transition taking place over distances of the order of Si lattice constant. Substantial relaxation of the hydrostatic stress and strain, in both... read less NOT USED (high confidence) J. Stangl, V. Holý, and G. Bauer, “Structural properties of self-organized semiconductor nanostructures,” Reviews of Modern Physics. 2004. link Times cited: 698 Abstract: Instabilities in semiconductor heterostructure growth can be… read moreAbstract: Instabilities in semiconductor heterostructure growth can be exploited for the self-organized formation of nanostructures, allowing for carrier confinement in all three spatial dimensions. Beside the description of various growth modes, the experimental characterization of structural properties, such as size and shape, chemical composition, and strain distribution is presented. The authors discuss the calculation of strain fields, which play an important role in the formation of such nanostructures and also influence their structural and optoelectronic properties. Several specific materials systems are surveyed together with important applications. read less NOT USED (high confidence) L. Cannavacciuolo and D. Landau, “Critical behavior of the three-dimensional compressible Ising antiferromagnet at constant volume: A Monte Carlo study,” Physical Review B. 2004. link Times cited: 13 Abstract: Extensive Monte Carlo simulations in the semi-grand-canonica… read moreAbstract: Extensive Monte Carlo simulations in the semi-grand-canonical ensemble are used to study the critical behavior of a three-dimensional compressible Ising model with antiferromagnetic interactions under constant volume conditions. Elastic forces between spins are introduced by the Stillinger-Weber potential and energy parameters are chosen in such a way that antiparallel spin ordering is favored, analogous to the antiferromagnetic coupling in the rigid Ising Hamiltonian. All the quantities analyzed strongly indicate that the system remains in the universality class of the standard (rigid) three-dimensional Ising model, in contrast with theoretical predictions. read less NOT USED (high confidence) Q. Tang, “A molecular dynamics simulation: the effect of finite size on the thermal conductivity in a single crystal silicon,” Molecular Physics. 2004. link Times cited: 22 Abstract: Non-equilibrium molecular dynamics (NEMD) simulations are pe… read moreAbstract: Non-equilibrium molecular dynamics (NEMD) simulations are performed to calculate thermal conductivity. The environment-dependent interatomic potential (EDIP) potential on crystal silicon is adopted as a model system. The issues are related to nonlinear response, local thermal equilibrium and statistical averaging. The simulation results by non-equilibrium molecular dynamics show that the calculated thermal conductivity decreases almost linearly as the film thickness reduced at the nanometre scale. The effect of size on the thermal conductivity is also obtained by a theoretic analysis of the kinetic theory and formulas of the heat capacity. The analysis reveals that the contributions of phonon mean free path (MFP) and phonon number in a finite cell to thermal conductivity are very important. read less NOT USED (high confidence) M. C. Moore, N. Kalyanasundaram, J. Freund, and H. Johnson, “Structural and sputtering effects of medium energy ion bombardment of silicon,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2004. link Times cited: 43 NOT USED (high confidence) J. Godet, L. Pizzagalli, S. Brochard, and P. Beauchamp, “Theoretical study of dislocation nucleation from simple surface defects in semiconductors,” Physical Review B. 2004. link Times cited: 78 Abstract: The plasticity of semiconductors has been a subject ofnumero… read moreAbstract: The plasticity of semiconductors has been a subject ofnumerous studies for the last decades in both fundamen-tal and applied research. Despite significant progress inthe understanding of the fundamental mechanisms in-volved, several issues remain, in particular for nanos-tructured semiconductors. In these materials, includ-ing for example nano-grained systems or nanolayers inheteroepitaxy, dimensions are usually too small to allowthe classical mechanisms of dislocation multiplication,such as Franck-Read sources. read less NOT USED (high confidence) R. Singh, S. Prakash, N. Shukla, and R. Prasad, “Sample dependence of the structural, vibrational, and electronic properties of a − Si : H : A density-functional-based tight-binding study,” Physical Review B. 2004. link Times cited: 23 Abstract: In order to investigate the sample dependence of various pro… read moreAbstract: In order to investigate the sample dependence of various properties of hydrogenated amorphous silicon (a-Si:H), we have generated four samples with 216 silicon atoms and 24 hydrogen atoms using the density functional based tight binding molecular dynamics simulations. The overall structural properties of these model samples are in agreement with the previous theoretical and experimental results. While the Si-Si and Si-H pair correlation functions are independent of preparation procedure as well as initial conditions, the H-H pair correlation functions are sample dependent. The distribution of hydrogen atoms in all the samples is nonuniform and depends upon the preparation procedure as well as the initial structure from which the hydrogenated amorphous silicon sample is generated. The Si-Si bond length and Si-Si-Si bond angle distributions are nearly independent of sample preparation procedure, but Si-H bond length distributions are sample dependent. The peaks in the vibrational density of states (VDOS) at high frequencies, which are due to the Si-H bond vibrations, are in reasonable accord with the experimental results. The positions of the high frequency peaks are found to be dependent on the local environment which changes from one sample to another. While the high frequency vibrational modes related to Si-Si bond vibrations are moderately localized, the vibrational modes related to Si-H bond vibrations in a-Si:H samples are highly localized. In samples generated read less NOT USED (high confidence) V. Shenoy, “Mechanics at small scales,” SPIE Optics + Photonics. 2004. link Times cited: 0 Abstract: This paper presents a short overview of the methods used for… read moreAbstract: This paper presents a short overview of the methods used for the study of mechanics at small scales. The key issue to be tackled is the presence of multiple scales starting from the atomic scale. The methods outlined include continuum, atomistic and mixed methods. read less NOT USED (high confidence) L. Wang and P. Clancy, “Molecular dynamics simulations of boron diffusion in SiGe,” Journal of Applied Physics. 2004. link Times cited: 10 Abstract: Transient enhanced diffusion (TED) of boron poses a limit to… read moreAbstract: Transient enhanced diffusion (TED) of boron poses a limit to the formation of ultrashallow junctions. To suppress TED of boron, other species (e.g., Ge) can be introduced into the Si substrate. Experiments have shown that boron diffusivity decreased rapidly as Ge concentration increased to 40% Ge. There is no consensus on the cause for this decrease in diffusivity. Here, an ab initio derived energy database was used to fit classical potential models in order to simulate boron diffusion in SiGe on larger length and time-frames than are possible using ab initio models. In this paper, a set of Stillinger-Weber potential parameters for Ge-B and Si-Ge-B has been constructed, allowing a molecular dynamics study of boron diffusion in SiGe alloys to be carried out. Molecular dynamics simulations of boron B diffusion in Si compared to that in SiGe alloys suggest that different trapping mechanisms dominate: B in Si is trapped in substitutional positions, whereas B in SiGe alloys is trapped in interstitial positions... read less NOT USED (high confidence) D. Humbird and D. Graves, “Molecular dynamics simulations of Si–F surface chemistry with improved interatomic potentials,” Plasma Sources Science and Technology. 2004. link Times cited: 17 Abstract: Molecular dynamics results using an improved Tersoff?Brenner… read moreAbstract: Molecular dynamics results using an improved Tersoff?Brenner style interatomic potential for Si?F (denoted by TB?HG) are presented. In simulations of F/Ar+, F+, and etching of silicon, the TB?HG potential predicts different behaviour from that of Stillinger and Weber (SW). With the SW potential, F atoms do not mix into Si surfaces, creating instead a roughened surface with F on the outside. With the TB?HG potential, F atoms are able to mix into Si, leading to higher F uptake and Si etch rate in all cases. The TB?HG potential is compared to the modified SW potential of Weakliem et al (SW?WWC) in simulations of F+ etching of Si. The quantitative values of steady-state F uptake and Si etch rate for the (SW?WWC and TB?HG) potentials are nearly identical, but surface structure and etch product distributions are qualitatively different. Evidence of spurious energetic barriers in the SW potential form is given. read less NOT USED (high confidence) J. Zimmerman, E. B. WebbIII, J. J. Hoyt, R. Jones, P. A. Klein, and D. Bammann, “Calculation of stress in atomistic simulation,” Modelling and Simulation in Materials Science and Engineering. 2004. link Times cited: 401 Abstract: Atomistic simulation is a useful method for studying materia… read moreAbstract: Atomistic simulation is a useful method for studying material science phenomena. Examination of the state of a simulated material and the determination of its mechanical properties is accomplished by inspecting the stress field within the material. However, stress is inherently a continuum concept and has been proven difficult to define in a physically reasonable manner at the atomic scale. In this paper, an expression for continuum mechanical stress in atomistic systems derived by Hardy is compared with the expression for atomic stress taken from the virial theorem. Hardy's stress expression is evaluated at a fixed spatial point and uses a localization function to dictate how nearby atoms contribute to the stress at that point; thereby performing a local spatial averaging. For systems subjected to deformation, finite temperature, or both, the Hardy description of stress as a function of increasing characteristic volume displays a quicker convergence to values expected from continuum theory than volume averages of the local virial stress. Results are presented on extending Hardy's spatial averaging technique to include temporal averaging for finite temperature systems. Finally, the behaviour of Hardy's expression near a free surface is examined, and is found to be consistent with the mechanical definition for stress. read less NOT USED (high confidence) D. Humbird and D. Graves, “Atomistic simulations of spontaneous etching of silicon by fluorine and chlorine,” Journal of Applied Physics. 2004. link Times cited: 50 Abstract: Updated interatomic potential energy functions for Si–F and … read moreAbstract: Updated interatomic potential energy functions for Si–F and Si–Cl are used in molecular dynamics simulations of spontaneous etching of Si. Steady halogen uptake and spontaneous silicon etching are predicted as F and Cl atoms impact initially crystalline Si. At 300 K, the simulated etch probability (silicon atoms etched per incident F atom) is 0.03 for F atoms and 0.005 for Cl. The major etch products are SiF4 and Si2F6 for F etching and SiCl4 for Cl. Etching is not observed with F2 or Cl2. At 300 K and below, the simulation predictions are within the range of reported experimental measurements of the surface coverage, etch reaction probability, and etch product distribution. Etch products that remain weakly bound to the surface are detected in significant quantities. At higher temperature (T>450 K), SiF2 and SiCl2 become the dominant etch products as the temperature is increased, in agreement with experiment, but the simulation underpredicts the etch reaction probability. The atomistic mechanisms of etch ... read less NOT USED (high confidence) L. Shen and Z. Chen, “An investigation of the effect of interfacial atomic potential on the stress transition in thin films,” Modelling and Simulation in Materials Science and Engineering. 2004. link Times cited: 34 Abstract: In order to better understand the mechanisms of tungsten (W)… read moreAbstract: In order to better understand the mechanisms of tungsten (W) film delamination from the silicon (Si) substrate, a three-dimensional molecular dynamics (MD) simulation is being conducted to investigate the formation of residual stress during the film deposition process. For the purpose of simplicity, a Morse pair potential is proposed in this paper to simulate the interactions between W and Si atoms during the film deposition process. It appears from numerical solutions that the residual stress field in the W film is very sensitive to the W–Si interfacial potential model proposed for the MD simulation. By calibrating the controlling parameters in the interfacial potential model using the comparison between the simulated stresses and experimental data, the film stress transition from tension to compression during the film deposition process could be qualitatively simulated via the proposed simulation procedure. The numerical results presented in this paper provide a better insight into the effect of interfacial atomic potential on the stress transition in thin films. In addition, it can be seen from the MD simulation that there might exist a phase transition from the crystalline Si to amorphous W–Si structure to crystalline W around the interface area. Well-designed experiments are required to verify the simulation results. read less NOT USED (high confidence) H. Ishii, A. Murakawa, and K. Kakimoto, “Isotope-concentration dependence of thermal conductivity of germanium investigated by molecular dynamics,” Journal of Applied Physics. 2004. link Times cited: 4 Abstract: Thermal conductivity of solid germanium as a function of the… read moreAbstract: Thermal conductivity of solid germanium as a function of the mole fraction of isotopes was estimated semi-quantitatively by using equilibrium molecular dynamics. The thermal conductivity of isotope-germanium was calculated by using an empirical potential of Stillinger–Weber potential. We employed the molecular dynamics based on Green–Kubo’s formula in which the autocorrelation function of heat flux was integrated as a function of duration time. The results of calculation showed that thermal conductivity of mixed isotope-germanium with large difference of mass is smaller than that with small mass difference, which is similar to experimental results. read less NOT USED (high confidence) J. Feldman, N. Bernstein, D. Papaconstantopoulos, and M. Mehl, “Tight-binding study of structure and vibrations of amorphous silicon,” Physical Review B. 2004. link Times cited: 11 Abstract: We present a tight-binding calculation that, for the first t… read moreAbstract: We present a tight-binding calculation that, for the first time, accurately describes the structural, vibrational and elastic properties of amorphous silicon. We compute the interatomic force constants and find an unphysical feature of the Stillinger-Weber empirical potential that correlates with a much noted error in the radial distribution function associated with that potential. We also find that the intrinsic first peak of the radial distribution function is asymmetric, contrary to usual assumptions made in the analysis of diffraction data. We use our results for the normal mode frequencies and polarization vectors to obtain the zero-point broadening effect on the radial distribution function, enabling us to directly compare theory and a high resolution x-ray diffraction experiment. read less NOT USED (high confidence) W. K. Liu, E. Karpov, S. Zhang, and H. S. Park, “An introduction to computational nanomechanics and materials,” Computer Methods in Applied Mechanics and Engineering. 2004. link Times cited: 405 NOT USED (high confidence) P. Kelires, “A constrained-equilibrium Monte Carlo method for quantum dots—the problem of intermixing,” Journal of Physics: Condensed Matter. 2004. link Times cited: 8 Abstract: Islands grown during semiconductor heteroepitaxy are in a th… read moreAbstract: Islands grown during semiconductor heteroepitaxy are in a thermodynamically metastable state. Experiments show that diffusion at the surface region, including the interior of the islands, is fast enough to establish local equilibrium. I review here applications of a Monte Carlo method which takes advantage of the quasi-equilibrium nature of quantum dots and is able to address the issue of intermixing and island composition. Both Ge islands grown on the bare Si(100) surface and C-induced Ge islands grown on Si(100) precovered with C are discussed. In the bare case, the interlinking of the stress field with the composition is revealed. Both are strongly inhomogeneous. In the C-induced case, the interplay of strain and chemical effects is the dominant key factor. Islands do not contain C under any conditions of coverage and temperature. read less NOT USED (high confidence) A. Blumenau, T. Frauenheim, S. Öberg, B. Willems, and G. van Tendeloo, “Dislocation Structures in Diamond: Density-Functional Based Modelling and High-Resolution Electron Microscopy,” Defect and Diffusion Forum. 2004. link Times cited: 5 Abstract: The core structures of perfect 60 and edge dislocations in d… read moreAbstract: The core structures of perfect 60 and edge dislocations in diamond are investigated atomistically in a density-functional based tight-binding approach, and their dissociation is discussed both in terms of structure and energy. Furthermore, high resolution electron microscopy is performed on dislocation cores in high-temperature, high-pressure annealed natural brown diamond, and HRTEM image simulation allows a comparison of theoretically predicted and experimentally observed structures. read less NOT USED (high confidence) J. Pollmann and P. Krüger, “Reconstruction models of cubic SiC surfaces,” Journal of Physics: Condensed Matter. 2004. link Times cited: 38 Abstract: The current understanding of the relaxation and reconstructi… read moreAbstract: The current understanding of the relaxation and reconstruction of low-index cubic SiC surfaces, as it derives from first-principles calculations, is briefly reviewed in comparison with surface-sensitive experimental data. The calculated structural properties are obtained from ab initio total energy and grand canonical potential minimization in the framework of the local density and generalized gradient approximations of density functional theory. Characteristic surface structural properties are related to the surface electronic structure and to the ionicity of the underlying bulk crystal. For a number of cubic surfaces, there is good agreement between first-principles results and the data. In other cases, most noticeably for Si-terminated SiC(001) surfaces, there is still considerable controversy with respect to the atomic and electronic structure in both experiment and theory. read less NOT USED (high confidence) H. Ji et al., “Simulation of implantation into HfO/sub 2/ by MD method,” The Fourth International Workshop on Junction Technology, 2004. IWJT ’04. 2004. link Times cited: 0 Abstract: Molecular dynamics (MD) method has not been reported to pred… read moreAbstract: Molecular dynamics (MD) method has not been reported to predict range profiles of implantation into HfO/sub 2/ and stopping power models especially electronic stopping power model has not been studied specifically. In this article, MD method is successfully applied to simulate B, As and P implantation into HfO/sub 2/. An efficient electronic stopping model with only one free parameter, i.e., the single electron radius, is carefully discussed. A reliable fitting value of the single electron radius is firstly given for B, As and P implantation into HfO/sub 2/. Using the obtained fitting value, simulation results agree with SIMS data excellently over the energy range of 5 - 40 keV. read less NOT USED (high confidence) T. Hawa and M. Zachariah, “Molecular dynamics study of particle-particle collisions between hydrogen-passivated silicon nanoparticles,” Physical Review B. 2004. link Times cited: 39 Abstract: One of the significant challenges in the use of nanoparticle… read moreAbstract: One of the significant challenges in the use of nanoparticles is the control of primary particle size and extent of agglomeration when grown from the gas phase. In this paper we evaluate a possible strategy of surface passivation. Here the particle--particle interaction of hydrogen-surface-terminated silicon nanoparticles has been evaluated using molecular dynamics simulation. Nanoparticles of the size between 200 and 6400 silicon atoms at 300--1800 K were studied with a reparametrized Kohen-Tully-Stillinger empirical interatomic potential. A hydrogen monolayer is shown to prevent coalescence between particles under thermal collision conditions. The critical approach energy for coalescence was found to increase with increasing particle size but decreases with increasing temperature. Both solid and liquid droplets were seen to bounce at thermal energies, and in some cases, ``superelastic'' collisions are observed, where the rebound kinetic energy of the droplet is higher than the approach energy. These results suggest that surface coatings can significantly retard nanoaerosol growth. read less NOT USED (high confidence) A. Tekin and B. Hartke, “Global geometry optimization of small silicon clusters with empirical potentials and at the DFT level,” Physical Chemistry Chemical Physics. 2004. link Times cited: 40 Abstract: We have performed global parameter optimization of selected … read moreAbstract: We have performed global parameter optimization of selected empirical potentials for silicon, resulting in improved performance for small to medium-sized silicon clusters, as judged by a comparison of globally optimized cluster structures to the structures accepted in the literature for the size range up to n = 10. Using global cluster structure optimizations with the resulting optimized model potential and ensuing local optimizations at the DFT level, we could find improved proposals for global minimum structures in the size region n = 10–16. This study confirms the applicability of our general global cluster optimization strategy for still larger silicon clusters. read less NOT USED (high confidence) D. Pettifor, M. Finnis, D. Nguyen-Manh, D. Murdick, X. W. Zhou, and H. Wadley, “Analytic bond-order potentials for multicomponent systems,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2004. link Times cited: 53 NOT USED (high confidence) K. Shintani, T. Nakajima, and S. Kameoka, “Atomistic model of limited-thickness Si(001) epitaxy at low temperatures,” Journal of Applied Physics. 2004. link Times cited: 7 Abstract: Limited-thickness homoepitaxial growth on a Si(001) surface … read moreAbstract: Limited-thickness homoepitaxial growth on a Si(001) surface at low temperatures is investigated by using the classical molecular-dynamics method with the Stillinger-Weber potential. The simulation begins with preliminary equilibration of the substrate at a specified temperature. 256 silicon atoms with the energy of 0.2 eV are then deposited one by one on the substrate. The simulations are performed at the temperatures 300, 500, 700, and 1000 K. At 300 and 500 K, the initial three or four monolayers grow epitaxially, and the subsequent layers form amorphouslike structures. At 700 and 1000 K, the deposited atoms form epitaxial structures throughout the simulation. In the epitaxial growth mode, 2×1 dimer rows are observed to align along alternately perpendicular 〈110〉 directions in successive atomic layers. Tracking a few atoms on the substrate surface reveals that these transient anisotropic surface structures are created by the breaking and reconstruction of dimers due to the impingement of deposited atoms... read less NOT USED (high confidence) P. Biswas, R. Atta-Fynn, and D. A. Drabold, “Reverse Monte Carlo modeling of amorphous silicon,” Physical Review B. 2004. link Times cited: 71 Abstract: An implementation of the Reverse Monte Carlo algorithm is pr… read moreAbstract: An implementation of the Reverse Monte Carlo algorithm is presented for the study of amorphous tetrahedral semiconductors. By taking into account a number of constraints that describe the tetrahedral bonding geometry along with the radial distribution function, we construct a model of amorphous silicon using the reverse monte carlo technique. Starting from a completely random configuration, we generate a model of amorphous silicon containing 500 atoms closely reproducing the experimental static structure factor and bond angle distribution and in improved agreement with electronic properties. Comparison is made to existing Reverse Monte Carlo models, and the importance of suitable constraints beside experimental data is stressed. read less NOT USED (high confidence) Y. Ma et al., “Statistical nature of cluster emission in nuclear liquid-vapour phase coexistence,” Journal of Physics G. 2004. link Times cited: 1 Abstract: The emission of nuclear clusters is investigated within the … read moreAbstract: The emission of nuclear clusters is investigated within the framework of the isospin-dependent lattice gas model and the classical molecular dynamics model. It is found that the emission of an individual cluster which is heavier than proton is almost Poissonian except near the transition temperature at which the system is leaving the liquid-vapour phase coexistence and thermal scaling is observed by the linear Arrhenius plots which are made from the average multiplicity of each cluster versus the inverse of temperature in the liquid-vapour phase coexistence. The slopes of the Arrhenius plots, i.e. the 'emission barriers', are extracted as a function of the mass or charge number and fitted by the formula embodied with the contributions of the surface energy and Coulomb interaction. Good agreements are obtained in comparison with the data for low-energy conditional barriers. In addition, the possible influences of the source size, Coulomb interaction and 'freeze-out' density and related physical implications are discussed. read less NOT USED (high confidence) A. Barnard, P. Båth, S. Russo, and I. Snook, “A Monte Carlo Study of Surface Reconstruction in (100) and (111) Diamond Surfaces and Nanodiamond,” Molecular Simulation. 2004. link Times cited: 5 Abstract: A Monte-Carlo (MC) study of the surface reconstruction and r… read moreAbstract: A Monte-Carlo (MC) study of the surface reconstruction and relaxation of the diamond (100) and (111) surfaces is presented. Surface reconstruction events have been simulated using as empirical 2+3 body potential fitted to ab initio data. MC simulations are first performed on thick diamond slabs with (100) and (111) surfaces in order to evaluate the quality of the potential. The results obtained are then compared to those obtained using computational methods and experimental results. Reconstruction results for nanodiamond crystals with (100) surfaces of sizes ranging from 0.5 to 2 nm are then presented and discussed. read less NOT USED (high confidence) N. Jakse et al., “Structural changes on supercooling liquid silicon,” Applied Physics Letters. 2003. link Times cited: 68 Abstract: X-ray diffraction experiments and ab initio molecular dynami… read moreAbstract: X-ray diffraction experiments and ab initio molecular dynamics (AIMD) simulations have been performed to investigate the atomic structure of liquid silicon into the deeply supercooled region. The levitation technique used has made it possible to extend the measurements down to a temperature of 1458 K, 230 K below the equilibrium melting point. The x-ray and AIMD results, which are in reasonable agreement, show conclusively that the tetrahedral order is reinforced and that the coordination number decreases as the liquid is supercooled, with implications for the liquid–liquid phase transition. read less NOT USED (high confidence) F. F. Abraham, “How fast can cracks move? A research adventure in materials failure using millions of atoms and big computers,” Advances in Physics. 2003. link Times cited: 39 Abstract: During the last decade, we have been simulating the dynamic … read moreAbstract: During the last decade, we have been simulating the dynamic failure of brittle and ductile solids at the atomic level using some of the world's fastest computers. Computer experiments encompassing crack dynamics in brittle fracture, crack blunting in ductile failure, and multi-dislocation entanglement in work-hardening are some examples and have given new and exciting insights into the failure processes of solids. Our presentation begins at an introduction level where basic concepts are presented before their application is needed for the understanding of specific phenomena. The story is primarily based on our past experiences, and our goal is to give the reader a fundamental appreciation for how materials fail. read less NOT USED (high confidence) R. Rudd, “Coarse-Grained Molecular Dynamics for Computer Modeling of Nanomechanical Systems,” International Journal for Multiscale Computational Engineering. 2003. link Times cited: 28 Abstract: Unique challenges for computer modeling and simulation arise… read moreAbstract: Unique challenges for computer modeling and simulation arise in the course of the development and design of nanoscale mechanical systems. Materials often exhibit unconventional behavior at the nanoscale that can affect device operation and failure. This uncertainty poses a problem because of the limited experimental characterization at these ultra-small length scales. In this Article we give an overview of how we have used concurrent multiscale modeling techniques to address some of these issues. Of particular interest are the dynamic and temperature-dependent processes found in nanomechanical systems. We focus on the behavior of sub-micron mechanical components of Micro-Electro-Mechanical Systems (MEMS) and Nano-Electro-Mechanical Systems (NEMS), especially flexural-mode resonators. The concurrent multiscale methodology we have developed for NEMS employs an atomistic description of millions of atoms in relatively small but key regions of the system, coupled to, and run concurrently with, a generalized finite element model of the periphery. We describe two such techniques. The more precise model, Coarse-Grained Molecular Dynamics (CGMD), describes the dynamics on a mesh of elements, but the equations of motion are built up from the underlying atomistic physics to ensure a smooth coupling between regions governed by different length scales. In many cases the degrees of smoothness ofmore » the coupling provided by CGMD is not necessary. The hybrid Coupling of Length Scales (CLS) methodology, combining molecular dynamics with conventional finite element modeling, provides a suitable technique for these cases at a greatly reduced computation expense. We review these models and some of the results we have obtained regarding size effects in the elasticity and dissipation of nanomechanical systems.« less read less NOT USED (high confidence) C. Ciobanu, D. Tambe, and V. Shenoy, “Comparative study of dimer-vacancies and dimer-vacancy lines on Si(001) and Ge(001),” Surface Science. 2003. link Times cited: 11 NOT USED (high confidence) J. Godet, L. Pizzagalli, S. Brochard, and P. Beauchamp, “Comparison between classical potentials and ab initio methods for silicon under large shear,” Journal of Physics: Condensed Matter. 2003. link Times cited: 47 Abstract: The homogeneous shear of the {111} planes along the directio… read moreAbstract: The homogeneous shear of the {111} planes along the direction of bulk silicon has been investigated using ab initio techniques, to better understand the strain properties of both shuffle and glide set planes. Similar calculations have been done with three empirical potentials, Stillinger–Weber, Tersoff and EDIP, in order to find the one giving the best results under large shear strains. The generalized stacking fault energies have also been calculated with these potentials to complement this study. It turns out that the Stillinger–Weber potential better reproduces the ab initio results, for the smoothness and the amplitude of the energy variation as well as the localization of shear in the shuffle set. read less NOT USED (high confidence) S. Hosokawa et al., “Sub-picosecond dynamics in liquid Si,” Journal of Physics: Condensed Matter. 2003. link Times cited: 26 Abstract: We are the first group to succeed in measuring the dynamic s… read moreAbstract: We are the first group to succeed in measuring the dynamic structure factor S(Q,ω) of liquid Si close to melting using high-resolution inelastic x-ray scattering. The spectra clearly demonstrate the existence of propagating short wavelength modes in the melt with a Q–ω relation similar to those in other liquid metal systems. A specific variation of the quasi-elastic line shape with increasing Q is observed close to the structure factor maximum. This observation is related to the onset of atomic correlations on the sub-picosecond timescale in the vicinity of a metal-to-insulator transition. Such observations have been made previously only in computer simulations of metallic systems with increasing covalent character. Our data provide the first experimental evidence for these ultrashort density correlations. read less NOT USED (high confidence) N. Ghoniem, E. Busso, N. Kioussis, and H.-C. Huang, “Multiscale modelling of nanomechanics and micromechanics: an overview,” Philosophical Magazine. 2003. link Times cited: 168 Abstract: Recent advances in analytical and computational modelling fr… read moreAbstract: Recent advances in analytical and computational modelling frameworks to describe the mechanics of materials on scales ranging from the atomistic, through the microstructure or transitional, and up to the continuum are reviewed. It is shown that multiscale modelling of materials approaches relies on a systematic reduction in the degrees of freedom on the natural length scales that can be identified in the material. Connections between such scales are currently achieved either by a parametrization or by a ‘zoom-out’ or ‘coarse-graining’ procedure. Issues related to the links between the atomistic scale, nanoscale, microscale and macroscale are discussed, and the parameters required for the information to be transferred between one scale and an upper scale are identified. It is also shown that seamless coupling between length scales has not yet been achieved as a result of two main challenges: firstly, the computational complexity of seamlessly coupled simulations via the coarse-graining approach and, secondly, the inherent difficulty in dealing with system evolution stemming from time scaling, which does not permit coarse graining over temporal events. Starting from the Born–Oppenheimer adiabatic approximation, the problem of solving quantum mechanics equations of motion is first reviewed, with successful applications in the mechanics of nanosystems. Atomic simulation methods (e.g. molecular dynamics, Langevin dynamics and the kinetic Monte Carlo method) and their applications at the nanoscale are then discussed. The role played by dislocation dynamics and statistical mechanics methods in understanding microstructure self-organization, heterogeneous plastic deformation, material instabilities and failure phenomena is also discussed. Finally, we review the main continuum-mechanics-based framework used today to describe the nonlinear deformation behaviour of materials at the local (e.g. single phase or grain level) and macroscopic (e.g. polycrystal) scales. Emphasis is placed on recent progress made in crystal plasticity, strain gradient plasticity and homogenization techniques to link deformation phenomena simultaneously occurring at different scales in the material microstructure with its macroscopic behaviour. In view of this wide range of descriptions of material phenomena involved, the main theoretical and computational difficulties and challenges are critically assessed. read less NOT USED (high confidence) Y. Wang, H. Zhang, X. Bian, and Z. Zhang, “Structural Relaxation Phenomenon in Amorphous Al85Ni10Ce5 Alloy during Natural Aging,” Glass Physics and Chemistry. 2003. link Times cited: 1 NOT USED (high confidence) V. Fomin, I. Golovnev, and A. Utkin, “Relation between the atomistic picture and continuum mechanics description of detonating solid-state explosives,” Shock Waves. 2003. link Times cited: 7 NOT USED (high confidence) J. Los and A. Fasolino, “Intrinsic long-range bond-order potential for carbon: Performance in Monte Carlo simulations of graphitization,” Physical Review B. 2003. link Times cited: 233 Abstract: We propose a bond order potential for carbon with built-in l… read moreAbstract: We propose a bond order potential for carbon with built-in long-range interactions. The potential is defined as the sum of an angular and coordination dependent short-range part accounting for the strong covalent interactions and a radial long-range part describing the weak interactions responsible, e.g., for the interplanar binding in graphite. The short-range part is a Brenner type of potential, with several modifications introduced to get an improved description of elastic properties and conjugation. Contrary to previous long-range extensions of existing bond order potentials, we prevent the loss of accuracy by compensating for the additional long-range interactions by an appropriate parametrization of the short-range part. We also provide a short-range bond order potential. In Monte Carlo simulations our potential gives a good description of the diamond to graphite transformation. For thin (111) slabs graphitization proceeds perpendicular to the surface as found in ab initio simulations, whereas for thick layers we find that graphitization occurs layer by layer. read less NOT USED (high confidence) L. Saviot, D. Murray, and M. C. M. D. Lucas, “Vibrations of free and embedded anisotropic elastic spheres: Application to low-frequency Raman scattering of silicon nanoparticles in silica,” Physical Review B. 2003. link Times cited: 75 Abstract: Vibrational mode frequencies and damping are calculated for … read moreAbstract: Vibrational mode frequencies and damping are calculated for an elastic sphere embedded in an infinite, homogeneous, isotropic elastic medium. Anisotropic elasticity of the sphere significantly shifts the frequencies in comparison to simplified calculations that assume isotropy. New low-frequency Raman light scattering data are presented for silicon spheres grown in a ${\mathrm{SiO}}_{2}$ glass matrix. Principal features of the Raman spectrum are not correctly described by a simple model of the nanoparticle as a free, isotropic sphere, but require both matrix effects and the anisotropy of the silicon to be taken into account. Libration, not vibration, is the dominant mechanism. read less NOT USED (high confidence) S. Yoo and X. Zeng, “Global geometry optimization of silicon clusters described by three empirical potentials,” Journal of Chemical Physics. 2003. link Times cited: 59 Abstract: The “basic-hopping” global optimization technique developed … read moreAbstract: The “basic-hopping” global optimization technique developed by Wales and Doye is employed to study the global minima of silicon clusters Sin(3⩽n⩽30) with three empirical potentials: the Stillinger–Weber (SW), the modified Stillinger–Weber (MSW), and the Gong potentials. For the small-sized SW and Gong clusters (3⩽n⩽15), it is found that the global minima obtained based on the basin-hopping method are identical to those reported by using the genetic algorithm [Iwamatsu, J. Chem. Phys. 112, 10976 (2000)], as well as with those by using molecular dynamics and the steepest-descent quench (SDQ) method [Feuston, Kalia, and Vashishta, Phys. Rev. B 37, 6297 (1988)]. However, for the mid-sized SW clusters (16⩽n⩽20), the global minima obtained differ from those based on the SDQ method, e.g., the appearance of the endohedral atom with fivefold coordination starting at n=17, as opposed to n=19. For larger SW clusters (20⩽n⩽30), it is found that the “bulklike” endohedral atom with tetrahedral coordination starts at n=... read less NOT USED (high confidence) C. Ciobanu, V. Shenoy, C. Wang, and K. Ho, “Structure and stability of the Si(1 0 5) surface,” Surface Science. 2003. link Times cited: 8 NOT USED (high confidence) J. Li, D. Liao, S. Yip, R. Najafabadi, and L. Ecker, “Force-based many-body interatomic potential for ZrC,” Journal of Applied Physics. 