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.
1171 Citations (575 used)
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USED (high confidence) W. Dednam, M. Caturla, A. E. Botha, E. SanFabián, J. Miralles, and E. Louis, “Probability distribution for heat exchange in plastic deformation.,” Physical review. E. 2021. link Times cited: 0 Abstract: Fluctuation theorems allow one to obtain equilibrium informa… read moreAbstract: Fluctuation theorems allow one to obtain equilibrium information from nonequilibrium experiments. The probability distribution function of the relevant magnitude measured along the irreversible nonequilibrium trajectories is an essential ingredient of fluctuation theorems. In small systems, where fluctuations can be larger than average values, probability distribution functions often deviate from being Gaussian, showing long tails, mostly exponential, and usually strongly asymmetric. Recently, the probability distribution function of the van Hove correlation function of the relevant magnitude was calculated, instead of that of the magnitude itself. The resulting probability distribution function is highly symmetric, obscuring the application of fluctuation theorems. Here, the discussion is illustrated with the help of results for the heat exchanged during plastic deformation of aluminum nanowires, obtained from molecular dynamics calculations. We find that the probability distribution function for the heat exchanged is centrally Gaussian, with asymmetric exponential tails further out. By calculating the symmetry function we show that this distribution is consistent with fluctuation theorems relating the differences between two equilibrium states to an infinite number of nonequilibrium paths connecting those two states. read less USED (high confidence) Q. Yang and P. Olsson, “Full energy range primary radiation damage model,” Physical Review Materials. 2021. link Times cited: 9 Abstract: A full energy range primary radiation damage model is presen… read moreAbstract: A full energy range primary radiation damage model is presented here. It is based on the athermal recombination corrected displacements per atom (arc-dpa) model but includes a proper treatment of the near threshold conditions for metallic materials. Both ab initio (AIMD) and classical molecular dynamics (MD) simulations are used here for various metals with body-centered cubic (bcc), face-centered cubic (fcc), and hexagonal close-packed (hcp) structures to validate the model. For bcc and hcp metals, the simulation results fit very well with the model. For fcc metals, although there are slight deviations between the model and direct simulation results, it is still a clear improvement on the arc-dpa model. The deviations are due to qualitative differences in the threshold energy surfaces of fcc metals with respect to bcc and hcp metals according to our classical MD simulations. We introduce the minimum threshold displacement energy (TDE) as a term in our damage model. We calculated minimum TDEs for various metal materials using AIMD. In general, the calculated minimum TDEs are in very good agreement with experimental results. Moreover, we noticed a discrepancy in the literature for fcc Ni and estimated the average TDE of Ni using both classical MD and AIMD. It was found that the average TDE of Ni should be \ensuremath{\sim}70 eV based on simulation and experimental data, not the commonly used literature value of 40 eV. The most significant implications of introducing this full energy range damage model will be for estimating the effect of weak particle-matter interactions, such as for \ensuremath{\gamma}- and electron-radiation-induced damage. read less USED (high confidence) J. Zhong, “Atomistic Simulation of Severely Adhesive Wear on a Rough Aluminum Substrate.” 2020. link Times cited: 0 Abstract: In this Chapter, a severely adhesive wear on a rough aluminu… read moreAbstract: In this Chapter, a severely adhesive wear on a rough aluminum (Al) substrate is simulated by molecular dynamics (MD) under a high velocity impact of a hard-asperity (a hard-tip) with the Al-asperity. Multiple simulations include effects of four factors: the inter-asperity bonding, the geometry overlap between two asperities, the impact velocity between two asperities and the starting temperature of the Al-substrate. It is observed that the deformation mechanism on the Al-substrate would involve a local melting (from 1200 to 2500 K) which forms liquid type layers (amorphous textures) in the contact area between two asperities. Also, temperature profiles on the hard-tip and the Al-substrate is depicted. Moreover, a method in the Design of Experiments (DOE) is employed to interpret above all simulations. The DOE results indicate that the inter-asperity bonding and the geometry overlap between two asperities would substantially increase the wear rate (for about 53.56% and 67.29% contributions), while the starting temperature of the Al-substrate and the impact velocity between two asperities would play less important roles (about 10.30% and 6.61%) in raising the wear rate. read less USED (high confidence) D. Marchand, A. Jain, A. Glensk, and W. Curtin, “Machine learning for metallurgy I. A neural-network potential for Al-Cu,” Physical Review Materials. 2020. link Times cited: 35 Abstract: High-strength metal alloys achieve their performance via car… read moreAbstract: High-strength metal alloys achieve their performance via careful control of precipitates and solutes. The nucleation, growth, and kinetics of precipitation, and the resulting mechanical properties, are inherently atomic scale phenomena, particularly during early-stage nucleation and growth. Atomistic modeling using interatomic potentials is a desirable tool for understanding the detailed phenomena involved in precipitation and strengthening, which requires length and timescales far larger than those accessible by first-principles methods. Current interatomic potentials for alloys are not, however, sufficiently accurate for such studies. Here a family of neural-network potentials (NNPs) for the Al-Cu system are presented as a first example of a machine learning potential that can achieve near-first-principles accuracy for many different metallurgically important aspects of this alloy. High-fidelity predictions of intermetallic compounds, elastic constants, dilute solid-solution energetics, precipitate-matrix interfaces, generalized stacking fault energies and surfaces for slip in matrix and precipitates, antisite defect energies, and other quantities, are shown. The NNPs also captures the subtle entropically induced transition between ${\ensuremath{\theta}}^{\ensuremath{'}}$ and $\ensuremath{\theta}$ at temperatures around 600 K. Many comparisons are made with the state-of-the-art angular-dependent potential for Al-Cu, demonstrating the significant quantitative benefit of a machine learning approach. A preliminary kinetic Monte Carlo study shows the NNP to predict the emergence of GP zones in Al-4at%Cu at $T=300$ K in agreement with experiments. These studies show that the NNP has significant transferability to defects and properties outside the structures used to train the NNP but also shows some errors highlighting that the use of any interatomic potential requires careful validation in application to specific metallurgical problems of interest. read less USED (high confidence) L. Kolotova and I. Gordeev, “Structure and Phase Transition Features of Monoclinic and Tetragonal Phases in U–Mo Alloys,” Crystals. 2020. link Times cited: 2 Abstract: Using molecular dynamics simulations, we studied the structu… read moreAbstract: Using molecular dynamics simulations, we studied the structural properties of orthorhombic, monoclinic, and body-centered tetragonal (bct) phases of U–Mo alloys. A sequence of shear transformations between metastable phases takes place upon doping of uranium with molybdenum from pure α -U: orthorhombic α ′ → monoclinic α ″ → bct γ 0 → body-centered cubic (bcc) with doubled lattice constant γ s → bcc γ . The effects of alloy content on the structure of these phases have been investigated. It has been shown that increase in molybdenum concentration leads to an increase in the monoclinic angle and is more similar to the γ 0 -phase. In turn, tetragonal distortion of the γ 0 -phase lattice with displacement of a central atom in the basic cell along the <001> direction makes it more like the α ″ -phase. Both of these effects reduce the necessary shift in atomic positions for the α ″ → γ 0 -phase transition. read less USED (high confidence) R. Brüning, D. A. Brown, H. Bera, and N. Jakse, “Molecular dynamics simulations of amorphous Ni–P alloy formation by rapid quenching and atomic deposition,” Journal of Physics: Condensed Matter. 2019. link Times cited: 2 Abstract: A combined experimental and simulation study is carried out … read moreAbstract: A combined experimental and simulation study is carried out to compare the properties of amorphous Ni100−xPx alloys obtained by electroless deposition and rapid melt-quenching. The onset of crystallization of experimental electroless deposited amorphous films is measured by differential scanning calorimetry experiments. Classical molecular dynamics simulations using Embedded Atom Model-based interactions are performed to obtain glassy Ni–P by melt-quenching the liquid with various quenching rates, as well as via low-energy chemical deposition to mimic experimental electroless deposition. It is shown that the deposited amorphous and glassy states display similar short-range order. The amorphous deposit corresponds to a glassy state obtained with a cooling rate of 109 K s−1, indicating that deposition yields generally more relaxed amorphous structures. The appearance of phosphorus-enriched surface on the simulated deposited thin film, comparable to experimental observations, is discussed. read less USED (high confidence) A. Hernandez, A. Balasubramanian, F. Yuan, S. Mason, and T. Mueller, “Fast, accurate, and transferable many-body interatomic potentials by symbolic regression,” npj Computational Materials. 2019. link Times cited: 51 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 USED (high confidence) D. K. Qi, M. Tang, L. Lu, F. Zhao, L. Wang, and S. Luo, “Macrodeformation twinning in a textured aluminum alloy via dynamic equal channel angular pressing,” Journal of Materials Science. 2018. link Times cited: 7 USED (high confidence) M. Wang, S. Jiang, and Y. Zhang, “Phase Transformation, Twinning, and Detwinning of NiTi Shape-Memory Alloy Subject to a Shock Wave Based on Molecular-Dynamics Simulation,” Materials. 2018. link Times cited: 27 Abstract: Martensitic transformation, reverse martensitic transformati… read moreAbstract: Martensitic transformation, reverse martensitic transformation, twinning, and detwinning of equiatomic nickel–titanium shape-memory alloy (NiTi SMA) under the action of a shock wave are studied using a molecular-dynamics simulation. In the loading process of a shock wave, B2 austenite is transformed into B19′ martensite, whereas in the unloading process of the shock wave, B19′ martensite is transformed into B2 austenite. With repeated loading and unloading of the shock wave, martensitic transformation occurs along with twinning, but reverse martensitic transformation appears along with detwinning. The mechanisms for the twinning and detwinning of NiTi SMA subjected to a shock wave are revealed in order to lay the theoretical foundation to investigate the shape-memory effect and superelasticity. read less USED (high confidence) M. Hodapp, G. Anciaux, J. Molinari, and W. Curtin, “Coupled atomistic/discrete dislocation method in 3D Part II: Validation of the method,” Journal of the Mechanics and Physics of Solids. 2018. link Times cited: 24 USED (high confidence) M. L. D. Reis, L. Proville, and M. Sauzay, “Modeling the climb-assisted glide of edge dislocations through a random distribution of nanosized vacancy clusters,” Physical Review Materials. 2018. link Times cited: 8 Abstract: A multiscale model is developed to simulate the climb-assist… read moreAbstract: A multiscale model is developed to simulate the climb-assisted glide of edge dislocations anchored by a random distribution of nanosized vacancy clusters. Atomic-scale simulations allowed us to characterize the interactions between an edge dislocation and nanovoids as a function of their sizes and shapes. The atomic-scale data were used to calibrate the parameters of an elastic line model, which we employed to evaluate the average glide distance of a dislocation with realistic dimensions. To complete our scheme, a standard model for the climb velocity of edge dislocations was enhanced with atomic-scale inputs in order to determine the deformation rate expected through the climb-assisted glide. Our predictions made for the archetypical case of Al are in good agreement with experiments of different types, i.e., tensile deformation tests and steady creep tests. read less USED (high confidence) Z. Zhang, J. Zhang, Y. Ni, W. Can, J. Kun, and R. Xuedi, “Multiscale Simulation of Surface Defect Influence in Nanoindentation by a Quasi-Continuum Method,” Micromachining. 2018. link Times cited: 4 Abstract: Microscopic properties of nanocrystal aluminum thin film hav… read moreAbstract: Microscopic properties of nanocrystal aluminum thin film have been investigated using the quasicontinuum method in order to study the influence of surface defects in nanoindentation. Various distances between the surface defect and indenter have been taken into account. The results show that as the distance between the pit and indenter increases, the nanohardness increases in a wave pattern associated with a cycle of three atoms, which is closely related to the crystal structure of periodic atoms arrangement on {1 1 1} atomic close-packed planes of face-centered cubic metal; when the adjacent distance between the pit and indenter is more than 16 atomic spacing, there is almost no effect on nanohardness. In addition, the theoretical formula for the necessary load for elastic-to-plastic transition of Al film has been modified with the initial surface defect size, which may contribute to the investigation of material property with surface defects. read less USED (high confidence) M. Chakraborty, C. Xu, and A. White, “Encoding and selecting coarse-grain mapping operators with hierarchical graphs.,” The Journal of chemical physics. 2018. link Times cited: 33 Abstract: Coarse-grained (CG) molecular dynamics (MD) can simulate sys… read moreAbstract: Coarse-grained (CG) molecular dynamics (MD) can simulate systems inaccessible to fine-grained (FG) MD simulations. A CG simulation decreases the degrees of freedom by mapping atoms from an FG representation into agglomerate CG particles. The FG to CG mapping is not unique. Research into systematic selection of these mappings is challenging due to their combinatorial growth with respect to the number of atoms in a molecule. Here we present a method of reducing the total count of mappings by imposing molecular topology and symmetry constraints. The count reduction is illustrated by considering all mappings for nearly 50 000 molecules. The resulting number of mapping operators is still large, so we introduce a novel hierarchical graphical approach which encodes multiple CG mapping operators. The encoding method is demonstrated for methanol and a 14-mer peptide. With the test cases, we show how the encoding can be used for automated selection of reasonable CG mapping operators. read less USED (high confidence) P. Andric and W. Curtin, “New theory for crack-tip twinning in fcc metals,” Journal of The Mechanics and Physics of Solids. 2018. link Times cited: 18 USED (high confidence) K. Dang and D. Spearot, “Pressure Dependence of the Peierls Stress in Aluminum,” JOM. 2018. link Times cited: 11 USED (high confidence) S. Scharring, M. Patrizio, H. Eckel, J. Roth, and M. Povarnitsyn, “Dynamic Material Parameters in Molecular Dynamics and Hydrodynamic Simulations on Ultrashort-Pulse Laser Ablation of Aluminum.” 2018. link Times cited: 1 USED (high confidence) X. Hu and Y. Ni, “The Effect of the Vertex Angles of Wedged Indenters on Deformation during Nanoindentation.” 2017. link Times cited: 2 Abstract: In order to study the effect of the angle of wedged indenter… read moreAbstract: In order to study the effect of the angle of wedged indenters during nanoindentation, indenters with half vertex angles of 60°, 70° and 80° are used for the simulations of nanoindentation on FCC aluminum (Al) bulk material by the multiscale quasicontinuum method (QC). The load-displacement responses, the strain energy-displacement responses, and hardness of Al bulk material are obtained. Besides, atomic configurations for each loading situation are presented. We analyze the drop points in the load-displacement responses, which correspond to the changes of microstructure in the bulk material. From the atom images, the generation of partial dislocations as well as the nucleation and the emission of perfect dislocations have been observed with wedged indenters of half vertex angles of 60° and 70°, but not 80°. The stacking faults move beneath the indenter along the direction [ 1 1 ¯ 0 ] . The microstructures of residual displacements are also discussed. In addition, hardness of the Al bulk material is different in simulations with wedged indenters of half vertex angles of 60° and 70°, and critical hardness in the simulation with the 70° indenter is bigger than that with the 60° indenter. The size effect of hardness in plastic wedged nanoindentation is observed. There are fewer abrupt drops in the strain energy-displacement response than in the load-displacement response, and the abrupt drops in strain energy-displacement response reflect the nucleation of perfect dislocations or extended dislocations rather than partial dislocations. The wedged indenter with half vertex angle of 70° is recommended for investigating dislocations during nanoindentation. read less USED (high confidence) P. Andric and W. Curtin, “New Theory for Mode I Crack-tip Dislocation Emission,” Journal of The Mechanics and Physics of Solids. 2017. link Times cited: 58 USED (high confidence) J. Chen and C. García-Cervera, “An efficient multigrid strategy for large-scale molecular mechanics optimization,” J. Comput. Phys. 2017. link Times cited: 6 USED (high confidence) K. Machado et al., “Study of NaF–AlF3 Melts by Coupling Molecular Dynamics, Density Functional Theory, and NMR Measurements,” Journal of Physical Chemistry C. 2017. link Times cited: 28 Abstract: Improvement of the industrial electrolytic process for alumi… read moreAbstract: Improvement of the industrial electrolytic process for aluminum production necessitates a thorough understanding of the underlying ionic structure of the electrolyte, which mainly comprises NaF and AlF3 at around 965 °C. The chemical and physical properties of this melt strongly depend on the aluminum speciation, which requires a multipronged approach in order to clarify its properties. Here we parametrize a new polarizable ion model (PIM) interatomic potential for the molten NaF–AlF3 system, which is used to study the liquid properties up to 50 mol % of AlF3 at high temperatures. The potential parameters are obtained by force fitting to density functional theory (DFT) reference data. Molecular dynamics (MD) simulations are combined with further DFT calculations to determine NMR chemical shifts for 27Al, 23Na, and 19F. An excellent agreement is obtained with experimental values. This enables the study of the dynamic properties of the melts such as viscosity, electrical conductivity, and self-diffusion coe... read less USED (high confidence) H. Mu, B. Xu, C. Ouyang, and X. Lei, “Highly optimized embedding atom method potential for Pt-Cu alloys,” Journal of Alloys and Compounds. 