2003. link Times cited: 48 Abstract: A classical potential for ZrC is developed in the form of a … read moreAbstract: A classical potential for ZrC is developed in the form of a modified second-moment approximation with emphasis on the strong directional dependence of the C–Zr interactions. The model has a minimal set of parameters, 4 for the pure metal and 6 for the cross interactions, which are fitted to the database of cohesive energies of B1–, B2–, and B3–ZrC, the heat of formation, and most importantly, the atomic force constants of B1–ZrC from first-principles calculations. The potential is then extensively tested against various physical properties, none of which were considered in the fitting. Finite temperature properties such as thermal expansion and melting point are in excellent agreement with experiments. We believe our model should be a good template for metallic ceramics. read less NOT USED (high confidence) W. Curtin and R. E. Miller, “Atomistic/continuum coupling in computational materials science,” Modelling and Simulation in Materials Science and Engineering. 2003. link Times cited: 536 Abstract: Important advances in multi-scale computer simulation techni… read moreAbstract: Important advances in multi-scale computer simulation techniques for computational materials science have been made in the last decade as scientists and engineers strive to imbue continuum-based models with more-realistic details at quantum and atomistic scales. One major class of multi-scale models directly couples a region described with full atomistic detail to a surrounding region modelled using continuum concepts and finite element methods. Here, the development of such coupled atomistic/continuum models is reviewed within a single coherent framework with the aim of providing both non-specialists and specialists with insight into the key ideas, features, differences and advantages of prevailing models. Some applications and very recent advances are noted, and important challenges for extending these models to their fullest potential are discussed. read less NOT USED (high confidence) A. C. Sparavigna, “Role of nonpairwise interactions on phonon thermal transport,” Physical Review B. 2003. link Times cited: 15 Abstract: In this paper, the phonon system for a perfect silicon latti… read moreAbstract: In this paper, the phonon system for a perfect silicon lattice is obtained by means of a model considering a phenomenological potential that includes both two- and three-body contributions. Phonon dispersions are discussed, and anharmonic contributions to the phonon Hamiltonian are evaluated. The model is compared with a model involving a pairwise potential, previously used by the author in the calculation of silicon thermal conductivity. The equation of motion is solved for both models, obtaining phonon dispersions practically indistinguishable and in good agreement with the experimental data. The role of nonpairwise interactions in phonon-phonon-scattering processes, relevant for the calculation of thermal conductivity, is then discussed. The thermal conductivity obtained with the present model including two- and three-body interactions has a good agreement with the experimental data, better than the one previously achieved with the model involving a central potential. read less NOT USED (high confidence) T. F. Middleton and D. Wales, “Energy landscapes of model glasses. II. Results for constant pressure,” Journal of Chemical Physics. 2003. link Times cited: 60 Abstract: New geometry optimization techniques are introduced for char… read moreAbstract: New geometry optimization techniques are introduced for characterizing local minima, transition states, and pathways corresponding to enthalpy surfaces at constant pressure. Results are obtained for comparison with the potential energy surfaces of model glass formers studied in previous work. The constant pressure condition, where the the box lengths of the simulation cell vary, makes the enthalpy surface less rugged than the potential energy surface corresponding to the same mean density. Analysis of barrier heights as a function of pressure provides insight into transport and relaxation processes. Elementary rearrangements can be separated into “diffusive” and “nondiffusive” processes, where the former involve changes in the nearest-neighbor coordination of at least one atom, and the latter do not. With increasing pressure the barrier heights for cage-breaking rearrangements rise, while those for cage-preserving rearrangements appear relatively unchanged. The “strong” or “fragile” character of the syste... read less NOT USED (high confidence) T. Itami et al., “Structure of liquid Sn over a wide temperature range from neutron scattering experiments and first-principles molecular dynamics simulation : A comparison to liquid Pb,” Physical Review B. 2003. link Times cited: 74 Abstract: The structure of liquid Sn was studied by neutron scattering… read moreAbstract: The structure of liquid Sn was studied by neutron scattering experiments in the widest temperature range that was ever performed. Though, on increasing temperature, the existence of the shoulder in the structure factor, $S(Q),$ becomes less clear in the change of the overall shape of the $S(Q),$ the structure related to this shoulder seems to be present even at 1873 K. The first-principle molecular-dynamics (FPMD) simulation was performed for the first time for liquid Sn by using the cell size of 64 particles. The calculated results well reproduced $S(Q)$ obtained by the neutron experiments. The angle distribution, ${g}^{(3)}(\ensuremath{\theta}{,r}_{c}),$ was evaluated for the angle between vectors from centered atom to other two atoms in spheres of cutoff radii ${r}_{c}\mathrm{'}\mathrm{s}.$ The ${g}^{(3)}(\ensuremath{\theta}{,r}_{c})$ shows that, with the decrease of ${r}_{c}$ from 0.4 to 0.3 nm, a rather sharp peak around 60 \ifmmode^\circ\else\textdegree\fi{} disappears and only a broad peak around 100 \ifmmode^\circ\else\textdegree\fi{} remains; the former peak may be derived from the feature of the closely packed structures and the latter one is close to the tetrahedral angle of 109 \ifmmode^\circ\else\textdegree\fi{}. In addition, the coordination number, n, of liquid Sn counted within the sphere of ${r}_{c}=0.3\mathrm{nm}$ is found to be 2--3 and does not change with the increase of temperature even up to 1873 K. These facts indicate that at least the fragment of the tetrahedral unit may be essentially kept even at 1873 K for liquid Sn. For comparison, the FPMD simulation was performed for the first time also for liquid Pb. No sign of the existence of the tetrahedral structure was observed for liquid Pb. Unfortunately, the self-diffusion coefficients, $D\mathrm{'}\mathrm{s},$ obtained from this FPMD for liquid Sn do not agree with those obtained by the microgravity experiments though the structure factors, $S(Q)\mathrm{'}\mathrm{s},$ are well reproduced. To remove the limitation of the small cell size of the FPMD, the classical molecular-dynamics simulations with a cell size of 2197 particles were performed by incorporating the present experimental structural information of liquid Sn. Obtained $D\mathrm{'}\mathrm{s}$ are in good agreement with the microgravity data. read less NOT USED (high confidence) F. Valiquette and N. Mousseau, “Energy landscape of relaxed amorphous silicon,” Physical Review B. 2003. link Times cited: 25 Abstract: We analyze the structure of the energy landscape of a well-r… read moreAbstract: We analyze the structure of the energy landscape of a well-relaxed 1000-atom model of amorphous silicon using the activation-relaxation technique ! ART nouveau" . Generating more than 40000 events starting from a single minimum, we find that activated mechanisms are local in nature, that they are distributed uniformly throughout the model, and that the activation energy is limited by the cost of breaking one bond, independently of the complexity of the mechanism. The overall shape of the activation-energy-barrier distribution is also insensitive to the exact details of the configuration, indicating that well-relaxed configurations see essentially the same environment. These results underscore the localized nature of relaxation in this material. read less NOT USED (high confidence) W. Cai, V. V. Bulatob, J. Chang, J. Li, and S. Yip, “Periodic image effects in dislocation modelling,” Philosophical Magazine. 2003. link Times cited: 181 Abstract: The use of periodic boundary conditions for modelling crysta… read moreAbstract: The use of periodic boundary conditions for modelling crystal dislocations is predicated on one's ability to handle the inevitable image effects. This communication deals with an often overlooked mathematical subtlety involved in dealing with the periodic dislocation arrays, that is conditional convergence of the lattice sums of image fields. By analysing the origin of conditional convergence and the numerical artefacts associated with it, we establish a mathematically consistent and numerically efficient procedure for regularization of the lattice sums and the corresponding image fields. The regularized solutions are free from the artefacts caused by conditional convergence and regain periodicity and translational invariance of the periodic supercells. Unlike the other existing methods, our approach is applicable to general anisotropic elasticity and arbitrary dislocation arrangements. The capabilities of this general methodology are demonstrated by application to a variety of situations encountered in atomistic and continuum modelling of crystal dislocations. The applications include introduction of dislocations in the periodic supercell for subsequent atomistic simulations, atomistic calculations of the core energies and the Peierls stress and continuum dislocation dynamics simulations in three dimensions. read less NOT USED (high confidence) U. Kaiser, J. Biskupek, and K. Gärtner, “’Magic-size’ GeSi and Si nanocrystals created by ion bombardment of hexagonal SiC; a molecular dynamics study,” Philosophical Magazine Letters. 2003. link Times cited: 5 Abstract: We recently showed that GeSi and Si nanocrystals created aft… read moreAbstract: We recently showed that GeSi and Si nanocrystals created after Ge- and Si-ion implantation into hexagonal SiC and subsequent annealing contain a high percentage of hexagonality. Here we demonstrate that the nanocrystals are of 'magic sizes' and are microtwinned. Both these features are explained by molecular dynamics calculations. read less NOT USED (high confidence) G. Liu, H. Zhuang, J. Beitz, C. Williams, and V. Vikhnin, “Structure and charge transfer dynamics of uranyl ions in boron oxide and borosilicate glasses,” Physics of the Solid State. 2002. link Times cited: 11 NOT USED (high confidence) T. Kakinaga, N. Baba, O. Tabata, Y. Isono, K. H. Ehrmann, and J. Korvink, “Simulator for observing the Si anisotropic chemical etching process in atomic scale,” Proceedings of 2002 International Symposium on Micromechatronics and Human Science. 2002. link Times cited: 0 Abstract: We propose a new concept of anisotropic silicon (Si) etching… read moreAbstract: We propose a new concept of anisotropic silicon (Si) etching simulation approach by combining three calculation modules, a molecular dynamics calculation module to define chemical reaction probability, a cellular-automata module to calculate etching rate, and Wulff-Jaccodine graphical method module to predict an etched shape. This configuration allows mm scale device simulation based on the atomic scale physical chemistry of anisotropic Si etching. In this paper, the performance of a newly developed cellular-automata module called CAES is presented as a first step towards the realization of our simulation concept. read less NOT USED (high confidence) S. Franz, “How glasses explore configuration space,” Journal of Physics: Condensed Matter. 2002. link Times cited: 3 Abstract: We review a statistical picture of the glassy state derived … read moreAbstract: We review a statistical picture of the glassy state derived from the analysis of the off-equilibrium fluctuation-dissipation relations. We define an ultralong-time limit where 'one-time quantities' are close to equilibrium while the response and correlation can still display ageing. In this limit it is possible to relate the fluctuation response relation to static breaking of ergodicity. The resulting picture suggests that even far from that limit, the fluctuation-dissipation ratio relates to the rate of growth of the configurational entropy with the free-energy density. read less NOT USED (high confidence) R. E. Miller and E. Tadmor, “The Quasicontinuum Method: Overview, applications and current directions,” Journal of Computer-Aided Materials Design. 2002. link Times cited: 479 NOT USED (high confidence) A. Satta, E. Pisanu, L. Colombo, and F. Cleri, “Microstructure evolution at a triple junction in polycrystalline silicon,” Journal of Physics: Condensed Matter. 2002. link Times cited: 7 Abstract: We studied two elementary microstructure evolution events ta… read moreAbstract: We studied two elementary microstructure evolution events taking place at a multiple-twin triple junction (TJ) in Si by means of molecular dynamics simulations with the Stillinger–Weber empirical potential. Starting from a relaxed configuration, we inserted a fourth grain in the TJ location and determined the critical radius and the instability mode by which the central grain disappears by progressively shrinking. In a second set of simulations, we introduced a microcrack in the grain boundary plane and made it advance towards the TJ under the effect of the external loading. A kind of brittle–ductile transition is observed when the fracture changes from intergranular to intragranular. read less NOT USED (high confidence) J. Goss et al., “Planar interstitial aggregates in Si,” Journal of Physics: Condensed Matter. 2002. link Times cited: 20 Abstract: Self-interstitials in silicon aggregate to form rod-like def… read moreAbstract: Self-interstitials in silicon aggregate to form rod-like defects aligned along [110] directions and inhabiting either {111} or {113} crystallographic planes. These systems are known to be electrically and optically active. We present the results of first-principles calculations on the structure and energetics for candidate structures contained within the {113}, {111} and {001} planes and compare the results with experiment. read less NOT USED (high confidence) A. Barnard, S. Russo, and I. Snook, “Comparative Hartree-Fock and density-functional theory study of cubic and hexagonal diamond,” Philosophical Magazine B. 2002. link Times cited: 27 Abstract: An analysis of the electronic properties of bulk cubic and h… read moreAbstract: An analysis of the electronic properties of bulk cubic and hexagonal diamond calculated using the ab initio packages CRYSTAL98 and the Vienna Ab initio Simulation Package is presented. We apply these ab initio methods to the study of cubic diamond, including the calculation of electronic properties (such as the band structure, electronic density of states, the indirect bandgap E indirect g, the valence band width and the conduction band width) and mechanical properties (such as the equilibrium lattice constant a 0 and the bulk modulus B). The combination of theoretical techniques that yield results that most accurately match experiment for cubic diamond are then used to calculate the electronic properties of the hexagonal diamond polymorph. read less NOT USED (high confidence) M. Tadic, F. Peeters, K. Janssens, M. Korkusinski, and P. Hawrylak, “Strain and band edges in single and coupled cylindrical InAs/GaAs and InP/InGaP self-assembled quantum dots,” Journal of Applied Physics. 2002. link Times cited: 72 Abstract: A comparative study is made of the strain distribution in cy… read moreAbstract: A comparative study is made of the strain distribution in cylindrical InAs/GaAs and InP/InGaP self-assembled quantum dots as obtained from isotropic elasticity theory, the anisotropic continuum mechanical model, and from atomistic calculations. For the isotropic case, the recently proposed approach [J. H. Davies, J. Appl. Phys. 84, 1358 (1998)] is used, while the finite-element method, the valence force field method, and Stillinger–Weber potentials are employed to calculate the strain in anisotropic structures. We found that all four methods result in strain distributions of similar shapes, but with notable quantitative differences inside the dot and near the disk–matrix boundary. The variations of the diagonal strains with the height of the quantum dot, with fixed radius, as calculated from all models, are almost linear. Furthermore, the energies of the band edges in the two types of quantum dots are extracted from the multiband effective-mass theory by inserting the strain distributions as obtained by t... read less NOT USED (high confidence) R. W. Hall and P. Wolynes, “Microscopic theory of network glasses.,” Physical review letters. 2002. link Times cited: 27 Abstract: A theory of the glass transition of network liquids is devel… read moreAbstract: A theory of the glass transition of network liquids is developed using self-consistent phonon and liquid state approaches. The dynamical transition and entropy crisis characteristic of random first-order transitions are mapped as a function of the degree of bonding and density. Using a scaling relation for a soft-core model to crudely translate the densities into temperatures, theory predicts that the ratio of the dynamical transition temperature to the laboratory transition temperature rises as the degree of bonding increases, while the Kauzmann temperature falls explaining why highly coordinated liquids are "strong" while van der Waals liquids without coordination are "fragile." read less NOT USED (high confidence) J. Godet, L. Pizzagalli, S. Brochard, and P. Beauchamp, “Surface step effects on Si (100) under uniaxial tensile stress, by atomistic calculations,” Scripta Materialia. 2002. link Times cited: 13 NOT USED (high confidence) S. W. Ellaway and D. Faux, “Effective elastic stiffnesses of InAs under uniform strain,” Journal of Applied Physics. 2002. link Times cited: 41 Abstract: The effective elastic stiffnesses C11, C12 and C44 of InAs a… read moreAbstract: The effective elastic stiffnesses C11, C12 and C44 of InAs and derived elastic constants are determined for states of uniform volumetric strain by atomistic simulation. The effective elastic stiffnesses C11 and C12 are found to increase significantly with strain whereas C44 is found to be nearly independent of strain. Results for the bulk modulus are consistent with high-pressure experiments and nonlinear elasticity theories. The effective Young’s modulus is found to be nearly independent of strain whereas the effective Poisson’s ratio increases by about 40% over the range 0%–20% volumetric strain. The use of effective elastic stiffnesses within the isotropic approximation leads to a hydrostatic strain for an InAs quantum dot which is 16% smaller than the uncorrected value. It is concluded that continuum techniques for calculating quantum-dot-induced strain in the InAs/GaAs system should include strain-dependent InAs elastic stiffnesses for maximum accuracy. read less NOT USED (high confidence) L. Wang, P. Clancy, M. Thompson, and C. Murthy, “Thermodynamic and kinetic studies of laser thermal processing of heavily boron-doped amorphous silicon using molecular dynamics,” Journal of Applied Physics. 2002. link Times cited: 14 Abstract: Laser thermal processing (LTP) has been proposed as a means … read moreAbstract: Laser thermal processing (LTP) has been proposed as a means to avoid unwanted transient enhanced diffusion and deactivation of dopants, especially boron and arsenic, during the formation of ultrashallow junctions. Although experimental studies have been carried out to determine the efficacy of LTP for pure Si and lightly B-doped junctions, the effects of high concentrations of dopants (above 2% B) on the thermodynamic and kinetic properties of the regrown film are unknown. In this study, a classical interatomic potential model [Stillinger–Weber (SW)] is used with a nonequilibrium molecular dynamics computer simulation technique to study the laser thermal processing of heavily B-doped Si in the range 2–10 at. % B. We observe only a small effect of boron concentration on the congruent melting temperature of the B:Si alloy, and thus the narrowing of the “process window” for LTP is predicted to be small. No significant tendency for boron to segregate was observed at either the regrowth front or the buried c-Si interface during fast regrowth. The B-doped region regrew as defect-free crystal with full activation of the boron atoms at low boron concentrations (2%), in good agreement with experiments. As the concentration of boron increased, the number of intrinsic Si defects and boron interstitials in the regrown materials increased, with a minor amount of boron atoms in clusters ( 150 ps, compared to 5 ps in tight binding). The importance of adequate system size is discussed. read less NOT USED (high confidence) S. Nakhmanson, D. A. Drabold, and N. Mousseau, “Comment on ‘Boson peak in amorphous silicon: A numerical study,’” Physical Review B. 2002. link Times cited: 4 Abstract: (Dated: July 27, 2001) Based on molecular-dynamics simulatio… read moreAbstract: (Dated: July 27, 2001) Based on molecular-dynamics simulations using the Stillinger-Weber interatomic potential, Finkemeier and von Niessen recently proposed that the presence of the Boson peak in a–Si can be attributed to coordination defects [Phys. Rev. B 63, 235204 (2001)] and claimed agreement with earlier simulation results for models of a–Si with voids [Phys. Rev. B 61, 5376 (2000)]. In this Comment we clarify this issue and suggest that (i) the atomistic models of Finkemeier and von Niessen do not represent realistic amorphous silicon and (ii) the results for the models with voids do not support the hypothesis that coordination defects are the main cause of the appearance of the Boson peak in this material. read less NOT USED (high confidence) A. S. Barnard, S. Russo, and G. Leach, “Nearest neighbour considerations in Stillinger-Weber type potentials for diamond,” Molecular Simulation. 2002. link Times cited: 5 Abstract: Results of a preliminary investigation into the effect of va… read moreAbstract: Results of a preliminary investigation into the effect of varying the interaction cutoff on the bulk properties of diamond using a Stillinger-Weber (SW) type potential for C (Diamond) are presented. The interaction cutoff is varied over a range that includes and excludes the second-nearest neighbours. Whilst the original SW potential for silicon only included first-nearest neighbours inside the interaction cut-off, subsequent parameterizations for carbon (diamond) have also included second-nearest neighbours. Elastic and vibration properties of diamond were calculated over a range of cutoff distances used and the results show that certain lattice properties exhibit an approximately linear dependence on the interaction cut-off. read less NOT USED (high confidence) C. Rountree, R. Kalia, E. Lidorikis, A. Nakano, L. Brutzel, and P. Vashishta, “ATOMISTIC ASPECTS OF CRACK PROPAGATION IN BRITTLE MATERIALS: Multimillion Atom Molecular Dynamics Simulations,” Annual Review of Materials Research. 2002. link Times cited: 173 Abstract: ▪ Abstract Atomistic aspects of dynamic fracture in a variet… read moreAbstract: ▪ Abstract Atomistic aspects of dynamic fracture in a variety of brittle crystalline, amorphous, nanophase, and nanocomposite materials are reviewed. Molecular dynamics (MD) simulations, ranging from a million to 1.5 billion atoms, are performed on massively parallel computers using highly efficient multiresolution algorithms. These simulations shed new light on (a) branching, deflection, and arrest of cracks; (b) growth of nanoscale pores ahead of the crack and how pores coalesce with the crack to cause fracture; and (c) the influence of these mechanisms on the morphology of fracture surfaces. Recent advances in novel multiscale simulation schemes combining quantum mechanical, molecular dynamics, and finite-element approaches and the use of these hybrid approaches in the study of crack propagation are also discussed. read less NOT USED (high confidence) D. Alfé, M. Sciences, U. D. O. Physics, Astronomy, and U. C. London, “Exchange-correlation energy and the phase diagram of Si,” Physical Review B. 2002. link Times cited: 32 Abstract: Previous first-principles calculations of the melting proper… read moreAbstract: Previous first-principles calculations of the melting properties of Si, based on the local-density approximation (LDA) for electronic exchange-correlation energy, underpredict the melting temperature by $\ensuremath{\sim}20$ %. We present new first-principles results indicating that a large part of this problem is due to noncancellation of exchange-correlation errors between the semiconducting solid and the metallic liquid. It is shown that other sources of error, particularly those due to system size and Brillouin-zone sampling, can be made negligible. The same LDA errors cause an underprediction of the pressure of the diamond-Si $\ensuremath{\rightarrow}$ beta-tin-Si transition. The generalized-gradient approximation considerably improves both features of the Si phase diagram. read less NOT USED (high confidence) S. Nakhmanson and N. Mousseau, “Crystallization study of model tetrahedral semiconductors,” Journal of Physics: Condensed Matter. 2002. link Times cited: 13 Abstract: The microscopic mechanisms leading to crystallization are no… read moreAbstract: The microscopic mechanisms leading to crystallization are not yet fully understood. This is due, in part, to the lack of atomistic as well as interatomic interaction models for a wide range of materials that can lead to crystallization on a computer-simulation timescale, i.e. < 100 ns. While the nucleation in close-packed systems has been extensively studied, there are almost no numerical results for covalent tetrahedral semiconductors. We present here the simulation results of crystallization from the liquid and amorphous states of a 1000-atom model of silicon, described with a modified Stillinger?Weber potential. With this potential, it is possible to crystallize the model in as little as a few nanoseconds, which opens a door to detailed studies of the nucleation processes in covalent systems. Using topological analysis, we also present a first characterization of the structural fluctuations of the nucleation centres in this system and give a rough estimate for the critical size of these centres. read less NOT USED (high confidence) J.-D. Chai, D. Stroud, J. Hafner, and G. Kresse, “Dynamic structure factor of liquid and amorphous Ge from ab initio simulations,” Physical Review B. 2002. link Times cited: 28 Abstract: We calculate the dynamic structure factor $S(k,\ensuremath{\… read moreAbstract: We calculate the dynamic structure factor $S(k,\ensuremath{\omega})$ of liquid Ge $(l$-Ge) at temperature $T=1250\mathrm{}\mathrm{K},$ and of amorphous Ge $(a$-Ge) at $T=300\mathrm{K},$ using ab initio molecular dynamics. The electronic energy is computed using density-functional theory, primarily in the generalized gradient approximation, together with a plane-wave representation of the wave functions and ultrasoft pseudopotentials. We use a 64-atom cell with periodic boundary conditions, and calculate averages over runs of up to about 16 ps. The calculated liquid $S(k,\ensuremath{\omega})$ agrees qualitatively with that obtained by Hosokawa et al. [Phys. Rev. B 63, 134205 (2001)] using inelastic x-ray scattering. In a-Ge, we find that the calculated $S(k,\ensuremath{\omega})$ is in qualitative agreement with that obtained experimentally by Maley et al. [Phys. Rev. Lett. 56, 1720 (1986)]. Our results suggest that the ab initio approach is sufficient to allow approximate calculations of $S(k,\ensuremath{\omega})$ in both liquid and amorphous materials. read less NOT USED (high confidence) N. Gayathri, S. Izvekov, and G. Voth, “Ab initio molecular dynamics simulation of the H/InP(100)–water interface,” Journal of Chemical Physics. 2002. link Times cited: 13 Abstract: A first principles simulation study of the H-terminated InP(… read moreAbstract: A first principles simulation study of the H-terminated InP(100)–water interface is presented with an aim to understand the electronic structure of the interface. The simulation has been carried out using the ab initio Car–Parrinello molecular dynamics method within a pseudopotential formalism and the Becke–Lee–Yang–Parr generalized gradient approximation to the exchange-correlation potential. Dissociative adsorption of H2O molecules onto H/InP(100) surfaces, leading to formation of In–OH and In–H bonds on the (100) surface, occurs at the interface, in a manner similar to the experimentally demonstrated dissociative adsorption of H2O onto n-InP(110) surface. This process indicates a very strong coupling between the semiconductor and the water states. Also, simulation carried out for two H/InP(100) surfaces reveal that more H2O dissociations occur near the rougher atomically corrugated surface, in accordance with observations from experimental studies designed to determine the morphological influences on H... read less NOT USED (high confidence) A. Barnard and S. Russo, “Development of an improved Stillinger-Weber potential for tetrahedral carbon using ab initio (Hartree-Fock and MP2) methods,” Molecular Physics. 2002. link Times cited: 28 Abstract: An improved interatomic potential for tetrahedral carbon is … read moreAbstract: An improved interatomic potential for tetrahedral carbon is presented. This potential is of the Stillinger-Weber (SW) type and has been determined from calculations performed on a select group of small hydrocarbon molecules, chosen for their similarities to the tetrahedral lattice of bulk diamond. Counterpoise corrected Hartree-Fock (HF) and second-order Møller-Plesset perturbation theory (MP2) calculations were performed on ethane, 2,2-dimethylpropane (neo-pentane, (C5H12), 2-dimethyl-3-dimethylbutane (neobutane, C8H18) and cyclohexane (C6H12) in order to determine the two-body (stretching) and three-body (bond bending) energies. The suitability of these molecules to model the properties of diamond was determined by comparison of CC bond length, well depth, CCC bond angle, simultaneous stretch and bend energy and force constants to those of bulk diamond. It was found that neopentane provided the best overall description of tetrahedral bonded carbon. The ab initio derived stretch and bend energies were fitted to the SW potential energy terms and the SW parameters calculated. The newly parametrized SW potential was then evaluated by calculating the stretch force constants, elastic constants and the X-point phonon modes of bulk diamond. read less NOT USED (high confidence) M. Kohyama, “TOPICAL REVIEW: Computational studies of grain boundaries in covalent materials,” Modelling and Simulation in Materials Science and Engineering. 2002. link Times cited: 74 Abstract: Computational studies of energetics, atomic and electronic s… read moreAbstract: Computational studies of energetics, atomic and electronic structures and various properties of grain boundaries in covalent materials such as semiconductors and covalent ceramics are reviewed. For coincidence tilt boundaries, atomic and electronic structures were investigated intensively by using various computational schemes such as many-body interatomic potentials, tight-binding method and first-principles method. Computational results were compared with experimental results using recent novel techniques of electron microscopy such as high-resolution transmission electron microscopy, atomic-resolution Z-contrast imaging and electron energy-loss spectroscopy. Such collaboration clarified the detailed nature of coincidence tilt boundaries constructed by structural units. The behaviour of dopants at semiconductor grain boundaries was also investigated by such collaboration. Computations of twist boundaries provided insight into the nature of disordered configurations at general grain boundaries, which should strongly affect the properties of polycrystalline semiconductors and structural ceramics. Recent computational studies dealt with the basic mechanical properties of grain boundaries in covalent materials, where the behaviour of interfacial bonds plays an essential role. read less NOT USED (high confidence) T. Frauenheim et al., “Atomistic simulations of complex materials: ground-state and excited-state properties,” Journal of Physics: Condensed Matter. 2002. link Times cited: 456 Abstract: The present status of development of the density-functional-… read moreAbstract: The present status of development of the density-functional-based tightbinding (DFTB) method is reviewed. As a two-centre approach to densityfunctional theory (DFT), it combines computational efficiency with reliability and transferability. Utilizing a minimal-basis representation of Kohn–Sham eigenstates and a superposition of optimized neutral-atom potentials and related charge densities for constructing the effective many-atom potential, all integrals are calculated within DFT. Self-consistency is included at the level of Mulliken charges rather than by self-consistently iterating electronic spin densities and effective potentials. Excited-state properties are accessible within the linear response approach to time-dependent (TD) DFT. The coupling of electronic and ionic degrees of freedom further allows us to follow the non-adiabatic structure evolution via coupled electron–ion molecular dynamics in energetic particle collisions and in the presence of ultrashort intense laser pulses. We either briefly outline or give references describing examples of applications to ground-state and excited-state properties. Addressing the scaling problems in size and time generally and for biomolecular systems in particular, we describe the implementation of the parallel ‘divide-and-conquer’ order-N method with DFTB and the coupling of the DFTB approach as a quantum method with molecular mechanics force fields. read less NOT USED (high confidence) G. Ackland, “Calculation of free energies from ab initio calculation,” Journal of Physics: Condensed Matter. 2002. link Times cited: 51 Abstract: The calculation of total energy from electronic structure is… read moreAbstract: The calculation of total energy from electronic structure is now well established, and recent interest has moved to evaluation of free energies and equations of state. This paper discusses various methods for evaluating free energies, for equilibrium phases, for reaction pathways and for phase transformations. read less NOT USED (high confidence) C. Angell, S. D. S. University, and S. C. College, “Specific heats Cp, Cv, Cconf and energy landscapes of glassforming liquids,” Journal of Non-crystalline Solids. 2002. link Times cited: 80 NOT USED (high confidence) N. Mousseau and G. Barkema, “Fast bond-transposition algorithms for generating covalent amorphous structures,” Current Opinion in Solid State & Materials Science. 2001. link Times cited: 8 NOT USED (high confidence) R. Komanduri, N. Chandrasekaran, and L. Raff, “Molecular dynamics simulation of the nanometric cutting of silicon,” Philosophical Magazine B. 2001. link Times cited: 139 Abstract: Molecular dynamics simulations of nanometric cutting of sing… read moreAbstract: Molecular dynamics simulations of nanometric cutting of single-crystal, defect-free, pure silicon were performed using the Tersoff potential over a wide range of rake angles (from -60° to +60°), widths of cut (1.1 to 4.34 ran), depths of cut (0.01 to 2.72 nm) and clearance angles (10° to 30°) to hwestigate the nature of material removal and surface generation process in ultraprecision machining and grinding. The observed material removal mechanisms can be divided into four components: (i) compression of the work material ahead of the tool; (ii) chip formation akin to an extrusion-like process; (iii) side flow; and (iv) subsurface deformation in the machined surface. Unlike in conventional machining of most ductile materials, where no volume or phase change is observed in the plastic deformation process, significant volume changes (from 18.38 to 14.19Å3), resulting in a densification of about 23% occur owing to phase transition from a diamond cubic (or α-silicon) to a bet (or β-tin structure) in the case of machining silicon. Such a structural change is typical of silicon undergoing a pressure-induced phase transformation. The extent of structural changes and their contributions to each of the four material removal mechanisms depend on the tool rake angle and the width of cut. The ratio of the width of cut to depth of cut w/d is the primary factor affecting the extent of side flow and subsurface compression. The tool rake angle and the w/d ratio are found to be dominant factors affecting the chip flow and shear zone compression ahead of the tool. Subsurface or near-surface deformation was observed with all rake angles and all cut depths down to 0.01 nm, indicating the need for an alternate final polishing process such as chemomechanical polishing to produce defect-free surfaces of silicon on an atomie scale. read less NOT USED (high confidence) A. Béré and A. Serra, “Atomic Structure of [0001] Tilt Boundaries in GaN,” Interface Science. 2001. link Times cited: 10 NOT USED (high confidence) P. Voyles et al., “Structure and physical properties of paracrystalline atomistic models of amorphous silicon,” Journal of Applied Physics. 2001. link Times cited: 85 Abstract: We have examined the structure and physical properties of pa… read moreAbstract: We have examined the structure and physical properties of paracrystalline molecular dynamics models of amorphous silicon. Simulations from these models show qualitative agreement with the results of recent mesoscale fluctuation electron microscopy experiments on amorphous silicon and germanium. Such agreement is not found in simulations from continuous random network models. The paracrystalline models consist of topologically crystalline grains which are strongly strained and a disordered matrix between them. We present extensive structural and topological characterization of the medium range order present in the paracrystalline models and examine their physical properties, such as the vibrational density of states, Raman spectra, and electron density of states. We show by direct simulation that the ratio of the transverse acoustic mode to transverse optical mode intensities ITA/ITO in the vibrational density of states and the Raman spectrum can provide a measure of medium range order. In general, we conc... read less NOT USED (high confidence) R. Rudd, “The Atomic Limit of Finite Element Modeling in MEMS: Coupling of Length Scales,” Analog Integrated Circuits and Signal Processing. 2001. link Times cited: 18 NOT USED (high confidence) H. Ohta and S. Hamaguchi, “Molecular dynamics simulation of silicon and silicon dioxide etching by energetic halogen beams,” Journal of Vacuum Science and Technology. 2001. link Times cited: 89 Abstract: Molecular dynamics simulations of silicon (Si) and silicon d… read moreAbstract: Molecular dynamics simulations of silicon (Si) and silicon dioxide (SiO2) etching by energetic halogen (fluorine or chlorine) atoms in the energy range of 50–150 eV are performed using new sets of interatomic potentials for Si–O–F and Si–O–Cl systems. Etch rates and selectivities obtained from numerical simulations are compared with available experimental data. Etching mechanisms in the atomic scale, especially the difference between chlorine and fluorine direct ion etching characteristics, are discussed on the basis of the simulation results. read less NOT USED (high confidence) S. Ogata, E. Lidorikis, F. Shimojo, A. Nakano, P. Vashishta, and R. Kalia, “Hybrid finite-element/molecular-dynamics/electronic-density-functional approach to materials simulations on parallel computers,” Computer Physics Communications. 2001. link Times cited: 142 NOT USED (high confidence) R. Fournier, “Theoretical study of the structure of silver clusters,” Journal of Chemical Physics. 2001. link Times cited: 237 Abstract: Neutral silver cluster isomers Agn (n=2 to 12) were studied … read moreAbstract: Neutral silver cluster isomers Agn (n=2 to 12) were studied by Kohn–Sham density functional theory. There is a strong even-odd oscillation in cluster stability due to spin subshell closing. Nearest-neighbor interatomic distances do not evolve continuously from the diatomic (2.53 A) to the bulk (2.89 A). After adding an empirical correction to the calculated values, we estimate that they are always near 2.68 A for 3⩽n⩽6, and near 2.74 A for 7⩽n⩽12. We find several low-energy isomers at all cluster sizes larger than seven atoms with one exception: Ag10 has a D2d twinned pentagonal bipyramid isomer predicted to be 0.20 eV more stable than any other isomer. The ellipsoidal jellium model predicts rather well the shapes of stable silver clusters. Other models (extended Huckel, empirical potential) fail to reproduce the energy ordering of cluster isomers. The structural attributes of low-energy silver cluster isomers Agn (n⩾7) are, in decreasing order of importance: a high mean coordination; a shape that conform... read less NOT USED (high confidence) F. Giessibl, H. Bielefeldt, S. Hembacher, and J. Mannhart, “Imaging of atomic orbitals with the Atomic Force Microscope — experiments and simulations,” Annalen der Physik. 2001. link Times cited: 51 Abstract: Atomic force microscopy (AFM) is a mechanical profiling tech… read moreAbstract: Atomic force microscopy (AFM) is a mechanical profiling technique that allows to image surfaces with atomic resolution. Recent progress in reducing the noise of this technique has led to a resolution level where previously undetectable symmetries of the images of single atoms are observed. These symmetries are related to the nature of the interatomic forces. The Si(111)‐(7 × 7) surface is studied by AFM with various tips and AFM images are simulated with chemical and electrostatic model forces. The calculation of images from the tip‐sample forces is explained in detail and the implications of the imaging parameters are discussed. Because the structure of the Si(111)‐(7 × 7) surface is known very well, the shape of the adatom images is used to determine the tip structure. The observability of atomic orbitals by AFM and scanning tunneling microscopy is discussed. read less NOT USED (high confidence) J. M. Stallons and E. Iglesia, “Simulations of the structure and properties of amorphous silica surfaces,” Chemical Engineering Science. 2001. link Times cited: 36 NOT USED (high confidence) C. N. Likos, “EFFECTIVE INTERACTIONS IN SOFT CONDENSED MATTER PHYSICS,” Physics Reports. 2001. link Times cited: 859 NOT USED (high confidence) D. Belashchenko and O. Ostrovski, “Molecular dynamics simulation of oxides with ionic–covalent bonds,” Thermochimica Acta. 2001. link Times cited: 16 NOT USED (high confidence) V. Bulatov et al., “Parameter-free modelling of dislocation motion: The case of silicon,” Philosophical Magazine A. 2001. link Times cited: 69 Abstract: In silicon and other materials with a high Peierls potential… read moreAbstract: In silicon and other materials with a high Peierls potential. dislocation motion takes place by nucleation and propagation of kink pairs. The rates of these unit processes are complex unknown functions of interatomic interactions in the dislocation core, stress and temperature. This work is an attempt to develop a quantitative physical description of dislocation motion in silicon based on understanding of the core structure and the energetics of core mechanisms of mobility. Atomistic simulations reveal multiple and complex kink mechanisms of dislocation translation; however, this complexity can be rationalized through the analysis of a straight kink-free dislocation, based on symmetry-breaking arguments. Further reduction is achieved by observing that the energetics of kink mechanisms is scaled by a single parameter, the energy required to break a bond in the core. To obtain accurate values of this energy we perform density functional calculations that lead us to conclude that the low mobility of the 30° dislocation results from its high bond-breaking energy. Armed with the knowledge of kink mechanisms, we develop a kinetic Monte Carlo model that makes direct use of the atomistic data as the material-defining input and predicts the dislocation velocity on the length and time scales accessible to experiments. This provides the connection between the atomistic aspects of the dislocation core and the mobility behaviour of single dislocations. read less NOT USED (high confidence) A. Chatterjee, T. Iwasaki, and T. Ebina, “Structural And Energetic Changes of Si (100) Surface With Fluorine in Presence of Water - A Density Functional Study,” International Journal of Molecular Sciences. 2001. link Times cited: 7 Abstract: Abstract: We report density functional electronic structure … read moreAbstract: Abstract: We report density functional electronic structure calculations to monitor thechange in the surface characteristics of the Si (100)-2x1 surface after fluorination followedby interaction with water. Embedded finite silicon clusters are used to model an extended Si(100)-2x1 surface. Two high symmetry pathways and subsequent adsorption sites wereexamined: (i) adsorption of an fluorine atom directing onto a silicon dangling bond to form amonocoordinated fluorine atom (ii) adsorption of a fluorine atom directing on top of silicondimer to form a bridging dicoordinated fluorine atom. However, in the later case we findthat no barrier exists for the bridging fluorine atom to slide towards silicon dimer danglingbond to form more stable mono coordinated Si-F bond. We calculated activation barriersand equilibrium surface configuration as a function of fluorine coverage upto 2.0 ML. Wecompared the stability of the fluorinated surface. The results were compared with existingexperimental and theoretical results. The reaction of water with HF treated Si surface ismonitored. It produces, as a first step, the exchange of Si-F with water to form Si-OHgroups reducing the concentration of the fluorine on the surface, followed by a rapture of Si-Si bonds and finally the Si-O-Si bridge formation in the lattice. read less NOT USED (high confidence) P. Pirouz, J. Demenet, and M. Hong, “On transition temperatures in the plasticity and fracture of semiconductors,” Philosophical Magazine A. 2001. link Times cited: 111 Abstract: Recent experiments on deformation of semiconductors show an … read moreAbstract: Recent experiments on deformation of semiconductors show an abrupt change in the variation in the critical resolved shear stress τY with temperature T. This implies a change in the deformation mechanism at a critical temperature T c. In the cases examined so far in our laboratories (Case Western Reserve University and Poitiers) and elsewhere, this critical temperature appears to coincide approximately with the brittle-to-ductile transition temperature T BDT. In this paper, new deformation experiments performed on the wide-bandgap semiconductor 4H-SiC over a range of temperatures at two strain rates are described together with a transmission electron microscopy characterization of induced dislocations below and above T c. Based on these, and results recently reported on a few III–V compound semiconductors, a new model for the deformation of tetrahedrally coordinated materials at low and high temperatures is proposed, and the relation of the transition in deformation mode to the transition in fracture mode (brittle to ductile) is discussed. read less NOT USED (high confidence) R. Rudd, “Concurrent Multiscale Modeling of Embedded Nanomechanics,” MRS Proceedings. 2001. link Times cited: 13 Abstract: We discuss concurrent multiscale simulations of dynamic and … read moreAbstract: We discuss concurrent multiscale simulations of dynamic and temperature-dependent processes found in nanomechanical systems coupled to larger scale surroundings. We focus on the behavior of sub-micron Micro-Electro-Mechanical Systems (MEMS), especially micro-resonators. The coupling of length scales methodology we have developed for MEMS employs an atomistic description of small but key regions of the system, consisting of millions of atoms, coupled concurrently to a finite element model of the periphery. The result is a model that accurately describes the behavior of the mechanical components of MEMS down to the atomic scale. This paper reviews some of the general issues involved in concurrent multiscale simulation, extends the methodology to metallic systems and describes how it has been used to identify atomistic effects in sub-micron resonators. read less NOT USED (high confidence) G. Barkema and N. Mousseau, “The activation–relaxation technique: an efficient algorithm for sampling energy landscapes,” Computational Materials Science. 2001. link Times cited: 39 NOT USED (high confidence) M. Mäki-Jaskari, “Simulations of strain relief at the crack tip in silicon,” Journal of Physics: Condensed Matter. 2001. link Times cited: 1 Abstract: The mechanism of strain relief for a tensile strained diamon… read moreAbstract: The mechanism of strain relief for a tensile strained diamond-structure silicon-atom system containing an initial cut is considered theoretically. Molecular dynamics and molecular mechanics simulations were employed as simulation methods. Loading under finite-temperature conditions starts cleavage crack initiation. Simulations made using tight-binding density functional molecular dynamics favour the traditional mechanism of brittle crack initiation. In this process, bonds are broken entirely at the tip of the cut. Under specific conditions, molecular dynamics simulation can lead to the formation of new stable structures. This transformation is associated with bond switching. The results for the bond-bending force from the energy models are compared and its influence on the results of the simulations is discussed. read less NOT USED (high confidence) S. Izvekov, A. Mazzolo, K. VanOpdorp, and G. Voth, “Ab initio molecular dynamics simulation of the Cu(110)–water interface,” Journal of Chemical Physics. 2001. link Times cited: 72 Abstract: The results of a first principles simulation of the Cu(110)–… read moreAbstract: The results of a first principles simulation of the Cu(110)–water interface are presented. The calculations were carried out using ab initio Car–Parrinello molecular dynamics simulation within a pseudopotential formalism and the BLYP generalized gradient approximation to the exchange-correlation potential. An analysis of the structural properties of the interface shows that absorption of H2O molecules occurs on the metal top sites which is in agreement with experimental results. The electronic structure of the interface has also been explored. It was found that there is a strong coupling of the water overlayer with the metal crystal electronic states. However, the surface-states charge density is undisturbed by the presence of water. The empty surface states are seen to not be quenched by the presence of water, which is also in qualitative agreement with existing experiments. read less NOT USED (high confidence) R. Pérez and P. Gumbsch, “An ab initio study of the cleavage anisotropy in silicon,” Acta Materialia. 2000. link Times cited: 124 NOT USED (high confidence) G. Csányi, T. Engeness, S. Ismail‐Beigi, and T. Arias, “New physics of the 30 ◦ partial dislocation in silicon revealed through ab initio calculation,” Journal of Physics: Condensed Matter. 2000. link Times cited: 3 Abstract: On the basis of ab initio calculation, we propose a new stru… read moreAbstract: On the basis of ab initio calculation, we propose a new structure for the fundamental excitation of the reconstructed 30° partial dislocation in silicon. This soliton has a rare structure involving a fivefold-coordinated atom near the dislocation core. The unique electronic structure of this defect is consistent with the electron spin-resonance signature of the hitherto enigmatic thermally stable R centre of plastically deformed silicon. We present the first ab initio determination of the free energy of the soliton, which is also in agreement with the experimental observation. This identification suggests the possibility of an experimental determination of the density of solitons, a key defect in understanding the plastic flow of the material. read less NOT USED (high confidence) T. Lenosky et al., “Highly optimized empirical potential model of silicon,” Modelling and Simulation in Materials Science and Engineering. 2000. link Times cited: 145 Abstract: We fit an empirical potential for silicon using the modified… read moreAbstract: We fit an empirical potential for silicon using the modified embedded atom (MEAM) functional form, which contains a nonlinear function of a sum of pairwise and three-body terms. The three-body term is similar to the Stillinger-Weber form. We parametrized our model using five cubic splines, each with 10 fitting parameters, and fitted the parameters to a large database using the force-matching method. Our model provides a reasonable description of energetics for all atomic coordinations, Z, from the dimer (Z = 1) to fcc and hcp (Z = 12). It accurately reproduces phonons and elastic constants, as well as point defect energetics. It also provides a good description of reconstruction energetics for both the 30° and 90° partial dislocations. Unlike previous models, our model accurately predicts formation energies and geometries of interstitial complexes - small clusters, interstitial-chain and planar {311} defects. read less NOT USED (high confidence) A. Kawamoto, J. Jameson, K. Cho, and R. Dutton, “Challenges for atomic scale modeling in alternative gate stack engineering,” IEEE Transactions on Electron Devices. 2000. link Times cited: 24 Abstract: We review the challenges for atomic scale modeling of altern… read moreAbstract: We review the challenges for atomic scale modeling of alternative gate dielectric stacks. We begin by highlighting recent achievements of state-of-the-art atomistic simulations of the Si-SiO/sub 2/ system, showing how such calculations have elucidated the microscopic origins of several important experimental phenomena. For the benefit of readers who may be unfamiliar with the simulation tools, we overview and compare the relevant methods. We then describe the difficulties encountered in extending these approaches to investigate high-k dielectric stacks, pointing out exciting research directions aimed at overcoming these challenges. We conclude by presenting a roadmap of computational goals for atomic scale modeling of alternative gate dielectrics. read less NOT USED (high confidence) K. Nordlund, P. Partyka, R. Averback, I. Robinson, and P. Ehrhart, “Atomistic simulation of diffuse x-ray scattering from defects in solids,” Journal of Applied Physics. 2000. link Times cited: 21 Abstract: Diffuse x-ray scattering is a powerful means to study the st… read moreAbstract: Diffuse x-ray scattering is a powerful means to study the structure of defects in crystalline solids. The traditional analysis of diffuse x-ray scattering experiments relies on analytical and numerical methods which are not well suited for studying complicated defect configurations. We present here an atomistic simulation method by which the diffuse x-ray scattering can be calculated for an arbitrary finite-sized defect in any material where reliable interatomic force models exist. We present results of the method for point defects, defect clusters and dislocations in semiconductors and metals, and show that surface effects on diffuse scattering, which might be important for the investigation of shallow implantation damage, will be negligible in most practical cases. We also compare the results with x-ray experiments on defects in semiconductors to demonstrate how the method can be used to understand complex damage configurations. read less NOT USED (high confidence) M. Iwamatsu, “Global geometry optimization of silicon clusters using the space-fixed genetic algorithm,” Journal of Chemical Physics. 2000. link Times cited: 53 Abstract: The space-fixed genetic algorithm originally proposed by Nie… read moreAbstract: The space-fixed genetic algorithm originally proposed by Niesse and Mayne [J. Chem. Phys. 105, 4700 (1996)] is modified and used to study the lowest energy structure of small silicon clusters by employing empirical interatomic potentials. In this new space-fixed genetic algorithm, a gradient-free simplex method, rather than the conventional gradient-driven conjugate gradient minimization employed by Niesse and Mayne, is selected by virtue of its flexibility and applicability to any form of interatomic potentials for which the calculation of derivatives is difficult. Using two empirical three-body potentials, we calculated the ground state structure up to Si15 successfully using this new genetic algorithm based on the simplex method. The effect of angular dependent three-body potentials on the cluster structures is examined and compared with the experimental results. read less NOT USED (high confidence) Scheerschmidt, Conrad, Kirmse, Schneider, and Neumann, “Electron microscope characterization of CdSe/ZnSe quantum dots based on molecular dynamics structure relaxations,” Ultramicroscopy. 2000. link Times cited: 20 NOT USED (high confidence) J. Zimmerman, H. Gao, and F. F. Abraham, “Generalized stacking fault energies for embedded atom FCC metals,” Modelling and Simulation in Materials Science and Engineering. 2000. link Times cited: 284 Abstract: Atomistic calculations for the 112 -generalized stacking fau… read moreAbstract: Atomistic calculations for the 112 -generalized stacking fault (GSF) energy curve are performed for various embedded atom models of FCC metals. Models include those by Voter and Chen; Angelo, Moody and Baskes; Oh and Johnson; Mishin and Farkas; and Ercolessi and Adams. The resulting curves show similar characteristics but vary in their agreement with the experimental estimates of the intrinsic stacking fault energy, sf , and with density functional theory (DFT) calculations of the GSF curve. These curves are used to obtain estimates of the unstable stacking fault energy, us , a quantity used in a criterion for dislocation nucleation. Curves for nickel and copper models show the theoretically expected skewed sinusoidal shape; however, several of the aluminium models produce an irregularly shaped GSF curve. Copper and aluminium values for us are underestimates of calculations from DFT, although some of the nickel models produce a value matching one of the available DFT results. Values for sf are either fitted to, or underestimate, the measured results. For use in simulations, the authors recommend using the Voter and Chen potential for copper, and either the Angelo, Moody and Baskes potential or the Voter and Chen potential for nickel. None of the potentials model aluminium well, indicating the need for a more-advanced empirical potential. read less NOT USED (high confidence) H. Koizumi, Y. Kamimura, and T. Suzuki, “Core structure of a screw dislocation in a diamond-like structure,” Philosophical Magazine A. 2000. link Times cited: 46 Abstract: The core structure of a screw dislocation in the diamond lat… read moreAbstract: The core structure of a screw dislocation in the diamond lattice has been calculated with the Stillinger-Weber potential for the interatomic interaction. The non-dissociated screw dislocation positioned at the centre of a unit hexagon normal to the dislocation line is a stable configuration A. A perfect screw centred on a longer edge of the unit hexagon is also a stable configuration B. Configuration B is more stable and has a lower energy than configuration A. Dissociated configurations of width w = na (a is the repeat distance in the slip direction and n = 1, 2, 3,…) are also stable. The geometrical feature of configuration B explains the cross-slip observed in III-V compounds at low temperatures. The Peierls stress of the perfect screw dislocation is 0.044G, where G is the shear modulus. This value corresponds to the experimental values of III-V compounds deduced from the temperature dependence of the critical shear stress at low temperatures. read less NOT USED (high confidence) C. Herrero, “Quantum atomic dynamics in amorphous silicon; a path-integral Monte Carlo simulation,” Journal of Physics: Condensed Matter. 2000. link Times cited: 10 Abstract: The quantum dynamics of atoms in amorphous silicon has been … read moreAbstract: The quantum dynamics of atoms in amorphous silicon has been addressed by using path-integral Monte Carlo simulations. Structural results (radial distribution functions) found from these simulations agree well with experimental data. We study the quantum delocalization of the silicon atoms around their equilibrium positions. This delocalization is larger for coordination defects (fivefold-coordinated Si atoms). Correlations in the atomic displacements are analysed as a function of the interatomic distance and compared with those derived from classical Monte Carlo simulations. At high temperatures, the classical limit is recovered. Our results are also compared with those derived from similar quantum simulations for crystalline silicon. Structural disorder favours a larger vibrational amplitude for the atoms in amorphous silicon. read less NOT USED (high confidence) N. Zotov, M. Marinov, N. Mousseau, and G. Barkema, “Dependence of the vibrational spectra of amorphous silicon on the defect concentration and ring distribution,” Journal of Physics: Condensed Matter. 1999. link Times cited: 36 Abstract: The Raman spectra of nine 216-atom models of amorphous silic… read moreAbstract: The Raman spectra of nine 216-atom models of amorphous silicon (a-Si) are calculated using the bond polarizability approximation of Raman scattering. These a-Si models, generated by the activation relaxation technique, have different concentrations of coordination defects, ring statistics and local strain distributions, which cause changes in the vibrational density of states and the Raman scattering. Analysis of the vibrational modes indicates that an increase in the number of coordination defects leads to an increase in the high-frequency localization and to mixing of the TA modes with other high-frequency modes. Calculation of partial Raman spectra indicates that five-coordinated Si atoms enhance the high-frequency part of the LO Raman peak at about 400 cm-1 and lead to characteristic band at about 600 cm-1 on the high-frequency side of the TO Raman peak. For their part, the three-coordinated Si atoms contribute to the low-frequency part of the LO peak. A weak correlation between the number of four-membered rings and the intensity of the LO Raman peak is also established although there is no correlation between the number of three- and four-membered rings and the total strain energy. read less NOT USED (high confidence) M. Schaible, “Empirical Molecular Dynamics Modeling of Silicon and Silicon Dioxide: A Review,” Critical Reviews in Solid State and Materials Sciences. 1999. link Times cited: 28 Abstract: A number of computational methods have been developed over t… read moreAbstract: A number of computational methods have been developed over the last 40 years to simulate the behavior of solid materials with small dimensions. On the macro-scale, Finite Element analysis calculates mechanical stress on micron-sized cantilevers and motors. On the atomic level, newer ab initio methods compute nuclear and electronic behavior of hundred atom models with unprecedented rigor. By implementing the laws of classic mechanics, empirical Molecular Dynamics (MD) programs help bridge these two computational extremes. MD identifies nonelectronic, particle motion for large 100,000 atom cells with good success. MD derives both equilibrium and nonequilibrium properties for many complex condensed regimes; quantitatively (and qualitatively) reaffirms empirical data; aids discovery of new materials processing techniques, and helps predict unknown physical phenomena often only observable under extreme environmental settings. One material of great technical importance to the semiconductor industry is silicon (... read less NOT USED (high confidence) C.-K. Kim, A. Kubota, and D. J. Economou, “Molecular dynamics simulation of silicon surface smoothing by low-energy argon cluster impact,” Journal of Applied Physics. 1999. link Times cited: 8 Abstract: The molecular dynamics simulation method was employed to stu… read moreAbstract: The molecular dynamics simulation method was employed to study the mechanism of silicon (001) surface smoothing by impact of Ar16 or Ar40 clusters with energy at or below 20 eV per constituent atom. Smoothing of a pyramid on top of an otherwise “flat” silicon surface was used as a model system to elucidate the mechanism of cluster-substrate interaction. Surface smoothing is achieved by lateral displacement of substrate atoms during cluster impact. There exists an optimum energy of around 4–5 eV per constituent atom of the cluster for efficient surface smoothing; this implies that a proper energy is required for effective lateral displacement. Cluster size also affects surface smoothing because lateral displacement depends on the nonlinear effect of multiple collisions in the near surface region. As anticipated, damage in the substrate increases with cluster energy. read less NOT USED (high confidence) C. Angell and S. Borick, “COMMENT: Comment on ‘Structure of supercooled liquid silicon’ by Ansell et al,” Journal of Physics: Condensed Matter. 1999. link Times cited: 24 Abstract: We correct a statement made in a recent paper (Angell S et a… read moreAbstract: We correct a statement made in a recent paper (Angell S et al 1998 J. Phys.: Condens. Matter 10 L73-8) that computer simulations on supercooled liquid silicon were not available. We further point out that the simulations that have been made provide an important confirmation of the findings of Angell et al, from the x-ray diffraction studies, that the Si coordination number rapidly decreases in the supercooling range. Of particular interest is the observation that, at the limit of the 340 K supercooling reported in Angell et al, the laboratory liquid has the same coordination number that the simulated system reaches at the temperature of its first order liquid-liquid transition. This implies that the crystallization is promoted by the liquid-liquid transition, as is also seen in the simulation. We point out other systems in which such provocative behaviour should be found. read less NOT USED (high confidence) C. T. Reeves, B. A. Ferguson, C. Mullins, G. Sitz, B. A. Helmer, and D. Graves, “Trapping dynamics of ethane on Si(100)-(2×1): Molecular beam experiments and molecular dynamics simulations,” Journal of Chemical Physics. 1999. link Times cited: 14 Abstract: The trapping probability, or physical adsorption probability… read moreAbstract: The trapping probability, or physical adsorption probability, of ethane on a clean Si(100)-(2×1) surface has been measured as a function of the incident translational energy and incident polar angle of the molecule at a surface temperature of 65 K. At all incident angles the trapping probability decreases as the translational energy of the incoming ethane molecule is increased from 0.05 to 1.3 eV. As the incident polar angle, with respect to the surface normal, is increased, the trapping probability decreases. This decrease in trapping probability with increasing polar angle contradicts the idea of normal energy scaling and has been seen in very few cases. Classical molecular dynamics calculations have been employed to study the cause of this unusual angular dependence. This simulation predicts trapping probabilities in good agreement with the experimental data. Analysis of the computed trajectories indicates that the initial site of impact within the unit cell, as well as energy exchange on initial impact with the surface, is important in determining the fate of an incident molecule. Normal momentum of the incident molecule is dissipated during the first impact much more efficiently than is parallel momentum. The simulations also indicate that the observed angular dependence can be explained in terms of parallel momentum accommodation. Large amounts of parallel momentum remaining after initial impact may be converted to normal momentum on subsequent impacts, causing molecules to scatter from the surface. Therefore, molecules that impact the surface at glancing angles and high translational kinetic energies are more likely to scatter from the surface than those at normal incidence or with lower translational kinetic energy. read less NOT USED (high confidence) A. Kiv, “Microstructure of the relaxed (001) Si surface,” Semiconductor physics, quantum electronics and optoelectronics. 1999. link Times cited: 3 Abstract: We have applied molecular dynamics method and semi-empirical… read moreAbstract: We have applied molecular dynamics method and semi-empirical potential [1] to obtain the realistic picture of Si surface layers relaxation. The starting configuration was taken as a parallelepiped containing 864 atoms. There were 12 layers with 72 atoms in each one. Periodic boundary conditions were used in two dimensions. read less NOT USED (high confidence) S. Volz and G. Chen, “Molecular dynamics simulation of thermal conductivity of silicon nanowires,” Applied Physics Letters. 1999. link Times cited: 401 Abstract: We investigate the thermal conductivity of silicon nanowires… read moreAbstract: We investigate the thermal conductivity of silicon nanowires based on molecular dynamics (MD) simulations. The simulated thermal conductivities of nanowires with square cross sections are found to be about two orders of magnitude smaller than those of bulk Si crystals in a wide range of temperatures (200–500 K) for both rigid and free boundary conditions. A solution of the Boltzmann transport equation is used to explore the possibility of explaining the MD results based on boundary scattering. read less NOT USED (high confidence) J. F. Justo, V. Bulatov, and S. Yip, “DISLOCATION CORE RECONSTRUCTION AND ITS EFFECT ON DISLOCATION MOBILITY IN SILICON,” Journal of Applied Physics. 1999. link Times cited: 31 Abstract: Through atomistic calculations of kink nucleation and migrat… read moreAbstract: Through atomistic calculations of kink nucleation and migration in the core of partial dislocations in silicon we demonstrate that symmetry-breaking structural reconstructions will strongly affect dislocation mobility. Core reconstructions give rise to multiple kink species, and, relative to kinks in an unreconstructed dislocation, an increase in kink formation and migration energies. These factors provide additional resistance to dislocation motion which scales with the energy reconstruction. Our results indicate that the observed variations of dislocation mobility in going from elemental to IV–IV, and further to III–V and II–VI zinc-blende semiconductors, can be attributed in part to the weakening of core reconstruction across the series. read less NOT USED (high confidence) B. A. Helmer and D. Graves, “Molecular dynamics simulations of Cl2+ impacts onto a chlorinated silicon surface: Energies and angles of the reflected Cl2 and Cl fragments,” Journal of Vacuum Science and Technology. 1999. link Times cited: 17 Abstract: We describe the energy and angle distributions of reflected … read moreAbstract: We describe the energy and angle distributions of reflected Cl2 molecules and Cl atom fragments obtained from molecular dynamics (MD) simulations of Cl2+ ion impacts onto a chlorinated silicon surface. We simulated Cl2+ ion impacts onto a silicon surface with 1 monolayer (ML) of adsorbed Cl atoms. The ion incident energies Ei were 20, 50, and 100 eV. We varied the ion incident angles θi from 0° to 85° from the surface normal. We report the Cl2 dissociation probability, as well as the scattering probabilities for both the Cl2 molecules and the Cl atom fragments. The effects of Ei and θi on these quantities are discussed. For the 100 eV Cl2+ impacts with θi⩾75°, we describe the distributions of energies Er and angles (polar θr and azimuthal φr) for the reflected Cl2 molecules and Cl atom fragments. In addition, we compare the average energies of the reflected molecules and atoms with the predictions of two simple models based on the binary collision approximation. read less NOT USED (high confidence) T. Sinno, H. Susanto, R. A. Brown, W. Ammon, and E. Dornberger, “Boron retarded self-interstitial diffusion in Czochralski growth of silicon crystals and its role in oxidation-induced stacking-fault ring dynamics,” Applied Physics Letters. 1999. link Times cited: 12 Abstract: The effect of boron doping on the position of the oxidation-… read moreAbstract: The effect of boron doping on the position of the oxidation-induced stacking-fault ring (OSF ring) during Czochralski (CZ) crystal growth is described using a comprehensive model for point defect dynamics including the role of boron. The important interactions between boron atoms and intrinsic point defects are selected on the basis of tight-binding estimates for the energies of formation for boron-point defect structures. Intrinsic point defect properties used are taken from a parameterized model of point defect dynamics for predicting OSF-ring dynamics. Entropies of formation for boron-point defect species are obtained by fitting the predictions of the model to experimental data for OSF-ring dynamics. The model successfully predicts OSF-ring dynamics for a variety of doping and growth conditions. The effect of boron on the OSF ring is caused by the retardation of point defect recombination at temperatures near the melting point caused by dynamic storage of self-interstitials in complexes with boron. read less NOT USED (high confidence) R. Sahara, H. Mizuseki, K. Ohno, S. Uda, T. Fukuda, and Y. Kawazoe, “Body-centered-cubic lattice model with many-body interactions representing the melting transition in Si,” Journal of Chemical Physics. 1999. link Times cited: 11 Abstract: A body-centered-cubic (BCC) lattice model with realistic man… read moreAbstract: A body-centered-cubic (BCC) lattice model with realistic many-body interactions is introduced and investigated by means of the Metropolis’ Monte Carlo method to describe both crystalline and molten states of Si. Under the simplest assumption that atoms surrounded by tetrahedral first-neighbors only have an energy lower than the other atoms, a clear first-order phase transition including hysteresis is observed between a solid with diamond structure and a melt. Nucleation and domain growth are dynamically observed in certain range of the supercooling. In order to introduce more realistic and accurate lattice-gas models, the Tersoff potential is renormalized and the interactions are mapped onto a BCC lattice. Then, it is found that the phase transition temperature and other thermodynamic properties are dramatically improved compared with the case using the Tersoff potential directly in the lattice model without renormalization. read less NOT USED (high confidence) M. Ghaly, K. Nordlund, and R. Averback, “Molecular dynamics investigations of surface damage produced by kiloelectronvolt self-bombardment of solids,” Philosophical Magazine. 1999. link Times cited: 271 Abstract: Molecular dynamics computer simulations were employed to stu… read moreAbstract: Molecular dynamics computer simulations were employed to study damage production mechanisms at solid surfaces during bombardment with kiloelectronvolt ions. Three separate mechanisms are identified: ballistic damage, viscous flow and microexplosions. Ballistic damage is created by the direct knock-on of atoms onto the surface as described within the binary collision approximation. Viscous flow refers to local melting and the forced flow of liquid onto the surface, and microexplosions occur when the high pressures in cascades lead to rupturing of the nearby surface. The relative importance of each mechanism depends on several parameters: atomic mass, melting temperature, atomic density, structure and atomic bonding of the target, and the mass and energy of the projectile. The simulations were performed for Pt. Au, Cu, Ni and Ge self-atom bombardment. Cascades in the interior of the targets were also examined to provide a comparison for the surface events. In addition several events of 4.5keV Ne an... read less NOT USED (high confidence) D. Hanson, J. Kress, and A. Voter, “AN INTERATOMIC POTENTIAL FOR REACTIVE ION ETCHING OF SI BY CL IONS,” Journal of Chemical Physics. 1999. link Times cited: 26 Abstract: An interatomic potential has been developed to describe the … read moreAbstract: An interatomic potential has been developed to describe the dynamics of Si/Cl systems, with particular relevance to reactive ion etching of Si by energetic Cl ions. We have modified the Stillinger–Weber (SW) potential of Feil et al. by adding two new terms: (1) an embedding term that corrects for the variation in Si–Cl bond strength as a function of the number of neighbors, and (2) a four-body term to describe the variation of the Si–Si bond strength as a function of the number of neighbors of each Si atom and the atom types (a bond order correction). Calculated Si etch rates obtained from molecular dynamics simulations using the new potential are in better agreement with recent experimental results than those obtained with the unmodified potential. Predictions of the stoichiometry of the etch products are also markedly different between the two potentials. read less NOT USED (high confidence) C. Wang, B. Pan, and K. Ho, “An environment-dependent tight-binding potential for Si,” Journal of Physics: Condensed Matter. 1999. link Times cited: 116 Abstract: We present a new generation of tight-binding model for silic… read moreAbstract: We present a new generation of tight-binding model for silicon which goes beyond the traditional two-centre approximation and allows the tight-binding parameters to scale according to the bonding environment. We show that the new model improves remarkably the accuracy and transferability of the potential for describing the structures and energies of silicon surfaces, in addition to the properties of silicon in the bulk diamond structure. read less NOT USED (high confidence) H. Gao, C. Ozkan, W. Nix, J. Zimmerman, and L. Freund, “Atomistic models of dislocation formation at crystal surface ledges in Si1-xGex/Si(100) heteroepitaxial thin films,” Philosophical Magazine. 1999. link Times cited: 35 Abstract: Mechanisms of defect formation near surface ledges of a diam… read moreAbstract: Mechanisms of defect formation near surface ledges of a diamond cubic crystal subjected to compressive strain parallel to the surface are investigated as precursory processes to dislocation nucleation in Si1-xGex/Si(100) heteroepitaxial thin films under surface diffusion conditions. This study is motivated by our preliminary calculations of dislocation formation at surface ledges in a model crystal characterized by the 6–12 Lennard-Jones interatomic potential, and by our controlled annealing experiments on evolution of a Si1-xGex/Si(100) film from an atomically flat, defect-free, surface morphology to an undulating surface morphology with cusp-like surface features and dislocation formation at the cusp valley. When subjecting such films to high temperature anneals, we observed nucleation and growth of three types of dislocations: the 60° glide dislocations, the 90° Lomer-Cottrell dislocations with stair rod Shockley partials and twinned wedge disclinations with twofold ∑9 coincidence boundaries b... read less NOT USED (high confidence) M. Lombardero, C. Martín, S. Jorge, F. Lado, and E. Lomba, “An integral equation study of a simple point charge model of water,” Journal of Chemical Physics. 1999. link Times cited: 57 Abstract: We present an extensive integral equation study of a simple … read moreAbstract: We present an extensive integral equation study of a simple point charge model of water for a variety of thermodynamic states ranging from the vapor phase to the undercooled liquid. The calculations are carried out in the molecular reference-hypernetted chain approximation and the results are compared with extensive molecular dynamics simulations. Use of a hard sphere fluid as a reference system to provide the input reference bridge function leads to relatively good thermodynamics. However, at low temperatures the computed microscopic structure shows deficiencies that probably stem from the lack of orientational dependence in this bridge function. This is in marked contrast with results previously obtained for systems that, although similarly composed of angular triatomic molecules, do not tend to the tetrahedral coordinations that are characteristic of water. read less NOT USED (high confidence) B. A. Helmer and D. Graves, “Molecular dynamics simulations of Ar+ and Cl+ impacts onto silicon surfaces: Distributions of reflected energies and angles,” Journal of Vacuum Science and Technology. 1998. link Times cited: 82 Abstract: Previous profile evolution studies of plasma-assisted etch p… read moreAbstract: Previous profile evolution studies of plasma-assisted etch processes have shown that ions scattered from sidewalls can lead to microtrench formation on the bottom of an etched feature [see, for example, Dalton et al., J. Electrochem. Soc. 140, 2395 (1993)]. In these studies, the ions impacting feature surfaces with incident angles above a critical value were assumed to reflect specularly from the surfaces. In the present article, we describe the energy and angle distributions of reflected atoms obtained from molecular dynamics (MD) simulations. We simulated Ar+ and Cl+ ions impacting model silicon surfaces. The ion incident energies Ei were 20, 50, and 100 eV. We varied the ion incident angles θi from 0° to 85° from the surface normal. The model silicon surfaces had chlorine coverages of 0 monolayers (ML) of Cl, 1 ML Cl, and 2.3 ML Cl. We determined the Ar and Cl reflection probabilities, i.e., the fraction of Ar and Cl atoms scattered from the surfaces during the 1–2 ps MD trajectories. For θi⩾75°, we fo... read less NOT USED (high confidence) P. B. Rasband, P. Clancy, and B. W. Roberts, “Tight-binding studies of the tendency for boron to cluster in c-Si. I. Development of an improved boron–boron model,” Journal of Applied Physics. 