2017. link Times cited: 6 USED (high confidence) D. Sun, D. Sun, C. Shang, Z. Liu, and X. Gong, “Intrinsic Features of an Ideal Glass,” Chinese Physics Letters. 2017. link Times cited: 6 Abstract: In order to understand the long-standing problem of the natu… read moreAbstract: In order to understand the long-standing problem of the nature of glass states, we performed intensive simulations on the thermodynamic properties and potential energy surface of an ideal glass. We found that the atoms of an ideal glass manifest cooperative diffusion, and show clearly different behavior from the liquid state. By determining the potential energy surface, we demonstrated that the glass state has a flat potential landscape, which is the critical intrinsic feature of ideal glasses. When this potential region is accessible through any thermal or kinetic process, the glass state can be formed and a glass transition will occur, regardless of any special structural character. With this picture, the glass transition can be interpreted by the emergence of configurational entropies, as a consequence of flat potential landscapes. read less USED (high confidence) S. Ryu and W. Cai, “Stability of Eshelby dislocations in FCC crystalline nanowires,” International Journal of Plasticity. 2016. link Times cited: 6 USED (high confidence) B. Yao, X. Tang, and Z. Yu, “Trapping of helium atoms in aluminum,” Journal of Nuclear Science and Technology. 2016. link Times cited: 0 Abstract: Using molecular dynamic simulation, the effect of vacancy cl… read moreAbstract: Using molecular dynamic simulation, the effect of vacancy clusters on the interstitial helium atoms was studied in the early stages of helium bubble formation in the vessel of fission reactor, aluminum. The simulation shows, that there is a slight propensity of helium interstitial clustering without initial vacancies in aluminum. When vacancy cluster was introduced, the behavior of interstitial helium atoms was strongly dependent on the ratio of vacancy to helium. The interstitial helium atoms will be attracted in the center of the vacancy cluster when the ratio of vacancy to helium is much larger than 1, and when the ratio approaches 1, the helium will recombine with the vacancies, and, form in substitutions. In the case of the ratio of vacancy to helium less than 1, some aluminum interstitials will be created. The result shows, that the vacancy cluster plays a role of a nucleation center for helium atoms to accelerate the helium bubble growth. read less USED (high confidence) K. L. Baker and W. Curtin, “Multiscale diffusion method for simulations of long-time defect evolution with application to dislocation climb,” Journal of The Mechanics and Physics of Solids. 2016. link Times cited: 15 USED (high confidence) N. Admal and E. Tadmor, “Material fields in atomistics as pull-backs of spatial distributions,” Journal of The Mechanics and Physics of Solids. 2016. link Times cited: 12 USED (high confidence) B. Szajewski, F. Pavia, and W. Curtin, “Robust atomistic calculation of dislocation line tension,” Modelling and Simulation in Materials Science and Engineering. 2015. link Times cited: 41 Abstract: The line tension Γ ?> of a dislocation is an important and f… read moreAbstract: The line tension Γ ?> of a dislocation is an important and fundamental property ubiquitous to continuum scale models of metal plasticity. However, the precise value of Γ ?> in a given material has proven difficult to assess, with literature values encompassing a wide range. Here results from a multiscale simulation and robust analysis of the dislocation line tension, for dislocation bow-out between pinning points, are presented for two widely-used interatomic potentials for Al. A central part of the analysis involves an effective Peierls stress applicable to curved dislocation structures that markedly differs from that of perfectly straight dislocations but is required to describe the bow-out both in loading and unloading. The line tensions for the two interatomic potentials are similar and provide robust numerical values for Al. Most importantly, the atomic results show notable differences with singular anisotropic elastic dislocation theory in that (i) the coefficient of the ln(L) ?> scaling with dislocation length L differs and (ii) the ratio of screw to edge line tension is smaller than predicted by anisotropic elasticity. These differences are attributed to local dislocation core interactions that remain beyond the scope of elasticity theory. The many differing literature values for Γ ?> are attributed to various approximations and inaccuracies in previous approaches. The results here indicate that continuum line dislocation models, based on elasticity theory and various core-cut-off assumptions, may be fundamentally unable to reproduce full atomistic results, thus hampering the detailed predictive ability of such continuum models. read less USED (high confidence) N. S. Weingarten and J. Larentzos, “Implementation of Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Software.” 2015. link Times cited: 7 Abstract: : To observe screw dislocation motion on an infinite glide p… read moreAbstract: : To observe screw dislocation motion on an infinite glide plane in atomistic simulations, shifted periodic boundary conditions (sPBC) must be utilized. We have implemented this capability in the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) software application code for use in classical molecular dynamics (MD) simulations. This report presents the justification for utilizing sPBC, followed by a description of the implementation methodology. Dislocation velocities as a function of applied stress are obtained for screw dislocations in aluminum (Al) at a temperature of 300 K, and compared to prior results to verify our implementation. read less USED (high confidence) A. V. Fedorov and A. V. Shul’gin, “Molecular dynamics modeling melting of of aluminum nanoparticles of the embedded atom method,” Combustion, Explosion, and Shock Waves. 2015. link Times cited: 13 USED (high confidence) J. Cho, T. Junge, J. Molinari, and G. Anciaux, “Toward a 3D coupled atomistic and discrete dislocation dynamics simulation: dislocation core structures and Peierls stresses with several character angles in FCC aluminum,” Advanced Modeling and Simulation in Engineering Sciences. 2015. link Times cited: 35 USED (high confidence) F. Pavia and W. Curtin, “Parallel algorithm for multiscale atomistic/continuum simulations using LAMMPS,” Modelling and Simulation in Materials Science and Engineering. 2015. link Times cited: 39 Abstract: Deformation and fracture processes in engineering materials … read moreAbstract: Deformation and fracture processes in engineering materials often require simultaneous descriptions over a range of length and time scales, with each scale using a different computational technique. Here we present a high-performance parallel 3D computing framework for executing large multiscale studies that couple an atomic domain, modeled using molecular dynamics and a continuum domain, modeled using explicit finite elements. We use the robust Coupled Atomistic/Discrete-Dislocation (CADD) displacement-coupling method, but without the transfer of dislocations between atoms and continuum. The main purpose of the work is to provide a multiscale implementation within an existing large-scale parallel molecular dynamics code (LAMMPS) that enables use of all the tools associated with this popular open-source code, while extending CADD-type coupling to 3D. Validation of the implementation includes the demonstration of (i) stability in finite-temperature dynamics using Langevin dynamics, (ii) elimination of wave reflections due to large dynamic events occurring in the MD region and (iii) the absence of spurious forces acting on dislocations due to the MD/FE coupling, for dislocations further than 10 Å from the coupling boundary. A first non-trivial example application of dislocation glide and bowing around obstacles is shown, for dislocation lengths of ∼50 nm using fewer than 1 000 000 atoms but reproducing results of extremely large atomistic simulations at much lower computational cost. read less USED (high confidence) A. V. Fedorov and A. Shulgin, “Molecular dynamics modeling melting of of aluminum nanoparticles of the embedded atom method,” Combustion, Explosion, and Shock Waves. 2015. link Times cited: 0 USED (high confidence) Y. Rosandi et al., “Melting of Al Induced by Laser Excitation of 2p Holes,” Materials Research Letters. 2015. link Times cited: 4 Abstract: Novel photon sources—such as XUV- or X-ray lasers—allow to s… read moreAbstract: Novel photon sources—such as XUV- or X-ray lasers—allow to selectively excite core excitations in materials. We study the response of a simple metal, Al, to the excitation of 2p holes using molecular dynamics simulations. During the lifetime of the holes, the interatomic interactions in the slab are changed; we calculate these using WIEN2k. We find that the melting dynamics after core-hole excitation is dominated by classical electron–phonon dynamics. The effects of the changed potential surface for excited Al atoms occur on the time scale of 100 fs, corresponding to the Debye time of the lattice. read less USED (high confidence) L. Wang, Y. Cai, F. Zhao, D. Fan, and S. Luo, “Shock-induced deformation of nanocrystalline Al: Characterization with orientation mapping and selected area electron diffraction,” Journal of Applied Physics. 2015. link Times cited: 33 Abstract: We investigate shock-induced deformation of columnar nanocry… read moreAbstract: We investigate shock-induced deformation of columnar nanocrystalline Al with large-scale molecular dynamics simulations and implement orientation mapping (OM) and selected area electron diffraction (SAED) for microstructural analysis. Deformation mechanisms include stacking fault formation, pronounced twinning, dislocation slip, grain boundary (GB) sliding and migration, and lattice or partial grain rotation. GBs and GB triple junctions serve as the nucleation sites for crystal plasticity including twinning and dislocations, due to GB weakening, and stress concentrations. Grains with different orientations exhibit different densities of twins or stacking faults nucleated from GBs. GB migration occurs as a result of differential deformation between two grains across the GB. High strain rates, appropriate grain orientation and GBs contribute to deformation twinning. Upon shock compression, intra-grain dislocation and twinning nucleated from GBs lead to partial grain rotation and the formation of subgrains, ... read less USED (high confidence) B. Szajewski and W. A. Curtin, “Analysis of spurious image forces in atomistic simulations of dislocations,” Modelling and Simulation in Materials Science and Engineering. 2015. link Times cited: 40 Abstract: Molecular dynamics simulations of dislocation/obstacle inter… read moreAbstract: Molecular dynamics simulations of dislocation/obstacle interactions are enhancing our physical understanding of plasticity. However, despite increasing computational power, the interaction between simulation cell boundaries and the long ranged fields of dislocations make spurious image effects inevitable. Here, these image effects are examined in detail, providing a general map of the spurious image stress as a function of simulation cell size, aspect ratio and bow-out for both nominally edge and screw dislocations. This is achieved using an approximate image solution of the resulting boundary value problem as well as an analytic model that captures most of the spurious image effects. A unique simulation cell shape is found to minimize spurious image effects for a fixed simulation volume (i.e. fixed total number of atoms) and specified initial dislocation line length. The results are used to estimate image stress effects in various literature studies involving dislocation bow-out. The image effects are non-negligible. Several case studies involving simulation cell dimensions are shown to converge due to a near-zero scaling of the image stress with respect to the simulation cell dimensions used. Finally, a direct comparison is made between a dislocation bow-out configuration under an applied load in a finite simulation cell and an image-free multiscale simulation of the same problem and the difference is shown to be consistent with our estimated image stresses. Overall, the results here provide guidance for both the development and interpretation of quantitative molecular dynamics studies involving curved dislocation structures. read less USED (high confidence) T. Wejrzanowski, M. Lewandowska, K. Sikorski, and K. Kurzydłowski, “Effect of grain size on the melting point of confined thin aluminum films,” Journal of Applied Physics. 2014. link Times cited: 17 Abstract: The melting of aluminum thin film was studied by a molecular… read moreAbstract: The melting of aluminum thin film was studied by a molecular dynamics (MD) simulation technique. The effect of the grain size and type of confinement was investigated for aluminum film with a constant thickness of 4 nm. The results show that coherent intercrystalline interface suppress the transition of solid aluminum into liquid, while free-surface gives melting point depression. The mechanism of melting of polycrystalline aluminum thin film was investigated. It was found that melting starts at grain boundaries and propagates to grain interiors. The melting point was calculated from the Lindemann index criterion, taking into account only atoms near to grain boundaries. This made it possible to extend melting point calculations to bigger grains, which require a long time (in the MD scale) to be fully molten. The results show that 4 nm thick film of aluminum melts at a temperature lower than the melting point of bulk aluminum (933 K) only when the grain size is reduced to 6 nm. read less USED (high confidence) Y. Li and Y. Ni, “Multiscale Simulation of Wedge Nanoindentation Based on the Repulsive Force-field Approach,” International Journal of Nonlinear Sciences and Numerical Simulation. 2014. link Times cited: 0 Abstract: A new method is proposed to perform the multiscale simulatio… read moreAbstract: A new method is proposed to perform the multiscale simulation of nanoindentation with wedge indenter. We designed a potential field to model the wedge indenter based on the repulsive force-field approach which was used to model round indenters. A smooth curve representing the indenter tip is used to avoid the singularity of an ideal wedge indenter. Simulation with our approach correctly shows essential features of wedge nanoindentation. The load responses during retraction is confirmed by elastic model based on the Oliver–Pharr approach. Significant indentation size effect that the contact hardness decreases with the increase of contact depth is compared with existing models. The atomic configurations of the film shows that perfect dislocations nucleate under the indenter with Burges vectors perpendicular to the indentation direction. The strain distribution under the indenter shows that the length of plastic zone in the indentation direction is much larger than the contact width. read less USED (high confidence) C. Huang et al., “Prediction of Thermal Conductivity of Aluminum Nanocluster-Filled Mesoporous Silica (Al/MCM-41),” International Journal of Thermophysics. 2013. link Times cited: 4 USED (high confidence) J. Yang, C. Mao, X. Li, and C. Liu, “On the Cauchy-Born approximation at finite temperature for alloys,” Discrete & Continuous Dynamical Systems - B. 2013. link Times cited: 4 USED (high confidence) J. Dantzig, J. Dantzig, P. Napoli, J. Friedli, J. Friedli, and M. Rappaz, “Dendritic Growth Morphologies in Al-Zn Alloys—Part II: Phase-Field Computations,” Metallurgical and Materials Transactions A. 2013. link Times cited: 71 USED (high confidence) C.-W. Lai and C.-S. Chen, “Influence of indenter shape on nanoindentation: an atomistic study,” Interaction and multiscale mechanics. 2013. link Times cited: 2 Abstract: The influence of indenter geometry on nanoindentation was st… read moreAbstract: The influence of indenter geometry on nanoindentation was studied using a static molecular dynamics simulation. Dislocation nucleation, dislocation locks, and dislocation movements during nanoindentation into Al (001) were studied. Spherical, rectangular, and Berkovich indenters were modeled to study the material behaviors and dislocation activities induced by their different shapes. We found that the elastic responses for the three cases agreed well with those predicted from elastic contact theory. Complicated stress fields were generated by the rectangular and Berkovich indenters, leading to a few uncommon nucleation and dislocation processes. The calculated mean critical resolved shear stresses for the Berkovich and rectangular indenters were lower than the theoretical strength. In the Berkovich indenter case, an amorphous region was observed directly below the indenter tip. In the rectangular indenter case, we observed that some dislocation loops nucleated on the plane. Furthermore, a prismatic loop originating from inside the material glided upward to create a mesa on the indenting surface. We observed an unusual softening phenomenon in the rectangular indenter case and proposed that heterogeneously nucleating dislocations are responsible for this. read less USED (high confidence) K. Okhotnikov, B. Stevensson, and M. Edén, “New interatomic potential parameters for molecular dynamics simulations of rare-earth (RE = La, Y, Lu, Sc) aluminosilicate glass structures: exploration of RE3+ field-strength effects.,” Physical chemistry chemical physics : PCCP. 2013. link Times cited: 39 Abstract: Sets of self-consistent oxygen-rare earth (RE = La, Y, Lu, S… read moreAbstract: Sets of self-consistent oxygen-rare earth (RE = La, Y, Lu, Sc) interatomic potential parameters are derived using a force-matching procedure and utilized in molecular dynamics (MD) simulations for exploring the structures of RE2O3-Al2O3-SiO2 glasses that feature a fixed molar ratio n(Al)/n(Si) = 1 but variable RE contents. The structures of RE aluminosilicate (AS) glasses depend markedly on the RE(3+) cation field strength (CFS) over both short and intermediate length-scales. We explore these dependencies for glasses incorporating the cations La(3+), Y(3+), Lu(3+) and Sc(3+), whose CFSs increase due to the concomitant shrinkage of the ionic radii: R(La) > R(Y) > R(Lu) > R(Sc). This trend is mirrored in decreasing average RE(3+) coordination numbers (Z(RE)) from Z(La) = 6.4 to Z(Sc) = 5.4 in the MD-derived data. However, overall the effects from RE(3+) CFS elevations on the local glass structures are most pronounced in the O and {Al([4]), Al([5]), Al([6])} speciations. The former display minor but growing populations of O([0]) ("free oxygen ion") and O([3]) ("oxygen tricluster") moieties. The abundance of AlO5 polyhedra increases significantly from ≈10% in La-based glasses to ≈30% in their Sc counterparts at the expense of the overall dominating AlO4 tetrahedra, whereas the amounts of AlO6 groups remain <5% throughout. We also discuss the Si([4])/Al([p]) (p = 4, 5, 6) intermixing and the nature of their oxygen bridges, where the degree of edge-sharing increases together with the RE(3+) CFS. read less USED (high confidence) M. C. Liu et al., “Assessing the interfacial strength of an amorphous–crystalline interface,” Acta Materialia. 