1998. link Times cited: 22 Abstract: A tight-binding model for B–B interactions has been develope… read moreAbstract: A tight-binding model for B–B interactions has been developed to study the stability of small boron clusters in crystalline silicon. The model was produced by fitting to the band structure determined by local-density approximation calculations on periodic supercells. This model is able to reproduce, relatively accurately, the cohesive energy of free boron clusters as determined by self-consistent field and configuration-interaction calculations. read less NOT USED (high confidence) J. D. Torre, M. Rouhani, R. Malek, D. Estève, and G. Landa, “Beyond the solid on solid model: An atomic dislocation formation mechanism,” Journal of Applied Physics. 1998. link Times cited: 14 Abstract: We investigate the growth of mismatched thin films by a kine… read moreAbstract: We investigate the growth of mismatched thin films by a kinetic Monte Carlo computer simulation. The strain is introduced through an elastic energy term based on a valence force field approximation and stress is relaxed along “atomic chains” at each step of the simulation. The calculations use a set of elementary atomic processes including, besides well-known standard processes, the collective incorporation of atoms. This leads us to introduce a new “hanging” position with only one bond created toward the substrate contrary to solid on solid models. This position plays a role of defects initiation, and thus an atomic dislocation nucleation mechanism is described. Finally, we present the influence of a step in the dislocations creation. read less NOT USED (high confidence) N. Ghoniem, “Atomic processes during damage production and defect retention,” Journal of Nuclear Materials. 1998. link Times cited: 9 NOT USED (high confidence) F. Stillinger, P. Debenedetti, and S. Sastry, “Resolving vibrational and structural contributions to isothermal compressibility,” Journal of Chemical Physics. 1998. link Times cited: 27 Abstract: The well-known and general “compressibility theorem” for pur… read moreAbstract: The well-known and general “compressibility theorem” for pure substances relates κT =−(∂ ln V/∂p)N,T to a spatial integral involving the pair correlation function g(2). The isochoric inherent structure formalism for condensed phases separates g(2) into two fundamentally distinct contributions: a generally anharmonic vibrational part, and a structural relaxation part. Only the former determines κT for low-temperature crystals, but both operate in the liquid phase. As a supercooled liquid passes downward in temperature through a glass transition, the structural contribution to κT switches off to produce the experimentally familiar drop in this quantity. The Kirkwood–Buff solution theory forms the starting point for extension to mixtures, with electroneutrality conditions creating simplifications in the case of ionic systems. read less NOT USED (high confidence) P. Keblinski, D. Wolf, F. Cleri, S. Phillpot, and H. Gleiter, “On the Nature of Grain Boundaries in Nanocrystalline Diamond,” MRS Bulletin. 1998. link Times cited: 72 Abstract: The atomic structures of a few representative large-unit-cel… read moreAbstract: The atomic structures of a few representative large-unit-cell grain boundaries thought to largely determine the behavior of nanocrystalline diamond are determined via Monte-Carlo simulation. In these highly disordered grain boundaries up to 80% of the C atoms exhibit local sp2 bonding. However, because the three-coordinated C atoms are poorly connected to each-other, graphite-like electrical conduction through the grain boundaries is unlikely without 'bridging' impurities. Surprisingly, based on their fracture energies, the high-energy, large-unit-cell boundaries are more stable against brittle decohesion into free surfaces than low-energy ones and perhaps even the perfect crystal. read less NOT USED (high confidence) G. Khaldeev and S. N. Petrov, “Computer simulation of electrochemical processes on interfaces,” Russian Chemical Reviews. 1998. link Times cited: 5 Abstract: The basic problems of computer simulation of mass and charge… read moreAbstract: The basic problems of computer simulation of mass and charge transfer in electrochemical processes such as electrocrystallisation and corrosion of metals are analysed. Three main approaches to the simulation of electrochemical problems are considered: the Ising (lattice gas) model, molecular dynamics (MD) and Monte Carlo (MC) methods. The principal equations used in simulation techniques and examples of the simulation of particular systems are presented. The bibliography includes 136 references. read less NOT USED (high confidence) M. Bachlechner et al., “Multimillion-atom molecular dynamics simulation of atomic level stresses in Si(111)/Si3N4(0001) nanopixels,” Applied Physics Letters. 1998. link Times cited: 33 Abstract: Ten million atom multiresolution molecular-dynamics simulati… read moreAbstract: Ten million atom multiresolution molecular-dynamics simulations are performed on parallel computers to determine atomic-level stress distributions in a 54 nm nanopixel on a 0.1 µm silicon substrate. Effects of surfaces, edges, and lattice mismatch at the Si(111)/Si3N4(0001) interface on the stress distributions are investigated. Stresses are found to be highly inhomogeneous in the nanopixel. The top surface of silicon nitride has a compressive stress of +3 GPa and the stress is tensile, –1 GPa, in silicon below the interface. read less NOT USED (high confidence) N. Kubota, D. J. Economou, and S. Plimpton, “Molecular dynamics simulations of low-energy (25–200 eV) argon ion interactions with silicon surfaces: Sputter yields and product formation pathways,” Journal of Applied Physics. 1998. link Times cited: 65 Abstract: The etch yield and subsurface damage are important issues in… read moreAbstract: The etch yield and subsurface damage are important issues in low energy (200 < eV) ion interactions with surfaces. In particular, atomic layer etching requires etching of electronic materials with monolayer precision and minimal interlayer atomic mixing. In this study, the molecular dynamics technique is used to simulate the impact of argon ions on chlorine-free and chlorine-passivated silicon surfaces, under conditions relevant to atomic layer etching. Thousands of individual ion impact simulations are performed on a massively parallel supercomputer. The silicon sputter yield is obtained for Ar ion energies ranging from 25 to 200 eV. Where possible, simulation results are compared to available experimental data. Volatile product formation during ion bombardment of ordered surfaces tends to follow distinct local trajectories. For example, the formation of products due to 120 eV Ar ions impacting onto Si(001)(2×1) at normal incidence has been found to occur mainly by a mechanism in which the Ar ion impacts... read less NOT USED (high confidence) K. Nordlund, M. Ghaly, and R. Averback, “Mechanisms of ion beam mixing in metals and semiconductors,” Journal of Applied Physics. 1998. link Times cited: 69 Abstract: Ion beam mixing was investigated in crystalline and amorphou… read moreAbstract: Ion beam mixing was investigated in crystalline and amorphous semiconductors and metals using molecular dynamics simulations. The magnitude of mixing in an amorphous element compared to its crystalline counterpart was found to be larger by a factor of 2 or more. Mixing in semiconductors was found to be significantly larger than in a face-centered-cubic (fcc) metal of corresponding mass and atomic density. The difference in mixing between amorphous and crystalline materials is attributed to local relaxation mechanisms occurring during the cooling down phase of the cascade. Comparison of mixing in semiconductors and metals shows that short range structural order also has a significant influence on mixing. The mixing results in fcc metals indicate that the role of the electron–phonon coupling in the evolution of collision cascades may be less significant than previously thought. read less NOT USED (high confidence) A. Laref, B. Bouhafs, H. Aourag, and N. Bouarissa, “Calculation of the electronic and elastic properties of carbon,” Journal of Physics: Condensed Matter. 1998. link Times cited: 5 Abstract: By accurately fitting tight-binding parameters to ab initio … read moreAbstract: By accurately fitting tight-binding parameters to ab initio band structures from different tetrahedral volumes, tight-binding parameters have been developed for carbon. The model has scaling form similar to the tight-binding Hamiltonian of Xu et al. However, the properties of the higher-coordinated metallic structure are well described by the model in addition to those of the lower-coordinated covalent structures. This one reproduces accurately the band structures of carbon polytypes and gives a good description of the elastic constants for carbon in diamond structure. Results for phonon frequencies in crystalline carbon are also presented. read less NOT USED (high confidence) L. J. Lewis and N. Mousseau, “Tight-binding molecular-dynamics studies of defects and disorder in covalently bonded materials,” Computational Materials Science. 1998. link Times cited: 13 NOT USED (high confidence) D. Kohen, J. Tully, and F. Stillinger, “Modeling the interaction of hydrogen with silicon surfaces,” Surface Science. 1998. link Times cited: 33 NOT USED (high confidence) M. Rouhani, R. Malek, S. Keršulis, and V. Mitin, “Computer simulation of the growth of heterostructure systems,” Microelectronics Journal. 1997. link Times cited: 1 NOT USED (high confidence) O. Braun, T. Valkering, J. V. Opheusden, and H. Zandvliet, “Substrate-induced pairing of Si ad-dimers on the Si(100) surface.,” Surface Science. 1997. link Times cited: 1 NOT USED (high confidence) E. Lomba, J. L. López‐Martín, J. Anta, J. Ho, Ye, and G. Kahl, “A theoretical approach to the tight-binding band structure of liquid carbon and silicon beyond linear approximations,” Journal of Chemical Physics. 1997. link Times cited: 3 Abstract: We present a study of the band structure of liquid Carbon an… read moreAbstract: We present a study of the band structure of liquid Carbon and Silicon modelled in a Tight-Binding Hamiltonian approximation by means of an integral equation approximation that includes non-linear corrections. The theoretical predictions are contrasted with Tight Binding Molecular Dynamics simulations in which the energy bands are obtained by direct diagonalization of the Hamiltonian matrix. The results for Silicon are excellent, whereas in liquid Carbon only some of the qualitative features of the band structure are captured by the non-linear corrections. We find that this can largely be understood as an effect of missing three-body correlation functions in the theoretical treatment of the energy bands. This is particularly crucial in the case of strongly directional and short range bonding, as it occurs in Carbon. read less NOT USED (high confidence) E. Chason et al., “Ion beams in silicon processing and characterization,” Journal of Applied Physics. 1997. link Times cited: 248 Abstract: General trends in integrated circuit technology toward small… read moreAbstract: General trends in integrated circuit technology toward smaller device dimensions, lower thermal budgets, and simplified processing steps present severe physical and engineering challenges to ion implantation. These challenges, together with the need for physically based models at exceedingly small dimensions, are leading to a new level of understanding of fundamental defect science in Si. In this article, we review the current status and future trends in ion implantation of Si at low and high energies with particular emphasis on areas where recent advances have been made and where further understanding is needed. Particularly interesting are the emerging approaches to defect and dopant distribution modeling, transient enhanced diffusion, high energy implantation and defect accumulation, and metal impurity gettering. Developments in the use of ion beams for analysis indicate much progress has been made in one-dimensional analysis, but that severe challenges for two-dimensional characterization remain. The ... read less NOT USED (high confidence) S. Carniato, G. Boureau, and J. Harding, “Modelling oxygen vacancies at the Si(100)-SiO2 interface,” Philosophical Magazine. 1997. link Times cited: 8 Abstract: Using a structural model proposed by Ourmazd et al. as a sta… read moreAbstract: Using a structural model proposed by Ourmazd et al. as a starting point, we have determined some properties of the Si(100)-SiO2 interface. To obtain this information, we have performed a Monte Carlo simulation of the interface, using semiempirical interaction potentials. In a first step, we have just relaxed the system. While on the one hand the relaxation allows us to reach the usual values of bond lengths, on the other hand the silica at the interface retains several features of the initial configurations. There is no tendency for the free volume to collapse in the interfacial region, and the density is somewhat larger than that of tridymite. Two varieties of Si-Si bonds have been found. Owing to constraints imposed by the very low oxygen pressure, the real system accommodates a number of oxygen vacancies. We have shown that these vacancies are much more easily accommodated at the interface, because of electrostatic interactions. read less NOT USED (high confidence) P. Keblinski, S. Phillpot, D. Wolf, and H. Gleiter, “On the Thermodynamic Stability of Amorphous Intergranular Films in Covalent Materials,” Journal of the American Ceramic Society. 1997. link Times cited: 68 Abstract: The thermodynamic origin, structure, and stability of the th… read moreAbstract: The thermodynamic origin, structure, and stability of the thin amorphous films commonly found in grain boundaries in covalent ceramics are investigated by molecular-dynamics simulation. to focus on the purely thermodynamic aspects, any kinetic effects associated with impurity-controlled interface chemistry are excluded by investigating pure silicon (described by the Stillinger-Weber three-body potential). For this single-component covalent model material, the authors demonstrate that all high-energy boundaries exhibit a universal amorphous structure, with a width of {approximately}0.25 nm, whereas low-energy boundaries are crystalline and much sharper. They also demonstrate that introduction of an amorphous film into a crystalline interface lowers the excess energy to a level similar to the energy of two bulk crystal-amorphous interfaces. The competition between a narrow crystalline boundary structure and a wider amorphous boundary structure is shown to be governed by the relative excess energies of the atoms in the grain boundaries and in the bulk amorphous phase. These observations suggest that, in principle, amorphous grain-boundary films do not require impurities for their stabilization and that, as first proposed by Clarke, an equilibrium grain-boundary phase of uniform thickness can be the result of purely thermodynamic rather than kinetic factors. read less NOT USED (high confidence) M. Baskes, “Calculation of the behaviour of Si ad-dimers on Si(001),” Modelling and Simulation in Materials Science and Engineering. 1997. link Times cited: 26 Abstract: The modified embedded atom method (MEAM) is used to investig… read moreAbstract: The modified embedded atom method (MEAM) is used to investigate the geometry and energetics of Si ad-dimers and adatoms on the reconstructed Si(001) surface. Site stability and saddle point energies are predicted for a large number of possible mechanisms. The calculations predict the relative stability of parallel and normal ad-dimers to be 80 meV, in excellent agreement with from experiment, the barrier to rotation of these dimers to be 0.66 eV compared with , and the activation energy for diffusion parallel to the dimer rows to be 0.74 eV compared with . These calculations are the first of any kind to predict quantitative agreement with experiment. We also predict substitutional Ni atoms near the surface are bound to the second and first layer below the dimer layer by 0.65 and 0.47 eV relative to bulk substitutional Ni atoms. The effect of these Ni impurities on the ad-dimer stability is predicted. A parallel ad-dimer is repelled by a substitutional Ni impurity by 30 meV compared with the 20 - 35 meV observed in experiment for an unknown substrate defect. read less NOT USED (high confidence) L. Marqués, J. Rubio, M. Jaraíz, L. Bailón, and J. Barbolla, “Dose effects on amorphous silicon sputtering by argon ions: A molecular dynamics simulation,” Journal of Applied Physics. 1997. link Times cited: 11 Abstract: We have investigated, using molecular dynamics techniques, t… read moreAbstract: We have investigated, using molecular dynamics techniques, the sputtering yield enhancement of amorphous silicon produced by argon ion accumulation within the target. Several amorphous silicon samples, with different argon contents, were bombarded with 1 keV argon ions at normal incidence. To study the influence of the target structure, we considered samples with different argon arrangements, either uniformly distributed or within solid bubbles. We have observed that silicon sputtering yield increases linearly with dose until steady state conditions are reached. This enhancement is produced by the shallow argon atoms through the weakening of Si–Si bonds. We have also observed that argon release takes place even long after the end of the collisional phase, and it is produced by ion-induced desorption and bubble destabilization. This enhanced argon yield determines the dose where target saturation and steady state conditions are reached. read less NOT USED (high confidence) M. Caturla, T. D. Rubia, L. A. Marqués, and G. Gilmer, “Ion-beam processing of silicon at keV energies: A molecular-dynamics study.,” Physical review. B, Condensed matter. 1996. link Times cited: 196 Abstract: We discuss molecular-dynamics simulations of ion damage in s… read moreAbstract: We discuss molecular-dynamics simulations of ion damage in silicon, with emphasis on the effects of ion mass and energy. We employ the Stillinger-Weber potential for silicon, suitably modified to account for high-energy collisions between dopant-silicon and silicon-silicon pairs. The computational cells contain up to 10{sup 6} atoms and these are bombarded by B and As atoms at incident energies from 1 keV up to 15 keV. We show that the displacement cascade results in the production of amorphous pockets as well as isolated point defects and small clusters with populations which have a strong dependence on ion mass and a weaker relationship to the ion energy. We show that the total number of displaced atoms agrees with the predictions of binary collision calculations for low-mass ions, but is a factor of 2 larger for heavy-ion masses. We compare the simulations to experiments and show that our results provide a clear and consistent physical picture of damage production in silicon under ion bombardment. We studied the stability of the damage produced by heavy ions at different temperatures and the nature of the recrystallization mechanism. The inhomogeneous nature of the damage makes the characterization of the process through a single activation energymore » very difficult. An {ital effective} activation energy is found depending on the pocket size. We discuss our results considering the Spaepen-Turnbull recrystallization model for an amorphous-crystalline planar interface. {copyright} {ital 1996 The American Physical Society.}« less read less NOT USED (high confidence) D. Mckenzie, “Tetrahedral bonding in amorphous carbon,” Reports on Progress in Physics. 1996. link Times cited: 365 Abstract: Electron configurations close to the tetrahedral hybridizati… read moreAbstract: Electron configurations close to the tetrahedral hybridization are found in pure amorphous carbon at a concentration which depends on preparation conditions. Tetrahedral bonding at levels of approximately 80% is found in amorphous carbons formed from beams of carbon ions with energies in a `window' between 20 eV and approximately 500 eV. Suitable techniques for its formation include cathodic arc deposition, ion beam deposition and laser ablation. Similar material appears to be formed by pressure treatment of fullerene precursors and by displacement damage in diamond. Highly tetrahedral forms of amorphous carbon (ta-C) show electronic, optical and mechanical properties which approach those of diamond and are quite different from amorphous carbons with low content. Useful techniques for determining the content include electron energy loss spectroscopy, electron and neutron diffraction and Raman spectroscopy. Considerable progress has been made in the understanding of this material by simulating its structure in the computer with a range of techniques from empirical potentials to ab initio quantum mechanics. The structure shows departures from an idealized glassy state of diamond which would have a random tetrahedral network structure as used to describe amorphous silicon and germanium. A surprising feature of the structure simulated using ab initio methods is the presence of small rings containing three or four carbon atoms. The electronic and optical properties are strongly influenced by the residual of carbon. Applications to electronic devices are at an early stage with the demonstration of photoconductivity and some simple junction devices. Applications as a wear resistant coating are promising, since the theoretically predicted high values of elastic constants, comparable to but less than those of diamond, are achieved experimentally, together with low friction coefficients. read less NOT USED (high confidence) C. Herrero and R. Ramírez, “Bond-centred hydrogen and muonium in silicon; a Feynman path-integral simulation,” Journal of Physics: Condensed Matter. 1996. link Times cited: 3 Abstract: Isolated hydrogen and muonium in crystalline silicon have be… read moreAbstract: Isolated hydrogen and muonium in crystalline silicon have been studied by the path-integral Monte Carlo method, using a parametrized Si - H interaction derived from earlier ab initio calculations. Hydrogen and deuterium are found to be stable at the bond-centre (BC) site, but this position is metastable for muonium. Average values of the kinetic and potential energy of the defects are compared with those expected for the hydrogen-like impurities within a harmonic approximation. The backwards relaxation of the Si-atom nearest neighbours of the impurity is found to be dependent on the impurity mass (higher host-atom relaxation for higher impurity mass). read less NOT USED (high confidence) K. K. Mon, “Size dependences of model nanostructure sound velocity,” Journal of Applied Physics. 1996. link Times cited: 1 Abstract: We study by means of numerical simulations the size dependen… read moreAbstract: We study by means of numerical simulations the size dependences for sound velocity of model nanostructures. We use molecular dynamics to obtain the zero temperature size dependences of the propagation velocity of mechanical perturbation for rod‐shaped nanostructures with free surfaces. The particles interact with the Stillinger–Weber potential for silicon. We consider the longitudinal sound propagation in the (001) direction only. The bulk limit is reached very quickly and the longitudinal velocity is already independent of the cross section for a nanofiber larger than 40×40 A. We also study velocity for structures without free surfaces and the effect of changing the magnitude of the triplet interaction potentials. read less NOT USED (high confidence) A. Ihlal, R. Rizk, and O. H. Duparc, “Correlation between the gettering efficiencies and the energies of interfaces in silicon bicrystals,” Journal of Applied Physics. 1996. link Times cited: 22 Abstract: A comparative study of the gettering efficiency of the twin … read moreAbstract: A comparative study of the gettering efficiency of the twin grain boundaries Σ=25, Σ=13, and Σ=9 has been carried out by means of electron‐beam‐induced current measurements performed on quenched silicon bicrystals precontaminated by Cu or Ni. The extent of the denuded zone appearing on both sides of each interface type has been considered as the ‘‘rating’’ of its gettering efficiency. For both contaminants, the same scaling of the gettering efficiencies of the boundaries has been observed and was found to be in the order Σ=9≪Σ=13<Σ=25. To account for this ranking, we have correlated the gettering efficiency to the excess energy of the grain boundary with respect to the bulk energy, as theoretically calculated. The computational procedures have been performed by means of molecular‐dynamics simulations using several potentials. On the basis of the specific disorder affecting the Σ=25 structure upon heat treatment, our calculations provided the same progression for the interfacial energies as that observed e... read less NOT USED (high confidence) P. Keblinski, S. Phillpot, D. Wolf, and H. Gleiter, “Relationship between nanocrystalline and amorphous microstructures by molecular dynamics simulation,” Nanostructured Materials. 1996. link Times cited: 19 NOT USED (high confidence) C. Wang and K. Ho, “Tight-binding molecular dynamics for materials simulations,” Journal of Computer-Aided Materials Design. 1996. link Times cited: 12 NOT USED (high confidence) C. Jayanthi and S. Wu, “Act locally and think globally,” Journal of Computer-Aided Materials Design. 1996. link Times cited: 0 NOT USED (high confidence) P. B. Rasband, P. Clancy, and M. Thompson, “Equilibrium concentrations of defects in pure and B‐doped silicon,” Journal of Applied Physics. 1996. link Times cited: 33 Abstract: Empirical tight‐binding (ETB) calculations have been used in… read moreAbstract: Empirical tight‐binding (ETB) calculations have been used in extensive searches for new point defect structures in pure silicon as well as silicon doped with boron. In general, these searches, which use a steepest‐descents energy minimization from random starting structures, have produced the same set of simple defects in pure silicon (tetrahedral interstitials, split interstitials, and simple vacancies) which have been widely studied. However, a variety of boron interstitials, and several new di‐interstitials (with and without boron) have been discovered. Similarities between these defects and defects found in ab initio and classical studies are discussed, as well as the accuracy of the theoretical results in general. A Stillinger–Weber (SW) model for Si–B interactions has been developed in order to obtain vibrational entropies for simple point defects. Using the SW potential, concentration prefactors have been obtained, and traditional Arrhenius plots for concentration have been produced. The theoretica... read less NOT USED (high confidence) M. E. Barone and D. Graves, “Molecular dynamics simulations of plasma - surface chemistry,” Plasma Sources Science and Technology. 1996. link Times cited: 27 Abstract: Molecular dynamics (MD) simulations were conducted of impact… read moreAbstract: Molecular dynamics (MD) simulations were conducted of impact (normal incidence; 10, 25 and 50 eV) onto an initially pure Si surface until approximately steady state Cl coverages had been obtained. A variety of quantities were obtained from these simulations, including steady state Cl coverages, the yields associated with various etching mechanisms and the degree of surface roughness that evolves during surface chlorination. The most direct comparison to experimental measures of etching yield are from vacuum beam experiments utilizing mass- and energy-selected ion beams. In order to compare to these measurements, we took chlorinated Si layers and impacted upon them at a variety of energies. Quantitative agreement between the simulations and measurements was obtained for ion energies in the range 20 - 75 eV and qualitative agreement was obtained for 75 - 300 eV. read less NOT USED (high confidence) C. Kui-ying, L. Hongbo, and H. Zhuangqi, “Structure features in binary liquid Li–Tl alloys,” Journal of Chemical Physics. 1995. link Times cited: 3 Abstract: With the help of potential mapping techniques, molecular dyn… read moreAbstract: With the help of potential mapping techniques, molecular dynamics simulations have been performed to study the local structure features in binary liquid Li–Tl alloys. The generalized nonlocal model pseudopotentials have been chosen as the bases for our calculations. Both the bond orientational order and pair analysis approach have been adopted as the basic structural functions to examine the structure features in binary liquid Li–Tl alloys. In addition, bonded pairs with various symmetries, icosahedra, defective icosahedra, Frank–Kasper polyhedra, etc., formed in the Li–Tl alloys are examined in detail, and the relationship between the structure features and composition has been established. The results show that the distribution of attractive parts of the potentials play an important role in characterizing the liquid structure. Finally, the results are discussed in detail. read less NOT USED (high confidence) A. A. Valuev, A. S. Kaklyugin, and H. E. Norman, “Molecular modelling of the chemical interaction of atoms and molecules with a surface,” Russian Chemical Reviews. 1995. link Times cited: 3 Abstract: The modelling of a surface as an assembly of moving atoms in… read moreAbstract: The modelling of a surface as an assembly of moving atoms interacting with one another and with an incident particle is examined. Both dynamic methods for the modelling of a surface (for short times) and probability methods (for long times) are analysed. The Massey adiabaticity criterion has been used to determine the regions of applicability of the methods of molecular dynamics. Within the framework of probability methods, the chemical bond is described with the aid of Harrison's generalised periodic system of the elements. Together with the general modeling problems, the reconstruction of the surface, physical and chemical sorption, as well as the modification of the surface and of its morphology as a result of the multiple repetition of elementary processes (precipitation, etching, corrosion) are discussed. The bibliography includes 169 references. read less NOT USED (high confidence) D. Timpel and K. Scheerschmidt, “HREM simulations of Ag particles in sodium silicate glasses refined by molecular dynamic relaxations,” Physica Status Solidi (a). 1995. link Times cited: 6 Abstract: Providing local information at an atomic level high resoluti… read moreAbstract: Providing local information at an atomic level high resolution electron microscopy (HREM) is applied to investigate Ag particles in sodium silicate glasses. Here, the structure of the embedded metallic particles, which influence the properties of glasses, is described by molecular dynamics relaxation calculations. The possibility of HREM to vizualize the structural modifications owing to relaxations is discussed on the basis of simulated HREM micrographs.
Hochauflosende Elektronenmikroskopie (HREM) wird wegen der direkten atomaren Strukturabbildung zur Untersuchung von Ag-Teilchen in Natriumsilikat-Glasern verwendet. Die Struktur der eingelagerten Metallteilchen, die wesentlichen Einflus auf die Glaseigenschaften hat, wird dabei durch molekulardynamische Relaxationsrechnungen beschrieben. Die Moglichkeiten der Sichtbarmachung struktureller Veranderungen im HREM infolge der Relaxationseffekte werden anhand von computersimulierten Abbildungen diskutiert. read less NOT USED (high confidence) R. Černý, P. Přikryl, K. El-kader, and V. Cháh, “Determination of the reflectivity of liquid semiconductors over a wide temperature range,” International Journal of Thermophysics. 1995. link Times cited: 5 NOT USED (high confidence) A. Skinner and J. Broughton, “Neural networks in computational materials science: training algorithms,” Modelling and Simulation in Materials Science and Engineering. 1995. link Times cited: 70 Abstract: Neural networks can be used in principle in an unbiased way … read moreAbstract: Neural networks can be used in principle in an unbiased way for a multitude of pattern recognition and interpolation problems within computational material science. Reliably finding the weights of large feed-forward neural networks with both accuracy and speed is crucial to their use. In this paper, the rate of convergence of numerous optimization techniques that can be used to determine the weights is compared for two problems related to the construction of atomistic potentials. Techniques considered were back propagation (steepest descent), conjugate gradient methods, real-string genetic algorithms, simulated annealing and a new swarm search algorithm. For small networks, where only a few optimal solutions exist, we find that conjugate-gradient methods are most successful. However, for larger networks where the parameter space to be searched is more complex, a hybrid scheme is most effective; genetic algorithm or simulated annealing to find a good initial starting set of weights, followed by a conjugate-gradient approach to home in on a final solution. These hybrid approaches are now our method of choice for training large networks. read less NOT USED (high confidence) Z. Jiang and R. A. Brown, “Study of Oxygen Diffusion and Clustering in Silicon using an Empirical Interatomic Potential,” arXiv: Materials Science. 1995. link Times cited: 0 Abstract: The diffusion path and diffusivity of oxygen in crystalline … read moreAbstract: The diffusion path and diffusivity of oxygen in crystalline silicon are computed using an empirical interatomic potential which was recently developed for modelling the interactions between oxygen and silicon atoms. The diffusion path is determined by constrained energy minimization, and the diffusivity is computed using jump rate theory. The calculated diffusivity is in excellent agreement with experiemental data. The same interatomic potntial also is used to study the formation of small clusters of oxygen atoms in silicon. The structures of these clusters are found by NPT molecular dynamics simulations, and their free energies are calculated by thermodynamic integration. These free energies are used to predict the temperature dependence of the equilibrium partitioning of oxygen into clusters of different sizes. The calculations show that, for given total oxygen concentration, most oxygen atoms are in clusters at temperature below 1300K, and that the average cluster size increases with decreasing temperature. These results are in qualitative agreement with effects of thermal annealing on oxygen precipitation in silicon crystals. read less NOT USED (high confidence) A. P. Smith et al., “Si adatom binding and diffusion on the Si(100) surface: Comparison of ab initio, semiempirical and empirical potential results,” Journal of Chemical Physics. 1995. link Times cited: 51 Abstract: The binding energies and configurations for single Si adatom… read moreAbstract: The binding energies and configurations for single Si adatoms on the Si(100) surface are investigated theoretically. Detailed comparisons between previously published and new calculations using classical potentials, semiempirical formulations, and density functional theory (DFT) are made. The DFT calculations used both the plane‐wave‐pseudopotential approach in a periodic slab geometry and the Gaussian‐orbital based all‐electron approach employing cluster geometries. In the local‐density approximation excellent agreement between the cluster and slab results was obtained. Inclusion of gradient corrections to the exchange‐correlation energy significantly improves absolute binding energies and changes relative energies by as much as 0.3–0.5 eV depending on the particular exchange‐correlation functional used. Binding energies and relative energies obtained using the classical potentials disagree with the gradient corrected DFT energies at about the 0.6–0.9 eV level, and most find qualitatively different local... read less NOT USED (high confidence) S. Erkoç, “An empirical many-body potential energy function constructed from pair-interactions,” Zeitschrift für Physik D Atoms, Molecules and Clusters. 1994. link Times cited: 25 NOT USED (high confidence) D. Stock, M. Nitschke, K. Gärtner, and T. Kandler, “Comparison of MC and MD calculations of slowing down of ions with low energies,” Radiation Effects and Defects in Solids. 1994. link Times cited: 5 Abstract: The energy loss of low energy ( Si crystal is calculated usi… read moreAbstract: The energy loss of low energy ( Si crystal is calculated using a Monte Carlo (MC) and a Molecular Dynamics (MD) computer code, respectively. The MC simulation is based on a modified binary collision model where large range interactions are treated separately within the momentum approximation. Because of the small thickness of the Si crystal the MD calculations are performed for the whole crystal considered, using the Stillinger-Weber many-body potential for silicon. For the B-Si interatomic interaction in both codes the same numerically calculated potential is used. By comparison of the MC and MD results the validity of the binary collision model is discussed. read less NOT USED (high confidence) O. H. H. Duparc and M. Torrent, “A new type of periodie boundary condition useful for high-temperature atomistic simulations of grain boundaries: Applications in semiconductors,” Interface Science. 1994. link Times cited: 21 NOT USED (high confidence) U. Trinczek and H. Teichler, “Line Energies of 30°- and 90°-Partial Dislocations in Silicon and Germanium†,” Physica Status Solidi (a). 1993. link Times cited: 8 Abstract: For the 30°- and 90°-partial dislocations in Si and Ge line … read moreAbstract: For the 30°- and 90°-partial dislocations in Si and Ge line energy calculations are considered. Basic requirements are discussed on empirical interaction potentials to make them suited for estimating the line energies. In case of the considered ‘reconstructed’ dislocation core geometries the potentials have to describe properly the elastic constants and the full phonon dispersion curves including the TA phonon branch flattening. For Weber's bond charge model, which fulfils the requirements, dislocation line energies are presented and compared with data from Keating, Tersoff, and Stillinger-Weber model calculations. read less NOT USED (high confidence) J. Fang, R. Johnston, and J. Murrell, “Potential energy functions for atomic solids: V. Application to alkali metal solids,” Molecular Physics. 1993. link Times cited: 18 Abstract: Empirical potential functions comprising two-body and three-… read moreAbstract: Empirical potential functions comprising two-body and three-body terms have been derived for the alkali metals by fitting parameters to the phonon frequencies, elastic constants, lattice energies and lattice distances of the body-centred-cubic (b.c.c.) solids. These potentials give, in all cases, very similar energies for the b.c.c., face-centred-cubic (f.c.c.) and hexagonal closest packing (h.c.p.) structures, with simple cubic (s.c.), diamond and various two-dimensional structures being much less stable. The lithium potential has been used to predict structures and stabilities of neutral Li n microclusters. No ‘magic number’ stabilities have been found. For n ≥ 6 the structures can, in the main, be described as face-fused tetrahedra, and ab initio calculations support these structures in some important cases (e.g. n = 6, 7). read less NOT USED (high confidence) W. Eckstein, S. Hackel, D. Heinemann, and B. Fricke, “Influence of the interaction potential on simulated sputtering and reflection data,” Zeitschrift für Physik D Atoms, Molecules and Clusters. 1992. link Times cited: 18 NOT USED (high confidence) J. Gardeniers and L. Giling, “Vapour growth of silicon: growth anisotropy and adsorption,” Journal of Crystal Growth. 1991. link Times cited: 8 NOT USED (high confidence) Y. Uemura, “Tight-Binding Approach to the Dangling Bond Feature of Covalent Crystals,” Physica Status Solidi B-basic Solid State Physics. 1991. link Times cited: 0 Abstract: A potential function is proposed which is responsible for da… read moreAbstract: A potential function is proposed which is responsible for dangling bond generation in defect structures of covalent crystals. The defect energy is calculated by the tight-binding method using this potential. All atoms in the defect region are relaxed in six degrees of freedom (three translations and three rotations of a tetrahedron considered at each atomic site). This method is applied to a (111) twist boundary for calculating the boundary energy and the structure. The boundary energy seems mainly to be governed by the dangling bond density which is determined by dividing the number of dangling bonds by the number of atoms included in a supercell at the interface. But in the low energy region, the dependence between them is not so simple. In the case of a low dangling bond density, the relationship between the boundary energy and the rotation angle resembles the result reported for the twist boundary in ionic crystals.
Nous avons proposee la fonction potentiel qui est responsable de la generation du lien pendant dans la structure defaut du cristal covalent. L'energie du defaut a ete calculee par l'approximation des liaisons fortes avec cette potentiel. Tous atoms dans la region imparfaite ont ete relaxee avex six degres (trois translations et trois rotations du tetraedre a chaque site atomic). Cette methode a ete appliquee au (111) borne tordue pour de calcul des energies et des structures. Conclusion, des energies de la borne ont ete principalement decidee par la densite du lien pendant qui a ete definie en divisant le nombre du lien pendant par le nombre des atoms inclus dans un supercellure a la borne. Mais, a la region des energie bas, la dependance entre elles n'est pas simple. Au cas ou la densite du lien pendant ete moins, la relation entre l'energie et l'angle de la rotation a ressemblee aux rapports pour les cristals ionic. read less NOT USED (high confidence) A. Al-Derzi, R. Johnston, J. Murrell, and J. Rodriguez-Ruiz, “Potential energy functions for atomic solids: III. Fitting phonon frequencies and elastic constants of diamond structures,” Molecular Physics. 1991. link Times cited: 39 NOT USED (high confidence) A. Mazzone, “Interatomic Potentials in Silicon,” Physica Status Solidi B-basic Solid State Physics. 1991. link Times cited: 2 Abstract: A study is made, based on molecular dynamics simulations, of… read moreAbstract: A study is made, based on molecular dynamics simulations, of the properties of interatomic potentials currently used to describe solid structures with covalent bonding. From these studies it appears that none of the available forms of potentials leads to a satisfactory description of bulk silicon.
Mittels Molekulardynamik-Simulation werden die Eigenschaften interatomarer Potentiale, die gegenwartig fur die Beschreibung von Festkorperstrukturen mit kovalenter Bindung herangezogen werden, untersucht. Aus den Untersuchungen folgt, das keine der vorhandenen Potentialformen zu einer befriedigenden Beschreibung von Volumensilizium fuhrt. read less NOT USED (high confidence) J. Holender and G. J. Morgan, “Molecular dynamics simulations of a large structure of amorphous Si and direct calculations of the structure factor,” Journal of Physics: Condensed Matter. 1991. link Times cited: 19 Abstract: There have been a number of simulations of fully bonded mode… read moreAbstract: There have been a number of simulations of fully bonded models of a-Si containing of the order of 102 atoms; comparison was then made with the pair distribution function deduced from neutron and X-ray scattering measurements on Si (or Ge). Obtaining the pair distribution function from the primary data produces a convoluted pair distribution function, and it seems sensible to compute the structure factor so as to make possible a direct comparison with experiment. The authors have taken the basic model of Wooten, Winer and Weaire and relaxed it slightly to conform the Stillinger-Weber potential. This is a periodic structure but they have put together 64 such blocks, heated them rapidly to remove the periodicity, then coded them rapidly to 0 K. The resulting structure factors agree extremely well with experimental measurements. read less NOT USED (high confidence) J. Murrell and J. Rodriguez-Ruiz, “Potential energy functions for atomic solids: II. Potential functions for diamond-like structures,” Molecular Physics. 1990. link Times cited: 38 Abstract: Potential functions comprising a sum of two- and three-body … read moreAbstract: Potential functions comprising a sum of two- and three-body terms have been obtained that reproduce the lattice energy, lattice constant, the three elastic constants and the Raman frequency of the diamond lattices of carbon, silicon and germanium. These potentials give the sc, bcc, fcc and hcp lattices of these elements a higher energy. The carbon potential gives a graphite lattice more stable than the diamond lattice, although the stability is overestimated. For silicon and germanium, in contrast, the graphitic structure is significantly less stable than the diamond structure. read less NOT USED (high confidence) M. Kohyama, S. Kose, M. Kinoshita, and R. Yamamoto, “The self-consistent tight-binding method: application to silicon and silicon carbide,” Journal of Physics: Condensed Matter. 1990. link Times cited: 27 Abstract: The self-consistent tight-binding (SCTB) model proposed by M… read moreAbstract: The self-consistent tight-binding (SCTB) model proposed by Majewski and Vogl (1987) has been extended to be applicable for calculations of lattice defects in solids or disordered systems with both ionic and covalent characters that cannot be treated using other types of tight-binding theories. The precise formulation of electronic structure, total energy and atomic forces in the supercell technique has been presented. In order to apply this method to lattice defects in SiC, the parameters and functional forms have been examined so as to reproduce the basic properties of Si, SiC and C. The nature of the bonding and the phase stability in Si and SiC have been analysed by the present SCTB method. read less NOT USED (high confidence) D. Remler and P. Madden, “Molecular dynamics without effective potentials via the Car-Parrinello approach,” Molecular Physics. 1990. link Times cited: 442 Abstract: An introduction to the Car-Parrinello molecular-dynamics met… read moreAbstract: An introduction to the Car-Parrinello molecular-dynamics method is given, written from the viewpoint of a molecular physicist. This scheme makes it possible to simulate atomic and molecular motion in cluster or bulk systems on an energy surface that is determined ‘on the fly’, by finding an adiabatic electronic state appropriate to the instantaneous nuclear positions. The crucial stability of the method is discussed at length. The development of computationally tractable expressions is considered in detail, using (local) density-functional techniques to describe the electronic energy surface. An extended account of these techniques is given, suitable for those unfamiliar with them. read less NOT USED (high confidence) T. Weber and F. Stillinger, “Dynamical branching during fluorination of the dimerized Si(100) surface: A molecular dynamics study,” Journal of Chemical Physics. 1990. link Times cited: 70 Abstract: Collections of classical trajectories have been numerically … read moreAbstract: Collections of classical trajectories have been numerically generated for individual F2 molecules impinging at normal incidence on a Si(100) surface at 0 K dimerized in a p(2×1) pattern. A linear combination of two‐atom and three‐atom interaction functions represents the potential energy. Trajectories fall into four categories: (a) non‐reactive F2 rebound, (b) monofluorination at a surface dangling bond with energetic expulsion into the vacuum of the remaining F atom, (c) difluorination of a pair of dangling bonds, and (d) monofluorination with retention of the second F in a weakly bound Si–F⋅⋅⋅F surface complex. Surface patterns for difluorination, (c), indicate absence of surface diffusion during this mode of chemisorption. Increasing either the translational kinetic energy or the vibrational excitation of the incident F2 appears to enhance its surface reactivity. read less NOT USED (high confidence) J. Murrell and R. E. Mottram, “Potential energy functions for atomic solids,” Molecular Physics. 1990. link Times cited: 109 Abstract: A potential energy function has been proposed for atomic sol… read moreAbstract: A potential energy function has been proposed for atomic solids consisting of two-body and three-body terms which over its range of parameters encompasses all simple crystal structures. Phase diagrams have been constructed as a function of a single parameter in the two-body term and one, of several, parameters in the three-body term, and these include as the most stable structures hcp, fcc, bcc, sc and diamond. The hcp and fcc lattices have been shown to distort to lower symmetries with appropriate three-body parameters and these distortions are in accord with known structures. A brief study has been made of the appropriate parameters for silicon. read less NOT USED (high confidence) K. Laasonen and R. Nieminen, “Molecular dynamics using the tight-binding approximation,” Journal of Physics: Condensed Matter. 1990. link Times cited: 46 Abstract: The authors present an extension of classical molecular dyna… read moreAbstract: The authors present an extension of classical molecular dynamics (MD) to include the forces calculated from electronic degrees of freedom using the tight-binding (TB) approximation. The combined MD-TB problem is solved using simulated annealing techniques. As an example they study the structures and energetics of small silicon clusters, containing up to 10 Si atoms. read less NOT USED (high confidence) J. Hafner and M. Tegze, “Structural and electronic properties of crystalline and glassy calcium-zinc compounds. I. Trigonal prismatic ordering or tetrahedral close packing,” Journal of Physics: Condensed Matter. 1989. link Times cited: 17 Abstract: The authors present a detailed molecular dynamics study of t… read moreAbstract: The authors present a detailed molecular dynamics study of the atomic structure of liquid and amorphous Ca-Zn alloys, based on inter-atomic forces derived from optimised first-principles pseudopotentials. In the Zn-rich limit, their results fit into the pattern characteristic for other sample-metal alloys; the liquid and the quench-condensed amorphous phase can be described as disordered tetrahedrally close packed. For the Ca-rich phases they find some distinctly different features; the most prominent is a pre-peak in the partial structure factor SZn-Zn(q) and in the number-density structure factor SNN(q), indicating topological short-range order. The analysis of the bond distances, coordination numbers and bond angles shows that the local order might be described as trigonal prismatic (distorted trigonal prisms of Ca, centred by Zn) in analogy to the trigonal prismatic structures of the crystalline intermetallic compounds Ca3Zn (Re3B-type), Ca5Zn3 (Cr5B3 type) and CaZn (CrB type). read less NOT USED (high confidence) P. Ashu and C. Matthai, “Computer simulation of Si and Ge adatoms and thin layers on Si substrates,” Journal of Physics: Condensed Matter. 1989. link Times cited: 4 Abstract: The molecular dynamics method is used to determine minimum e… read moreAbstract: The molecular dynamics method is used to determine minimum energy configurations of Si and Ge adatoms on a Si surface. Results for thin layers of Ge on Si substrates and Si-Ge superlattices are also presented. read less NOT USED (high confidence) Z. Badirkhan, A. Ferrante, M. Rovere, and M. Tosi, “Statistical mechanical models for liquid and amorphous structure in covalently bonded systems,” Il Nuovo Cimento D. 1989. link Times cited: 1 NOT USED (high confidence) M. Kohyama, R. Yamamoto, Y. Ebata, and M. Kinoshita, “Atomic forces in the self-consistent tight-binding model,” Physica Status Solidi B-basic Solid State Physics. 1989. link Times cited: 11 Abstract: The self-consistent tight-binding (SCTB) model for structura… read moreAbstract: The self-consistent tight-binding (SCTB) model for structural and electronic properties of solids, which can treat both ionicity and covalency on an equal footing, is re-formulated so as to be applicable to general and disordered systems and is analyzed in comparison with the tight-binding bond (TBB) model. It is shown that atomic forces in the SCTB model are given very simply as well as in other tight-binding type theories. Atomic forces consist of three types of contributions, which are those from the interatomic Coulomb interaction, from the covalent energy, and from the overlap repulsion. By using the present formulation, it is possible to calculate quantum-mechanically the structural and electronic properties of extended defects or disordered systems of sp-bondod materials with both the properties, ionicity and covalency, which have not yet been treated enough theoretically or quantitatively.
Ein selbstkonsistentes Modell der starken Bindung (SCTB) fur strukturelle und elektronische Eigenschaften von festen Korpern, das Ionen- und Kovalenz-Eigenschaften gleichermasen behandeln kann, wird fur die Anwendung auf allgemeine und fehlgeordnete Systeme reformuliert und im Vergleich zum Modell der starken Bindung (TBB) analysiert. Es wird bewiesen, das die atomaren Krafte im SCTB-Modell wie bei anderen Theorien der starken Bindung sehr einfach gegeben werden. Die atomaren Krafte bestehen aus drei Arten von Beitragen, die der inter-atomaren Coulomb-Wechselwirkung, der kovalenten Energie, und der Uberlappungsabstosung. Mit der vorliegenden Formulierung ist es moglich, quantenmechanisch die strukturellen und elektronischen Eigenschaften von ausgedehnten Defekten oder fehlgeordneten Systemen von sp-gebundenen Materialien mit Ionen- und Kovalenz-Eigenschaften zu berechnen, die noch nicht genugend theoretisch oder quantitativ behandelt worden sind. read less NOT USED (high confidence) S. Erkoç, “A new empirical many‐body potential energy function. Application to microclusters,” Physica Status Solidi B-basic Solid State Physics. 1989. link Times cited: 37 Abstract: A new empirical many-body potential energy function is propo… read moreAbstract: A new empirical many-body potential energy function is proposed which comprises two- and three-body interactions. The two-body potential is a kind of hybrid function and the three-body potential is expressed in terms of the two-body interactions. The parameters of the potential energy function can be easily evaluated using dimer data and the bulk cohesive energy of the system considered. The proposed potential energy function is parameterized for several elements in f.c.c., b.c.c., and diamond structures and is applied for the investigation of structural stability and energetics of microclusters. The agreement between the present results and literature values is good.
Eine neue empirische Viel-Korper-Potentialfunktion wird vorgeschlagen, die Zwei- und Dreikorperwechselwirkungen beschreibt. Das Zwei-Korperpotential ist eine Art von Hybridfunktion und das Drei-Korper-Potential wird durch Zwei-Korperwechselwirkungen ausgedruckt. Die Parameter der Potentialenergiefunktion konnen mit Dimerdaten und der Volumenkohasionsenergie des betrachteten Systems einfach berechnet werden. Die vorgeschlagene Potentialfunktion wird fur einige Elemente in k.f.z.-, k.r.z.- und Diamant-Strukturen parametrisiert und zur Untersuchung der Strukturstabilitat und Energetik von Mikroclustern angewendet. Die Ubereinstimmung zwischen den vorgelegten Ergebnissen und Literaturwerten ist gut. read less NOT USED (high confidence) H. Iyetomi and P. Vashishta, “Generalisation of the density-functional theory and three-body interactions in classical fluids,” Journal of Physics: Condensed Matter. 1989. link Times cited: 9 Abstract: An external field coupled with the two-body density distribu… read moreAbstract: An external field coupled with the two-body density distribution function leads to a generalisation of the density-functional theory in which the free energy is regarded as a functional not only of the density but also of the two-body distribution function. The generalised formalism is applied to the liquid structure theory in the presence of a weak three-body potential. The first-order calculation shows that the three-body effects are fully incorporated into the theory through modification of the pair potential by virtue of the variational property of the free-energy functional. read less NOT USED (high confidence) X. Zeng and D. Stroud, “The solid-liquid interfacial tension of diamond-structure Si and Ge,” Journal of Physics: Condensed Matter. 1989. link Times cited: 10 Abstract: The authors extend their previously developed Ginzburg-Landa… read moreAbstract: The authors extend their previously developed Ginzburg-Landau theory for the solid-liquid interfaces of BCC elements to treat the diamond-structure elements Si and Ge. They use as an order parameter the amplitude of the (220) components of the density of solid. This order parameter is inserted into a simplified density-functional theory for the freezing of Si and Ge, and used to estimate explicitly the crystal-melt interfacial tensions. read less NOT USED (high confidence) A. Ferrante and M. Tosi, “Bond particle model for semiconductor melts and its application to the liquid structure of germanium,” Journal of Physics: Condensed Matter. 1989. link Times cited: 10 Abstract: A simple type of liquid-state model is proposed to describe … read moreAbstract: A simple type of liquid-state model is proposed to describe on a primitive level the melt of an elemental group IV semiconductor as a mixture of atoms and bond particles. The latter, on increase of a coupling strength parameter become increasingly localised between pairs of atoms up to local tetrahedral coordination of atoms by bond particles. Angular interatomic correlations are built into the model as bond particle localisation grows, even though the bare interactions between the components of the liquid are formally described solely in terms of central pair potentials. The model is solved for liquid structure by standard integral equation techniques of liquid-state theory and by Monte Carlo simulation, for values of the parameters which are appropriate to liquid germanium down to strongly supercooled states. The calculated liquid structure is compared with the results of diffraction experiments on liquid germanium near freezing and discussed in relation to diffraction data on amorphous germanium. The model suggests simple melting criteria for elemental and polar semiconductors, which are empirically verified. read less NOT USED (high confidence) S. Phillpot, J. Lutsko, D. Wolf, and S. Yip, “Growth kinetics of grain-boundary induced melting: A molecular-dynamics study,” MRS Proceedings. 1988. link Times cited: 0 Abstract: The growth kinetics of melting nucleated at a high-angle twi… read moreAbstract: The growth kinetics of melting nucleated at a high-angle twist boundary in silicon are investigated using molecular dynamics. Melting is found to be a two-stage process. In the first stage order is lost within a single plane at the interface and the density of the solid increases to that of the liquid. In the second stage the atomic coordination changes and an isotropic liquid is formed. 11 refs., 4 figs., 1 tab. read less NOT USED (high confidence) D. Chokappa and P. Clancy, “The influence of an interface in the promotion of melting,” Molecular Physics. 1988. link Times cited: 6 Abstract: The effect of the presence of a solid/liquid interface in pr… read moreAbstract: The effect of the presence of a solid/liquid interface in preventing the superheating and supercooling found in previous surfaceless systems is investigated using isothermal (constant-NVT) molecular dynamics. The particles interact via a Lennard-Jones potential cut at c = 2·5. Computer simulations are performed at temperatures around the expected melting point for three different pressures, close to P* = 0·0, 0·67 and 9·0. The results show that there is no evidence of any superheating of the lattice or supercooling of the liquid. This points to the significant importance of the presence of an interface in melting and freezing phenomena. Since only thermodynamically stable points are produced, the method can be used to determine the melting point of the system. It is shown that the melting point thus produced is more accurate than that obtained using the hysteresis loop found in surfaceless systems. This is particularly apparent at higher pressures. read less NOT USED (high confidence) F. Stillinger and R. LaViolette, “Sensitivity of liquid‐state inherent structure to details of intermolecular forces,” Journal of Chemical Physics. 1985. link Times cited: 27 Abstract: Temperature dependence of short‐range order has been systema… read moreAbstract: Temperature dependence of short‐range order has been systematically studied in two model atomic liquids, using molecular dynamics computer simulation linked to steepest‐descent mapping of configurations onto potential minima. Owing primarily to differing attractive forces, the natural crystal structures differ for the two models (face‐centered‐cubic vs primitive hexagonal). Only one of these crystals is geometrically consistent with the number of particles (256) and boundary conditions (periodic, cubic cell) used for both. Nevertheless, both liquids were found to exhibit temperature dependence of short‐range order arising solely from vibrational smearing of underlying temperature‐independent inherent structure. The latter differs substantially for the two models, and in each case resembles a highly defective version of the corresponding crystal. read less NOT USED (high confidence) Y. Yang et al., “Taking materials dynamics to new extremes using machine learning interatomic potentials,” Journal of Materials Informatics. 2021. link Times cited: 5 Abstract: Understanding materials dynamics under extreme conditions of… read moreAbstract: Understanding materials dynamics under extreme conditions of pressure, temperature, and strain rate is a scientific quest that spans nearly a century. Atomic simulations have had a considerable impact on this endeavor because of their ability to uncover materials’ microstructure evolution and properties at the scale of the relevant physical phenomena. However, this is still a challenge for most materials as it requires modeling large atomic systems (up to millions of particles) with improved accuracy. In many cases, the availability of sufficiently accurate but efficient interatomic potentials has become a serious bottleneck for performing these simulations as traditional potentials fail to represent the multitude of bonding. A new class of potentials has emerged recently, based on a different paradigm from the traditional approach. The new potentials are constructed by machinelearning with a high degree of fidelity from quantum-mechanical calculations. In this review, a brief introduction to the central ideas underlying machine learning interatomic potentials is given. In particular, the coupling of machine learning models with domain knowledge to improve accuracy, computational efficiency, and interpretability is highlighted. Subsequently, we demonstrate the effectiveness of the domain knowledge-based approach in certain select problems related to the kinetic response of warm dense materials. It is hoped that this review will inspire further advances in the understanding of matter under extreme conditions. read less NOT USED (high confidence) D.-K. Cao, “Pair distribution functions in molecular dynamics simulations of interfaces.” 2020. link Times cited: 0 Abstract: Pair Distribution Functions in Molecular Dynamics Simulation… read moreAbstract: Pair Distribution Functions in Molecular Dynamics Simulations of Interface by Deng Cao Thin films of silicon nitride on silicon are well suited materials for many applications including photovoltaics. Large-scale molecular-dynamics simulations of silicon/silicon nitride interfaces under externally applied tensile strain are performed in an attempt to improve understanding of this interface. The simulations reveal stress release in form of fracture, slip, pit formation, and interface phase transition under high stress condition. The silicon/silicon nitride interface is described as an eight-component system thereby offering valuable information in some of the thirty-six different pair distribution functions. We find that fracture in silicon nitride, with a centerpiece breaking off the sides, is reflected in a return to the original height of the first peak of the Si-N pair distribution function indicating that this centerpiece is essentially unstretched. Slip and pit formation in silicon as well as formation of domains of two different interface phases are identified by additional peaks in the pair distribution functions at and across the interface. Understanding selective pair distribution functions calculated at various stages of a particular simulation offer the opportunity to analyze structural and mechanical failure of large systems without knowing the detailed properties of individual atoms in the system. In particular, the occurrence of peaks reflecting new interatomic distances allows early predictions of failure. read less NOT USED (high confidence) V. Levitas, H. Chen, and L. Xiong, “Phase Transitions and Their Interaction with Dislocations in Silicon.” 2018. link Times cited: 2 NOT USED (high confidence) H. Meidani, J. Hooper, D. Bedrov, and R. Kirby, “CALIBRATION AND RANKING OF COARSE-GRAINED MODELS IN MOLECULAR SIMULATIONS USING BAYESIAN FORMALISM,” International Journal for Uncertainty Quantification. 2017. link Times cited: 4 Abstract: CALIBRATION AND RANKING OF COARSE-GRAINED MODELS IN MOLECULA… read moreAbstract: CALIBRATION AND RANKING OF COARSE-GRAINED MODELS IN MOLECULAR SIMULATIONS USING BAYESIAN FORMALISM Hadi Meidani,1,∗ Justin B. Hooper,2 Dmitry Bedrov,2 & Robert M. Kirby3 1Department of Civil and Environmental Engineering, 1211 Newmark Civil Engineering Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61822, USA 2Department of Materials Science & Engineering, 206 Civil and Materials Engineering Building, University of Utah, Salt Lake City, UT 84112, USA 3School of Computing, 3750 Warnock Engineering Building, University of Utah, Salt Lake City, UT 84112, USA read less NOT USED (high confidence) Z. Zhang and H. Urbassek, “Indentation into an Al/Si composite: enhanced dislocation mobility at interface,” Journal of Materials Science. 2017. link Times cited: 21 NOT USED (high confidence) E. Neyts and P. Brault, “Molecular Dynamics Simulations for Plasma‐Surface Interactions,” Plasma Processes and Polymers. 2017. link Times cited: 51 Abstract: Plasma-surface interactions are in general highly complex du… read moreAbstract: Plasma-surface interactions are in general highly complex due to the interplay of many concurrent processes. Molecular dynamics simulations provide insight in some of these processes, subject to the accessible time and length scales, and the availability of suitable force fields. In this introductory tutorial-style review, we aim to describe the current capabilities and limitations of molecular dynamics simulations in this field, restricting ourselves to low-temperature non-thermal plasmas. Attention is paid to the simulation of the various fundamental processes occurring, including sputtering, etching, implantation, and deposition, as well as to what extent the basic plasma components can be accounted for, including ground state and excited species, electric fields, ions, photons, and electrons. A number of examples is provided, giving an bird's eye overview of the current state of the field. read less NOT USED (high confidence) B. K. Madappa, “Mobility of Hydrogen-Vacancy Complexes in Nickel.” 2016. link Times cited: 0 Abstract: Atomistic simulations of the mechanism of hydrogen pileup ar… read moreAbstract: Atomistic simulations of the mechanism of hydrogen pileup around a vacancy and its effect on the vacancy mobility are performed to investigate possible mechanisms for hydrogen embrittlement in nickel.We show that the vacancy is capable of trapping 12 hydrogen atoms.The trapping energy is found to be approximately equal to -0.14 eV.We find that the interstitial hydrogen in the bulk lattice prefers to be located at octahedral interstitial positions which is in agreement with previous works.The influence of the vacancy defect is not limited to its volume but also extends to the octahedral sites of its first-nearest-neighbours.The hydrogen atoms prefer to cluster around the single vacancy.We also look at the effect of pressure on the trapping and migration energies of the hydrogen-vacancy complex.We find that the magnitude of the energy is influenced by stress.The hydrogen atom cloud around the vacancy defect also exerts some resistance towards the migration of the defect. read less NOT USED (high confidence) F. G. VanGessel, “Fully Anisotropic Solution of the Three Dimensional Boltzmann Transport Equation.” 2016. link Times cited: 0 Abstract: Title of dissertation: Fully Anisotropic Solution of the Thr… read moreAbstract: Title of dissertation: Fully Anisotropic Solution of the Three Dimensional Boltzmann Transport Equation Francis G. VanGessel, Masters of Science, 2016 Thesis directed by: Professor Peter W. Chung Department of Mechanical Engineering The development of accurate modeling techniques for nanoscale thermal transport is an active area of research. Modern day nanoscale devices have length scales of tens of nanometers and are prone to overheating, which reduces device performance and lifetime. Therefore, accurate temperature profiles are needed to predict the reliability of nanoscale devices. The majority of models that appear in the literature obtain temperature profiles through the solution of the Boltzmann transport equation (BTE). These models often make simplifying assumptions about the nature of the quantized energy carriers (phonons). Additionally, most previous work has focused on simulation of planar two dimensional structures. This thesis presents a method which captures the full anisotropy of the Brillouin zone within a three dimensional solution to the BTE. The anisotropy of the Brillouin zone is captured by solving the BTE for all vibrational modes allowed by the Born Von-Karman boundary conditions. read less NOT USED (high confidence) S. Urata and S. Li, “Higher order Cauchy–Born rule based multiscale cohesive zone model and prediction of fracture toughness of silicon thin films,” International Journal of Fracture. 2016. link Times cited: 18 NOT USED (high confidence) S. Kazachenko and A. Thakkar, “How Can One Locate the Global Energy Minimum for Hydrogen-Bonded Clusters?” 2016. link Times cited: 0 NOT USED (high confidence) A. McGaughey and J. Larkin, “PREDICTING PHONON PROPERTIES FROM EQUILIBRIUM MOLECULAR DYNAMICS SIMULATIONS,” Annual Review of Heat Transfer. 2014. link Times cited: 84 Abstract: The objective of this chapter is to describe how equilibrium… read moreAbstract: The objective of this chapter is to describe how equilibrium molecular dynamics simulations (with the help of harmonic lattice dynamics calculations) can be used to predict phonon properties and thermal conductivity using normal mode decomposition. The molecular dynamics and lattice dynamics methods are reviewed and the normal mode decomposition technique is described in detail. The application of normal mode decomposition is demonstrated through case studies on crystalline, alloy, and amorphous Lennard-Jones phases. Notable works that used normal mode decomposition are presented and the future of molecular dynamics simulations in phonon transport modeling is discussed. read less NOT USED (high confidence) J. Shiomi, “NONEQUILIRIUM MOLECULAR DYNAMICS METHODS FOR LATTICE HEAT CONDUCTION CALCULATIONS,” Annual Review of Heat Transfer. 2014. link Times cited: 38 NOT USED (high confidence) P. Seleson, M. Parks, and M. Gunzburger, “Peridynamic State-Based Models and the Embedded-Atom Model,” Communications in Computational Physics. 2014. link Times cited: 27 Abstract: We investigate connections betweennonlocal continuum models … read moreAbstract: We investigate connections betweennonlocal continuum models andmolec- ular dynamics. A continuous upscaling of molecular dynamics models of the form of the embedded-atom model is presented, providing means for simulating molecular dynamics systems at greatly reduced cost. Results are presented for structured and structureless material models, supported by computational experiments. The nonlocal continuum models are shown to be instances of the state-based peridynamics theory. Connections relating multibody peridynamic models and upscaled nonlocal contin- uum models are derived. read less NOT USED (high confidence) K. Miyake et al., “Characterization of polymer layer formation during SiO2/SiN etching by fluoro/hydrofluorocarbon plasmas,” Japanese Journal of Applied Physics. 2014. link Times cited: 10 Abstract: In reactive-ion etching (RIE) of silicon oxide (SiO2) or sil… read moreAbstract: In reactive-ion etching (RIE) of silicon oxide (SiO2) or silicon nitride (SiN) by fluorocarbon (FC) or hydrofluorocarbon (HFC) plasmas, fluorinated carbon layers may be formed on the etched surfaces and affect their etching rates. In this study, the properties of SiO2 and SiN etching by FC or HFC plasmas are examined in light of the formation mechanism of such carbon layers by molecular dynamics (MD) simulation. Furthermore, in this study, the electronegativity effect of fluorine (F) is taken into account in the interatomic potential functions for C–F and Si–F bonds and MD simulations here show SiO2 and SiN sputtering yields are closer to those obtained from ion beam experiments. It has been found from MD simulations that the SiN sputtering yield during etching by HFC ions is higher than that by FC ions owning to the fact that hydrogen in the HFC ion beam tends to impede the formation of a fluorocarbon layer on SiN and therefore energetic fluorine ions/atoms are more readily available to etch SiN underneath the polymer layer. read less NOT USED (high confidence) C. Jiang, D. Morgan, and I. Szlufarska, “Structures and stabilities of small carbon interstitial clusters in cubic silicon carbide,” Acta Materialia. 2014. link Times cited: 19 NOT USED (high confidence) T. Zohdi, “Numerical simulation of the impact and deposition of charged particulate droplets,” J. Comput. Phys. 2013. link Times cited: 57 NOT USED (high confidence) D. Schopf, “Effective potentials for numerical investigations of complex intermetallic phases.” 2013. link Times cited: 0 Abstract: The class of Complex Metallic Alloys (CMAs) is interesting f… read moreAbstract: The class of Complex Metallic Alloys (CMAs) is interesting for its wide range of physical properties. There are materials that exhibit high hardness at low density or good corrosion resistance, which is important for technological applications. Other compounds are superconductors, have strong anisotropic transport coefficients or exhibit a novel magnetic memory effect. The theoretical investigation of CMAs is often very challenging because of their inherent complexity and large unit cells with up to several thousand atoms. Molecular dynamics simulations with classical interaction potentials are well suited for this task – they can handle hundreds of thousands of atoms in reasonable time. Such simulations can provide insight into static and dynamic processes at finite temperatures on an atomistic level.
The accuracy of these simulations depends strongly on the quality of the employed interaction potentials. To generate physically relevant potentials the force-matching method can be applied. A computer code called potfit has been developed at the Institute for Theoretical and Applied Physics (ITAP) especially for this task. It uses a large database of quantum-mechanically calculated reference data, forces on individual atoms and cohesive energies, to generate effective potentials. The parameters of the potential are optimized in such a way that the reference data are reproduced as accurately as possible.
The potfit program has been greatly enhanced as part of this thesis. The optimization of analytic potentials, new interaction models as well as a new optimization algorithm were implemented. Potentials for two different complex metallic alloy systems have been generated and used to study their properties with molecular dynamics simulations.
The first system is an approximant to the decagonal Al-Pd-Mn quasicrystal. A potential which can reproduce the cohesive energy with high accuracy was generated. With the help of this potential a refinement of the experimentally poorly determined structure model could be performed.
The second class of potentials was fitted for intermetallic clathrate systems. They have interesting thermoelectric properties which originate from their special structure. Silicon- and germanium-based clathrate potentials were derived and the influence of the complex structure on the thermal conductivity has been studied.
Komplexe Intermetallische Verbindungen (CMAs) sind aufgrund ihrer vielfaltigen physikalischen Eigenschaften sehr interessant fur technologische Anwendungen. Dabei ist z.B. hohe Harte bei geringer Dichte und Korrosionsbestandigkeit wichtig. Neben Supraleitern gibt es Materialien mit anisotropen Transporteigenschaften oder einem neuartigen magnetischen Memory Effekt. Theoretische Untersuchungen von CMAs stellen durch ihre inharente Komplexitat und die riesigen Einheitszellen mit mehreren tausend Atomen oft eine grose Herausforderung dar. Molekulardynamiksimulationen mit effektiven Potenzialen konnen dazu eingesetzt werden; sie ermoglichen die Berechnung von hunderttausenden von Atome in annehmbarer Zeit. Damit kann ein Einblick in sowohl statische als auch dynamische Prozesse auf atomarer Ebene gewonnen werden.