2013. link Times cited: 54 USED (high confidence) M. C. Nguyen, L. Ke, X. Zhao, V. Antropov, C. Wang, and K. Ho, “Atomic Structure and Magnetic Properties of HfCo_7 Alloy,” IEEE Transactions on Magnetics. 2013. link Times cited: 6 Abstract: Co rich Hf-Co alloys demonstrate promising properties as pot… read moreAbstract: Co rich Hf-Co alloys demonstrate promising properties as potential permanent magnet systems. However their structure has not been well established by experiment. We performed a search for low-energy structures of the HfCo7 system with recently developed adaptive genetic algorithm. Among the low-energy structures with 16 and 32 atoms per unit cell, we found structural motifs similar to the permanent magnet SmCo5. For the unit cell size larger than 40 atoms, we found a phase separation into pure hcp Co and Hf2Co7 in agreement with the experiment. Calculated magnetization and temperature of magnetic phase transition are similar to those for hcp Co. Overall considered HfCo7 system represents a mix of in- and out-of-plane magnetic anisotropies systems with possible site dependence of magnetic anisotropy. read less USED (high confidence) Y. Rosandi and H. Urbassek, “Melting of Al by ultrafast laser pulses: dynamics at the melting threshold,” Applied Physics A. 2013. link Times cited: 9 USED (high confidence) X. Li, “Coarse‐graining molecular dynamics models using an extended Galerkin projection method,” International Journal for Numerical Methods in Engineering. 2012. link Times cited: 17 Abstract: We present a new framework for coarse‐graining molecular dyn… read moreAbstract: We present a new framework for coarse‐graining molecular dynamics models for crystalline solids. The reduction method is based on a Galerkin projection to a subspace, whose dimension is much smaller than that of the full atomistic model. To effectively reduce artificial reflections of phonons at the interface, we construct extended subspaces with increasing accuracy by adding more coarse‐grained variables near the interface between lattice defects and the surrounding region. This approach is equivalent to the generalized Langevin model. But it eliminates the need to precompute the memory function, a well‐known practical difficulty. Further, the variational formulation preserves the stability of the molecular models. Copyright © 2014 John Wiley & Sons, Ltd. read less USED (high confidence) J. Yang, X. Wu, and X. Li, “A generalized Irving-Kirkwood formula for the calculation of stress in molecular dynamics models.,” The Journal of chemical physics. 2012. link Times cited: 45 Abstract: In non-equilibrium molecular dynamics simulations, continuum… read moreAbstract: In non-equilibrium molecular dynamics simulations, continuum mechanics quantities can be computed from the position and momentum of the particles based on the classical Irving-Kirkwood formalism. For practical purposes, the implementations of Irving-Kirkwood formulas often involve a spatial averaging using a smooth kernel function. The resulting formula for the stress has been known as Hardy stress. Usually results obtained this way still need to be further processed to reduce the fluctuation, e.g., by ensemble or time averaging. In this paper we extend Hardy's formulas by systematically incorporating both spatial and temporal averaging into the expression of continuum quantities. The derivation follows the Irving-Kirkwood formalism, and the average quantities still satisfy conservation laws in continuum mechanics. We will discuss the selection of kernel functions and present several numerical tests. read less USED (high confidence) H. Hsu, J. Chien, L. Chu, S. Ju, Y. Feng, and S. Fu, “Nanoscale bondability study on copper-aluminum intermetallic compound using molecular dynamics simulation,” 2012 7th International Microsystems, Packaging, Assembly and Circuits Technology Conference (IMPACT). 2012. link Times cited: 3 Abstract: In this paper, the growth mechanism of intermetallic compoun… read moreAbstract: In this paper, the growth mechanism of intermetallic compound (IMC) layer between Copper (Cu) free air ball (FAB) and Aluminum (Al) bond pad is carefully examined. The test vehicle is pd-coated Cu wirebonds on Al pad in plastic ball grid array (PBGA) package. Palladium (Pd), the anti-oxide material coated on Cu wire will be blended in the Cu FAB when the ball is formed by an electrical flame-off (EFO). Preliminary results demonstrated that IMC cracks from the edge of bonding interface and spreads into the center area. This is the cause of open fail. The IMC between Cu and Al was initially generated in the form of CuAl2, and gradually increased the content of Cu and turned into CuAl when the working temperature was increased. The final stage of IMC growth is Cu9Al4 and the aluminum pad will be vanished as the result of Cu diffusivity. Bondability on nanoscale IMC of CuAl2, CuAl and Cu9Al4 are also cautiously investigated by using molecular dynamics (MD) simulations. Atomic-level tensile stress and tensile strain are predicted to examine the bonding strength of two IMCs along the bonding interface. Interfacial fracture is different in different tensile speed as well as the working temperature. A series of experimental works and MD simulations are conducted in this research. read less USED (high confidence) G. Longo, S. Bhattacharya, and S. Scandolo, “A Molecular Dynamics Study of the Role of Adatoms in SAMs of Methylthiolate on Au(111): A New Force Field Parameterized from Ab Initio Calculations,” Journal of Physical Chemistry C. 2012. link Times cited: 13 Abstract: Starting from ab initio calculations and using a force match… read moreAbstract: Starting from ab initio calculations and using a force matching procedure, we have developed a new force field for molecular dynamics simulations of self-assembled monolayers of methylthiolate (MT) on Au(111) surfaces. This new force field is able to reproduce several observed features of SAMs of MT on Au(111) surface, such as the formation of gold vacancy islands and the (√3 × √3)R30 lattice. We have studied the dynamics of Au adatoms and monatomic vacancies on the Au(111) surface for the SAM of MT at room temperature. It is observed that monatomic vacancies coarsen to form large vacancy islands while the adatoms group to form clusters. Both results are in agreement with experiments. At elevated temperatures, Au adatoms that are lifted from the surface leave an atomic vacancy on it. The liquid-like diffusion of gold adatoms on the SAM surface occurs by hopping between pairs of methylthiolate to which the adatom is temporarily bound. Our findings indicate that structural models of the c(4 × 2) unit cell i... read less USED (high confidence) S. Brinckmann, D. Mahajan, and A. Hartmaier, “A scheme to combine molecular dynamics and dislocation dynamics,” Modelling and Simulation in Materials Science and Engineering. 2012. link Times cited: 12 Abstract: Many engineering challenges occur on multiple interacting le… read moreAbstract: Many engineering challenges occur on multiple interacting length scales, e.g. during fracture atoms separate on the atomic scale while plasticity develops on the micrometer scale. To investigate the details of these events, a concurrent multiscale model is required which studies the problem at appropriate length- and time-scales: the atomistic scale and the dislocation dynamics scale. The AtoDis multiscale model is introduced, which combines atomistics and dislocation dynamicsinto a fully dynamic model that is able to simulate deformation mechanisms at finite temperature. The model uses point forces to ensure mechanical equilibrium and kinematic continuity at the interface. By resolving each interface atom analytically, and not numerically, the framework uses a coarse FEM mesh and intrinsically filters out atomistic vibrations. This multiscale model allows bi-directional dislocation transition at the interface of both models with no remnant atomic disorder. Thereby, the model is able to simulate a larger plastic zone than conventional molecular dynamics while reducing the need for constitutive dislocation dynamics equations. This contribution studies dislocation nucleation at finite temperature and investigates the absorption of dislocations into the crack wake. read less USED (high confidence) L. Li, J. Shao, Y.-F. Li, S. Duan, and J. Liang, “Atomistic simulation of fcc—bcc phase transition in single crystal Al under uniform compression,” Chinese Physics B. 2012. link Times cited: 4 Abstract: By molecular dynamics simulations employing an embedded atom… read moreAbstract: By molecular dynamics simulations employing an embedded atom model potential, we investigate the fcc-to-bcc phase transition in single crystal Al, caused by uniform compression. Results show that the fcc structure is unstable when the pressure is over 250 GPa, in reasonable agreement with the calculated value through the density functional theory. The morphology evolution of the structural transition and the corresponding transition mechanism are analysed in detail. The bcc (011) planes are transited from the fcc (111) plane and the (111) plane. We suggest that the transition mechanism consists mainly of compression, shear, slid and rotation of the lattice. In addition, our radial distribution function analysis explicitly indicates the phase transition of Al from fcc phase to bcc structure. read less USED (high confidence) H. Men and Z. Fan, “Effects of lattice mismatch on interfacial structures of liquid and solidified Al in contact with hetero-phase substrates: MD simulations,” IOP Conference Series: Materials Science and Engineering. 2012. link Times cited: 8 Abstract: In this study, the effects of the misfit on in-plane structu… read moreAbstract: In this study, the effects of the misfit on in-plane structures of liquid Al and interfacial structure of solidified Al in contact with the heterophase substrates have been investigated, using molecular dynamics (MD) simulations. The MD simulations were conducted for Al/fcc (111) substrates with varied misfits. The order parameter and atomic arrangement indicated that the in-plane ordering of the liquid at the interface decreases significantly with an increase of the misfit, i.e., solid-like for small misfit and liquid-like for large misfit. Further, our MD simulation results revealed that a perfect orientation relationship forms at the interface between the substrate and the solidified Al for a misfit of less than -3% and the boundary is coherent. With an increase in the misfit, Shockley partial and extended dislocations form at the interface, and the boundary becomes a semi-coherent or low-angle twist boundary. read less USED (high confidence) S. Hocker, P. Beck, S. Schmauder, J. Roth, and H. Trebin, “Simulation of crack propagation in alumina with ab initio based polarizable force field.,” The Journal of chemical physics. 2011. link Times cited: 22 Abstract: We present an effective atomic interaction potential for cry… read moreAbstract: We present an effective atomic interaction potential for crystalline α-Al(2)O(3) generated by the program potfit. The Wolf direct, pairwise summation method with spherical truncation is used for electrostatic interactions. The polarizability of oxygen atoms is included by use of the Tangney-Scandolo interatomic force field approach. The potential is optimized to reproduce the forces, energies, and stresses in relaxed and strained configurations as well as {0001}, {1010}, and {1120} surfaces of Al(2)O(3). Details of the force field generation are given, and its validation is demonstrated. We apply the developed potential to investigate crack propagation in α-Al(2)O(3) single crystals. read less USED (high 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 USED (high confidence) S. Starikov et al., “Laser ablation of gold: Experiment and atomistic simulation,” JETP Letters. 2011. link Times cited: 21 USED (high confidence) M. Dewald and W. Curtin, “Multiscale modeling of dislocation/grain-boundary interactions: III. 60° dislocations impinging on Σ3, Σ9 and Σ11 tilt boundaries in Al,” Modelling and Simulation in Materials Science and Engineering. 2011. link Times cited: 75 Abstract: The interactions between 60° dislocation pile-ups with grain… read moreAbstract: The interactions between 60° dislocation pile-ups with grain boundaries (GBs) are studied using multiscale modeling. Careful quantitative analyses of complex processes associated with 60° dislocation absorption and transmission phenomena at Σ3, Σ9 and Σ11 symmetric tilt boundaries in Al are interpreted in terms of a set of modified Lee–Robertson–Birnbaum (MLRB) criteria. Our results and the MLRB criteria (i) explain experimental observations, (ii) rationalize new mechanisms such as deformation twinning and formation of extended stacking faults, (iii) show that reactions can be controlled more strongly by the leading partial of an incoming dislocation rather than the full Burgers vector and (iv) demonstrate that non-Schmid stresses, e.g. shear and compressive stresses along the GB, GB dislocation processes and step-height changes on the GB all influence the critical nucleation stress, but to differing degrees among different tilt boundaries. The MLRB criteria do not capture the effects of local GB structure that can also influence behavior. Quantitative metrics based on the MLRB criteria are formulated, using the simulation results, for various absorption and transmission phenomena. These metrics can be used as input into mesoscale models such as discrete dislocation plasticity, so that atomic-scale observations can inform higher-scale predictions plasticity. read less USED (high confidence) S. Sonntag, C. Trichet Paredes, J. Roth, and H. Trebin, “Molecular dynamics simulations of cluster distribution from femtosecond laser ablation in aluminum,” Applied Physics A. 2011. link Times cited: 40 USED (high confidence) 李莉, 邵建立, 段素青, and 梁九卿, “Orientation dependence of structural transition in fcc Al driven under uniaxial compression by atomistic simulations,” Chinese Physics B. 2011. link Times cited: 4 Abstract: By molecular dynamics simulations employing an embedded atom… read moreAbstract: By molecular dynamics simulations employing an embedded atom method potential, we have investigated structural transformations in single crystal Al caused by uniaxial strain loading along the [001], [011] and [111] directions. We find that the structural transition is strongly dependent on the crystal orientations. The entire structure phase transition only occurs when loading along the [001] direction, and the increased amplitude of temperature for [001] loading is evidently lower than that for other orientations. The morphology evolutions of the structural transition for [011] and [111] loadings are analysed in detail. The results indicate that only 20% of atoms transit to the hcp phase for [011] and [111] loadings, and the appearance of the hcp phase is due to the partial dislocation moving forward on {111}fcc family. For [011] loading, the hcp phase grows to form laminar morphology in four planes, which belong to the {111}fcc family; while for [111] loading, the hcp phase grows into a laminar structure in three planes, which belong to the {111}fcc family except for the (111) plane. In addition, the phase transition is evaluated by using the radial distribution functions. read less USED (high confidence) J. Barrat and D. Rodney, “Portable Implementation of a Quantum Thermal Bath for Molecular Dynamics Simulations,” Journal of Statistical Physics. 2011. link Times cited: 42 USED (high confidence) A. Nair, D. Warner, R. Hennig, and W. Curtin, “Coupling quantum and continuum scales to predict crack tip dislocation nucleation,” Scripta Materialia. 2010. link Times cited: 28 USED (high confidence) X. Zhang, Q. Peng, and G. Lu, “Self-consistent embedding quantum mechanics/molecular mechanics method with applications to metals,” Physical Review B. 2010. link Times cited: 11 Abstract: We present a quantum mechanics QM/molecular mechanics MM met… read moreAbstract: We present a quantum mechanics QM/molecular mechanics MM method for coupling Kohn-Sham density-functional theory with classical atomistic simulations based on a self-consistent embedding theory. The formalism and numerical implementation of the method are described. The QM/MM method is employed to study extended defects—a grain boundary and an edge dislocation in Al by focusing on hydrogen H-defect interactions. We find that it is energetically more favorable for H impurities to segregate at the grain boundary and the dislocation core as opposed to the bulk. We provide direct first-principles evidence that both the grain boundary and the dislocation could serve as a “pipe” to accelerate H diffusion and shed light on the corresponding atomistic mechanisms. The results demonstrate that the QM/MM method is a powerful approach in dealing with extended defects in materials. read less USED (high confidence) Q. Peng, X. Zhang, C. Huang, E. Carter, and G. Lu, “Quantum mechanical study of solid solution effects on dislocation nucleation during nanoindentation,” Modelling and Simulation in Materials Science and Engineering. 2010. link Times cited: 10 Abstract: A multiscale quasicontinuum density functional theory method… read moreAbstract: A multiscale quasicontinuum density functional theory method is used to study the solid solution effect on dislocation nucleation during nanoindentation. Specifically, an Al thin film with Mg impurities is considered. We find that the solid solution effect depends sensitively on the local configuration of the impurities. Although a random distribution of the impurities increases the hardness of the material, linear distributions of the impurities actually lower the hardness. In both cases, the strengthening/softening effects are due to dislocation nucleation. Consistent with recent experiments, the change of the ideal strength is found to be small. Different incipient plasticity behaviors are observed: in the pure material, two full dislocations are nucleated under the indentor. For a random distribution of impurities, two partial dislocations are formed instead. For linear distributions of impurities, only one partial dislocation is formed. Thus the nucleation of dislocations is sensitive to the local distribution of impurities in an alloy. read less USED (high confidence) L. Yi-de, H. Qing-hai, C. Qi-long, and L. Chang-song, “Diffusion activation energy versus the favourable energy in two-order-parameter model::A molecular dynamics study of liquid Al,” Chinese Physics B. 2010. link Times cited: 2 Abstract: In the preent work, we find that both diffusion activation e… read moreAbstract: In the preent work, we find that both diffusion activation energy Ea(D) and Ea(Sex) increase linearly with pressure and have the same slope (0.022±0.001 eV/GPa) for liquid Al. The temperature and pressure dependence of excess entropy is well fitted by the expression −Sex(T,P)/kB = a(P)+b(P)T+c(P) exp (Ef/kBT), which together with the small ratio of Ef/kBT leads to the relationship of excess entropy to temperature and pressure, i.e. Sex −cEf/T, where c is about 12 and Ef ( = ΔE − PΔV) is the favourable energy. Therefore, there exists a simple relation between Ea(Sex) and Ef i.e. Ea(Sex) cEf. read less USED (high confidence) A. Franchini, V. Bortolani, G. Santoro, and M. Brigazzi, “Sliding friction of N2 on Pb(111),” Journal of Physics: Condensed Matter. 