Die Ergebenisse solcher Simulationen hangen jedoch sehr stark von der Qualitat der eingesetzten Wechselwirkung ab. Um physikalisch gerechtfertigte Potenziale zu erzeugen, kann die Force-Matching-Methode angewandt werden. Dazu wurde am Institut fur Theoretische und Angewandte Physik (ITAP) ein Programm mit dem Namen potfit entwickelt. Es verwendet eine grose Datenbank von quantenmechanisch berechneten Referenzgrosen wie z.B. Krafte auf die einzelnen Atome und die Kohasionsenergie, um effektive Potenziale zu generieren. Die freien Parameter des Potenzials werden optimiert, um die Referenzdaten so gut wie moglich zu reproduzieren.
Fur diese Arbeit wurde potfit deutlich erweitert. Es konnen nun analytisch definierte Potenziale optimiert werden, neue Wechselwirkungen wurden implementiert und ein neuer Optimierungsalgorithmus wurde hinzugefugt. Damit wurden effektive Potenziale fur zwei verschiedene CMA Systeme gefittet und deren Eigenschaften mit Molekulardynamik untersucht.
Fur die Approximanten eines decagonalen Al-Pd-Mn Quasikristalls, den Xi-Phasen, wurde ein Potenzial fur die Strukturbestimmung erzeugt. Es kann die Kohasionsenergien verschiedener Strukturen mit groser Genauigkeit wiedergeben. Ein aus experimentellen Daten ungenau bestimmtes Strukturmodell konnte damit erheblich verbessert werden.
Auserdem wurden Potenziale fur Intermetallische Klathrate erzeugt. Diese Systeme besitzen interessante thermoelektrische Eigenschaften aufgrund ihrer speziellen Kafigstruktur. Effektive Wechselwirkungen fur silizium- und germaniumbasierte Klathrate wurden erzeugt. Damit wurde der Einfluss der komplexen Struktur auf die thermische Leitfahigkeit des Gitters untersucht. read less NOT USED (high confidence) W. Noid, “Systematic methods for structurally consistent coarse-grained models.,” Methods in molecular biology. 2013. link Times cited: 57 NOT USED (high confidence) T. Hori, T. Shiga, S. Maruyama, and J. Shiomi, “Mode-Dependent Phonon Transport Analysis of Silicon Crystal by Molecular Dynamics Method,” Transactions of the Japan Society of Mechanical Engineers. B. 2012. link Times cited: 4 Abstract: In this work, we have investigated phonon transport in silic… read moreAbstract: In this work, we have investigated phonon transport in silicon crystal using molecular dynamics and lattice dynamics methods. The phonon relaxation time is derived from molecular phase space trajectories through two different analysis methods using normal mode projection and spectral energy density. By performing the calculations for wavevectors spanning the entire first Brillouin zone, we find that these two relaxation-time calculation methods give almost the same results despite the fundamental difference in the underlying theories. With the obtained phonon relaxation time and group velocity calculated by lattice dynamics method, we have quantified the contribution from each phonon mode to the overall thermal conductivity. In addition, by calculating the cumulative thermal conductivity, we have quantified contributions to thermal conductivity from phonons with different mean free paths to gain insight into the scale effect of heat conduction in nanoscale. read less NOT USED (high confidence) J. Zang and Y.-pu Zhao, “Silicon nanowire reinforced by single-walled carbon nanotube and its applications to anti-pulverization electrode in lithium ion battery,” Composites Part B-engineering. 2012. link Times cited: 49 NOT USED (high confidence) C. H. Baker, C. Wu, R. N. Salaway, L. Zhigilei, and P. Norris, “Vibrational Contribution to Thermal Conductivity of Silicon Near Solid-Liquid Transition.” 2011. link Times cited: 2 Abstract: Although thermal transport in silicon is dominated by phonon… read moreAbstract: Although thermal transport in silicon is dominated by phonons in the solid state, electrons also participate as the system approaches, and exceeds, its melting point. Thus, the contribution from both phonons and electrons must be considered in any model for the thermal conductivity, k, of silicon near the melting point. In this paper, equilibrium molecular dynamics simulations measure the vibration mediated thermal conductivity in Stillinger-Weber silicon at temperatures ranging from 1400 to 2000 K — encompassing the solid-liquid phase transition. Non-equilibrium molecular dynamics is also employed as a confirmatory study. The electron contribution may then be estimated by comparing these results to experimental measurements of k. The resulting relationship may provide a guide for the modeling of heat transport under conditions realized in high temperature applications, such as laser irradiation or rapid thermal processing of silicon substrates.Copyright © 2011 by ASME read less NOT USED (high confidence) S. Sonntag, “Computer simulations of laser ablation from simple metals to complex metallic alloys.” 2011. link Times cited: 10 Abstract: In this work, a method for computer simulations of laser abl… read moreAbstract: In this work, a method for computer simulations of laser ablation in metals is presented. The ambitious task to model the physical processes, that occur on different time and length scales, is overcome to some extent by the combination of two techniques: Molecular dynamics and finite differences. The former is needed to achieve atomistic resolution of the processes involved. Material failure like melting, vaporization or spallation occur on the atomic scale. Light absorption and electronic heat conduction, which plays the major role in metals, is described by a generalized heat conduction equation solved by the finite differences method. From the so-called Two-Temperature Model temperature, density and pressure evolution - both in time and space - can be derived. With this, various studies on laser heated metals were done. For reasons discussed in more detail later, aluminum was chosen as a model system for most simulations on isotropic materials. As a more complex structure, the metallic alloy Al13Co4 was used because of its special material properties. As an approximant to the decagonal phase of Al-Ni-Co, the alloy shows an anisotropy in its transport properties, e.g. an anisotropic heat conduction.
It will be shown, that the model is able to describe the physics in laser heated solids on time scales from 100 fs up to the ns-scale properly. Great insight was gained about the processes occuring during and shortly after the laser pulse. Many of the quantities interesting for experimentalists can be predicted by the theory. From the simulations relevant parameters like the electron-cooling time or the important ablation threshold were calculated. All values match their experimental counterpart very well.
Die vorliegende Arbeit beschaftigt sich mit der Laserablation in Metallen. Ziel ist es, mit Hilfe von numerischen Simulationen das Verhalten von Metallen nach der Bestrahlung mit intensiven Laserpulsen vorherzusagen. Die Arbeit ist inhaltlich in zwei Teile gegliedert. In der ersten Halfte werden theoretische Grundlagen, eine qualitative Beschreibung der Ablation und die Implementierung des Modells gegeben. Im zweiten Teil folgen Ergebnisse sowie, falls vorhanden, Vergleiche mit Experimenten. Die Arbeit schliest mit einer Zusammenfassung und einem Ausblick. read less NOT USED (high confidence) T. Zushi, Y. Kamakura, K. Taniguchi, I. Ohdomari, and T. Watanabe, “Molecular Dynamics Simulation on Longitudinal Optical Phonon Mode Decay and Heat Transport in a Silicon Nano-Structure Covered with Oxide Films,” Japanese Journal of Applied Physics. 2011. link Times cited: 6 Abstract: A series of molecular dynamics (MD) simulations have been co… read moreAbstract: A series of molecular dynamics (MD) simulations have been conducted to investigate the heat transport in terms of the phonon dynamics in nanoscale silicon (Si). This work is motivated by a concern over the stagnation of heat at the drain region of nanoscopic transistors, owing to this, a large amount of optical phonons with a low group velocity are emitted from hot electrons, which are ballistically transferred through channel region. The point of this work is the explicit inclusion of the SiO2 film in the MD simulation of the Si lattice. The calculation results show that longitudinal optical (LO) phonons decay faster as Si lattice thickness decreases and turn into acoustic phonons. In contrast, thermal diffusion rate decreases with Si lattice thickness. Both the decay rate of LO phonons and thermal diffusion rate are not governed by oxide thickness. These results imply that the phonon scattering at the SiO2/Si interface is enhanced by thinning the Si layer. In nanoscopic devices, a thin Si layer is effective in diminishing the optical phonons with a low group velocity, but it hinders the subsequent heat transport. read less NOT USED (high confidence) A. Connelly, K. Travis, R. Hand, N. Hyatt, and E. Maddrell, “Composition–Structure Relationships in Simplified Nuclear Waste Glasses: 1. Mixed Alkali Borosilicate Glasses,” Journal of the American Ceramic Society. 2011. link Times cited: 21 Abstract: Mixed alkali borosilicate glasses show a complex relationshi… read moreAbstract: Mixed alkali borosilicate glasses show a complex relationship between composition and structure. These relationships are often difficult to fully investigate using standard laboratory methods. Therefore, we present here a systematic molecular dynamics (MD) study of composition–structure relationships in sodium lithium borosilicate glasses. Results are compared with the published laboratory glass data. These glasses are of importance to the U.K. nuclear waste vitrification program where an understanding of glass structure can improve greatly the understanding of long-term glass properties and waste element solubility. The MD-simulated glasses produced in this work show close agreement with laboratory glasses for bond lengths, atom coordinations and bond angles of all species. Particularly, the change in coordination of boron is accurately reproduced over a wide compositional range without the use of a three-body potential for the O–B–O angle. The change in the polymerization and mixing of the silicate and borate networks with composition in the MD-simulated glasses was shown to agree well with that seen in laboratory glasses. read less NOT USED (high confidence) A. Connelly, K. Travis, R. Hand, N. Hyatt, and E. Maddrell, “Composition–Structure Relationships in Simplified Nuclear Waste Glasses: 2. The Effect of ZrO2 Additions,” Journal of the American Ceramic Society. 2011. link Times cited: 15 Abstract: The presence of large quantities of ZrO2 in certain high-lev… read moreAbstract: The presence of large quantities of ZrO2 in certain high-level nuclear waste streams presents a significant problem due to the relatively low solubility of ZrO2 in oxide glasses. Here, molecular dynamic modeling was used to give insights into the structure of two sodium–lithium borosilicate glasses with additions of ZrO2. The structural environment of Zr within the molecular dynamics (MD)-simulated glasses correlated well with that shown in the literature. There has been limited study previously into the changes in bulk glass structure with ZrO2 additions. This work shows that addition of ZrO2 changes the coordination of boron and the polymerization of the glass network due to the requirement for 1 mol of alkali oxide for charge compensation. The change in boron coordination is shown to be nonlinear with the addition of ZrO2. We have also shown a possible method of predicting the solubility limits of oxides within glasses from MD simulations. read less NOT USED (high confidence) T. Dumitricǎ, “Computational Nanomechanics of Quasi-one-dimensional Structures in a Symmetry-Adapted Tight Binding Framework.” 2010. link Times cited: 2 NOT USED (high confidence) M. Timonova and B. Thijsse, “Optimizing the MEAM potential for silicon,” Modelling and Simulation in Materials Science and Engineering. 2010. link Times cited: 25 Abstract: By applying simulated annealing techniques we fit the modifi… read moreAbstract: By applying simulated annealing techniques we fit the modified embedded atom method (MEAM) potential to a database of ab initio energies for silicon and construct an improved parametrization of this potential. In addition, we introduce a new, reference-free version of the MEAM potential. This MEAM version is also fitted to the silicon data and shows an even better agreement, although the improvement is modest. Finally, we investigate whether increasing the number of different angular terms in the MEAM potential from 3 to 4 will lead to a better potential. The aim of this work is to determine a broad-ranged potential, one that is reliable in many different low- and high-energy atomic geometries in silicon crystals, molecules, near defects and under strain. To verify this, the performance of the new potentials is tested in different circumstances that were not explicitly included in the fit: relaxed defect energies, thermal expansion, melting temperature and liquid silicon. The new MEAM parametrizations found in this work, called MEAM-M and RF-MEAM, are shown to be overall more accurate than previous potentials—although a few defect energies are exceptions—and we recommend them for future work. The melting temperatures are closer to the experiment than those of other MEAM potentials, but they are still too high. read less NOT USED (high confidence) C. Ciobanu, C. Wang, D. P. Mehta, and K. Ho, “Predicting the Atomic Configuration of 1- and 2-Dimensional Nanostructures via Global Optimization Methods.” 2010. link Times cited: 1 NOT USED (high confidence) J. Turney, A. McGaughey, and C. Amon, “Critically Assessing the Application of Quantum Corrections to Classical Thermal Conductivity Predictions.” 2009. link Times cited: 0 Abstract: Quantum corrections can be used to map the thermal conductiv… read moreAbstract: Quantum corrections can be used to map the thermal conductivity predicted in a classical framework [e.g., a molecular dynamics (MD) simulation] to a corresponding value in a quantum system. This procedure is accomplished by equating the total energies and energy fluxes of the classical and quantum systems. The validity of these corrections is questionable because they are introduced in an ad hoc manner and are not derived from first principles. In this work, the validity of these quantum corrections is examined by comparing the thermal conductivity of Stillinger-Weber silicon calculated using a full quantum mechanical treatment to a quantum-corrected value predicted from a classical framework between temperatures of 10 K and 1000 K. The quantum and classical predictions are obtained using anharmonic lattice dynamics calculations. We find discrepancies between the quantum-corrected predictions and the quantum predictions obtained directly. We investigate the causes of these discrepancies and from our findings, conclude that quantum thermal conductivities cannot be predicted by applying simple corrections to the values obtained from a purely classical framework.Copyright © 2009 by ASME read less NOT USED (high confidence) J. Snyman and S. Kok, “A reassessment of the Snyman–Fatti dynamic search trajectory method for unconstrained global optimization,” Journal of Global Optimization. 2009. link Times cited: 10 NOT USED (high confidence) J. Yuhang, M. Qingyuan, and Z. Wei, “Atomistic simulations of the tensile and melting behavior of silicon nanowires,” Journal of Semiconductors. 2009. link Times cited: 0 Abstract: Molecular dynamics simulations with Stillinger–Weber potenti… read moreAbstract: Molecular dynamics simulations with Stillinger–Weber potential are used to study the tensile and melting behavior of single-crystalline silicon nanowires (SiNWs). The tensile tests show that the tensile behavior of the SiNWs is strongly dependent on the simulation temperature, the strain rate, and the diameter of the nanowires. For a given diameter, the critical load significantly decreases as the temperature increases and also as the strain rate decreases. Additionally, the critical load increases as the diameter increases. Moreover, the melting tests demonstrate that both melting temperature and melting heat of the SiNWs decrease with decreasing diameter and length, due to the increase in surface energy. The melting process of SiNWs with increasing temperature is also investigated. read less NOT USED (high confidence) J. Wernik and S. Meguid, “Coupling atomistics and continuum in solids: status, prospects, and challenges,” International Journal of Mechanics and Materials in Design. 2008. link Times cited: 46 NOT USED (high confidence) L. Marqués, L. Pelaz, I. Santos, P. López, and M. Aboy, “Atomistic Simulation Techniques in Front-End Processing,” MRS Proceedings. 2008. link Times cited: 0 Abstract: Atomistic process models are beginning to play an important … read moreAbstract: Atomistic process models are beginning to play an important role as direct simulation approaches for front-end processes and materials, and also as a pathway to improve continuum modeling. Detailed insight into the underlying physics using ab-initio methods and classical molecular dynamics simulations will be needed for understanding the kinetics of reduced thermal budget processes and the role of impurities. However, the limited sizes and time scales accessible for detailed atomistic techniques usually lead to the difficult task of relating the information obtained from simulations to experimental data. The solution consists of the use of a hierarchical simulation scheme: more fundamental techniques are employed to extract parameters and models that are then feed into less detailed simulators which allow direct comparison with experiments. This scheme will be illustrated with the atomistic modeling of the ion-beam induced amorphization and recrystallization of silicon. The model is based on the bond defect or IV pair, which is used as the building block of the amorphous phase. It is shown that the recombination of this defect depends on the surrounding bond defects, which accounts for the cooperative nature of the amorphization and recrystallization processes. The implementation of this model in a kinetic Monte Carlo code allows extracting data directly comparable with experiments. read less NOT USED (high confidence) J. Turney, A. McGaughey, and C. Amon, “Effects of Confinement and Surface Reconstruction on the Lattice Dynamics and Thermal Transport Properties of Thin Films.” 2007. link Times cited: 1 Abstract: Phonon transport in argon and silicon thin films is examined… read moreAbstract: Phonon transport in argon and silicon thin films is examined using harmonic lattice dynamics theory and the Lennard-Jones and Stillinger-Weber potentials. Film thicknesses ranging from 0.8 to 33.5 nm for argon and 0.4 to 8.6 nm for silicon are examined at a temperature of 0 K. Both reconstructed films and films built using the bulk unit cell are considered. Phonon dispersion curves for the in-plane direction and the density of states are computed from lattice dynamics and compared to predictions for a bulk system. The results from the lattice dynamics calculations are used to predict the thermal conductivities of the bulk and thin film structures.Copyright © 2007 by ASME read less NOT USED (high confidence) E. Landry, A. McGaughey, and M. Hussein, “Molecular Dynamics Prediction of the Thermal Conductivity of Si/Ge Superlattices.” 2007. link Times cited: 7 Abstract: Molecular dynamics simulations and the non-equilibrium direc… read moreAbstract: Molecular dynamics simulations and the non-equilibrium direct method are used to predict the thermal conductivity of a Si/Ge superlattice modeled by the Stillinger-Weber potential at a temperature of 300 K. We focus on the methodology of making the thermal conductivity prediction (limited effort has been made to model Si/Ge nanocomposites in the literature) and find that proper selection of the size and composition of the thermal reservoirs is important.Copyright © 2007 by ASME read less NOT USED (high confidence) G. Csányi, G. Moras, J. Kermode, M. Payne, A. Mainwood, and A. Vita, “Multiscale modeling of defects in semiconductors : a novel molecular-dynamics scheme,” Topics in Applied Physics. 2007. link Times cited: 5 NOT USED (high confidence) K. Scheerschmidt and M. Planck, “Empirical Molecular Dynamics: Possibilities, Requirements, and Limitations.” 2007. link Times cited: 9 NOT USED (high confidence) W. Wang, “An adaptive multi-scale computational method for modeling nonlinear deformation in nanoscale materials.” 2006. link Times cited: 1 Abstract: In this dissertation a coupled multi-scale computational mod… read moreAbstract: In this dissertation a coupled multi-scale computational model for simulating nonlinear deformation processes in crystalline metals at finite temperatures is developed. The computational model uses the finite element method to model the coarse scale response of the material. The constitutive response in the finite element will be modeled through interatomic potentials acting on the underlying homogeneous crystal lattice that characterizes its nanostructure. An adaptive remeshing technique is proposed to automatically delineate regions of severe deformation where homogeneity of the microstructure/deformation is violated. In these regions the finite element will be replaced by a set of deformed atoms which interact with each other through the interatomic potential. The resulting coupled multi-scale model will be used to study defect generation and growth, through a computational nanoindentation experiment, in practical 2D and 3D problems. read less NOT USED (high confidence) D. Murdick, X. W. Zhou, and H. Wadley, “Low-temperature atomic assembly of stoichiometric gallium arsenide from equiatomic vapor,” Journal of Crystal Growth. 2006. link Times cited: 18 NOT USED (high confidence) T. Hawa and M. Zachariah, “Coalescence kinetics of unequal sized nanoparticles,” Journal of Aerosol Science. 2006. link Times cited: 128 NOT USED (high confidence) N. Kalyanasundaram, M. C. Moore, J. Freund, and H. Johnson, “Structure and Stress Evolution Due to Medium Energy Ion Bombardment of Silicon.” 2006. link Times cited: 1 NOT USED (high confidence) Y. Chen, G. Wang, D. Li, and J. Lukes, “THERMAL EXPANSION AND ISOTOPIC COMPOSITION EFFECTS ON LATTICE THERMAL CONDUCTIVITIES OF CRYSTALLINE SILICON.” 2006. link Times cited: 1 Abstract: Equilibrium molecular dynamics simulation is used to calcula… read moreAbstract: Equilibrium molecular dynamics simulation is used to calculate lattice thermal conductivities of crystal silicon in the temperature range from 400K to 1600K. Simulation results confirmed that thermal expansion, which resulted in the increase of the lattice parameter, caused the decrease of the lattice thermal conductivity. The simulated results proved that thermal expansion imposed another type resistance on phonon transport in crystal materials. Isotopic and vacancy effects on lattice thermal conductivity are also investigated and compared with the prediction from the modified Debye Callaway model. It is demonstrated in the MD simulation results that the isotopic effect on lattice thermal conductivity is little in the temperature range from 400K to 1600K for isotopic concentration below 1%, which implies the isotopic scattering on phonon due to mass difference can be neglected over the room temperature. The remove of atoms from the crystal matrix caused mass difference and elastic strain between the void and the neighbor atoms, which resulted in vacancy scattering on phonons. Simulation results demonstrated this mechanism is stronger than that caused by isotopic scattering on phonons due to mass difference. A good agreement is obtained between the MD simulation results of silicon crystal with vacancy defects and the data predicted from the modified Debye Callaway model. This conclusion is helpful to demonstrate the validity of Klemens' Rayleigh model for impurity scattering on phonons.Copyright © 2006 by ASME read less NOT USED (high confidence) M. Arndt and M. Griebel, “Derivation of Higher Order Gradient Continuum Models from Atomistic Models for Crystalline Solids,” Multiscale Model. Simul. 2005. link Times cited: 78 Abstract: We propose a new upscaling scheme for the passage from atomi… read moreAbstract: We propose a new upscaling scheme for the passage from atomistic to continuum mechanical models for crystalline solids. It is based on a Taylor expansion of the deformation function and allows us to capture the microscopic properties and the discreteness effects of the underlying atomistic system up to an arbitrary order. The resulting continuum mechanical model involves higher order terms and gives a description of the specimen within the quasi-continuum regime. Furthermore, the convexity of theatomistic potential is retained, which leads to well-posed evolution equations. We numerically compare our technique to other common upscaling schemes for the example of an atomic chain. Then we apply our approach to a physically more realistic many-body potential of crystalline silicon. Here the above-mentioned advantages of our technique hold for the newly obtained macroscopic model as well. read less NOT USED (high confidence) S. Sinha and K. Goodson, “Review: Multiscale Thermal Modeling in Nanoelectronics,” International Journal for Multiscale Computational Engineering. 2005. link Times cited: 48 Abstract: Subcontinuum phonon conduction phenomena impede the cooling … read moreAbstract: Subcontinuum phonon conduction phenomena impede the cooling of field-effect transistors with gate lengths less than 100 nm, which degrades their performance and reliability. Thermal modeling of these nanodevices requires attention to a broad range of length scales and physical phenomena, ranging from continuum heat diffusion to atomic-scale interactions and phonon confinement. This review describes the state of the art in subcontinuum thermal modeling. Although the focus is on the silicon field-effect transistor, the models are general enough to apply to other semiconductor devices as well. Special attention is given to the recent advances in applying statistical and atomistic simulation methods to thermal transport. read less NOT USED (high confidence) J. Murthy, S. Narumanchi, J. A. Pascual-Gutiérrez, T. Wang, C. Ni, and S. Mathur, “Review of Multiscale Simulation in Submicron Heat Transfer,” International Journal for Multiscale Computational Engineering. 2005. link Times cited: 76 Abstract: Over thelastdecade, interestin thesimulationof microandnano-… read moreAbstract: Over thelastdecade, interestin thesimulationof microandnano-scale heattransferhasleadto thedevelopmentof a varietyof modelsandnumerical methods for phonon transpor t in semiconductorsanddielectrics.These models spandirect simulationusingmoleculardynamics,a rangeof modelsof varying fidelity basedon theBoltzmanntranspor t equation, aswell as simplerhyperbolic extensionsto theclassicalFourier heatconduction equation. Thepaperreviews thebasicsof phonontransport in crystals,available models for phonon transpor t, aswell asnumerical methods for solving the equationsresultingfrom thesemodels. Recommend ationsaremadefor futurework. read less NOT USED (high confidence) D. Humbird and D. Graves, “Atomistic simulations of Ar+-ion-assisted etching of silicon by fluorine and chlorine,” Journal of Vacuum Science and Technology. 2005. link Times cited: 24 Abstract: We present simulations of Si etching with F and Cl radicals … read moreAbstract: We present simulations of Si etching with F and Cl radicals in the presence of inert ion bombardment. Si etch yields predicted by the simulation are in good agreement with experiments. The atomic-scale mechanisms of ion-enhanced etching are classified as enhanced spontaneous etching, chemically enhanced physical sputtering, and chemical sputtering. The primary effects of ions are to increase the local surface coverage of etchant species by increasing the sticking coefficient of arriving radicals and by mediating diffusion of etchant into the subsurface during impact, and create volatile products by inducing chemical reactions within the halogenated surface layer. Ion-assisted effects are most pronounced at low neutral-to-ion ratio and decline as this ratio increases. Explicit ion enhancements to the etch yield are greater for Cl than for F. read less NOT USED (high confidence) A. Gannepalli, “Theoretical and experimental explorations in atomic force microscopy.” 2004. link Times cited: 1 Abstract: Nanotechnology is the capability to build by controlling the… read moreAbstract: Nanotechnology is the capability to build by controlling the arrangement of individual atoms and molecules. Such a technology would be founded on the ability to control, manipulate and investigate matter at the atomic scale. The invention of atomic force microscope (AFM) and the advances in microcantilever based scanning probe technology have significantly enhanced the experimental capability to probe and modify matter at the nanoscale. However, it is still severely limited in achieving the necessary bandwidth, sensitivity and resolution. To further the advances in this field an in-depth understanding of the nature and effects of the tip-sample interactions is imperative. A complementary approach involving theoretical investigations and experimental advances is best suited to overcome the current limitations of this technology. This thesis investigates the atomistic phenomena associated with material modification at the tipsample contact theoretically because such information is inaccessible to experimental observation. Molecular dynamics studies of nanoindentation of crystalline silicon and gold, representative of semi conductor and metallic substrates, shed light on the mechanics of plastic deformation and defect forma tion. Silicon undergoes a densification transformation to amorphous phase in the deformed region via the formation of interstitials. In gold a pyramidal defect structure is formed via a three step mechanism consisting of nucleation, glide and reaction of dislocations. This mechanism dictates the dependence of defect structure on the crystallography of the indented surface as observed in experimental studies performed by other researchers. The experimental studies develop a new small amplitude non-contact AFM technique. In this frequency modulation method, changes in the cantilever's resonance induced by the tip-sample inter actions are detected from its thermal noise response. By eliminating the need for positive feedback it enables maintaining an extremely small tip-sample separation for extended periods of time at room temperatures. Consequently, this technique is particularly suited for studying highly localized slowly evolving atomic or molecular scale phenomena at ambient temperatures. The experiments performed in ambient room conditions have achieved tip-sample separations less than 2 nm for time periods in excess of 30 min. At such small separations a narrowband signal at 250 Hz is imaged with a force sensitivity of 14 fN in a bandwidth of 0.4 Hz. read less NOT USED (high confidence) W. Cai, V. Bulatov, J. Chang, J. Li, and S. Yip, “Chapter 64 – Dislocation Core Effects on Mobility.” 2004. link Times cited: 128 NOT USED (high confidence) J. A. Zimmerman, E. B. WebbIII, J. J. Hoyt, R. E. Jones, P. A. Klein, and D. J. Bammann, “Calculation of stress in atomistic simulation,” Modelling and Simulation in Materials Science and Engineering. 2004. link Times cited: 3 Abstract: Atomistic simulation is a useful method for studying materia… read moreAbstract: Atomistic simulation is a useful method for studying material science phenomena. Examination of the state of a simulated material and the determination of its mechanical properties is accomplished by inspecting the stress field within the material. However, stress is inherently a continuum concept and has been proven difficult to define in a physically reasonable manner at the atomic scale. In this paper, an expression for continuum mechanical stress in atomistic systems derived by Hardy is compared with the expression for atomic stress taken from the virial theorem. Hardy's stress expression is evaluated at a fixed spatial point and uses a localization function to dictate how nearby atoms contribute to the stress at that point; thereby performing a local spatial averaging. For systems subjected to deformation, finite temperature, or both, the Hardy description of stress as a function of increasing characteristic volume displays a quicker convergence to values expected from continuum theory than volume averages of the local virial stress. Results are presented on extending Hardy's spatial averaging technique to include temporal averaging for finite temperature systems. Finally, the behaviour of Hardy's expression near a free surface is examined, and is found to be consistent with the mechanical definition for stress. read less NOT USED (high confidence) L. Shen and Z. Chen, “An investigation of the effect of interfacial atomic potential on the stress transition in thin films,” Modelling and Simulation in Materials Science and Engineering. 2004. link Times cited: 2 Abstract: In order to better understand the mechanisms of tungsten (W)… read moreAbstract: In order to better understand the mechanisms of tungsten (W) film delamination from the silicon (Si) substrate, a three-dimensional molecular dynamics (MD) simulation is being conducted to investigate the formation of residual stress during the film deposition process. For the purpose of simplicity, a Morse pair potential is proposed in this paper to simulate the interactions between W and Si atoms during the film deposition process. It appears from numerical solutions that the residual stress field in the W film is very sensitive to the W–Si interfacial potential model proposed for the MD simulation. By calibrating the controlling parameters in the interfacial potential model using the comparison between the simulated stresses and experimental data, the film stress transition from tension to compression during the film deposition process could be qualitatively simulated via the proposed simulation procedure. The numerical results presented in this paper provide a better insight into the effect of interfacial atomic potential on the stress transition in thin films. In addition, it can be seen from the MD simulation that there might exist a phase transition from the crystalline Si to amorphous W–Si structure to crystalline W around the interface area. Well-designed experiments are required to verify the simulation results. read less NOT USED (high confidence) Y. Ge and J. Head, “Global optimization of SixHy at the ab initio level via an iteratively parametrized semiempirical method,” International Journal of Quantum Chemistry. 2003. link Times cited: 9 Abstract: Previously we searched for the ab initio global minima of se… read moreAbstract: Previously we searched for the ab initio global minima of several SixHy clusters by a genetic algorithm in which we used the AM1 semiempirical method to facilitate a rapid energy calculation for the many different cluster geometries explored. However, we found that the AM1 energy ranking significantly differs from the ab initio energy ranking. To better guarantee locating the ab initio global minimum while retaining the efficiency of the AM1 method, we present an improved iterative global optimization strategy. The method involves two separate genetic algorithms that are invoked consecutively. One is the cluster genetic algorithm (CGA), mentioned above, to find the semiempirical SixHy cluster global minimum. A second and separate parametrization genetic algorithm (PGA) is used to reparametrize the AM1 method using some of the ab initio data generated from the CGA to form a training set of different reference clusters but with fixed SixHy stoichiometry. The cluster global optimization search (CGA) and the semiempirical parametrization (PGA) steps are performed iteratively until the semiempirical GA reparametrized AM1 (GAM1) calculations give low-energy optimized structures that are consistent with the globally optimized ab initio structure. We illustrate the new global optimization strategy by attempting to find the ab initio global minima for the Si6H2 and Si6H6 clusters. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 95: 617- 626, 2003 read less NOT USED (high confidence) W. A. Curtin and R. E. Miller, “Atomistic/continuum coupling in computational materials science,” Modelling and Simulation in Materials Science and Engineering. 2003. link Times cited: 84 Abstract: Important advances in multi-scale computer simulation techni… read moreAbstract: Important advances in multi-scale computer simulation techniques for computational materials science have been made in the last decade as scientists and engineers strive to imbue continuum-based models with more-realistic details at quantum and atomistic scales. One major class of multi-scale models directly couples a region described with full atomistic detail to a surrounding region modelled using continuum concepts and finite element methods. Here, the development of such coupled atomistic/continuum models is reviewed within a single coherent framework with the aim of providing both non-specialists and specialists with insight into the key ideas, features, differences and advantages of prevailing models. Some applications and very recent advances are noted, and important challenges for extending these models to their fullest potential are discussed. read less NOT USED (high confidence) G. Schaaf et al., “Simulation of Dislocations in Icosahedral Quasicrystals with IMD.” 2002. link Times cited: 2 NOT USED (high confidence) E. Bitzek et al., “Recent Developments in IMD: Interactions for Covalent and Metallic Systems.” 2001. link Times cited: 11 NOT USED (high confidence) K. Scheerschmidt, “Molecular dynamics simulations of wafer bonding,” MRS Proceedings. 2001. link Times cited: 0 Abstract: Molecular dynamics simulations using empirical potentials ha… read moreAbstract: Molecular dynamics simulations using empirical potentials have been employed to describe atomic inte ractions at interfaces created by the macroscopic wafer bonding process. Investigating perfect o r distorted s urfaces of different s emiconductor materials as well as of silica enables one to study the elementary processes and the resulting defects at the interfaces, and to characterize the ability of the potentials used. T wist r otation due to misalignment and bonding over steps influence strongly the bondability of larger areas. Empirical potentials developed by the bond o rder tight-binding approximation incl ude -bonds and yield enhanced interface structures, energies, and transferability to new materials systems. read less NOT USED (high confidence) S. Alfthan, A. Kuronen, and K. Kaski, “Crystalline-Amorphous Interface: Molecular Dynamics Simulation of Thermal Conductivity,” MRS Proceedings. 2001. link Times cited: 3 Abstract: : Effect of a crystalline-amorphous interface on heat conduc… read moreAbstract: : Effect of a crystalline-amorphous interface on heat conduction has been studied using atomistic simulations of a silicon system. System with amorphous silicon was created using the bond-switching Monte Carlo simulation method and heat conduction near room temperature was studied by molecular dynamics simulations of this system. read less NOT USED (high confidence) J. Hahn and H. Trebin, “Molecular Dynamics of Covalent Crystals.” 2000. link Times cited: 3 NOT USED (high confidence) D. Alfé, G. D. Wijs, G. Kresse, and M. Gillan, “Recent Developments in ab initio Thermodynamics,” International Journal of Quantum Chemistry. 2000. link Times cited: 28 Abstract: It has recently become possible to calculate the free energy… read moreAbstract: It has recently become possible to calculate the free energy and other thermodynamic functions of solids and liquids using density functional theory to treat the quantum mechanics of the electrons. We present the main ideas that have made this possible, emphasizing the key role of thermodynamic integration and the importance of well-adapted reference systems in the computation of the free energy. We show how ab initio methods have been used to calculate the melting and other phase-equilibrium properties of simple materials, and the thermal-equilibrium concentrations of point defects in crystals. We point out the possibility of adapting techniques that are already available in order to calculate chemical potentials, solubilities, equilibrium constants, and other thermodynamic functions that are important in physical chemistry. c 2000 John Wiley & Sons, Inc. Int J Quant Chem 77: 871-879, 2000 read less NOT USED (high confidence) J. A. Zimmerman, H. Gao, and F. F. Abraham, “Generalized stacking fault energies for embedded atom FCC metals,” Modelling and Simulation in Materials Science and Engineering. 2000. link Times cited: 27 Abstract: Atomistic calculations for the 112 -generalized stacking fau… read moreAbstract: Atomistic calculations for the 112 -generalized stacking fault (GSF) energy curve are performed for various embedded atom models of FCC metals. Models include those by Voter and Chen; Angelo, Moody and Baskes; Oh and Johnson; Mishin and Farkas; and Ercolessi and Adams. The resulting curves show similar characteristics but vary in their agreement with the experimental estimates of the intrinsic stacking fault energy, sf , and with density functional theory (DFT) calculations of the GSF curve. These curves are used to obtain estimates of the unstable stacking fault energy, us , a quantity used in a criterion for dislocation nucleation. Curves for nickel and copper models show the theoretically expected skewed sinusoidal shape; however, several of the aluminium models produce an irregularly shaped GSF curve. Copper and aluminium values for us are underestimates of calculations from DFT, although some of the nickel models produce a value matching one of the available DFT results. Values for sf are either fitted to, or underestimate, the measured results. For use in simulations, the authors recommend using the Voter and Chen potential for copper, and either the Angelo, Moody and Baskes potential or the Voter and Chen potential for nickel. None of the potentials model aluminium well, indicating the need for a more-advanced empirical potential. read less NOT USED (high confidence) P. Ruterana, A. Béré, and G. Nouet, “Formation and stability of the prismatic stacking fault in wurtzite (Al,Ga,In) nitrides,” MRS Proceedings. 1999. link Times cited: 0 Abstract: The formation of the {l_brace}1{bar 2}10{r_brace} stacking f… read moreAbstract: The formation of the {l_brace}1{bar 2}10{r_brace} stacking fault, which has two atomic configurations in Wurtzite (Ga,Al,In)N, has been investigated by high resolution electron microscopy and energetic calculations. It originates from steps at the SiC surface and it can form on a flat (0001) sapphire surface. A modified Stillinger-Weber potential was used in order to investigate the relative stability of the two atomic configurations. They have comparable energy in AlN, whereas the 1/2 {l_brace}1{bar 2}10{r_brace} configuration is more stable in GaN and InN. In GaN layers, only the 1/2 {l_brace}1{bar 2}10{r_brace} configuration was observed. The 1/6 configuration was found in small areas inside the AlN buffer layer where it folded rapidly to the basal plane, and when back into the prismatic plane, it took the 1/2 {l_brace}1{bar 2}10{r_brace} atomic configuration. read less NOT USED (high confidence) S. W. Yim, N. Sonwalkar, and N. Saka, “Molecular dynamics simulation of boundary lubricated interfaces,” Journal of Computer-Aided Materials Design. 1999. link Times cited: 8 NOT USED (high confidence) M. Dornheim and H. Teichler, “Atomistic Modeling of Misfit Dislocations for Ge/(001)Si and Ge/(111)Si,” Physica Status Solidi (a). 1999. link Times cited: 12 Abstract: For Ge films on (001)- and (111)-Si the energy of coherent a… read moreAbstract: For Ge films on (001)- and (111)-Si the energy of coherent and semicoherent interfaces with misfit dislocations is numerically analyzed by use of the atomistic, anharmonic bond charge model. The model describes correctly the elastic properties of the Ge film and the Si substrate, the bond angle stiffness reduction for short wavelength deformations as found in the dislocation cores, and the third order elastic constants. A generalization of the model to deal with mixed Ge–Si bonds is provided. For Ge/(001)Si misfit dislocations of 90° Lomer type are considered, for Ge/(111)Si a trigonal network of 90° glide-set partials with stacking faults between them. In both cases, the estimated critical thickness for the coherent interface is in fair accordance with experimental observations. read less NOT USED (high confidence) L. Porter, S. Yip, M. Yamaguchi, H. Kaburaki, and M. Tang, “EMPIRICAL BOND-ORDER POTENTIAL DESCRIPTION OF THERMODYNAMIC PROPERTIES OF CRYSTALLINE SILICON,” Journal of Applied Physics. 1997. link Times cited: 67 Abstract: Thermodynamic properties of silicon (diamond cubic phase) ar… read moreAbstract: Thermodynamic properties of silicon (diamond cubic phase) are calculated using an empirical many-body potential developed by Tersoff [Phys. Rev. Lett. 56, 632 (1986)] based on the concept of bond order. It is shown that this model gives predictions in good agreement with experiment for those properties governed by energetics (free energy, entropy, and heat capacity). The thermal expansion coefficient is less well described, which is traced to the fact that the model potential, in its present version, is overly stiff and therefore unable to account properly for the volume dependence of the transverse acoustic modes. Furthermore, sensitivity of the potential to whether each atom remains bonded to only four neighbors indicates that the short-range nature of the potential may necessitate model improvement before it is suitable for studies of thermomechanical properties at elevated temperatures or large deformations. read less NOT USED (high confidence) K. Nordlund, P. Partyka, and R. Averback, “Fully Atomistic Analysis of Diffuse X-Ray Scattering Spectra of Silicon Defects,” MRS Proceedings. 1997. link Times cited: 6 Abstract: Diffuse X-ray scattering is a useful method for studying def… read moreAbstract: Diffuse X-ray scattering is a useful method for studying defects in silicon and metals. Although the traditional approaches of analyzing experimental diffuse X-ray scattering data have given much information about the size of defects and defect clusters, they are not very well suited for determining the atomic configuration. We present a fully atomistic computational method to calculate the diffuse X-ray scattering line profile of an arbitrary atomic configuration, and compare line profiles of point defects and Frenkel pair configurations with experiment. read less NOT USED (high confidence) A. Omeltchenko, “Nanoscale Structures and Fracture Processes in Advanced Ceramics: Million-Atom MD Simulations on Parallel Architectures.” 1997. link Times cited: 0 Abstract: Properties and processes in silicon nitride and graphite are… read moreAbstract: Properties and processes in silicon nitride and graphite are investigated using molecular-dynamics (MD) simulations. Scalable and portable multiresolution algorithms are developed and implemented on parallel architectures to simulate systems containing 106 atoms interacting via realistic potentials. Structural correlations, mechanical properties, and thermal transport are studied in microporous silicon nitride as a function of density. The formation of pores is observed when the density is reduced to 2.6 g/cc, and the percolation occurs at a density of 2.0 g/cc. The density variation of the thermal conductivity and the Young’s modulus are well described by power laws with scaling exponents of 1.5 and 3.6, respectively. Dynamic fracture in a single graphite sheet is investigated. For certain crystalline orientations, the crack becomes unstable with respect to branching at a critical speed of -60% of the Rayleigh velocity. The origin of the branching instability is investigated by calculating local-stress distributions. The branched fracture profile is characterized by a roughness exponent, a 0.7, above a crossover length of 50A. For smaller length scales and within the same branch, a 0.4. Crack propagation is studied in nanophase silicon nitride prepared by sintering nanoclusters of size 60A. The system consists of crystalline cluster interiors, amorphous intercluster regions, and isolated pores. These microstructures cause crack branching and meandering, and the clusters undergo significant rearrangement due to plastic deformation of interfacial regions. As a result, the system can withstand enormous deformation (30%). In contrast, a crystalline sample in the same geometry cleaves under an applied strain of only 3%. read less NOT USED (high confidence) B. Dünweg, S. Kämmerer, and M. Presber, “Phase Diagrams of Alloys and Adsorbed Monolayers: Some Recent Results.” 1997. link Times cited: 0 NOT USED (high confidence) T. Einstein, “Chapter 11 – Interactions Between Adsorbate Particles.” 1996. link Times cited: 28 NOT USED (high confidence) J. Siepmann and M. Sprik, “Influence of surface topology and electrostatic potential on water/electrode systems,” Journal of Chemical Physics. 1995. link Times cited: 306 Abstract: We have used the classical molecular dynamics technique to s… read moreAbstract: We have used the classical molecular dynamics technique to simulate the ordering of a water film adsorbed on an atomic model of a tip of a scanning tunneling microscope approaching a planar metal surface. For this purpose, we have developed a classical model for the water–substrate interactions that solely depends on the coordinates of the particles and does not require the definition of geometrically smooth boundary surfaces or image planes. The model includes both an electrostatic induction for the metal atoms (determined by means of an extended Lagrangian technique) and a site‐specific treatment of the water–metal chemisorption. As a validation of the model we have investigated the structure of water monolayers on metal substrates of various topology [the (111), (110), and (100) crystallographic faces] and composition (Pt, Ag, Cu, and Ni), and compared the results to experiments. The modeling of the electrostatic induction is compatible with a finite external potential imposed on the metal. This featur... read less NOT USED (high confidence) T. Mittelbach, “Moleküldynamische Untersuchungen an Si-Clustern,” Zeitschrift für Physikalische Chemie. 1992. link Times cited: 1 NOT USED (high confidence) J. Murrell, “The many‐body expansion of the potential energy function for elemental clusters,” International Journal of Quantum Chemistry. 1990. link Times cited: 16 Abstract: The many-body expansion of the potential energy function of … read moreAbstract: The many-body expansion of the potential energy function of elemental clusters is examined in general terms in regard to its convergence for microclusters and the bulk phase. The system Be n and Li n are examined in detail. For Li it is clear that the many-body expansion has no low-order converegence, but it is shown that a potential of the form V=aV (2) +bV (3) gives good binding energies for Li n (3read less NOT USED (definite) L. Safina, J. Baimova, and R. Mulyukov, “Nickel nanoparticles inside carbon nanostructures: atomistic simulation,” Mechanics of Advanced Materials and Modern Processes. 2019. link Times cited: 17 NOT USED (definite) L. de Sousa Oliveira, V. Vargiamidis, and N. Neophytou, “Modeling Thermoelectric Performance in Nanoporous Nanocrystalline Silicon,” IEEE Transactions on Nanotechnology. 2019. link Times cited: 5 Abstract: Introducing hierarchical disorder from multiple defects into… read moreAbstract: Introducing hierarchical disorder from multiple defects into materials through nanostructuring is one of the most promising directions to achieve extremely low thermal conductivities and thus improve thermoelectric performance. The success of nanostructuring relies on charge carriers having shorter mean-free-paths than phonons so that the latter can be selectively scattered. Nevertheless, introducing disorder into a material often comes at the expense of scattering charge carriers as well as phonons. In order to determine the tradeoff between the degradation of the lattice thermal conductivity and of the power factor due to this, we perform a theoretical investigation of both phonon and electron transport in nanocrystalline, nanoporous Si geometries. We use molecular dynamics for phonon transport calculations and the non-equilibrium Green's function method for electronic transport. We report on the engineering tradeoff that the porosity (number of pores and their in-between distance) has on the overall thermoelectric performance for the material optimization. We indeed find that the reduction in thermal conductivity is stronger compared to the reduction in the power factor, for the low porosities considered in this study (up to 5%), and that the ZT figure of merit can experience a large increase, especially when grain boundaries are included, compared to just nanoporosity. read less NOT USED (definite) L. Steinberg, J. Russo, and J. Frey, “A new topological descriptor for water network structure,” Journal of Cheminformatics. 2019. link Times cited: 8 NOT USED (definite) H. Meng, D. Ma, X. Yu, L. Zhang, Z. Sun, and N. Yang, “Thermal conductivity of molybdenum disulfide nanotube from molecular dynamics simulations,” International Journal of Heat and Mass Transfer. 2019. link Times cited: 21 NOT USED (definite) R. Aguirre, S. Abdullah, X. W. Zhou, and D. Zubia, “Molecular Dynamics Calculations of Grain Boundary Mobility in CdTe,” Nanomaterials. 2019. link Times cited: 4 Abstract: Molecular dynamics (MD) simulations have been applied to stu… read moreAbstract: Molecular dynamics (MD) simulations have been applied to study mobilities of Σ3, Σ7 and Σ11 grain boundaries in CdTe. First, an existing MD approach to drive the motion of grain boundaries in face-centered-cubic and body-centered-cubic crystals was generalized for arbitrary crystals. MD simulations were next performed to calculate grain boundary velocities in CdTe crystals at different temperatures, driving forces, and grain boundary terminations. Here a grain boundary is said to be Te-terminated if its migration encounters sequentially Cd·Te−Cd·Te… planes, where “·” and “−” represent short and long spacing respectively. Likewise, a grain boundary is said to be Cd-terminated if its migration encounters sequentially Te·Cd−Te·Cd… planes. Grain boundary mobility laws, suitable for engineering time and length scales, were then obtained by fitting the MD results to Arrhenius equation. These studies indicated that the Σ3 grain boundary has significantly lower mobility than the Σ7 and Σ11 grain boundaries. The Σ7 Te-terminated grain boundary has lower mobility than the Σ7 Cd-terminated grain boundary, and that the Σ11 Cd-terminated grain boundary has lower mobility than the Σ11 Te-terminated grain boundary. read less NOT USED (definite) S. Brown et al., “Direct imaging of ultrafast lattice dynamics,” Science Advances. 2019. link Times cited: 28 Abstract: We image a previously unidentified ultrafast lattice respons… read moreAbstract: We image a previously unidentified ultrafast lattice response in silicon, providing insight into deformation kinetics. Under rapid high-temperature, high-pressure loading, lattices exhibit complex elastic-inelastic responses. The dynamics of these responses are challenging to measure experimentally because of high sample density and extremely small relevant spatial and temporal scales. Here, we use an x-ray free-electron laser providing simultaneous in situ direct imaging and x-ray diffraction to spatially resolve lattice dynamics of silicon under high–strain rate conditions. We present the first imaging of a new intermediate elastic feature modulating compression along the axis of applied stress, and we identify the structure, compression, and density behind each observed wave. The ultrafast probe x-rays enabled time-resolved characterization of the intermediate elastic feature, which is leveraged to constrain kinetic inhibition of the phase transformation between 2 and 4 ns. These results not only address long-standing questions about the response of silicon under extreme environments but also demonstrate the potential for ultrafast direct measurements to illuminate new lattice dynamics. read less NOT USED (definite) J. Cao, Y. Wang, J. Shi, J. Chai, and K. Cai, “Initial Relative Position Influencing Self-Assembly of a Black Phosphorus Ribbon on a CNT,” International Journal of Molecular Sciences. 2018. link Times cited: 6 Abstract: It is difficult to obtain a nanotube from phosphorus with a … read moreAbstract: It is difficult to obtain a nanotube from phosphorus with a 3sp2 electron configuration by chemical synthesis. However, a physical fabrication approach, such as self-assembly, is worth trying. In an experiment, when using a carbon nanotube (CNT) to trigger self-assembly of a black phosphorus (BP) ribbon, the final configuration of the BP component may be sensitive to the initial relative position of the CNT to the BP ribbon. For instance, using the same CNT with different initial relative positions to the BP ribbon, the BP ribbon may finally become a nanotube, or a scroll, or just wind upon the CNT, or escape from the CNT, etc. In this study, the sensitivity is investigated using molecular dynamics simulations. Numerical results illustrate some essentials for potential fabrication of a BP nanotube from ribbon. read less NOT USED (definite) D. Dong et al., “Multiscale Modeling of Structure, Transport and Reactivity in Alkaline Fuel Cell Membranes: Combined Coarse-Grained, Atomistic and Reactive Molecular Dynamics Simulations,” Polymers. 2018. link Times cited: 21 Abstract: In this study, molecular dynamics (MD) simulations of hydrat… read moreAbstract: In this study, molecular dynamics (MD) simulations of hydrated anion-exchange membranes (AEMs), comprised of poly(p-phenylene oxide) (PPO) polymers functionalized with quaternary ammonium cationic groups, were conducted using multiscale coupling between three different models: a high-resolution coarse-grained (CG) model; Atomistic Polarizable Potential for Liquids, Electrolytes and Polymers (APPLE&P); and ReaxFF. The advantages and disadvantages of each model are summarized and compared. The proposed multiscale coupling utilizes the strength of each model and allows sampling of a broad spectrum of properties, which is not possible to sample using any of the single modeling techniques. Within the proposed combined approach, the equilibrium morphology of hydrated AEM was prepared using the CG model. Then, the morphology was mapped to the APPLE&P model from equilibrated CG configuration of the AEM. Simulations using atomistic non-reactive force field allowed sampling of local hydration structure of ionic groups, vehicular transport mechanism of anion and water, and structure equilibration of water channels in the membrane. Subsequently, atomistic AEM configuration was mapped to ReaxFF reactive model to investigate the Grotthuss mechanism in the hydroxide transport, as well as the AEM chemical stability and degradation mechanisms. The proposed multiscale and multiphysics modeling approach provides valuable input for the materials-by-design of novel polymeric structures for AEMs. read less NOT USED (definite) C.-S. Liao, Y. Zhao, and G. Ouyang, “Strain-Modulated Band Engineering in Two-Dimensional Black Phosphorus/MoS2 van der Waals Heterojunction,” ACS Omega. 2018. link Times cited: 22 Abstract: We investigate the band shift and band alignment of two-dime… read moreAbstract: We investigate the band shift and band alignment of two-dimensional (2D) black phosphorus (BP)/MoS2 van der Waals heterojunction (vdW HJ) via uniaxial strain in terms of first-principles calculations and atomic-bond-relaxation method. We find that the band gap of 2D BP/MoS2 HJ decreases linearly with applied tensile strain and Mo–S bond breaks down at 10% tensile strain. Meanwhile, the band gap slightly increases and then monotonically decreases under compressive strain and there appears a semiconductor-to-metal transition at −11 and −12% strain in the y and x directions, respectively. Moreover, 2D BP/MoS2 HJ maintains type-II band alignment for strain applied in the y direction whereas type-II/I band transition appears at −5% strain in the x direction. Moreover, we propose an analytical model to address the strain-modulated band engineering of 2D BP/MoS2 vdW HJ at the atomic level. Our results suggest a promising way to explain the intrinsic mechanism of strain engineering and manipulate the electronic properties of 2D vdW HJs. read less NOT USED (definite) C. Chen, H. Li, H. Xiang, and X. Peng, “Molecular Dynamics Simulation on B3-GaN Thin Films under Nanoindentation,” Nanomaterials. 2018. link Times cited: 17 Abstract: The B3-GaN thin film was investigated by performing large-sc… read moreAbstract: The B3-GaN thin film was investigated by performing large-scale molecular dynamics (MD) simulation of nanoindentation. Its plastic behavior and the corresponding mechanism were studied. Based on the analysis on indentation curve, dislocation density, and orientation dependence, it was found that the indentation depths of inceptive plasticity on (001), (110), and (111) planes were consistent with the Schmid law. The microstructure evolutions during the nanoindentation under different conditions were focused, and two formation mechanisms of prismatic loop were proposed. The “lasso”-like mechanism was similar to that in the previous research, where a shear loop can translate into a prismatic loop by cross-slip; and the extended “lasso”-like mechanism was not found to be reported. Our simulation showed that the two screw components of a shear loop will glide on another loop until they encounter each other and eventually produce a prismatic dislocation loop. read less NOT USED (definite) L. de Sousa Oliveira, V. Vargiamidis, and N. Neophytou, “Transport simulations in hierarchically disordered nanostructures for thermoelectric material design,” 2018 IEEE 13th Nanotechnology Materials and Devices Conference (NMDC). 2018. link Times cited: 0 Abstract: Hierarchically nanostructured materials, where disorder is i… read moreAbstract: Hierarchically nanostructured materials, where disorder is introduced in various length scales (at the atomic scale, the nanoscale, and the mesoscale) is one of the most promising directions to achieve extremely low thermal conductivities and improve thermoelectric performance. Here we theoretically investigate one such system, a nanocrystalline material with nanopores that are introduced between the crystalline regions. We use the Nonequilibrium Green's Function method for electronic transport and Molecular Dynamics for phonon transport. read less NOT USED (definite) R. Dettori and L. Colombo, “THERMAL PROPERTIES OF TPD-BASED ORGANIC GLASSES,” Istituto Lombardo - Accademia di Scienze e Lettere - Incontri di Studio. 2018. link Times cited: 1 Abstract: Glassy materials are condensed matter systems showing physic… read moreAbstract: Glassy materials are condensed matter systems showing physical properties in between solids and liquids and retaining information about the thermal history they have been subjected to and the way they have been prepared. Formally, this implies that their configurational energy landscape is a complex multi-dimensional surface, showing quite a few basins with different depths, widths, and shapes: the system can be trapped in any of them, assuming very unlike physical properties. Recently, it has been demonstrated experimentally that a glassy system can be grown by physical vapor deposition of organic molecules on a substrate. The physics of such organic glasses is enriched by a new feature, namely: the anisotropic molecular structure of the basic building blocks used to assemble the film. TPD-based organic glasses have been generated by atomistic simulations that mimic vapor deposition and their thermal properties have been accordingly calculated. Simulations generate a rational phenomenology, providing robust evidence that heat transfer is not isotropic but, rather, correlated to an inherent molecular property, namely the axial structure of the TPD molecule. Furthermore, we present the first theoretical prediction of the specific heat trend versus temperature, showing in the quantum regime an intriguing anomaly with respect to crystalline systems. read less NOT USED (definite) D. Olson, X. Li, C. Ortner, and B. V. Koten, “Force-based atomistic/continuum blending for multilattices,” Numerische Mathematik. 2018. link Times cited: 0 NOT USED (definite) M. Friedrich and U. Stefanelli, “Graphene ground states,” Zeitschrift für angewandte Mathematik und Physik. 2018. link Times cited: 0 NOT USED (definite) M. Friedrich and U. Stefanelli, “Ripples in Graphene: A Variational Approach,” Communications in Mathematical Physics. 2018. link Times cited: 5 NOT USED (definite) H. Nakano, H. Tetsuka, M. Spencer, and T. Morishita, “Chemical modification of group IV graphene analogs,” Science and Technology of Advanced Materials. 2018. link Times cited: 28 Abstract: Mono-elemental two-dimensional (2D) crystals (graphene, sili… read moreAbstract: Mono-elemental two-dimensional (2D) crystals (graphene, silicene, germanene, stanene, and so on), termed 2D-Xenes, have been brought to the forefront of scientific research. The stability and electronic properties of 2D-Xenes are main challenges in developing practical devices. Therefore, in this review, we focus on 2D free-standing group-IV graphene analogs (graphene quantum dots, silicane, and germanane) and the functionalization of these sheets with organic moieties, which could be handled under ambient conditions. We highlight the present results and future opportunities, functions and applications, and novel device concepts. read less NOT USED (definite) S. Torquato, “Hyperuniform states of matter,” Physics Reports. 2018. link Times cited: 256 NOT USED (definite) A. Bari, S. Rubaiee, A. Ahmed, and A. Masud, “A molecular dynamic study of change in thermodynamic functions of silicon FCC cell with the change in temperature,” Journal of Naval Architecture and Marine Engineering. 2017. link Times cited: 0 Abstract: In modern days silicon is being extensively used in making e… read moreAbstract: In modern days silicon is being extensively used in making electronic semiconductor-based chips and ICs. In this research, the change in different thermodynamic properties of silicon like lattice heat capacity, molar enthalpy and Debye temperature at constant pressure, with the change in temperature, has been investigated by using molecular dynamics (MD) simulation method. Knowing silicon thermodynamic functions are quite important, because many electronic companies are nowadays trying a lot to reduce the heat generated by their semiconductor chips as excessive heating of the chip not only warms up the device quickly but also reduces the chip life. The results obtained from this simulation help engineers to design electronic chips more efficiently. For simulation Accelrys Materials Studio (Version 5.0) software has been used. The simulation was run for silicon FCC diamond structured cell. The analysis tool used in the simulation is known as CASTEP (Cambridge Sequential Total Energy Package). This tool is specialized for performing molecular level thermodynamic analysis to generate data and graphs for the change in different temperature dependent properties of the molecular system. The interaction between silicon atoms was expressed by the Kohn-Sham potential and MD calculation was conducted on crystalline state of silicon at temperatures between 0 and 1000 K. Here, density function theory (DFT) based tool has been used to derive density of state relations. Results obtained by the simulation were compared with published experimental values and it was found that the simulation results were close to the experimental values. read less NOT USED (definite) M. Yu and S. Kenny, “Modelling the deposition process on the CdTe/CdS interface,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2017. link Times cited: 1 NOT USED (definite) J. Burg et al., “Hyperconnected molecular glass network architectures with exceptional elastic properties,” Nature Communications. 2017. link Times cited: 21 NOT USED (definite) C. Ruestes, I. A. Alhafez, and H. Urbassek, “Atomistic Studies of Nanoindentation—A Review of Recent Advances.” 2017. link Times cited: 45 Abstract: This review covers areas where our understanding of the mech… read moreAbstract: This review covers areas where our understanding of the mechanisms underlying nanoindentation has been increased by atomistic studies of the nanoindentation process. While such studies have been performed now for more than 20 years, recent investigations have demonstrated that the peculiar features of nanoplasticity generated during indentation can be analyzed in considerable detail by this technique. Topics covered include: nucleation of dislocations in ideal crystals, effect of surface orientation, effect of crystallography (fcc, bcc, hcp), effect of surface and bulk damage on plasticity, nanocrystalline samples, and multiple (sequential) indentation. In addition we discuss related features, such as the influence of tip geometry on the indentation and the role of adhesive forces, and how pre-existing plasticity affects nanoindentation. read less NOT USED (definite) X. W. Zhou and R. Jones, “A Stillinger-Weber Potential for InGaN,” Journal of Materials Science Research. 2017. link Times cited: 9 Abstract: Reducing defects in InGaN films deposited on GaN substrates … read moreAbstract: Reducing defects in InGaN films deposited on GaN substrates has been critical to fill the “green” gap for solid-state lighting applications. To enable researchers to use molecular dynamics vapor deposition simulations to explores ways to reduce defects in InGaN films, we have developed and characterized a Stillinger-Weber potential for InGaN. We show that this potential reproduces the experimental atomic volume, cohesive energy, and bulk modulus of the equilibrium wurtzite / zinc-blende phases of both InN and GaN. Most importantly, the potential captures the stability of the correct phase of InGaN compounds against a variety of other elemental, alloy, and compound configurations. This is validated by the potential’s ability to predict crystalline growth of stoichiometric wurtzite and zinc-blende InxGa1-xN compounds during vapor deposition simulations where adatoms are randomly injected to the growth surface. read less NOT USED (definite) É. Maras, L. Pizzagalli, T. Ala‐Nissila, H. Jónsson, and H. Jónsson, “Atomic Scale Formation Mechanism of Edge Dislocation Relieving Lattice Strain in a GeSi overlayer on Si(001),” Scientific Reports. 2017. link Times cited: 13 NOT USED (definite) R. J. Wang, C. Wang, and Y. Feng, “Effective geometric size and bond-loss effect in nanoelasticity of GaN nanowires,” International Journal of Mechanical Sciences. 2017. link Times cited: 7 NOT USED (definite) A. Gautam, N. Pingua, A. Goyal, and P. A. Apte, “Dynamical Instability Causes the Demise of a Supercooled Tetrahedral Liquid,” Journal of Statistical Physics. 2017. link Times cited: 0 NOT USED (definite) J. Han, L. Zhang, R. Car, and E. Weinan, “Deep Potential: a general representation of a many-body potential energy surface,” arXiv: Computational Physics. 2017. link Times cited: 153 Abstract: We present a simple, yet general, end-to-end deep neural net… read moreAbstract: We present a simple, yet general, end-to-end deep neural network representation of the potential energy surface for atomic and molecular systems. This methodology, which we call Deep Potential, is "first-principle" based, in the sense that no ad hoc approximations or empirical fitting functions are required. The neural network structure naturally respects the underlying symmetries of the systems. When tested on a wide variety of examples, Deep Potential is able to reproduce the original model, whether empirical or quantum mechanics based, within chemical accuracy. The computational cost of this new model is not substantially larger than that of empirical force fields. In addition, the method has promising scalability properties. This brings us one step closer to being able to carry out molecular simulations with accuracy comparable to that of quantum mechanics models and computational cost comparable to that of empirical potentials. read less NOT USED (definite) M. Radek et al., “Ion-Beam-Induced Atomic Mixing in Ge, Si, and SiGe, Studied by Means of Isotope Multilayer Structures,” Materials. 2017. link Times cited: 6 Abstract: Crystalline and preamorphized isotope multilayers are utiliz… read moreAbstract: Crystalline and preamorphized isotope multilayers are utilized to investigate the dependence of ion beam mixing in silicon (Si), germanium (Ge), and silicon germanium (SiGe) on the atomic structure of the sample, temperature, ion flux, and electrical doping by the implanted ions. The magnitude of mixing is determined by secondary ion mass spectrometry. Rutherford backscattering spectrometry in channeling geometry, Raman spectroscopy, and transmission electron microscopy provide information about the structural state after ion irradiation. Different temperature regimes with characteristic mixing properties are identified. A disparity in atomic mixing of Si and Ge becomes evident while SiGe shows an intermediate behavior. Overall, atomic mixing increases with temperature, and it is stronger in the amorphous than in the crystalline state. Ion-beam-induced mixing in Ge shows no dependence on doping by the implanted ions. In contrast, a doping effect is found in Si at higher temperature. Molecular dynamics simulations clearly show that ion beam mixing in Ge is mainly determined by the thermal spike mechanism. In the case of Si thermal spike, mixing prevails at low temperature whereas ion beam-induced enhanced self-diffusion dominates the atomic mixing at high temperature. The latter process is attributed to highly mobile Si di-interstitials formed under irradiation and during damage annealing. read less NOT USED (definite) S. Ambrogio et al., “Modeling resistive switching materials and devices across scales,” Journal of Electroceramics. 2017. link Times cited: 18 NOT USED (definite) K. Klymko, D. Mandal, and K. Mandadapu, “Statistical mechanics of transport processes in active fluids: Equations of hydrodynamics.,” The Journal of chemical physics. 2017. link Times cited: 16 Abstract: The equations of hydrodynamics including mass, linear moment… read moreAbstract: The equations of hydrodynamics including mass, linear momentum, angular momentum, and energy are derived by coarse-graining the microscopic equations of motion for systems consisting of rotary dumbbells driven by internal torques. In deriving the balance of linear momentum, we find that the symmetry of the stress tensor is broken due to the presence of non-zero torques on individual particles. The broken symmetry of the stress tensor induces internal spin in the fluid and leads us to consider the balance of internal angular momentum in addition to the usual moment of momentum. In the absence of spin, the moment of momentum is the same as the total angular momentum. In deriving the form of the balance of total angular momentum, we find the microscopic expressions for the couple stress tensor that drives the spin field. We show that the couple stress contains contributions from both intermolecular interactions and the active forces. The presence of spin leads to the idea of balance of moment of inertia due to the constant exchange of particles in a small neighborhood around a macroscopic point. We derive the associated balance of moment of inertia at the macroscale and identify the moment of inertia flux that induces its transport. Finally, we obtain the balances of total and internal energy of the active fluid and identify the sources of heat and heat fluxes in the system. read less NOT USED (definite) M. Moqadam, E. Riccardi, T. T. Trinh, A. Lervik, and T. S. van Erp, “Rare event simulations reveal subtle key steps in aqueous silicate condensation.,” Physical chemistry chemical physics : PCCP. 2017. link Times cited: 17 Abstract: A replica exchange transition interface sampling (RETIS) stu… read moreAbstract: A replica exchange transition interface sampling (RETIS) study combined with Born-Oppenheimer molecular dynamics (BOMD) is used to investigate the dynamics, thermodynamics and the mechanism of the early stages of the silicate condensation process. In this process, two silicate monomers, of which one is an anionic species, form a negatively charged five-coordinated silicate dimer. In a second stage, this dimer can fall apart again, forming the original monomers, or release a water molecule into the solution. We studied the association and dissociation reaction in the gas phase, and the dissociation and water removal step in the aqueous phase. The results on the aqueous phase dissociation suggest two possible mechanisms. The breakage of the bond between the intermediate oxygen and the five-coordinated silicon is sometimes accompanied by a proton transfer. After dissociation into silicate monomers, the anionic monomer is either the previously four-coordinated silicon or the previously five-coordinated silicon depending on whether the hydrogen transfer occurs or not. Our results show that the mechanism of proton transfer is highly predominant. Water removal simulations also show two possible mechanisms distinguished by the proton transfer reaction path. Proton transfer can occur either via a direct or via a water mediated reaction step. The calculations reveal that although both mechanisms contribute to the water removal process, the direct proton transfer is slightly favorable and occurs roughly in six out of ten occasions. read less NOT USED (definite) E. Mainini, H. Murakawa, P. Piovano, and U. Stefanelli, “Carbon-nanotube geometries: Analytical and numerical results,” Discrete and Continuous Dynamical Systems - Series S. 2016. link Times cited: 10 Abstract: We investigate carbon-nanotubes under the perspective ofgeom… read moreAbstract: We investigate carbon-nanotubes under the perspective ofgeometry optimization. Nanotube geometries are assumed to correspondto atomic configurations whichlocally minimize Tersoff-type interactionenergies. In the specific cases of so-called zigzag and armchairtopologies, candidate optimal configurations are analytically identifiedand their local minimality is numerically checked. Inparticular, these optimal configurations do not correspond neither tothe classical Rolled-up model [ 5 ] nor to themore recent polyhedral model [ 3 ]. Eventually, theelastic response of the structure under uniaxial testing is numericallyinvestigated and the validity of the Cauchy-Born rule is confirmed. read less NOT USED (definite) A. Glielmo, P. Sollich, and A. Vita, “Accurate interatomic force fields via machine learning with covariant kernels,” Physical Review B. 2016. link Times cited: 147 Abstract: We present a novel scheme to accurately predict atomic force… read moreAbstract: We present a novel scheme to accurately predict atomic forces as vector quantities, rather than sets of scalar components, by Gaussian process (GP) regression. This is based on matrix-valued kernel functions, on which we impose the requirements that the predicted force rotates with the target configuration and is independent of any rotations applied to the configuration database entries. We show that such covariant GP kernels can be obtained by integration over the elements of the rotation group $\mathit{SO}(d)$ for the relevant dimensionality $d$. Remarkably, in specific cases the integration can be carried out analytically and yields a conservative force field that can be recast into a pair interaction form. Finally, we show that restricting the integration to a summation over the elements of a finite point group relevant to the target system is sufficient to recover an accurate GP. The accuracy of our kernels in predicting quantum-mechanical forces in real materials is investigated by tests on pure and defective Ni, Fe, and Si crystalline systems. read less NOT USED (definite) Z. Fan, W. Chen, V. Vierimaa, and A. Harju, “Efficient molecular dynamics simulations with many-body potentials on graphics processing units,” Comput. Phys. Commun. 2016. link Times cited: 116 NOT USED (definite) S. Winczewski, J. Dziedzic, and J. Rybicki, “Central-force decomposition of spline-based modified embedded atom method potential,” Modelling and Simulation in Materials Science and Engineering. 