2010. link Times cited: 1 Abstract: Molecular dynamics simulations of the sliding friction betwe… read moreAbstract: Molecular dynamics simulations of the sliding friction between two thick solid slabs are performed. The upper body is formed of light N2 particles and the substrate of heavy Pb atoms. Among the various mechanisms that are responsible for the friction, we consider the phonon–phonon interaction between the two blocks. To provide evidence of the phonon interaction, we compare two different systems. For the first we consider the substrate as formed of atoms fixed in the equilibrium (111) positions. In the second system the Pb atoms can be displaced from the ideal positions, under their mutual interactions. A comparison with recently obtained experimental data will be discussed. read less USED (high confidence) Y. Rosandi and H. Urbassek, “Ultrashort-pulse laser irradiation of metal films: the effect of a double-peak laser pulse,” Applied Physics A. 2010. link Times cited: 16 USED (high confidence) N. Admal and E. Tadmor, “A Unified Interpretation of Stress in Molecular Systems,” Journal of Elasticity. 2010. link Times cited: 200 USED (high confidence) W. Shan and U. Nackenhorst, “An adaptive FE–MD model coupling approach,” Computational Mechanics. 2010. link Times cited: 29 USED (high confidence) A. Stukowski and K. Albe, “Dislocation detection algorithm for atomistic simulations,” Modelling and Simulation in Materials Science and Engineering. 2010. link Times cited: 163 Abstract: We present a novel computational method that makes it possib… read moreAbstract: We present a novel computational method that makes it possible to directly extract dislocation lines and their associated Burgers vectors from three-dimensional atomistic simulations. The on-the-fly dislocation detection algorithm is based on a fully automated Burgers circuit analysis, which locates dislocation cores and determines their Burgers vector. Through a subsequent vectorization step, the transition from the atomistic system to a discrete dislocation representation is achieved. Using a parallelized implementation of the algorithm, the dislocation analysis can be efficiently performed on the fly within a molecular dynamics simulation. This enables the visualization and investigation of dislocation processes occurring on sub-picosecond time scales, whose observation is otherwise impeded by the presence of other crystal defects or simply by the huge amount of data produced by large-scale atomistic simulations. The presented method is able to identify individual segments as well as networks of perfect, partial and twinning dislocations. The dislocation density can be directly determined and even more sophisticated information is made accessible by our dislocation analysis, including dislocation reactions and junctions, as well as stacking fault and twin boundary densities. read less USED (high confidence) J. Marian, G. Venturini, B. L. Hansen, J. Knap, M. Ortiz, and G. Campbell, “Finite-temperature extension of the quasicontinuum method using Langevin dynamics: entropy losses and analysis of errors,” Modelling and Simulation in Materials Science and Engineering. 2009. link Times cited: 49 Abstract: The concurrent bridging of molecular dynamics and continuum … read moreAbstract: The concurrent bridging of molecular dynamics and continuum thermodynamics presents a number of challenges, mostly associated with energy transmission and changes in the constitutive description of a material across domain boundaries. In this paper, we propose a framework for simulating coarse dynamic systems in the canonical ensemble using the quasicontinuum method (QC). The equations of motion are expressed in reduced QC coordinates and are strictly derived from dissipative Lagrangian mechanics. The derivation naturally leads to a classical Langevin implementation where the timescale is governed by vibrations emanating from the finest length scale occurring in the computational cell. The equations of motion are integrated explicitly via Newmark's method, which is parametrized to ensure overdamped dynamics. In this fashion, spurious heating due to reflected vibrations is suppressed, leading to stable canonical trajectories. To estimate the errors introduced by the QC reduction in the resulting dynamics, we have quantified the vibrational entropy losses in Al uniform meshes by calculating the thermal expansion coefficient for a number of conditions. We find that the entropic depletion introduced by coarsening varies linearly with the element size and is independent of the nodal cluster diameter. We rationalize the results in terms of the system, mesh and cluster sizes within the framework of the quasiharmonic approximation. The limitations of the method and alternatives to mitigate the errors introduced by coarsening are discussed. This work represents the first of a series of studies aimed at developing a fully non-equilibrium finite-temperature extension of QC. read less USED (high confidence) P. Schuck, J. Marian, J. B. Adams, and B. Sadigh, “Vibrational properties of straight dislocations in bcc and fcc metals within the harmonic approximation,” Philosophical Magazine. 2009. link Times cited: 7 Abstract: We calculate the vibrational spectra of straight screw and e… read moreAbstract: We calculate the vibrational spectra of straight screw and edge dislocations in several body-centered cubic (bcc) (Mo and Fe) and face-centered cubic (fcc) (Cu and Al) metals within the harmonic approximation. We take advantage of the translational symmetry of straight dislocations to efficiently calculate their phonon eigenstates in the harmonic limit. This allows us to calculate the low-temperature contribution of straight screw and edge dislocations to the heat capacity of each respective metal, and show that the dominant temperature dependence below 5 K is linear. Comparison with heat capacity measurements of heavily cold-worked Cu reveals very good agreement with our calculations. At higher temperatures, the contribution from the non-linear terms becomes significant. As a result, maxima in the straight dislocation heat capacities are observed in the temperature range from 9% to 16% of the Debye temperature. We investigate the appearance of localized and resonance peaks in the vibrational spectra induced by dislocations, and study in detail their spatial spread around the dislocation cores by projecting vibrational eigenstates onto individual atoms. We study the deviation of these atomic-level vibrational free energies from that of the perfect crystal as a function of distance to the dislocation cores, and establish that, similar to the dislocation energy, the vibrational free energy of an isolated dislocation behaves logarithmically in the long-range limit. Finally, we obtain vibrational spectra for propagating waves along the dislocation line and find that the dispersion for these waves is consistent with the notion of kink formation and motion for screw dislocations. read less USED (high confidence) Y. Kulkarni and R. Asaro, “Are some nanotwinned fcc metals optimal for strength, ductility and grain stability?,” Acta Materialia. 2009. link Times cited: 81 USED (high confidence) J. M. Winey, A. Kubota, and Y. Gupta, “A thermodynamic approach to determine accurate potentials for molecular dynamics simulations: thermoelastic response of aluminum,” Modelling and Simulation in Materials Science and Engineering. 2009. link Times cited: 101 Abstract: An accurate description of the thermoelastic response of sol… read moreAbstract: An accurate description of the thermoelastic response of solids is central to classical simulations of compression- and deformation-induced condensed matter phenomena. To achieve the correct thermoelastic description in classical simulations, a new approach is presented for determining interatomic potentials. In this two-step approach, values of atomic volume and the second- and third-order elastic constants measured at room temperature are extrapolated to T = 0 K using classical thermo-mechanical relations that are thermodynamically consistent. Next, the interatomic potentials are fitted to these T = 0 K pseudo-values. This two-step approach avoids the low-temperature quantum regime, providing consistency with the assumptions of classical simulations and enabling the correct thermoelastic response to be recovered in simulations at room temperature and higher. As an example of our approach, an EAM potential was developed for aluminum, providing significantly better agreement with thermoelastic data compared with previous EAM potentials. The approach presented here is quite general and can be used for other potential types as well, the key restriction being the inapplicability of classical atomistic simulations when quantum effects are important. read less USED (high confidence) A. Franchini, V. Bortolani, G. Santoro, and M. Brigazzi, “Theoretical investigation of the anticorrugation effects on the tribological properties of the Xe/Cu interface,” Journal of Physics: Condensed Matter. 2009. link Times cited: 3 Abstract: We present a molecular dynamics study of the slip time and s… read moreAbstract: We present a molecular dynamics study of the slip time and static friction for a slab of Xe deposited on a slab of Cu. To put in evidence the role played by the phonon field of the two blocks, we compare results obtained with a substrate formed by fixed atoms with one formed by mobile atoms. In the last case the scattering between Xe and Cu mobile atoms is inelastic and there is an exchange of momentum and energy between the two blocks which produces disorder in the interface plane. This disorder favors a decrease of the static friction and a consequent increase of the slip time. We describe the interaction between Xe and Cu with a phenomenological multi-ion potential which gives rise to an anticorrugation of the charge distribution and reproduces very well the ab initio density functional calculations. Our model potential is a linear superposition of a corrugating potential and an anticorrugating one. For this reason we can study the static friction by passing from an anticorrugated to a fully corrugated system. We also investigate the slip time and we compare our results with recent experimental data measured with the quartz crystal microbalance technique. read less USED (high confidence) S. Hendy and D. Schebarchov, “Superheating in metal nanoparticles with non-melting surfaces,” The European Physical Journal D. 2009. link Times cited: 5 USED (high confidence) G. Wu, G. Lu, C. García-Cervera, and E. Weinan, “Density-gradient-corrected embedded atom method,” Physical Review B. 2009. link Times cited: 9 Abstract: Through detailed comparisons between Embedded Atom Method (E… read moreAbstract: Through detailed comparisons between Embedded Atom Method (EAM) and first-principles calculations for Al, we find that EAM tends to fail when there are large electron density gradients present. We attribute the observed failures to the violation of the uniform density approximation (UDA) underlying EAM. To remedy the insufficiency of UDA, we propose a gradient-corrected EAM model which introduces gradient corrections to the embedding function in terms of exchange-correlation and kinetic energies. Based on the perturbation theory of "quasiatoms" and density functional theory, the new embedding function captures the essential physics missing in UDA, and paves the way for developing more transferable EAM potentials. With Voter-Chen EAM potential as an example, we show that the gradient corrections can significantly improve the transferability of the potential. read less USED (high confidence) M. Mendelev, R. Ott, M. Kramer, and D. Sordelet, “Determining strain in amorphous alloys: Uncertainties with analyzing structural changes during deformation,” Journal of Applied Physics. 2009. link Times cited: 1 Abstract: Molecular dynamics simulations were utilized to test the rel… read moreAbstract: Molecular dynamics simulations were utilized to test the reliability of strain values obtained from diffraction data for noncrystalline alloys. We found that in the case of a one-component system, the strain value obtained from the pair correlation functions underestimates the actual value because of a small degree of atomic relaxations, which minimize the effects of the applied deformation. In the case of multicomponent systems, the different pairs are affected by applied deformation to different extents; moreover, this implies that the strain value determined from diffraction data should depend on the type of scattering. read less USED (high confidence) S. Namilae, B. Radhakrishnan, and J. R. Morris, “Atomistic simulation of the effect of Ga on crack tip opening in Al bicrystals,” Modelling and Simulation in Materials Science and Engineering. 2008. link Times cited: 6 Abstract: Liquid metal embrittlement (LME) in the Al–Ga system is stud… read moreAbstract: Liquid metal embrittlement (LME) in the Al–Ga system is studied using molecular dynamics simulations. Crack tip opening loads are exerted on symmetric tilt Al bicrystals in the presence of liquid Ga. In general, the speed of crack propagation increases in the presence of Ga. However, there is significant variation in the dynamic behavior of the different boundaries studied here. We observe the formation of a sub-grain by grain boundary dissociation (grain boundary phase transformation) in [1 1 0] Σ9 and [1 1 0] Σ11 grain boundaries; this results in crack blunting even in the presence of Ga. In the Σ3 twin, the absence of alternating compressive and tensile stresses present in other boundaries results in fast Ga penetration after the crack path is formed. The structure of grain boundaries apart from thermodynamic considerations significantly affects LME. read less USED (high confidence) I. N. Kar’kin, L. E. Kar’kina, and Y. Gornostyrev, “Effect of chemical interaction on the stability of metal clusters in FCC metals,” The Physics of Metals and Metallography. 2008. link Times cited: 2 USED (high confidence) A. Franchini, M. Brigazzi, G. Santoro, and V. Bortolani, “Theory of static friction: temperature and corrugation effects,” Journal of Physics: Condensed Matter. 2008. link Times cited: 10 Abstract: We present a study of the static friction, as a function of … read moreAbstract: We present a study of the static friction, as a function of temperature, between two thick solid slabs. The upper one is formed of light particles and the substrate of heavy particles. We focus our attention on the interaction between the phonon fields of the two blocks and on the interface corrugation, among the various mechanisms responsible for the friction. To give evidence of the role played by the dynamical interaction of the substrate with the upper block, we consider both a substrate formed by fixed atoms and a substrate formed by mobile atoms. To study the effect of the corrugation, we model it by changing the range parameter σ in the Lennard-Jones interaction potential. We found that in the case of the mobile substrate there is a large momentum transfer from the substrate to the upper block. This momentum transfer increases on increasing the temperature and produces a large disorder in the upper block favouring a decrease of the static friction with respect to the case for a rigid substrate. Reducing the corrugation, we found that with a rigid substrate the upper block becomes nearly commensurate, producing an enhancement of the static friction with respect to that with a mobile substrate. read less USED (high confidence) A. Acharya, A. Beaudoin, and R. E. Miller, “New Perspectives in Plasticity Theory: Dislocation Nucleation, Waves, and Partial Continuity of Plastic Strain Rate,” Mathematics and Mechanics of Solids. 2008. link Times cited: 67 Abstract: A field theory of dislocation mechanics and plasticity is il… read moreAbstract: A field theory of dislocation mechanics and plasticity is illustrated through new results at the nano, meso, and macro scales. Specifically, dislocation nucleation, the occurrence of wave-type response in quasi-static plasticity, and a jump condition at material interfaces and its implications for analysis of deformation localization are discussed. read less USED (high confidence) J. A. Rinehimer, M. Widom, J. Northrup, and R. M. Feenstra, “Molecular dynamics and first‐principles computations of Ga adlayers on GaN(0001),” physica status solidi (b). 2008. link Times cited: 7 Abstract: Structural models for Ga adlayer(s) on GaN(0001) are investi… read moreAbstract: Structural models for Ga adlayer(s) on GaN(0001) are investigated using both molecular dynamics and first‐principles computations. An energetically favourable model is deduced that is consistent with observed low‐energy electron diffraction data. The model contains regions of uniaxial contraction of the topmost Ga adlayer on the surface (rather than uniform biaxial contraction, as in previous models), multiple domains of which form a hexagonal arrangement on the surface. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) read less USED (high confidence) X. Zhang and G. Lu, “Quantum mechanics/molecular mechanics methodology for metals based on orbital-free density functional theory,” Physical Review B. 2007. link Times cited: 28 Abstract: We present a quantum mechanics QM/molecular mechanics MM for… read moreAbstract: We present a quantum mechanics QM/molecular mechanics MM formalism for coupling density functional theory DFT based quantum simulations to classical atomistic simulations for metals. The multiscale methodology is applicable to systems where important quantum phenomena are confined to a small region, but their impacts could be felt over much larger scales. The concurrent coupling between QM and MM regions is treated quantum mechanically via the orbital-free density functional theory OFDFT. We propose two energetic formulations for the QM region: one is based on OFDFT and the other based on the Kohn-Sham KS DFT. In the first case, the degree of freedom is the electron charge density in the QM region, and the total energy functional is directly minimized with respect to the charge density. In the second case, the degrees of freedom are KS orbitals in the QM region. An embedding potential representing the influence of the larger MM region onto the QM region is included in the KS Hamiltonian for the QM region, which is solved selfconsistently. Calculations for a perfect lattice and vacancy clusters of aluminum demonstrate that the present QM/MM approaches yield excellent results both in terms of energetics and electron density. read less USED (high confidence) D. Rodney, “Activation enthalpy for kink-pair nucleation on dislocations: Comparison between static and dynamic atomic-scale simulations,” Physical Review B. 2007. link Times cited: 68 Abstract: We show in the case of a high-Peierls-stress Lomer dislocati… read moreAbstract: We show in the case of a high-Peierls-stress Lomer dislocation in an aluminum crystal that the dependence of the kink-pair activation enthalpy on the stress obtained from static nudged elastic band method calculations agrees with that extracted from dynamical, constant strain-rate simulations. In order to perform the dynamical simulations, we first propose flexible boundary conditions to replace the rigid conditions that are usually applied. This removes the spurious forces on the dislocation that arise because of the mismatch between the elastic strain imposed by the rigid conditions and the plastic strain associated with the dislocation motion. Second, we present a statistical analysis to rigorously extract enthalpy-stress relations from dynamical simulations. We find that the activation enthalpy becomes zero for a stress (which we call the Peierls stress for kink nucleation) smaller than that required to move athermally a rigid straight dislocation (called here the Peierls stress for rigid motion). This effect may explain the discrepancy often reported in the literature between the Peierls stress predicted by atomistic calculations, determined on short two dimensional dislocations, i.e., the Peierls stress for rigid motion, and the Peierls stress extracted from experiments, which corresponds to that when kink pairs form on three dimensional dislocations without the help of thermal fluctuations, i.e., the Peierls stress for kink nucleation. read less USED (high confidence) J. Fish et al., “Concurrent AtC coupling based on a blend of the continuum stress and the atomistic force,” Computer Methods in Applied Mechanics and Engineering. 2007. link Times cited: 137 USED (high confidence) M. Dewald and W. A. Curtin, “Multiscale modelling of dislocation/grain boundary interactions. II. Screw dislocations impinging on tilt boundaries in Al,” Philosophical Magazine. 2007. link Times cited: 126 Abstract: The interaction of dislocations with grain boundaries (GBs) … read moreAbstract: The interaction of dislocations with grain boundaries (GBs) determines a number of important aspects of the mechanical performance of materials, including strengthening and fatigue resistance. Here, the coupled atomistic/discrete-dislocation (CADD) multiscale method, which couples a discrete dislocation continuum region to a fully atomistic region, is used to study screw-dislocations interacting with Σ3, Σ11, and Σ9 symmetric tilt boundaries in Al. The low-energy Σ3 and Σ11 boundaries absorb lattice dislocations and generate extrinsic grain boundary dislocations (GBDs). As multiple screw dislocations impinge on the GB, the GBDs form a pile-up along the GB and provide a back stress that requires increasing applied load to push the lattice dislocations into the GB. Dislocation transmission is never observed, even with large GBD pile-ups near the dislocation/GB intersection. Results are compared with experiments and previous, related simulations. The Σ9 grain boundary, composed from a more complex set of structural units, absorbs screw dislocations that remain localized, with no GBD formation. With increasing applied stress, new screw dislocations are then nucleated into the opposite grain from structural units in the GB that are nearby but not at the location where the original dislocation intersected the boundary. The detailed behaviour depends on the precise location of the incident dislocations and the extent of the pile-up. Transmission can occur on both Schmid and non-Schmid planes and can depend on the shear stresses on the GB plane. A continuum yield locus for transmission is formulated. In general, the overall dissociation and/or transmission behaviour is also determined by the Burgers vectors and associated steps of the primitive vectors of the grain boundary, and the criteria for dislocation transmission formulated by Lee et al . [Scripta Metall. 23 799 (1989); Phil. Mag. A 62 131 (1990); Metall. Trans. A 21 2437 (1990)] are extended to account for these factors. read less USED (high confidence) M. Brigazzi, G. Santoro, A. Franchini, and V. Bortolani, “Simulations of the temperature dependence of static friction at the N2/Pb interface,” Journal of Physics: Condensed Matter. 2007. link Times cited: 14 Abstract: A molecular dynamics approach for studying the static fricti… read moreAbstract: A molecular dynamics approach for studying the static friction between two bodies, an insulator and a metal, as a function of the temperature is presented. The upper block is formed by N2 molecules and the lower block by Pb atoms. In both slabs the atoms are mobile. The interaction potential in each block describes properly the lattice dynamics of the system. We show that the lattice vibrations and the structural disorder are responsible for the behaviour of the static friction as a function of the temperature. We found that a large momentum transfer from the Pb atoms to the N2 molecules misplaces the N2 planes in the proximity of the interface. Around T = 20 K this effect produces the formation of an hcp stacking at the interface. By increasing the temperature, the hcp stacking propagates into the slab, toward the surface. Above T = 25 K, our analysis shows a sharp, rapid drop of more than three order of magnitude in the static friction force due to the misplacing of planes in the stacking of the fcc(111) layers, which are no longer in the minimum energy configuration. Above T = 35 K, we also observe a tendency for the splitting of planes and the formation of steps near the surface. By increasing the temperature we obtain the subsequent melting of the N2 slab interface layer at T = 50 K. The temperature behaviour of the calculated static friction is in good agreement with recent measurements made with the quartz crystal microbalance (QCM) method on the same system. read less USED (high confidence) Y. Liu, E. Giessen, and A. Needleman, “An analysis of dislocation nucleation near a free surface,” International Journal of Solids and Structures. 2007. link Times cited: 24 USED (high confidence) W. Curtin, D. Olmsted, and L. Hector, “A predictive mechanism for dynamic strain ageing in aluminium–magnesium alloys,” Nature Materials. 2006. link Times cited: 229 USED (high confidence) E. Clouet, “The vacancy - edge dislocation interaction in fcc metals: a comparison between atomic simulations and elasticity theory,” Acta Materialia. 2006. link Times cited: 92 USED (high confidence) R. Schäublin, “Nanometric crystal defects in transmission electron microscopy,” Microscopy Research and Technique. 2006. link Times cited: 17 Abstract: Transmission electron microscopy (TEM) is revisited in order… read moreAbstract: Transmission electron microscopy (TEM) is revisited in order to define methods for the identification of nanometric defects. Nanometric crystal defects play an important role as they influence, generally in a detrimental way, physical properties. For instance, radiation‐induced damage in metals strongly degrades mechanical properties, rendering the material stronger but brittle. The difficulty in using TEM to identify the nature and size of such defects resides in their small size. TEM image simulations are deployed to explore limits and possible ways to improve on spatial resolution and contrast. The contrast of dislocation loops, cavities, and a stacking fault tetrahedra (SFT) are simulated in weak beam, interfering reflections (HRTEM), and scanned condensed electron probe (STEM) mode. Results indicate that STEM is a possible way to image small defects. In addition, a new objective aperture is proposed to improve resolution in diffraction contrast. It is investigated by simulations of the weak beam imaging of SFT and successfully applied in experimental observations. Microsc. Res. Tech. 69:305–316, 2006. © 2006 Wiley‐Liss, Inc. read less USED (high confidence) M. Mills, N. Baluc, and P. Sarosi, “HRTEM of dislocation cores and thin‐foil effects in metals and intermetallic compounds,” Microscopy Research and Technique. 2006. link Times cited: 14 Abstract: Examples of the observation and analysis of dislocation core… read moreAbstract: Examples of the observation and analysis of dislocation cores and dislocation fine structure in metals and intermetallics using high resolution transmission electron microscopy are discussed. Specific examples include the 60° dislocations in aluminum, a〈011〉 edge dislocations in NiAl, and screw dislocations in Ni3Al. The effect of the thin TEM foils on the structure and imaging of these dislocations is discussed in light of embedded atom method calculations for several configurations and coupled with image simulations. Some generalizations based on these calculations are discussed. These analyses enables determination of the spreading or decomposition of the edge component of the cores, both in and out of the glide plane, which can have significant implications for the modeling of macroscopic behavior. Microsc. Res. Tech. 69:317–329, 2006. © 2006 Wiley‐Liss, Inc. read less USED (high confidence) M. Dewald and W. Curtin, “Analysis and minimization of dislocation interactions with atomistic/continuum interfaces,” Modelling and Simulation in Materials Science and Engineering. 2006. link Times cited: 30 Abstract: Spurious forces are shown to arise when dislocations interac… read moreAbstract: Spurious forces are shown to arise when dislocations interact with atom/continuum interfaces in some classes of multiscale models due to the use of linear elasticity in continuum descriptions of the material deformations and/or the singular dislocation fields. For Al, such forces can reach 500 MPa for dislocations within a few Angstroms of the interface and can remain significant at distances of ∼20 Å on the atomistic side and ∼15 Å on the continuum side of the interface, inhibiting the creation of truly seamless coupling. Replacement of the continuum representation of the dislocation displacement fields by a ‘template’ of the full atomistic displacement fields within a radius of Rcore = 50 Å is shown to significantly reduce the magnitude and range of the spurious forces. Implementation of the template method permits dislocations to approach within less than 10 Å of the interface from both atomistic and continuum sides, permitting higher accuracy in the multiscale simulations as well as reduced size of the atomistic region. read less USED (high confidence) S. Debiaggi, M. Koning, and A. M. Monti, “Theoretical study of the thermodynamic and kinetic properties of self-interstitials in aluminum and nickel,” Physical Review B. 2006. link Times cited: 10 Abstract: The formation thermodynamics and migration properties of sel… read moreAbstract: The formation thermodynamics and migration properties of self-interstitials in aluminum and nickel are investigated as a function of temperature using atomistic simulation techniques and embedded-atom-type interatomic potentials. Molecular dynamics and nonequilibrium free-energy techniques are employed to investigate anharmonic effects on the ${H}_{O}$ $⟨100⟩$ dumbbell formation properties. The equilibrium concentration of this defect is compared to those of vacancies and divacancies. The results are then analyzed in the framework of the interstitialcy model, according to which very high vibrational formation entropies should be expected for self-interstitials at high temperatures. The kinetics of self-interstitial migration is also investigated using different atomistic techniques, revealing the simultaneous activity of more than one distinct interstitial configuration as the temperature increases. read less USED (high confidence) S. Hocker, F. Gähler, and P. Brommer, “Molecular dynamics simulation of aluminium diffusion in decagonal quasicrystals,” Philosophical Magazine. 2006. link Times cited: 10 Abstract: Al diffusion in decagonal Al–Ni–Co and Al–Cu–Co quasicrystal… read moreAbstract: Al diffusion in decagonal Al–Ni–Co and Al–Cu–Co quasicrystals is investigated by molecular dynamics simulations. Results obtained with newly developed embedded-atom method potentials are compared with our previous work with effective pair potentials. With both types of potential, strong aluminium diffusion is observed above two-thirds of the melting temperature, and the general behaviours of the system are quite similar. The diffusion constant is measured as a function of temperature and pressure, and the activation enthalpies and activation volumes are determined from the resulting Arrhenius plot. For a number of important diffusion processes, the energy barriers are determined with molecular statics simulations. The qualitative behaviour of the dynamics is also confirmed by ab-initio simulations. read less USED (high confidence) Z. Xu and R. C. Picu, “Dislocation–solute cluster interaction in Al–Mg binary alloys,” Modelling and Simulation in Materials Science and Engineering. 2006. link Times cited: 21 Abstract: The close-range interaction of dislocations and solute clust… read moreAbstract: The close-range interaction of dislocations and solute clusters in the Al–Mg binary system is studied by means of atomistic simulations. We evaluate the binding energy per unit length of dislocations to the thermodynamically stable solute atmospheres that form around their cores, at various temperatures and average solid solution concentrations. A measure of the cluster size that renders linear the relationship between the binding energy per unit length and the cluster size is identified. The variation of the interaction energy between a dislocation and a cluster residing at a finite distance from its core is evaluated and it is shown that the interaction is negligible once the separation is larger than approximately 15 Burgers vectors. The data are relevant for the dynamics of dislocation pinning during dynamic strain ageing in solid solution alloys and for static ageing. read less USED (high confidence) K. Janssens, D. Olmsted, E. Holm, S. Foiles, S. Plimpton, and P. Derlet, “Computing the mobility of grain boundaries,” Nature Materials. 2006. link Times cited: 218 USED (high confidence) P. Tangney, “On the theory underlying the Car-Parrinello method and the role of the fictitious mass parameter.,” The Journal of chemical physics. 2006. link Times cited: 59 Abstract: The theory underlying the Car-Parrinello extended-Lagrangian… read moreAbstract: The theory underlying the Car-Parrinello extended-Lagrangian approach to ab initio molecular dynamics (CPMD) is reviewed and reexamined using "heavy" ice as a test system. It is emphasized that the adiabatic decoupling in CPMD is not a decoupling of electronic orbitals from the ions but only a decoupling of a subset of the orbital vibrational modes from the rest of the necessarily coupled system of orbitals and ions. Recent work [J. Chem. Phys. 116, 14 (2002)] has pointed out that, due to the orbital-ion coupling that remains once adiabatic decoupling has been achieved, a large value of the fictitious mass mu can lead to systematic errors in the computed forces in CPMD. These errors are further investigated in the present work with a focus on those parts of these errors that are not corrected simply by rescaling the masses of the ions. It is suggested that any comparison of the efficiencies of Born-Oppenheimer molecular dynamics (BOMD) and CPMD should be performed at a similar level of accuracy. If accuracy is judged according to the average magnitude of the systematic errors in the computed forces, the efficiency of BOMD compares more favorably to that of CPMD than previous comparisons have suggested. read less USED (high confidence) S. Oh, Y. Kauffmann, C. Scheu, W. Kaplan, and M. Rühle, “Ordered Liquid Aluminum at the Interface with Sapphire,” Science. 2005. link Times cited: 291 Abstract: Understanding the nature of solid-liquid interfaces is impor… read moreAbstract: Understanding the nature of solid-liquid interfaces is important for many processes of technological interest, such as solidification, liquid-phase epitaxial growth, wetting, liquid-phase joining, crystal growth, and lubrication. Recent studies have reported on indirect evidence of density fluctuations at solid-liquid interfaces on the basis of x-ray scattering methods that have been complemented by atomistic simulations. We provide evidence for ordering of liquid atoms adjacent to an interface with a crystal, based on real-time high-temperature observations of alumina-aluminum solid-liquid interfaces at the atomic-length scale. In addition, crystal growth of alumina into liquid aluminum, facilitated by interfacial transport of oxygen from the microscope column, was observed in situ with the use of high-resolution transmission electron microscopy. read less USED (high confidence) Y. Lee, J. Y. Park, S. Y. Kim, S. Jun, and S. Im, “Atomistic simulations of incipient plasticity under Al(1 1 1) nanoindentation,” Mechanics of Materials. 2005. link Times cited: 134 USED (high confidence) S. Qu, V. Shastry, W. Curtin, and R. E. Miller, “A finite-temperature dynamic coupled atomistic/discrete dislocation method,” Modelling and Simulation in Materials Science and Engineering. 2005. link Times cited: 108 Abstract: A method for simultaneously thermostatting an atomistic regi… read moreAbstract: A method for simultaneously thermostatting an atomistic region and absorbing energetic pulses impinging on the atomistic/continuum interface from the atomistic region is developed to operate within the framework of the coupled atomistic/discrete dislocation method. The approach inserts an additional Langevin damping term and a random force term into the equations of motion for atoms in a ‘stadium’ boundary region near the atom/continuum interface, with the damping coefficient ramped linearly over the width of the region, as suggested by Holian and Ravelo. The remaining interior atom dynamics are computed using a standard MD algorithm with no artificial damping or thermostatting. The continuum region deformations are computed using static FEM updated stochastically over time scales comparable to the Debye frequency of the atoms using time-averaged displacements at the atom/continuum interface, thereby providing an evolution of the continuum region that tracks the atomistic deformation. The method is evaluated by studying the ability of the coupled system: (i) to equilibrate the inner atomistic region at a desired temperature under conditions of no external or internal loading, (ii) to produce the proper canonical thermal fluctuations and (iii) to absorb deformation pulses initiated in the interior region and incident upon the atomistic/continuum boundary. With an optimal maximum damping coefficient of approximately 1/2 of the Debye frequency, temperature stability is attained at values very close to the target temperature. The temperature variance agrees well with the canonical expectation for various temperatures. For the same damping parameters and at low temperature, high-energy deformation pulses propagate unimpeded up to the stadium boundary region and then are completely damped out upon approach to the atomistic/continuum interface with no measurable reflections. At higher temperatures, thermal fluctuations in the total energy make analyses difficult, but damping of high-energy deformation pulses is achieved within the limits of the thermal noise in the system while observation of the time-dependent displacements shows no observable reflections. read less USED (high confidence) A. Buldum et al., “Multiscale Modeling, Simulations, and Experiments of Coating Growth on Nanofibers. Part Ii. Deposition,” Journal of Applied Physics. 