2016. link Times cited: 0 Abstract: Central-force decompositions are fundamental to the calculat… read moreAbstract: Central-force decompositions are fundamental to the calculation of stress fields in atomic systems by means of Hardy stress. We derive expressions for a central-force decomposition of the spline-based modified embedded atom method (s-MEAM) potential. The expressions are subsequently simplified to a form that can be readily used in molecular-dynamics simulations, enabling the calculation of the spatial distribution of stress in systems treated with this novel class of empirical potentials. We briefly discuss the properties of the obtained decomposition and highlight further computational techniques that can be expected to benefit from the results of this work. To demonstrate the practicability of the derived expressions, we apply them to calculate stress fields due to an edge dislocation in bcc Mo, comparing their predictions to those of linear elasticity theory. read less NOT USED (definite) G. Cisneros et al., “Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions,” Chemical Reviews. 2016. link Times cited: 292 Abstract: Almost 50 years have passed from the first computer simulati… read moreAbstract: Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought “universal model” capable of describing the behavior of water under different conditions and in different environments. read less NOT USED (definite) K. Jolley and R. Smith, “Iron phosphate glasses: structure determination and radiation tolerance,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2016. link Times cited: 20 NOT USED (definite) E. Holmström et al., “Dependence of short and intermediate-range order on preparation in experimental and modeled pure a-Si,” Journal of Non-crystalline Solids. 2016. link Times cited: 16 NOT USED (definite) É. Maras, O. Trushin, A. Stukowski, T. Ala‐Nissila, and H. Jónsson, “Global transition path search for dislocation formation in Ge on Si(001),” Comput. Phys. Commun. 2016. link Times cited: 281 NOT USED (definite) D. Varshney, S. Shriya, S. Jain, M. Varshney, and R. Khenata, “Mechanically induced stiffening, thermally driven softening, and brittle nature of SiC,” Journal of Advanced Ceramics. 2016. link Times cited: 3 NOT USED (definite) J. Ding, E. Ma, M. Asta, and R. Ritchie, “Second-Nearest-Neighbor Correlations from Connection of Atomic Packing Motifs in Metallic Glasses and Liquids,” Scientific Reports. 2015. link Times cited: 79 NOT USED (definite) G. Wang, G. Loh, R. Pandey, and S. Karna, “Out-of-plane structural flexibility of phosphorene,” Nanotechnology. 2015. link Times cited: 43 Abstract: Phosphorene has been rediscovered recently, establishing its… read moreAbstract: Phosphorene has been rediscovered recently, establishing itself as one of the most promising two-dimensional group-V elemental monolayers with direct band gap, high carrier mobility, and anisotropic electronic properties. In this paper, surface buckling and its effect on its electronic properties are investigated by using molecular dynamics simulations together with density functional theory calculations. We find that phosphorene shows superior structural flexibility along the armchair direction allowing it to have large curvatures. The semiconducting and direct band gap nature are retained with buckling along the armchair direction; the band gap decreases and transforms to an indirect band gap with buckling along the zigzag direction. The structural flexibility and electronic robustness along the armchair direction facilitate the fabrication of devices with complex shapes, such as folded phosphorene and phosphorene nano-scrolls, thereby offering new possibilities for the application of phosphorene in flexible electronics and optoelectronics. read less NOT USED (definite) X. W. Zhou, M. E. Foster, R. Jones, P. Yang, H. Fan, and F. Doty, “A modified Stillinger-Weber potential for TlBr and its polymorphic extension,” Journal of Materials Science Research. 2015. link Times cited: 6 Abstract: TlBr is promising for g- and x- radiation detection, but suf… read moreAbstract: TlBr is promising for g- and x- radiation detection, but suffers from rapid performance degradation under the operating external electric fields. To enable molecular dynamics (MD) studies of this degradation, we have developed a Stillinger-Weber type of TlBr interatomic potential. During this process, we have also addressed two problems of wider interests. First, the conventional Stillinger-Weber potential format is only applicable for tetrahedral structures (e.g., diamond-cubic, zinc-blende, or wurtzite). Here we have modified the analytical functions of the Stillinger-Weber potential so that it can now be used for other crystal structures. Second, past modifications of interatomic potentials cannot always be applied by a broad community because any new analytical functions of the potential would require corresponding changes in the molecular dynamics codes. Here we have developed a polymorphic potential model that simultaneously incorporates Stillinger-Weber, Tersoff, embedded-atom method, and any variations (i.e., modified functions) of these potentials. We have implemented this polymorphic model in MD code LAMMPS, and demonstrated that our TlBr potential enables stable MD simulations under external electric fields. read less NOT USED (definite) S. K. Jain, G. Barkema, N. Mousseau, C. Fang, and M. Huis, “Strong Long-Range Relaxations of Structural Defects in Graphene Simulated Using a New Semiempirical Potential,” Journal of Physical Chemistry C. 2015. link Times cited: 22 Abstract: We present a new semiempirical potential for graphene, which… read moreAbstract: We present a new semiempirical potential for graphene, which includes also an out-of-plane energy term. This novel potential is developed from density functional theory (DFT) calculations for small numbers of atoms and can be used for configurations with millions of atoms. Our simulations show that buckling caused by typical defects such as the Stone–Wales (SW) defect extends to hundreds of nanometers. Surprisingly, this long-range relaxation lowers the defect formation energy dramatically—by a factor of 2 or 3—implying that previously published DFT-calculated defect formation energies suffer from large systematic errors. We also show the applicability of the novel potential to other long-range defects including line dislocations and grain boundaries, all of which exhibit pronounced out-of-plane relaxations. We show that the energy as a function of dislocation separation diverges logarithmically for flat graphene but converges to a constant for free-standing buckled graphene. A potential in which the atom... read less NOT USED (definite) H. Tetlow, J. Boer, I. Ford, D. Vvedensky, J. Coraux, and L. Kantorovich, “Growth of Epitaxial Graphene: Theory and Experiment,” arXiv: Materials Science. 2014. link Times cited: 222 NOT USED (definite) J.-W. Jiang, B. Wang, J.-S. Wang, and H. S. Park, “A review on the flexural mode of graphene: lattice dynamics, thermal conduction, thermal expansion, elasticity and nanomechanical resonance,” Journal of Physics: Condensed Matter. 2014. link Times cited: 111 Abstract: Single-layer graphene is so flexible that its flexural mode … read moreAbstract: Single-layer graphene is so flexible that its flexural mode (also called the ZA mode, bending mode, or out-of-plane transverse acoustic mode) is important for its thermal and mechanical properties. Accordingly, this review focuses on exploring the relationship between the flexural mode and thermal and mechanical properties of graphene. We first survey the lattice dynamic properties of the flexural mode, where the rigid translational and rotational invariances play a crucial role. After that, we outline contributions from the flexural mode in four different physical properties or phenomena of graphene—its thermal conductivity, thermal expansion, Young's modulus and nanomechanical resonance. We explain how graphene's superior thermal conductivity is mainly due to its three acoustic phonon modes at room temperature, including the flexural mode. Its coefficient of thermal expansion is negative in a wide temperature range resulting from the particular vibration morphology of the flexural mode. We then describe how the Young's modulus of graphene can be extracted from its thermal fluctuations, which are dominated by the flexural mode. Finally, we discuss the effects of the flexural mode on graphene nanomechanical resonators, while also discussing how the essential properties of the resonators, including mass sensitivity and quality factor, can be enhanced. read less NOT USED (definite) J.-W. Jiang, “Graphene versus MoS2: A short review,” Frontiers of Physics. 2014. link Times cited: 140 NOT USED (definite) S. L. Meadley and C. Angell, “Water and its relatives: the stable, supercooled and particularly the stretched, regimes,” arXiv: Chemical Physics. 2014. link Times cited: 5 Abstract: While the water molecule is simple, its condensed phase liqu… read moreAbstract: While the water molecule is simple, its condensed phase liquid behavior is so complex that no consensus description has emerged despite three centuries of effort. Here we identify features of its behavior that are the most peculiar, hence suggest ways forward. We examine the properties of water at the boundaries of common experience, including stable states at high pressure, the supercooled state at normal and elevated pressure, and the stretched ("negative pressure") state, out to the limits of mechanical stability. The familiar anomalies at moderate pressures (viscosity and density (TMD) behavior, etc.), are not explained by H-bond breaking, according to common bond-breaking criteria. A comparison of data on the TMD, at both positive and negative pressures, with the predictions of popular pair potential models, shows dramatic discrepancies appearing in the stretched liquid domain. This prompts questions on the second critical point (TC2) hypothesis that has been guiding much current thinking. We turn to related systems for guidance, reviewing a hierarchy of water-like anomalies. We conclude that water models are far from complete and that proper understanding of water will depend on success in mastering the measurement of liquid behavior in the negative pressure domain - which we discuss. read less NOT USED (definite) P. Ballone, “Modeling Potential Energy Surfaces: From First-Principle Approaches to Empirical Force Fields,” Entropy. 2013. link Times cited: 9 Abstract: Explicit or implicit expressions of potential energy surface… read moreAbstract: Explicit or implicit expressions of potential energy surfaces (PES) represent the basis of our ability to simulate condensed matter systems, possibly understanding and sometimes predicting their properties by purely computational methods. The paper provides an outline of the major approaches currently used to approximate and represent PESs and contains a brief discussion of what still needs to be achieved. The paper also analyses the relative role of empirical and ab initio methods, which represents a crucial issue affecting the future of modeling in chemical physics and materials science. read less NOT USED (definite) T. Hofer, “From macromolecules to electrons—grand challenges in theoretical and computational chemistry,” Frontiers in Chemistry. 2013. link Times cited: 7 Abstract: Among the many achievements of the twentieth century the acc… read moreAbstract: Among the many achievements of the twentieth century the accelerating development of microprocessors and their capabilities is one of the most impressive accomplishments, influencing virtually every aspect of daily life. The impact of this new technological resource was (and still is) of particular importance for theoretical approaches in science and engineering. Although many theories (Schrodinger, 1926a,b; Dirac, 1928; Feynman et al., 2010) required for an accurate treatment of quantum systems such as light and matter have been formulated prior to the construction of vacuum tube computers and the invention of the transistor, the applicability of these methodologies is strongly linked to the capacities of the employed computational equipment. read less NOT USED (definite) E. Bouchbinder, T. Goldman, and J. Fineberg, “The dynamics of rapid fracture: instabilities, nonlinearities and length scales,” Reports on Progress in Physics. 2013. link Times cited: 179 Abstract: The failure of materials and interfaces is mediated by crack… read moreAbstract: The failure of materials and interfaces is mediated by cracks, almost singular dissipative structures that propagate at velocities approaching the speed of sound. Crack initiation and subsequent propagation—the dynamic process of fracture—couples a wide range of time and length scales. Crack dynamics challenge our understanding of the fundamental physics processes that take place in the extreme conditions within the almost singular region where material failure occurs. Here, we first briefly review the classic approach to dynamic fracture, namely linear elastic fracture mechanics (LEFM), and discuss its successes and limitations. We show how, on the one hand, recent experiments performed on straight cracks propagating in soft brittle materials have quantitatively confirmed the predictions of this theory to an unprecedented degree. On the other hand, these experiments show how LEFM breaks down as the singular region at the tip of a crack is approached. This breakdown naturally leads to a new theoretical framework coined ‘weakly nonlinear fracture mechanics’, where weak elastic nonlinearities are incorporated. The stronger singularity predicted by this theory gives rise to a new and intrinsic length scale, ℓnl. These predictions are verified in detail through direct measurements. We then theoretically and experimentally review how the emergence of ℓnl is linked to a new equation for crack motion, which predicts the existence of a high-speed oscillatory crack instability whose wavelength is determined by ℓnl. We conclude by delineating outstanding challenges in the field. read less NOT USED (definite) H. Li and F.-hua Sun, “Recent Advances in Mechanical Properties of Nanowires.” 2012. link Times cited: 1 Abstract: Over the recent decade, nanowires (NWs) have attracted great… read moreAbstract: Over the recent decade, nanowires (NWs) have attracted great attention due to their small size and thus large surface area to volume ratio which results in interesting surface effect. As the devices become smaller and smaller, NWs serve as basic building blocks for future elec‐ tronic and electromechanical systems, such as performing sensitive mass and force detec‐ tion, acting as high frequency resonators and so on. The potential of NWs in future application has led to significant interest in experimental and theoretical characterization of the size-dependent properties of NWs. Constructing and determining NWs with better me‐ chanical properties than the corresponding bulk materials are a challenge even though the technical equipments are improving. Meantime, another important thing is how to integrate NWs with the existing technology. Material simulations of investigating mechanical proper‐ ties of NWs are still an important technique until now. This is essential to understand the inherent mechanism of the NWs’ deformation. The deformation mechanism depends on several aspects including the intrinsic material properties, crystal structures, surface geome‐ try, applied stress state, axial and surface orientation and exposed transverse surfaces. Until now many experimental techniques have been utilized to investigate mechanical properties. Scanning tunneling microscope (STM) was employed to study atomic contact of NWs and their conductance [1-3] in early experiments. Since a novel nanobridge structure of Au NWs is generated by electron-beam irradiation on a thin Au film in an ultrahigh vacuum trans‐ mission electron microscope (TEM) [4], many researches have been carried out to study the properties of this stable structure. A specific developed STM supplemented with a force sen‐ sor is used in order to reveal the process of forming thin Au NWs [5]. Atomic force micro‐ scope(AFM) has also attracted particular attention due to its high spatial resolution and force-sensing capabilities[6] and was used for bending tests of single crystal, micromachined read less NOT USED (definite) K. Hadley and C. McCabe, “Coarse-grained molecular models of water: a review,” Molecular Simulation. 2012. link Times cited: 134 Abstract: Coarse-grained (CG) models have proven to be very effective … read moreAbstract: Coarse-grained (CG) models have proven to be very effective tools in the study of phenomena or systems involving large time- and length-scales. By decreasing the degrees of freedom in the system and using softer interactions than seen in atomistic models, larger time steps can be used and much longer simulation times can be studied. CG simulations are widely used to study systems of biological importance that are beyond the reach of atomistic simulation, necessitating a computationally efficient and accurate CG model for water. In this review, we discuss the methods used for developing CG water models and the relative advantages and disadvantages of the resulting models. In general, CG water models differ with regard to how many waters each CG group or bead represents, whether analytical or tabular potentials have been used to describe the interactions, and how the model incorporates electrostatic interactions. How the models are parameterised, which typically depends on their application, is also discussed. read less NOT USED (definite) D. Wales, “Decoding the energy landscape: extracting structure, dynamics and thermodynamics,” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2012. link Times cited: 66 Abstract: Describing a potential energy surface in terms of local mini… read moreAbstract: Describing a potential energy surface in terms of local minima and the transition states that connect them provides a conceptual and computational framework for understanding and predicting observable properties. Visualizing the potential energy landscape using disconnectivity graphs supplies a graphical connection between different structure-seeking systems, which can relax efficiently to a particular morphology. Landscapes involving competing morphologies support multiple potential energy funnels, which may exhibit characteristic heat capacity features and relaxation time scales. These connections between the organization of the potential energy landscape and structure, dynamics and thermodynamics are common to all the examples presented, ranging from atomic and molecular clusters to biomolecules and soft and condensed matter. Further connections between motifs in the energy landscape and the interparticle forces can be developed using symmetry considerations and results from catastrophe theory. read less NOT USED (definite) K. Eriguchi, “Application of Molecular Dynamics Simulations to Plasma Etch Damage in Advanced Metal-Oxide-Semiconductor Field-Effect Transistors.” 2012. link Times cited: 0 Abstract: According to "the international technology roadmap for … read moreAbstract: According to "the international technology roadmap for semiconductors (ITRS)" (SIA, 2009), the shrinkage of silicon-based metal–oxide–semiconductor field-effect transistor (MOSFET) – an elemental device (unit) in ultra-large-scale integrated (ULSI) circuits – has been accelerating due to expanding demands for the higher performance and the lower power operation. The characteristic dimensions of current MOSFETs in mass productions are around 30 – 50 nm. Figure 1 shows the scaling trend of the key feature sizes in ULSI circuits predicted by Semiconductor Industry Association, USA. Various types of MOSFETs are designed for the specific purposes, i.e., low standby power (LSP), low operation power (LOP), and high performance (HP) operations, and built in ULSI circuits such as dynamic random access memory (DRAM) and micro-processing unit (MPU). New structured MOSFETs such as fully-depleted (FD) and metal-gate (MG) devices have been recently proposed. Since physical gate length (Lg) and source / drain extension depth (Ext) are the key feature sizes determining MOSFET performance (Sze & Ng, 2007), the shrinkage of Lg and Ext is a primal focus in the development of MOSFETs. These sizes have become a few nanometers, comparable to the scale of atomistic simulation domain. read less NOT USED (definite) D. Rodney, A. Tanguy, and D. Vandembroucq, “Modeling the mechanics of amorphous solids at different length scale and time scale,” Modelling and Simulation in Materials Science and Engineering. 2011. link Times cited: 244 Abstract: We review the recent literature on the simulation of the str… read moreAbstract: We review the recent literature on the simulation of the structure and deformation of amorphous solids, including oxide and metallic glasses. We consider simulations at different length scale and time scale. At the nanometer scale, we review studies based on atomistic simulations, with a particular emphasis on the role of the potential energy landscape and of the temperature. At the micrometer scale, we present the different mesoscopic models of amorphous plasticity and show the relation between shear banding and the type of disorder and correlations (e.g. elastic) included in the models. At the macroscopic range, we review the different constitutive laws used in finite-element simulations. We end with a critical discussion on the opportunities and challenges offered by multiscale modeling and information transfer between scales to study amorphous plasticity. read less NOT USED (definite) N. Admal and E. Tadmor, “A Unified Interpretation of Stress in Molecular Systems,” Journal of Elasticity. 2010. link Times cited: 200 NOT USED (definite) V. Kuzkin, “Comment on the calculation of forces for multibody interatomic potentials.” 2010. link Times cited: 0 Abstract: The system of particles interacting via multibody interatomi… read moreAbstract: The system of particles interacting via multibody interatomic potential of general form is considered. Possible variants of partition of the total force acting on a single particle into pair contributions are discussed. Two definitions for the force acting between a pair of particles are compared. The forces coincide only if the particles interact via pair or embedded-atom potentials. However in literature both definitions are used in order to determine Cauchy stress tensor. A simplest example of the linear pure shear of perfect square lattice is analyzed. It is shown that, Hardy’s definition for the stress tensor gives different results depending on the radius of localization function. The differences strongly depend on the way of the force definition. read less NOT USED (definite) B. Sadigh, P. Erhart, A. Stukowski, and A. Caro, “Composition-dependent interatomic potentials: A systematic approach to modelling multicomponent alloys,” Philosophical Magazine. 2009. link Times cited: 16 Abstract: We propose a simple scheme to construct composition-dependen… read moreAbstract: We propose a simple scheme to construct composition-dependent interatomic potentials for multicomponent systems that, when superposed onto the potentials for the pure elements, can reproduce not only the heat of mixing of the solid solution in the entire concentration range but also the energetics of a wider range of configurations including intermetallic phases. We show that an expansion in cluster interactions provides a way to systematically increase the accuracy of the model, and that it is straightforward to generalise this procedure to multicomponent systems. Concentration-dependent interatomic potentials can be built upon almost any type of potential for the pure elements including embedded atom method (EAM), modified EAM, bond-order, and Stillinger–Weber type potentials. In general, composition-dependent N-body terms in the total energy lead to explicit (N + 1)-body forces, which potentially render them computationally expensive. We present an algorithm that overcomes this problem and that can speed up the calculation of the forces for composition-dependent pair potentials in such a way as to make them computationally comparable in efficiency and scaling behaviour to standard EAM potentials. We also discuss the implementation in Monte Carlo simulations. Finally, we exemplarily review the composition-dependent EAM model for the Fe–Cr system. read less NOT USED (definite) X. Zhang, M. Gharbi, P. Sharma, and H. Johnson, “Quantum field induced strains in nanostructures and prospects for optical actuation,” International Journal of Solids and Structures. 2009. link Times cited: 10 NOT USED (definite) T. Yamamoto, S. Ohnishi, Y. Chen, and S. Iwata, “Effective Interatomic Potentials Based on The First-Principles Material Database,” Data Sci. J. 2009. link Times cited: 0 Abstract: Effective interatomic potentials are frequently utilized for… read moreAbstract: Effective interatomic potentials are frequently utilized for large-scale simulations of materials. In this work, we generate an effective interatomic potential, with Niobium as an example, using the force-matching method derived from a material database which is created by the first-principle molecular dynamics. It is found that the potentials constructed in the present work are more transferable than other existing potential models. We further discuss how the first-principles material database should be organized for generation of additional potential. read less NOT USED (definite) B. Garrison and Z. Postawa, “Computational view of surface based organic mass spectrometry.,” Mass spectrometry reviews. 2008. link Times cited: 125 Abstract: Surface based mass spectrometric approaches fill an importan… read moreAbstract: Surface based mass spectrometric approaches fill an important niche in the mass analysis portfolio of tools. The particular niche depends on both the underlying physics and chemistry of molecule ejection as well as experimental characteristics. In this article, we use molecular dynamics computer simulations to elucidate the fundamental processes giving rise to ejection of organic molecules in atomic and cluster secondary ion mass spectrometry (SIMS), massive cluster impact (MCI) mass spectrometry, and matrix-assisted laser desorption ionization (MALDI) mass spectrometry. This review is aimed at graduate students and experimental researchers. read less NOT USED (definite) V. Coffman et al., “A comparison of finite element and atomistic modelling of fracture,” Modelling and Simulation in Materials Science and Engineering. 2008. link Times cited: 21 Abstract: Are the cohesive laws of interfaces sufficient for modelling… read moreAbstract: Are the cohesive laws of interfaces sufficient for modelling fracture in polycrystals using the cohesive zone model? We examine this question by comparing a fully atomistic simulation of a silicon polycrystal with a finite element simulation with a similar overall geometry. The cohesive laws used in the finite element simulation are measured atomistically. We describe in detail how to convert the output of atomistic grain boundary fracture simulations into the piecewise linear form needed by a cohesive zone model. We discuss the effects of grain boundary microparameters (the choice of section of the interface, the translations of the grains relative to one another and the cutting plane of each lattice orientation) on the cohesive laws and polycrystal fracture. We find that the atomistic simulations fracture at lower levels of external stress, indicating that the initiation of fracture in the atomistic simulations is likely dominated by irregular atomic structures at external faces, internal edges, corners and junctions of grains. Thus, the cohesive properties of interfaces alone are not likely to be sufficient for modelling the fracture of polycrystals using continuum methods. read less NOT USED (definite) Q. Tang and F. Chen, “MD simulation of phase transformations due to nanoscale cutting on silicon monocrystals with diamond tip,” Journal of Physics D: Applied Physics. 2006. link Times cited: 43 Abstract: A three-dimensional molecular dynamics simulation is perform… read moreAbstract: A three-dimensional molecular dynamics simulation is performed to study atomic force microscopy cutting on silicon monocrystal surface. The displacive phase transformation from the four-coordinated diamond cubic phase to the six-coordinated β-silicon phase is observed due to localized high pressure. During phase transformation, atoms are of high potential and temperature, and the values of pressure and temperature are in good agreement with those according to the phase diagram. read less NOT USED (definite) F. Giessibl, “Advances in atomic force microscopy,” Reviews of Modern Physics. 2003. link Times cited: 1783 Abstract: This article reviews the progress of atomic force microscopy… read moreAbstract: This article reviews the progress of atomic force microscopy in ultrahigh vacuum, starting with its invention and covering most of the recent developments. Today, dynamic force microscopy allows us to image surfaces of conductors and insulators in vacuum with atomic resolution. The most widely used technique for atomic-resolution force microscopy in vacuum is frequency-modulation atomic force microscopy (FM-AFM). This technique, as well as other dynamic methods, is explained in detail in this article. In the last few years many groups have expanded the empirical knowledge and deepened our theoretical understanding of frequency-modulation atomic force microscopy. Consequently spatial resolution and ease of use have been increased dramatically. Vacuum atomic force microscopy opens up new classes of experiments, ranging from imaging of insulators with true atomic resolution to the measurement of forces between individual atoms. read less NOT USED (definite) Kirmse, Schneider, Scheerschmidt, Conrad, and Neumann, “TEM characterization of self‐organized CdSe/ZnSe quantum dots,” Journal of Microscopy. 1999. link Times cited: 10 Abstract: CdSe quantum dots (QDs) grown on ZnSe were investigated by v… read moreAbstract: CdSe quantum dots (QDs) grown on ZnSe were investigated by various transmission electron microscopy (TEM) techniques including diffraction contrast imaging, high‐resolution and analytical transmission electron microscopy both of plan‐view as well as cross‐section specimens. The size of the QDs ranges from about 5–50 nm, where from the contrast features in plan‐view imaging two classes can be differentiated. In the features of the smaller dots there is no inner fine structure resolvable. The larger ones exhibit contrast features of fourfold symmetry as expected for pyramid‐like islands. Corresponding simulations of diffraction contrast images of truncated CdSe pyramids with the edges of the basal plane orientated parallel to <100> are in relatively good agreement with this assumption. In TEM diffraction contrast imaging of cross‐section samples the locations of the quantum dots are visualized by additional dark contrast features. The QDs have a distinct larger extension in growth direction compared to the almost uniformly thick CdSe wetting layer. The presence of the CdSe QDs was also confirmed by energy‐dispersive X‐ray spectroscopy. read less NOT USED (definite) F. Fang, X. Zhang, W. Gao, Y. B. Guo, G. Byrne, and H. N. Hansen, “Nanomanufacturing—Perspective and applications,” Cirp Annals-manufacturing Technology. 2017. link Times cited: 113 NOT USED (definite) “Diagonal flipping of a Rhombus as elementary act of a polymorphic transformation. Calculation of energy threshold for the transformation in metals,” arXiv: Materials Science. 2018. link Times cited: 0 Abstract: Diagonal flipping of a rhombus consisting of two triangles s… read moreAbstract: Diagonal flipping of a rhombus consisting of two triangles sharing a common edge with atoms (ions) in vertices of the triangles is considered as an elementary act of the polymorphic transformation in metals. The estimation of the energy threshold for the diagonal flipping has been carried out for various combination of rhombus vertices occupation by Fe, Cr, and Mn atoms. The energy threshold has been calculated in the framework of Morse interatomic pair potential. Numerical coefficients for the approximation of the pair potential function have been scaled by experimental values of the sublimation energy and temperature dependencies of elastic constants for Fe, Cr, Mn. Values of the energy threshold at 1193 K were estimated equal to 195, 150 and 94 kJ/mole for pure Cr, Fe and Mn respectively, i.e. in the same sequence as values of elastic bulk modulus for these metals. The substitution of one Fe atom by Cr or Mn atom results in alteration of the energy threshold. This alteration is dependent on the angle type at this vertex (an acute or obtuse angle), as well as on the ratio of bulk modulus values of iron and alloying element. read less NOT USED (definite) “Embedded electromagnetically sensitive particle motion in functionalized fluids,” Computational Particle Mechanics. 2014. link Times cited: 0 NOT USED (definite) “Machine learning valence force field model,” arXiv: Computational Physics. 2018. link Times cited: 0 Abstract: The valence force field (VFF) model is a concise physical in… read moreAbstract: The valence force field (VFF) model is a concise physical interpretation of the atomic interaction in terms of the bond and angle variations in the explicit quadratic functional form, while the machine learning (ML) method is a flexible numerical approach to make predictions based on some pre-obtained training data without the need of any explicit functions. We propose a so-called ML-VFF model, by combining the clear physical essence of the VFF model and the numerical flexibility of the ML method. Instead of imposing any explicit functional forms for the atomic interaction, the ML-VFF model predicts the potential and force with the Gaussian regression approach. We take graphene as an example to illustrate the ability of the ML-VFF model to make accurate predictions with relatively low computational expenses. We also discuss some key advantages and drawbacks of the ML-VFF model. read less NOT USED (definite) “Neural Message Passing for Quantum Chemistry,” International Conference on Machine Learning. 2017. link Times cited: 0 Abstract: Supervised learning on molecules has incredible potential to… read moreAbstract: Supervised learning on molecules has incredible potential to be useful in chemistry, drug discovery, and materials science. Luckily, several promising and closely related neural network models invariant to molecular symmetries have already been described in the literature. These models learn a message passing algorithm and aggregation procedure to compute a function of their entire input graph. At this point, the next step is to find a particularly effective variant of this general approach and apply it to chemical prediction benchmarks until we either solve them or reach the limits of the approach. In this paper, we reformulate existing models into a single common framework we call Message Passing Neural Networks (MPNNs) and explore additional novel variations within this framework. Using MPNNs we demonstrate state of the art results on an important molecular property prediction benchmark; these results are strong enough that we believe future work should focus on datasets with larger molecules or more accurate ground truth labels. read less NOT USED (definite) “GIBS: A grand-canonical Monte Carlo simulation program for simulating ion-biomolecule interactions,” arXiv: Biomolecules. 2017. link Times cited: 0 Abstract: The ionic environment of biomolecules strongly influences th… read moreAbstract: The ionic environment of biomolecules strongly influences their structure, conformational stability, and inter-molecular interactions.This paper introduces GIBS, a grand-canonical Monte Carlo (GCMC) simulation program for computing the thermodynamic properties of ion solutions and their distributions around biomolecules. This software implements algorithms that automate the excess chemical potential calculations for a given target salt concentration. GIBS uses a cavity-bias algorithm to achieve high sampling acceptance rates for inserting ions and solvent hard spheres in simulating dense ionic systems. In the current version, ion-ion interactions are described using Coulomb, hard-sphere, or Lennard-Jones (L-J) potentials; solvent-ion interactions are described using hard-sphere, L-J and attractive square-well potentials; and, solvent-solvent interactions are described using hard-sphere repulsions. This paper and the software package includes examples of using GIBS to compute the ion excess chemical potentials and mean activity coefficients of sodium chloride as well as to compute the cylindrical radial distribution functions of monovalent (Na$^+$, Rb$^+$), divalent (Sr$^{2+}$), and trivalent (CoHex$^{3+}$) around fixed all-atom models of 25 base-pair nucleic acid duplexes. GIBS is written in C++ and is freely available community use; it can be downloaded at this https URL. read less NOT USED (definite) “Fast, accurate, and transferable many-body interatomic potentials by genetic programming,” ArXiv. 2019. link Times cited: 0 Abstract: The length and time scales of atomistic simulations are limi… read moreAbstract: The length and time scales of atomistic simulations are limited by the computational cost of the methods used to predict material properties. In recent years there has been great progress in the use of machine learning algorithms to develop fast and accurate interatomic potential models, but it remains a challenge to develop models that generalize well and are fast enough to be used at extreme time and length scales. To address this challenge, we have developed a machine learning algorithm based on genetic programming that is capable of discovering accurate, computationally efficient many-body potential models. The key to our approach is to explore a hypothesis space of models based on fundamental physical principles and select models within this hypothesis space based on their accuracy, speed, and simplicity. The focus on simplicity reduces the risk of overfitting the training data and increases the chances of discovering a model that generalizes well. Our algorithm was validated by rediscovering an exact Lennard Jones potential and a Sutton Chen embedded atom method potential from training data generated using these models. By using training data generated from density functional theory calculations, we found potential models for elemental copper that are simple, as fast as embedded atom models, and capable of accurately predicting properties outside of their training set. Our approach requires relatively small sets of training data, making it possible to generate training data using highly accurate methods at a reasonable computational cost. We present our approach, the forms of the discovered models, and assessments of their transferability, accuracy and speed. read less NOT USED (definite) “Characterization of Optimal Carbon Nanotubes Under Stretching and Validation of the Cauchy–Born Rule,” Archive for Rational Mechanics and Analysis. 2018. link Times cited: 0 NOT USED (definite) “Transverse dipole-dipole effective interaction for sheet arrangements,” arXiv: Atomic Physics. 2009. link Times cited: 0 Abstract: We have succeeded to develop a model pair interaction which … read moreAbstract: We have succeeded to develop a model pair interaction which when added to a system of interacting particles can be tuned to arrange the interacting objects into sheets. The interaction is based on the decomposition of the dipole-dipole interaction into two components, one parallel and one perpendicular to the connecting line between the dipoles, and keeping only perpendicular part here. Various aspects of this simple interaction are discussed, in particular in connection to two recent papers on self assembly of carbon nanostructures. On the other hand, the features discussed are quite general and might be of interest in different areas of microscopic modeling. read less
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