2005. link Times cited: 10 Abstract: This work is Part II of an integrated experimental/modeling … read moreAbstract: This work is Part II of an integrated experimental/modeling investigation of a procedure to coat nanofibers and core-clad nanostructures with thin-film materials using plasma-enhanced physical vapor deposition. In the experimental effort, electrospun polymer nanofibers are coated with aluminum materials under different operating conditions to observe changes in the coating morphology. This procedure begins with the sputtering of the coating material from a target. Part I [J. Appl. Phys. 98, 044303 (2005)] focused on the sputtering aspect and transport of the sputtered material through the reactor. That reactor level model determines the concentration field of the coating material. This field serves as input into the present species transport and deposition model for the region surrounding an individual nanofiber. The interrelationships among processing factors for the transport and deposition are investigated here from a detailed modeling approach that includes the salient physical and chemical phenomena.... read less USED (high confidence) A. Buldum et al., “Multiscale Modeling, Simulations, and Experiments of Coating Growth on Nanofibers. Part I. Sputtering,” Journal of Applied Physics. 2005. link Times cited: 9 Abstract: This paper is Part I of an integrated experimental/modeling … read moreAbstract: This paper is Part I of an integrated experimental/modeling investigation of a procedure to coat nanofibers and core-clad nanostructures with thin-film materials using plasma-enhanced physical vapor deposition. In the experimental effort, electrospun polymer nanofibers are coated with aluminum under varying operating conditions to observe changes in the coating morphology. This procedure begins with the sputtering of the coating material from a target. This paper focuses on the sputtering process and transport of the sputtered material through the reactor. The interrelationships among the processing factors for the sputtering and transport are investigated from a detailed modeling approach that describes the salient physical and chemical phenomena. Solution strategies that couple continuum and atomistic models are used. At the continuum scale, the sheath region and the reactor dynamics near the target surface are described. At the atomic level, molecular-dynamics (MD) simulations are used to study the sputtering and deposition mechanisms. Ion kinetic energies and fluxes are passed from the continuum sheath model to the MD simulations. These simulations calculate sputtering and sticking probabilities that in turn are used to calculate parameters for the continuum reactor model. The reactor model determines the concentration field of the coating material. read less USED (high confidence) F. Tavazza, R. Wagner, A. Chaka, and L. Levine, “Vacancy formation energy near an edge dislocation: A hybrid quantum-classical study,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2005. link Times cited: 2 USED (high confidence) W. Fan and X. Gong, “Superheated melting of grain boundaries,” Physical Review B. 2005. link Times cited: 14 Abstract: Based on a model of the melting of grain boundaries GB, we d… read moreAbstract: Based on a model of the melting of grain boundaries GB, we discuss the possibility of the existence of a superheated GB state. The molecular dynamics simulation presented here shows that the superheated GB state can be realized in the high symmetric tilt GB. The sizes of liquid nuclei exceeding a critical size determined whether or not the superheating grain boundary melted. Our results also indicate that an increase of the melting point due to pressure is smaller than the superheating due to a nucleation mechanism. read less USED (high confidence) J. Marian, J. Knap, and M. Ortiz, “Nanovoid deformation in aluminum under simple shear,” Acta Materialia. 2005. link Times cited: 85 USED (high confidence) F. Sansoz and J. Molinari, “Mechanical behavior of Σ tilt grain boundaries in nanoscale Cu and Al: A quasicontinuum study,” Acta Materialia. 2005. link Times cited: 220 USED (high confidence) P. Jing, T. K. *, J. Young, and B. Wirth, “Multi-scale simulations of the effects of irradiation-induced voids and helium bubbles on the mechanical properties of aluminium,” Philosophical Magazine. 2005. link Times cited: 12 Abstract: As a result of irradiation, pressurized helium bubbles are o… read moreAbstract: As a result of irradiation, pressurized helium bubbles are observed in large number densities in some metals, which produce mechanical property changes. This paper presents the results of a computational multi-scale study (dislocation dynamics, DD, and molecular dynamics simulations, MD) to quantify the effect of He bubbles on material hardening from the impediment to dislocation motion. The effects of voids were studied using MD, and the effects of He bubbles, with a mean size of 2.5 nm and number densities from 3 × 1022 m−3 to 6 × 1022 m−3, were investigated using DD over a range of internal He pressures ranging from 125 to 750 MPa. The MD simulations elucidated the dislocation pinning action of voids and bubbles. Also, within the range of parameters studied, the DD simulations showed a clear, but weak correlation between the number density of He bubbles, and the internal He pressure, on the flow stress of the metal. read less USED (high confidence) J. Vandersall and B. Wirth, “Supersonic dislocation stability and nano-twin formation at high strain rate,” Philosophical Magazine. 2004. link Times cited: 26 Abstract: Improved understanding of the plastic deformation of metals … read moreAbstract: Improved understanding of the plastic deformation of metals during high-strain-rate shock loading is key to predicting their resulting material properties. This paper presents the results of molecular-dynamics simulations which address two fundamental questions related to materials deformation: the stability of supersonic dislocations and the mechanism of nano-twin formation. The results show that aluminium plastically deforms by the subsonic motion of edge dislocations when subjected to applied shear stresses of up to 600 MPa. Although higher applied stresses initially drive transonic dislocations, this motion is transient, and the dislocations decelerate to a sustained subsonic saturation velocity. Slowing of the transonic dislocation is controlled by the interaction with excited Rayleigh waves. 800 MPa marks a critical shear stress at which dislocation glide gives way to nano-twin formation via the homogeneous nucleation of Shockley partial dislocation dipoles. At still higher applied stresses, additional dislocation dipole nucleation produces a mid-stacking fault transformation of the twinned material. read less USED (high confidence) J. M. S. †, O. Politano, S. Garruchet, A. Sanfeld, and A. Steinchen, “Theoretical and numerical considerations on the surface energy for deformed isotropic nanocrystals,” Philosophical Magazine. 2004. link Times cited: 5 Abstract: In this paper we start by presenting an analytical analysis … read moreAbstract: In this paper we start by presenting an analytical analysis to determine the variation in the surface energy of isotropic solids when they are deformed in the elastic domain. This part of our work was based on a recent formulation proposed by Sanfeld and Steinchen and modified for the case of pure solids. We continue our presentation by deducing the form of the surface energy variation by means of molecular dynamics simulations at a finite temperature (300 K). These simulations were performed with single nanocrystals of Al and deformed in the elastic regime along one direction parallel to the surface. These simulations also allowed us to determine the variation in the interplanar spacing of the atomic layers near the surface. Our simulations for the (100), (110) and (111) surfaces exhibit the same multilayer relaxation tendency obtained by other numerical and experimental results. read less USED (high confidence) S. L. Frederiksen, K. Jacobsen, K. S. Brown, and J. Sethna, “Bayesian ensemble approach to error estimation of interatomic potentials.,” Physical review letters. 2004. link Times cited: 106 Abstract: Using a Bayesian approach a general method is developed to a… read moreAbstract: Using a Bayesian approach a general method is developed to assess error bars on predictions made by models fitted to data. The error bars are estimated from fluctuations in ensembles of models sampling the model-parameter space with a probability density set by the minimum cost. The method is applied to the development of interatomic potentials for molybdenum using various potential forms and databases based on atomic forces. The calculated error bars on elastic constants, gamma-surface energies, structural energies, and dislocation properties are shown to provide realistic estimates of the actual errors for the potentials. read less USED (high confidence) J. Marian, J. Knap, and M. Ortiz, “Nanovoid cavitation by dislocation emission in aluminum.,” Physical review letters. 2004. link Times cited: 102 Abstract: This Letter is concerned with the determination of the trans… read moreAbstract: This Letter is concerned with the determination of the transition paths attendant to nanovoid growth in aluminum under hydrostatic tension. The analysis is, therefore, based on energy minimization at 0 K. Aluminum is modeled by the Ercolessi-Adams embedded-atom method, and spurious boundary artifacts are mitigated by the use of the quasicontinuum method. Our analysis reveals several stages of pressure buildup separated by yield points. The first yield point corresponds to the formation of highly stable tetrahedral dislocation junctions around the surfaces of the void. The second yield point is caused by the dissolution of the tetrahedral structures and the emission of conventional 1/2<110>[111] and anomalous 1/2<110>[001] dislocation loops. read less USED (high confidence) S. Jun, Y. Lee, S. Y. Kim, and S. Im, “Large-scale molecular dynamics simulations of Al(111) nanoscratching,” Nanotechnology. 2004. link Times cited: 66 Abstract: Molecular dynamics simulations of nanoscratching are perform… read moreAbstract: Molecular dynamics simulations of nanoscratching are performed with emphasis on the correlation between the scratching conditions and the defect mechanism in the substrate. More than six million atoms are described by the embedded atom method (EAM) potential. The scratching process is simulated by high-speed ploughing on the Al(111) surface with an atomic force microscope (AFM) tip that is geometrically modelled to be of a smoothed conical shape. A repulsive model potential is employed to represent the interaction between the AFM tip and the Al atoms. Through the visualization technique of atomic coordination number, dislocations and vacancies are identified as the two major defect types prevailing under nanoscratching. Their structures and movements are investigated for understanding the mechanisms of defect generation and evolution under various scratching conditions. The glide patterns of Shockley partial dislocation loops are obviously dependent upon the scratching directions in conjunction with the slip system of face-centred cubic (fcc) single crystals. It is shown that the shape of the AFM tip directly influences the facet formation on the scratched groove. The penetration depth into the substrate during scratching is further verified to affect both surface pile-up and residual defect generations that are important in assessing the change of material properties after scratching. read less USED (high confidence) M. Fago, R. Hayes, E. Carter, and M. Ortiz, “Density-functional-theory-based local quasicontinuum method: Prediction of dislocation nucleation,” Physical Review B. 2004. link Times cited: 77 Abstract: We introduce the density functional theory (DFT) local quasi… read moreAbstract: We introduce the density functional theory (DFT) local quasicontinuum method: a first principles multiscale material model that embeds DFT unit cells at the subgrid level of a finite element computation. The method can predict the onset of dislocation nucleation in both single crystals and those with inclusions, although extension to lattice defects awaits new methods. We show that the use of DFT versus embedded-atom method empirical potentials results in different predictions of dislocation nucleation in nanoindented face-centered-cubic aluminum. read less USED (high confidence) G. Ackland, M. Mendelev, D. Srolovitz, S. Han, and A. Barashev, “Development of an interatomic potential for phosphorus impurities in α-iron,” Journal of Physics: Condensed Matter. 2004. link Times cited: 542 Abstract: We present the derivation of an interatomic potential for th… read moreAbstract: We present the derivation of an interatomic potential for the iron–phosphorus system based primarily on ab initio data. Transferability in this system is extremely problematic, and the potential is intended specifically to address the problem of radiation damage and point defects in iron containing low concentrations of phosphorus atoms. Some preliminary molecular dynamics calculations show that P strongly affects point defect migration. read less USED (high confidence) D. Fischer, A. Curioni, S. Billeter, and W. Andreoni, “Effects of nitridation on the characteristics of silicon dioxide: dielectric and structural properties from ab initio calculations.,” Physical review letters. 2004. link Times cited: 27 Abstract: By combining ab initio calculations and classical molecular … read moreAbstract: By combining ab initio calculations and classical molecular dynamics, we determine how the inclusion of nitrogen in a silica matrix changes its dielectric constant, and elucidate the underlying mechanisms. We find that there is an entire range of nitrogen concentrations (up to approximately 25%) for which the structural pattern of the oxide is preserved in bulk SiON, and the dielectric constant increases mainly because of the variation of the ionic polarizability. This behavior is not sensitive to hydrogen passivation of nitrogen. The few defects, which are associated with electron states near the gap, are mainly centered on undercoordinated nitrogen and undercoordinated silicon, and tend to be removed by hydrogen. read less USED (high confidence) M. Forsblom, N. Sandberg, and G. G. ‡, “Vibrational entropy of dislocations in Al,” Philosophical Magazine. 2004. link Times cited: 8 Abstract: The region nearest to a lattice defect must be described by … read moreAbstract: The region nearest to a lattice defect must be described by an atomistic model, while a continuum model suffices further away from the defect. We study such a separation into two regions for an edge dislocation. In particular we focus on the excess defect energy and vibrational entropy, when the dislocation core is described by a cluster of about 500–100 atoms, embedded in a large discrete and relaxed, but static, lattice. The interaction between the atoms is given by a potential of the embedded-atom model type referring to Al. The dynamic matrix of the vibrations in the cluster is fully diagonalized. The excess entropy ΔS near the core has positive and negative contributions, depending on the sign of the local strain. Typically, ΔS/k B ≈ 2 per atomic repeat length along the dislocation core in fcc Al. In the elastic continuum region far from the dislocation core the excess entropy shows the same logarithmic divergence as the elastic energy. Although the work refers to a specific material and defect type, the results are of a generic nature. read less USED (high confidence) J. Li, T. Zhu, S. Yip, K. Vliet, and S. Suresh, “Elastic criterion for dislocation nucleation,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2004. link Times cited: 55 USED (high confidence) M. Koning et al., “Modeling of dislocation-grain boundary interactions in FCC metals,” Journal of Nuclear Materials. 2003. link Times cited: 143 USED (high confidence) G.-X. Li, Y. Liang, Z. G. Zhu, and C. S. Liu, “Microstructural analysis of the radial distribution function for liquid and amorphous Al,” Journal of Physics: Condensed Matter. 2003. link Times cited: 27 Abstract: Constant-pressure molecular dynamics simulations and analysi… read moreAbstract: Constant-pressure molecular dynamics simulations and analysis of the local atomic structures have been performed to study the conventional and 'inherent' structural evolution of liquid Al during rapid solidification. The results show that the radial distribution functions g(r) exhibit a second-peak splitting feature not only for the general structures of the amorphous states but also for the inherent structure of liquid states. The second peak of g(r) decomposes into three main components, each corresponding to different pairs. The first subpeak in the inherent structure of the liquid arises from 2211 and 2331 pairs (which correspond to triangles with a common side and the tetrahedra sharing a face respectively), while the first subpeak in the amorphous state arises from 2331 pairs; in both cases the second subpeak is due to the 2101 pairs (linear trimers). The existence of a shoulder or the splitting in the second peak of g(r) in the amorphous state, and even in the undercooled liquid state, results mainly from the increase in number of and aggregation of the tetrahedra, which in turn give rise to the presence of entities with local icosahedral order. read less USED (high confidence) K. Vliet, J. Li, T. Zhu, S. Yip, and S. Suresh, “Quantifying the early stages of plasticity through nanoscale experiments and simulations,” Physical Review B. 2003. link Times cited: 368 Abstract: Nucleation and kinetics of defects at the atomic scale provi… read moreAbstract: Nucleation and kinetics of defects at the atomic scale provide the most fundamental information about the mechanical response of materials and surfaces. Recent advances in experimental and computational analyses allow us to study this phenomenon in the context of nanoindentation and localized mechanical probing of surfaces. Here, we present an analytical formulation of the elastic limit that predicts the location and slip character of a homogeneously nucleated defect in crystalline metals, and extend this formulation to the atomic scale in the form of an energy-based, local elastic stability criterion, termed the L criterion. We demonstrate that this approach can be incorporated efficiently into computational methods such as molecular dynamics and finite-element models. Furthermore, we validate and calibrate the L criterion directly through nanoindentation experiments and two-dimensional experimental analogs such as the bubble raft model. We outline explicitly a compact and efficient application of the L criterion within the context of a nonlinear, interatomic potential finite-element model~IPFEM!. Further, we report three-dimensional molecular dynamics simulations in several face-centered cubic systems that elucidate the transition from the initiation to the early stages of plasticity during nanoindentation of metals, as characterized by homogeneous and heterogeneous nucleation of up to hundreds of dislocations. Correlation of these simulations with direct observations from nanoindentation experiments provides atomistic insights into the early stages of plasticity. read less USED (high confidence) H. Yu, J. B. Adams, and L. Hector, “Molecular dynamics simulation of high-speed nanoindentation,” Modelling and Simulation in Materials Science and Engineering. 2002. link Times cited: 27 Abstract: A series of molecular dynamics simulations has been performe… read moreAbstract: A series of molecular dynamics simulations has been performed to study high-speed nanoindentation of a hard pyramidal tip into Al substrates. The effects of several process variables are investigated, including system temperature, tip-substrate bonding, indentation force, and surface orientation. We discuss the results and the deformation mechanisms that occur during indentation. read less USED (high confidence) T. Vegge and K. Jacobsen, “Atomistic simulations of dislocation processes in copper,” Journal of Physics: Condensed Matter. 2002. link Times cited: 38 Abstract: We discuss atomistic simulations of dislocation processes in… read moreAbstract: We discuss atomistic simulations of dislocation processes in copper based on effective medium theory interatomic potentials. Results on screw dislocation structures and processes are reviewed with particular focus on point defect mobilities and processes involving cross slip. For example, the stability of screw dislocation dipoles is discussed. We show that the presence of jogs will strongly influence cross slip barriers and dipole stability. We furthermore present some new results on jogged edge dislocations and edge dislocation dipoles. The jogs are found to be extended, and simulations of vacancy controlled climb show the jogs to climb easily in their extended form. The stability of small vacancy dipoles is discussed and it is seen that the introduction of jogs may lead to the formation of Z-type faulted vacancy dipoles. read less USED (high confidence) F. Baumann et al., “Multiscale Modeling of Thin-Film Deposition: Applications to Si Device Processing,” MRS Bulletin. 2001. link Times cited: 77 Abstract: Metallization is the back end of the integrated-circuit (IC)… read moreAbstract: Metallization is the back end of the integrated-circuit (IC) fabrication process where the transistor interconnections are formed. Figure 1 shows the metallized part of a static random-access memory chip. Metal lines for electrical connections (Al and Cu) in Si devices are deposited as blanket films and then etched or polished away to define the conducting lines. read less USED (high confidence) X. Duan, D. Sun, and X. Gong, “Hypermolecular dynamics simulations of monovacancy diffusion,” Computational Materials Science. 2001. link Times cited: 8 USED (high confidence) A. Landa, P. Wynblatt, D. J. Siegel, J. B. Adams, O. Mryasov, and X. Liu, “DEVELOPMENT OF GLUE-TYPE POTENTIALS FOR THE Al-Pb SYSTEM: PHASE DIAGRAM CALCULATION,” Acta Materialia. 2000. link Times cited: 67 USED (high confidence) D. Shu, D. Sun, X. Gong, and W. Lau, “A molecular-dynamics study of the anisotropic surface-melting properties of Al(110),” Surface Science. 1999. link Times cited: 7 USED (high confidence) E. Tadmor, R. E. Miller, R. Phillips, and M. Ortiz, “Nanoindentation and incipient plasticity,” Journal of Materials Research. 1999. link Times cited: 253 Abstract: This paper presents a large-scale atomic resolution simulati… read moreAbstract: This paper presents a large-scale atomic resolution simulation of nanoindentation into a thin aluminum film using the recently introduced quasicontinuum method. The purpose of the simulation is to study the initial stages of plastic deformation under the action of an indenter. Two different crystallographic orientations of the film and two different indenter geometries (a rectangular prism and a cylinder) are studied. We obtain both macroscopic load versus indentation depth curves, as well as microscopic quantities, such as the Peierls stress and density of geometrically necessary dislocations beneath the indenter. In addition, we obtain detailed information regarding the atomistic mechanisms responsible for the macroscopic curves. A strong dependence on geometry and orientation is observed. Two different microscopic mechanisms are observed to accommodate the applied loading: (i) nucleation and subsequent propagation into the bulk of edge dislocation dipoles and (ii) deformation twinning. read less USED (high confidence) C.-L. Liu, X.-Y. Liu, and L. Borucki, “Defect generation and diffusion mechanisms in Al and Al–Cu,” Applied Physics Letters. 1999. link Times cited: 36 Abstract: A defect generation mechanism, namely, the grain-boundary Fr… read moreAbstract: A defect generation mechanism, namely, the grain-boundary Frenkel pair model, and corresponding diffusion mechanisms during electromigration are developed using atomic simulation techniques in Al and Al–Cu. We contend that large numbers of interstitials and vacancies exist at grain boundaries and both contribute to mass transport. Cu preferentially segregates to the interstitial sites at grain boundaries via a Frenkel pair generation process and reduces the overall grain-boundary diffusivity due to the stronger Al–Cu binding. Predictions from our models are in excellent agreement with available experimental data and observations. read less USED (high confidence) H.-C. Huang, G. Gilmer, and T. D. Rubia, “An atomistic simulator for thin film deposition in three dimensions,” Journal of Applied Physics. 1998. link Times cited: 202 Abstract: We describe an atomistic simulator for thin film deposition … read moreAbstract: We describe an atomistic simulator for thin film deposition in three dimensions (ADEPT). The simulator is designed to bridge the atomic and mesoscopic length scales by using efficient algorithms, including an option to speed up surface diffusion using events with multiple diffusion hops. Sputtered particles are inserted and assigned ballistic trajectories with angular distributions appropriate for magnetron sputtering. Atoms on the surface of the film execute surface diffusion hops with rates that depend on the local configuration, and are consistent with microscopic reversibility. The potential energies are chosen to match information obtained from a database of first principles and molecular dynamics (MD) calculations. Efficient computation is accomplished by selecting atoms with probabilities that are proportional to their hop rates. A first implementation of grain boundary effects is accomplished by including an orientation variable with each occupied site. Energies and mobilities are assigned to atom... read less USED (high confidence) X. Liu, W. Xu, S. Foiles, and J. B. Adams, “Atomistic studies of segregation and diffusion in Al-Cu grain boundaries,” Applied Physics Letters. 1998. link Times cited: 57 Abstract: The segregation of Cu atoms at Al [110] Σ11 and [001] Σ5 til… read moreAbstract: The segregation of Cu atoms at Al [110] Σ11 and [001] Σ5 tilt grain boundaries was studied. Cu atoms were found to segregate to asymmetric sites at the Σ11 boundary and form zig-zag planar aggregates at the interface. Segregation is dominated by atomic size and local hydrostatic stress. Cu atoms prefer to occupy the prime diffusion path sites at both grain boundaries. Cu segregation raises the vacancy formation and diffusion activation energies at Σ11 grain boundaries, thus slowing the rate of atomic diffusion. 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) V. Shenoy, R. E. Miller, E. Tadmor, D. Rodney, R. Phillips, and M. Ortiz, “An adaptive finite element approach to atomic-scale mechanics—the quasicontinuum method,” Journal of The Mechanics and Physics of Solids. 1997. link Times cited: 660 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) V. Shenoy and R. Phillips, “Finite-sized atomistic simulations of screw dislocations,” Philosophical Magazine. 1996. link Times cited: 25 Abstract: The interaction of screw dislocations with an applied stress… read moreAbstract: The interaction of screw dislocations with an applied stress is studied using atomistic simulations in conjunction with a continuum treatment of the role played by the far-field boundary condition. A finite cell of atoms is used to consider the response of dislocations to an applied stress and this introduces an additional force on the dislocation due to the presence of the boundary. Continuum mechanics is used to calculate the boundary force which is subsequently accounted for in the equilibrium condition for the dislocation. Using this formulation, the lattice resistance curve and the associated Peierls stress are calculated for screw dislocations in several close-packed metals. As a concrete example of the boundary force method, we compute the bow-out of a pinned screw dislocation; the line tension of the dislocation is calculated from the results of the atomistic simulations using a variational principle that explicitly accounts for the boundary force. read less USED (high confidence) P. Andric, “The mechanics of crack-tip dislocation emission and twinning.” 2019. link Times cited: 1 Abstract: Dislocation emission from a crack tip is a necessary mechani… read moreAbstract: Dislocation emission from a crack tip is a necessary mechanism for crack tip blunting and toughening. A material is intrinsically ductile under Mode I loading when the critical stress intensity KIe for dislocation emission is lower than the critical stress intensity KIc for cleavage. In intrinsically ductile fcc metals, a first partial dislocation is emitted, followed either by a trailing partial dislocation (“ductile” behavior) or a twinning partial dislocation (“quasi-brittle”). K Ie for the first partial dislocation emission is usually evaluated using the approximate Rice theory, which predicts a dependence on the elastic constants and the unstable stacking fault energy γusf . Here, atomistic simulations across a wide range of fcc metals show that K Ie is systematically larger (10–30%) than predicted. However, the critical crack-tip shear displacement is up to 40% smaller than predicted. The discrepancy arises because Mode I emission is accompanied by the formation of a surface step that is not considered in the Rice theory. A new theory for Mode I emission is presented based on the ideas that (i) the stress resisting step formation at the crack tip creates “lattice trapping” against dislocation emission such that (ii) emission is due to a mechanical instability at the crack tip. The new theory naturally includes the energy to form the step, and reduces to the Rice theory (no trapping) when the step energy is small. The new theory predicts a higher K Ie at a smaller critical shear displacement, rationalizing deviations of simulations from the Rice theory. The twinning tendency is estimated using the Tadmor and Hai extension of the Rice theory. Atomistic simulations reveal that the predictions of the critical stress intensity factor K Ie for crack tip twinning are also systematically lower (20–35%) than observed. Energy change during nucleation reveal that twining partial emission is not accompanied by creation of a surface step while emission of the trailing partial creates a step. The absence of the step during twinning motivates a model for twinning nucleation that accounts for the fact that nucleation does not occur directly at the crack tip. New predictions are in excellent agreement with all simulations that show twinning. A second mode of twinning is found wherein the crack first advances by cleavage and then emits the twinning partial at the new crack tip. The stacking fault stress dependence is analyzed through (i) the generalized stacking fault potential energy (GSFE) and (ii) the generalized stacking fault enthalpy (GSFH). At an imposed shear displacement, there is also an associated inelastic normal displacement ∆n around the fault. Atomistic simulations with interatomic potentials and/or first principle calculations reveal that read less USED (high confidence) B. Alcott, “Nanoscale Electrical and Coarse-grained Molecular Dynamics Studies of Influenza Hemagglutinin-mediated Membrane Fusion Pores.” 2017. link Times cited: 0 Abstract: Nanoscale Electrical and Coarse-grained Molecular Dynamics S… read moreAbstract: Nanoscale Electrical and Coarse-grained Molecular Dynamics Studies of Influenza Hemagglutinin-mediated Membrane Fusion Pores Brett Eugene Alcott Fusion of viral and host membranes is a key step during infection by membrane-enclosed viruses. The fusion pore plays a critical role, and must dilate to release the viral genome. Prior studies of fusion mediated by influenza A hemagglutinin (HA) revealed ~2-5 nm pores that flickered before dilating to >10 nm. The mechanisms involved are unknown. Here we studied HA-mediated fusion pore dynamics using a novel single-pore assay (supported by a novel, robust, single-cell optical assay for fusion between HA-expressing cells and nanodiscs), combined with computational simulations accessing extraordinarily long (ms) timescales. We measured pores between HA-expressing fibroblasts and bilayer nanodiscs. From pore currents we infer pore size with millisecond time resolution. Unlike previous in vitro studies, the use of nanodiscs limited the membrane contact areas and maximum pore sizes, better mimicking the initial phases of virus-endosome fusion. In wild-type (WT) HA-mediated fusion pores, pores flickered about a mean pore size ~1.7 nm. In contrast, fusion pores formed by GPIanchored HA nucleated at less than half the WT rate; results were consistent with earlier findings that showed that while GPI-HA pores stabilize at larger initial conductances than WT, they were not able to enlarge beyond their initial size. We developed radically coarse-grained, explicit lipid molecular dynamics simulations of the fusion pore reconstituted with post-fusion, trans HA hairpins. With WT HA, fusion pores were small, similar to experiment. Over time hairpins gradually converted from trans to cis. With lipid-anchored HA, the trans → cis transition was much accelerated. Once most hairpins had converted to cis, because apposing membranes were released, the fusion pore was able to dilate to sizes close to protein-free. Additionally, in crowded simulations with HA densities approximating those found in HA clusters, we found that HA aggregation, promoted by TMDTMD interactions, delayed fusion pore dilation by inhibiting the trans → cis transition. Our results suggest that pore dilation requires the trans → cis transition. We hypothesize that this transition is accelerated in GPI-HA by the more mobile lipid anchor, and may explain the larger observed nascent fusion pores. read less USED (high confidence) P. Wang et al., “Atomistic simulation for deforming complex alloys with application toward TWIP steel and associated physical insights,” Journal of The Mechanics and Physics of Solids. 2017. link Times cited: 42 USED (high confidence) G. Venturini, J. Marian, J. Knap, G. Campbell, and M. Ortiz, “Thermal Expansion Behavior of AL and TA Using a Finite-Temperature Extension of the Quasicontinuum Method,” International Journal for Multiscale Computational Engineering. 2011. link Times cited: 3 Abstract: Numerical methods that bridge the atomistic andcontinuum sca… read moreAbstract: Numerical methods that bridge the atomistic andcontinuum scales concurrently have been applied successfully to anumber of materials science problems involving both nonlinear andlong-range deformation fields. However, extension of thesemethods to finite temperature, nonequilibrium dynamics isdifficult due to the intrinsic incoherency between moleculardynamics and continuum thermodynamics, which possess differentcrystal vibrational spectra and therefore result in unphysicalwave reflections across domain boundaries. Here we review ourrecent finite temperature extension of the three-dimensional,non-local quasicontinuum (QC) method based on Langevin dynamicsand carry out an analysis of the systematic errors associated withthe entropic depletion that results from the QC reduction. Weapply the method to Al and Ta structured meshes ranging fromatomistic resolution to minimum-node representations using thethermal expansion coefficient as the standard metric. We findthat, while Al errors scale linearly with the number of meshnodes, Ta displays a very erratic behavior that degrades rapidlywith mesh coarsening. read less USED (high confidence) G. Venturini, “Topics in Multiscale Modeling of Metals and Metallic Alloys.” 2011. link Times cited: 6 Abstract: In a number of areas of application, the behavior of systems… read moreAbstract: In a number of areas of application, the behavior of systems depends sensitively on properties that pertain to the atomistic scale, i. e., the angstrom and femtosecond scales. However, generally the behaviors of interest are macroscopic and are characterized by slow evolution on the scale of meters and years. This broad disparity of length and time scales places extraordinary challenges in computational material science.
The overarching objective of this dissertation is to address the problem of multiple space and time scales in atomistic systems undergoing slow macroscopic evolution while retaining full atomistic detail. Our approach may be summarized as follows:
(1) The issue of accounting for finite temperature in coarse grained systems has not been solved entirely. For finite temperature systems at equilibrium, constructing an effective free energy in terms of a reduced set of atomic degrees of freedom is still an open area of research. In particular, the thermal vibrations of the missing degrees of freedom need to be accounted for. This is specially important if the aim of the simulation is to determine the dynamic properties of a system, or to allow the transmission of dynamic information between regions of different spatial discretization. To this end, we introduce a framework to simulate (spatially) coarse dynamic systems using the Quasicontinuum method (QC). The equations of motion are strictly derived from dissipative Lagrangian mechanics, which provides a classical Langevin implementation where the characteristic time is governed by the vibrations of the finest length scale in the computational cell. In order to assess the framework's ability to transmit information across scales, we study the phonon impoverish spectra in coarse regions and the resulting underestimation of thermal equilibrium properties.
(2) Atomistic simulations have been employed for the past thirty years to determine structural and thermodynamic (equilibrium) properties of solids and their defects over a wide range of temperatures and pressures. The traditional Monte Carlo (MC) and Molecular Dynamics (MD) methods, while ideally suited to these calculations, require appreciable computational resources in order to calculate the long-time averages from which properties are obtained. In order to permit a reasonably quick, but accurate determination of the equilibrium properties of interest, we present an extension of the “maximum entropy” method to build effective alloy potentials while avoiding the treatment of all the system's atomic degrees of freedom. We assess the validity of the model by testing its ability to reproduce experimental measurements.
(3) Based upon these effective potentials, we present a numerical framework capable of following the time evolution of atomistic systems over time windows currently beyond the scope of traditional atomistic methods such as Molecular Dynamics (MD) or Monte Carlo (MC). This is accomplished while retaining the underlying atomistic description of the material. We formulate a discrete variational setting in which the simulation of time-dependent phenomena is reduced to a sequence of incremental problems, each characterized by a variational principle. In this fashion we are able to study the interplay between deformation and diffusion using time steps or strain rates that are orders of magnitude larger or smaller than their MD|MC counterparts.
(4) We formulate a new class of “Replica Time Integrators” (RTIs) that allows for the two-way transmission of thermal phonons across mesh interfaces. This two-way transmission is accomplished by representing the state of the coarse region by a collection of identical copies or “replicas” of itself. Each replica runs at its own slow time step and is out-of-phase with respect to the others by one fast time step. Then, each replica is capable of absorbing from the fine region the elementary signal that is in phase with the replica. Conversely, each replica is capable of supporting --and transmitting to the fine region-- an elementary signal of a certain phase. Since fine and coarse regions evolve asynchronously in time, RTIs permit both spatial and temporal coarse graining of the system of interest. Using a combination of phase-error analysis and numerical testing we find that RTIs are convergent, and allow step waves and thermal phonons to cross mesh interfaces in both directions losslessly. read less USED (high confidence) T. Luther, “Adaptation of atomistic and continuum methods for multiscale simulation of quasi-brittle intergranular damage.” 2010. link Times cited: 0 Abstract: The numerical simulation of damage using phenomenological mo… read moreAbstract: The numerical simulation of damage using phenomenological models on the macroscale was state of the art for many decades. However, such models are not able to capture the complex nature of damage, which simultaneously proceeds on multiple length scales. Furthermore, these phenomenological models usually contain damage parameters, which are physically not interpretable. Consequently, a reasonable experimental determination of these parameters is often impossible. In the last twenty years, the ongoing advance in computational capacities provided new opportunities for more and more detailed studies of the microstructural damage behavior. Today, multiphase models with several million degrees of freedom enable for the numerical simulation of micro-damage phenomena in naturally heterogeneous materials. Therewith, the application of multiscale concepts for the numerical investigation of the complex nature of damage can be realized. The presented thesis contributes to a hierarchical multiscale strategy for the simulation of brittle intergranular damage in polycrystalline materials, for example aluminum. The numerical investigation of physical damage phenomena on an atomistic microscale and the integration of these physically based information into damage models on the continuum meso- and macroscale is intended. Therefore, numerical methods for the damage analysis on the micro- and mesoscale including the scale transfer are presented and the transition to the macroscale is discussed. The investigation of brittle intergranular damage on the microscale is realized by the application of the nonlocal Quasicontinuum method, which fully describes the material behavior by atomistic potential functions, but reduces the number of atomic degrees of freedom by introducing kinematic couplings. Since this promising method is applied only by a limited group of researchers for special problems, necessary improvements have been realized in an own parallelized implementation of the 3D nonlocal Quasicontinuum method. The aim of this implementation was to develop and combine robust and efficient algorithms for a general use of the Quasicontinuum method, and therewith to allow for the atomistic damage analysis in arbitrary grain boundary configurations. The implementation is applied in analyses of brittle intergranular damage in ideal and nonideal grain boundary models of FCC aluminum, considering arbitrary misorientations. From the microscale simulations traction separation laws are derived, which describe grain boundary decohesion on the mesoscale. Traction separation laws are part of cohesive zone models to simulate the brittle interface decohesion in heterogeneous polycrystal structures. 2D and 3D mesoscale models are presented, which are able to reproduce crack initiation and propagation along cohesive interfaces in polycrystals. An improved Voronoi algorithm is developed in 2D to generate polycrystal material structures based on arbitrary distribution functions of grain size. The new model is more flexible in representing realistic grain size distributions. Further improvements of the 2D model are realized by the implementation and application of an orthotropic material model with Hill plasticity criterion to grains. The 2D and 3D polycrystal models are applied to analyze crack initiation and propagation in statically loaded samples of aluminum on the mesoscale without the necessity of initial damage definition. read less USED (high confidence) T. Tsuru, Y. Kaji, and Y. Shibutani, “Minimum Energy Motion and Core Structure of Pure Edge and Screw Dislocations in Aluminum,” Journal of Computational Science and Technology. 2010. link Times cited: 4 Abstract: The minimum energy motions of pure edge and screw dislocatio… read moreAbstract: The minimum energy motions of pure edge and screw dislocations in aluminum were investigated by atomistic transition state analysis. While the Peierls-Nabarro model and its modifications duplicate the essential nature of a dislocation within a crystalline lattice, the atomic-level relaxation of the dislocation core should be considered to estimate the minimum energy barrier. The relaxed atomic structure within and around the dislocation core is derived from the material’s inherent intrinsic properties and is therefore difficult to solve solely by simple analytical models. In this study, the minimum energy barriers and core structures for the quasi-static motions of pure edge and screw dislocations were investigated by the parallelized nudged elastic band method with the embedded atom method potential. We found that the local potential energy is distributed asymmetrically around the dislocation line for the most stable state and that it is bilaterally symmetrical at the transition state of the dislocation motion. The short-ranged structural relaxation of the core rearrangement as well as the wide-ranging elastic stress field is of great importance in realistic dislocation motion. read less USED (high confidence) B. Eidel and A. Stukowski, “A variational formulation of the quasicontinuum method based on energy sampling in clusters,” Journal of The Mechanics and Physics of Solids. 2009. link Times cited: 103 USED (high confidence) P. Brommer et al., “Vibrational properties of MgZn2,” Zeitschrift für Kristallographie - Crystalline Materials. 2009. link Times cited: 6 Abstract: We present here simulation results on the dynamical structur… read moreAbstract: We present here simulation results on the dynamical structure factor of the C14 Laves Phase of MgZn2, the simplest of the Mg–(Al,Zn) Frank-Kasper alloy phases. The dynamical structure factor was determined in two ways. Firstly, the dynamical matrix was obtained in harmonic approximation from ab-initio forces. The dynamical structure factor can then be computed from the eigenvalues of the dynamical matrix. Alternatively, Molecular Dynamics simulations of a larger sample were used to measure the correlation function corresponding to the dynamical structure factor. Both results are compared to data from neutron scattering experiments. This comparison also includes the intensity distribution, which is a very sensitive test. We find that the dynamical structure factor determined with either method agrees reasonably well with the experiment. In particular, the intensity transfer from acoustic to optic phonon modes can be reproduced correctly. This shows that simulation studies can complement phonon dispersion measurements. read less USED (high confidence) D. Irving, C. Padgett, and D. Brenner, “Coupled molecular dynamics/continuum simulations of Joule heating and melting of isolated copper–aluminum asperity contacts,” Modelling and Simulation in Materials Science and Engineering. 2008. link Times cited: 12 Abstract: Atomic-level dynamics of Joule heating, melting and plastic … read moreAbstract: Atomic-level dynamics of Joule heating, melting and plastic dynamics at loaded nanometer-scale Cu and Al asperity contacts are modeled using an ad hoc coupling between a numerical solution to a heat transport equation, a virtual resistor network for describing electric current flow and a molecular dynamics simulation using the embedded atom method. Under constant voltage conditions the simulations demonstrate the formation of an Al melt that removes faceting from a Cu asperity via surface disordering at the melt–solid interface. Constant current simulations demonstrate initial disordering of both copper and aluminum at the interface. Flow from the aluminum melt increases the contact area, which lowers the resistance and drops the voltage to below that needed for melting. For the system with a loaded copper asperity, the interface recrystallizes and the dynamics transition from molten flow to plastic damage via dislocation emission. For an aluminum asperity, the asperity remains disordered after the voltage drop and no dislocation emission occurs into the copper or aluminum substrate. read less USED (high confidence) M. Nuggehally, M. Shephard, R. C. Picu, and J. Fish, “Adaptive Model Selection Procedure for Concurrent Multiscale Problems,” International Journal for Multiscale Computational Engineering. 2007. link Times cited: 25 Abstract: An adaptive method for the selection of models in a concurre… read moreAbstract: An adaptive method for the selection of models in a concurrent multiscale approach is presented. Different models from a hierarchy are chosen in different subdomains of the problem domain adaptively in an automated problem simulation. A concurrent atomistic to continuum (AtC) coupling method [27], based on a blend of the continuum stress and the atomistic force, is adopted for the problem formulation. Two error indicators are used for the hierarchy of models consisting of a linear elastic model, a nonlinear elastic model, and an embedded atom method (EAM) based atomistic model. A nonlinear indicator ηNL−L , which is based on the relative error in the energy between the nonlinear model and the linear model, is used to select or deselect the nonlinear model subdomain. An atomistic indicator is a stress-gradient-based criterion to predict dislocation nucleation, which was developed by Miller and Acharya [6]. A material-specific critical value associated with the dislocation nucleation criterion is used in selecting and deselecting the atomistic subdomain during an automated simulation. An adaptive strategy uses limit values of the two indicators to adaptively modify the subdomains of the three different models. Example results are illustrated to demonstrate the adaptive method. read less USED (high confidence) Al, M. Dewald, and W. Curtin, “Multiscale modelling of dislocation/grain-boundary interactions: I. Edge dislocations impinging on Σ11 (1 1 3) tilt boundary in Al,” Modelling and Simulation in Materials Science and Engineering. 2006. link Times cited: 122 Abstract: Dislocation and grain-boundary processes contribute signific… read moreAbstract: Dislocation and grain-boundary processes contribute significantly to plastic behaviour in polycrystalline metals, but a full understanding of the interaction between these processes and their influence on plastic response has yet to be achieved. The coupled atomistic discrete-dislocation method is used to study edge dislocation pile-ups interacting with a Σ11-⟨1 1 3⟩ symmetric tilt boundary in Al at zero temperature under various loading conditions. Nucleation of grain-boundary dislocations (GBDs) at the dislocation/grain-boundary intersection is the dominant mechanism of deformation. Dislocation pile-ups modify both the stress state and the residual defects at the intersection, the latter due to multiple dislocation absorption into the boundary, and so change the local grain-boundary/dislocation interaction phenomena as compared with cases with a single dislocation. The deformation is irreversible upon unloading and reverse loading if multiple lattice dislocations absorb into the boundary and damage in the form of microvoids and loss of crystalline structure accumulates around the intersection. Based on these results, the criteria for dislocation transmission formulated by Lee, Robertson and Birnbaum are extended to include the influences of grain-boundary normal stress, shear stress on the leading pile-up dislocation and minimization of step height at the intersection. Two possible yield loci for the onset of GBD nucleation versus compressive stress and relevant shear stresses are derived from the simulations. These results, and similar studies on other boundaries and dislocation characters, guide the formulation of continuum constitutive behaviours for use in discrete-dislocation or strain-gradient plasticity modelling. read less USED (high confidence) D. Olmsted, R. E. Phillips, and W. Curtin, “Modelling diffusion in crystals under high internal stress gradients,” Modelling and Simulation in Materials Science and Engineering. 2004. link Times cited: 23 Abstract: Diffusion of vacancies and impurities in metals is important… read moreAbstract: Diffusion of vacancies and impurities in metals is important in many processes occurring in structural materials. This diffusion often takes place in the presence of spatially rapidly varying stresses. Diffusion under stress is frequently modelled by local approximations to the vacancy formation and diffusion activation enthalpies which are linear in the stress, in order to account for its dependence on the local stress state and its gradient. Here, more accurate local approximations to the vacancy formation and diffusion activation enthalpies, and the simulation methods needed to implement them, are introduced. The accuracy of both these approximations and the linear approximations are assessed via comparison to full atomistic studies for the problem of vacancies around a Lomer dislocation in Aluminium. Results show that the local and linear approximations for the vacancy formation enthalpy and diffusion activation enthalpy are accurate to within 0.05 eV outside a radius of about 13 Å (local) and 17 Å (linear) from the centre of the dislocation core or, more generally, for a strain gradient of roughly up to 6 × 106 m−1 and 3 × 106 m−1, respectively. These results provide a basis for the development of multiscale models of diffusion under highly non-uniform stress. read less 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 USED (high confidence) V. Shenoy, “Multi-scale modeling strategies in materials science—The quasicontinuum method,” Bulletin of Materials Science. 2003. link Times cited: 15 USED (low confidence) S. Hayakawa and H. Xu, “Development of an interatomic potential for L12 precipitates in Fe–Ni–Al alloys,” Computational Materials Science. 2024. link Times cited: 0 USED (low confidence) A. Perveen, H. Liang, D. V. Alexandrov, M. U. Dad, and Y. Yang, “Engulfment and Pushing of Cylindrical Liquid Nano-Inclusion by Advancing Crystal/Melt Interface: An Atomistic Simulation Study,” Nanomaterials. 2023. link Times cited: 0 Abstract: We reported a molecular dynamics (MD) simulation study of an… read moreAbstract: We reported a molecular dynamics (MD) simulation study of an advancing pure Al(100)/melt interface that encounters a foreign immiscible liquid Pb cylindrical nano-inclusion. When the advancing interface approaches the inclusion, the interface may engulf, push to an extent and then engulf or push the nano-inclusion away from the solidifying phase depending on the velocity of the interface. Here, we investigated cylindrical liquid Pb nano-inclusion pushing or engulfment by a growing crystal Al that strongly depends on the velocity of the crystal/melt interface, and a critical velocity (vc) is deduced. If the velocity of the interface is less than vc, then the inclusion is pushed and engulfed otherwise. The relationship between vc and the radius of the nano-inclusion is expressed using a power function that agrees well with the previous studies. For velocity above the vc, the crystal/melt interface plays a vital role; it hinders the matrix atoms from setting below the cylindrical nano-inclusion due to insufficient mass transfer below the inclusion, resulting in the engulfment. read less USED (low confidence) A. Goncharov, A. Yunda, I. Kolinko, G. Kornich, and D. Shyrokorad, “Modeling the Deposition of Thin Films of Transition Metal Nitrides,” Coatings. 2023. link Times cited: 0 Abstract: This paper presents an overview of studies dedicated to the … read moreAbstract: This paper presents an overview of studies dedicated to the atomic-discrete modeling of the growth process of film coatings that comprise mononitrides of transition and post-transition metals. The main modeling approaches are the Monte Carlo and molecular dynamics methods as well as their combinations with analytical contributions. The molecular dynamics method is more accurate compared to the Monte Carlo method but has disadvantages related to the time scale. Given this, the adoption of accelerated molecular dynamics methods is viewed as a promising approach for directly simulating the specified processes. These methods can be implemented just after the relaxation of the collision stage in the area of the deposited particle between the deposition events to simulate the realistic density of the incident beam and accompanied long-term mass transfer processes. read less USED (low confidence) J. S. Lee et al., “Atomistic investigation into the formation of axial weak twins during the compression of single-crystal Mg nanopillars,” Acta Materialia. 2023. link Times cited: 0 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 USED (low confidence) T. Yang, X. Han, W. Li, X. Chen, and P. Liu, “Angular dependent potential for Al-Zr binary system to study the initial heterogeneous nucleation behavior of liquid Al on L12-Al3Zr,” Computational Materials Science. 2023. link Times cited: 0 USED (low confidence) D. He, Z. Rui, X. Lyu, J. Zhuo, H. Sun, and Y. Dong, “Effect of Nanopillars on the Wetting State and Adhesion Characteristics of Molten Aluminum Droplets.,” Langmuir : the ACS journal of surfaces and colloids. 2023. link Times cited: 1 Abstract: To solve the adhesion problem between molten aluminum and va… read moreAbstract: To solve the adhesion problem between molten aluminum and vacuum ladle liner during the electrolytic aluminum production process, the wetting state and adhesion properties of molten aluminum droplets on substrate surfaces with different nanopillars are investigated based on molecular dynamics. The results show that the adhesion strength of molten aluminum droplets in different wetting states has the pattern Young state > Wenzel state > Cassie state. Effects of increasing nanopillar height or interval are poles apart in the wetting state and adhesion characteristics of aluminum molten droplets. The critical height and critical interval of the nanopillar where the wetting state transition occurs are obtained. The increase of the nanopillar width can induce the wetting state transition from the Cassie state to the Wenzel state. In addition, the phantom wall method is applied to study the variation of the separation force. It is found that a peak in the separation force curve occurs when the molten droplet separates from the bottom of the nanopillar interval or the top of the nanopillar. The separation force curves of the droplets in the Young state and the Cassie state have single peaks, while the droplets in the Wenzel state have double peaks. read less USED (low confidence) L. Chalamet, D. Rodney, and Y. Shibuta, “Coarse-grained molecular dynamic model for metallic materials,” Computational Materials Science. 2023. link Times cited: 3 USED (low confidence) J. Cui, F. Zeng, and Y. Wang, “A coarse‐grained molecular dynamics study on the mechanical behavior of carbon nanotubes reinforced vulcanized natural rubber composites,” Polymer Composites. 2023. link Times cited: 0 Abstract: In the present study, coarse‐grained (CG) molecular models o… read moreAbstract: In the present study, coarse‐grained (CG) molecular models of carbon nanotubes (CNTs) strengthened vulcanized natural rubber (VNR) composites are constructed to systematically investigate the effects of length, inter‐tube cross‐linking, and polymer‐grafting of CNTs on the stress–strain behavior of VNR composites under uniaxial tension. The interfacial CG force field between CNTs and VNR is derived via the energy matching approach. The results demonstrate that increasing the length of CNTs is able to effectively enhance the mechanical performance of VNR composites, and the reinforcing efficiency increases gradually and tends to stabilize with increasing CNT length. Moreover, the cross‐linking and polymer‐grafting of CNTs are also effective approaches to significantly enhance the mechanical performance of VNR composites. The enhancement mechanism of CNTs is interpreted from the perspective of CNT networks, VNR networks, CNT‐VNR interface networks, and the interfacial load‐transfer behavior. Specifically, the dispersion of CNTs, the orientation of CNTs and VNR molecular chains, and the wrapping and interlocking behaviors between CNTs and the VNR matrix reveal a detailed structure‐mechanics relationship of CNTs‐reinforced VNR composites at the molecular level. These findings present theoretical instruction for the structural design of high‐performance rubber composites.
A coarse‐grained model of carbon nanotube‐natural rubber composites is built.
The composite network structures are quantitatively characterized.
The length, cross‐linking, and grafting effects of carbon nanotubes are studied.
The reinforcement mechanisms of carbon nanotubes are revealed.
read less USED (low confidence) R. Shi, H. Qian, and Z. Lu, “Coarse‐grained molecular dynamics simulation of polymers: Structures and dynamics,” Wiley Interdisciplinary Reviews: Computational Molecular Science. 2023. link Times cited: 0 Abstract: For the simulations of polymeric systems, coarse‐grained (CG… read moreAbstract: For the simulations of polymeric systems, coarse‐grained (CG) molecular dynamics simulations are computationally demanding not only because of their high computational efficiency, but also these CG models can provide sufficient structural and dynamical properties at both micro‐ and meso‐scopic levels. During the past decades, developments of these CG models are roughly in two directions, that is, generic and chemically system‐specific models. The developme of the formmer focuses on the capability of the model to capature the general properties of the system, for instance, scaling relations between both structural and dynamic properties with respect to chain length. On the other hand, to bridging the gap between physics and chemistry, chemically‐specifi models are also widely developed which are able to retain the inherent chemical–physical properties for a given polymer system. However, due to the reduction of atomistic degree of freedom a faithful reproduction of structure and especialy dynamics properties of the system is the maijor challenge. In this review, after a brief introduction of some widely used generic models, we present an overview of both recent achievements and remainning challendges in the development of chemically‐specific CG approaches, for the simulations of polymer systems. read less USED (low confidence) J.-E. Brandenburg, L. Barrales-Mora, S. Tsurekawa, and D. Molodov, “Dynamic behavior of grain boundaries with misorientations in the vicinity of Σ3 coherent and incoherent twin boundaries in Al bicrystals,” Acta Materialia. 2023. link Times cited: 1 USED (low confidence) A. Duff, R. Sakidja, H. C. Walker, R. Ewings, and D. Voneshen, “Automated potential development workflow: Application to BaZrO3,” Comput. Phys. Commun. 2023. link Times cited: 0 USED (low confidence) T. Ohkubo, N. Komiyama, H. Masu, K. Kishikawa, and M. Kohri, “Molecular Dynamics Studies of the Ho(III) Aqua-tris(dibenzoylmethane) Complex: Role of Water Dynamics.,” Inorganic chemistry. 2023. link Times cited: 0 Abstract: The seven-coordinate Ho(III) aqua-tris(dibenzoylmethane)(DBM… read moreAbstract: The seven-coordinate Ho(III) aqua-tris(dibenzoylmethane)(DBM) complex, referred to as Ho-(DBM)3·H2O, was first reported in the late 1960s. It has a threefold symmetric structure, with Ho at the center of three dibenzoylmethane ligands and hydrogen-bonded water to ligands. It is considered that the hydrogen bonds between the water molecule and the ligands surrounding Ho play an important role in the formation of its symmetrical structure. In this work, we developed new force-field parameters for classical molecular dynamics (CMD) simulations to theoretically elucidate the structure and dynamics of Ho-(DBM)3·H2O. To develop the force field, structural optimization and molecular dynamics were performed on the basis of ab initio calculations using the plane-wave pseudopotential method. The force-field parameters for CMD were then optimized to reproduce the data obtained from ab initio calculations. Validation of the developed force field showed good agreement with the experimental crystalline structure and ab initio data. The vibrational properties of water in Ho-(DBM)3·H2O were investigated by comparison with bulk liquid water. The vibrational motion of water was found to have a characteristic mode originating from stationary rotational motion along the c-axis of Ho(III) aqua-tris(dibenzoylmethane). Contrary to expectations, the hydrogen-bond dynamics of water in Ho-(DBM)3·H2O were found to be almost equivalent to those of bulk liquid water except for librational motion. This development route for force-field parameters for CMD and the establishment of water dynamics can advance the understanding of water-coordinated metal complexes with high coordination numbers such as Ho-(DBM)3·H2O. read less USED (low confidence) S. Mahajan and T. Tang, “Automated Parameterization of Coarse-Grained Polyethylenimine under a Martini Framework,” Journal of chemical information and modeling. 2023. link Times cited: 0 Abstract: As a versatile polymer in many applications, synthesized pol… read moreAbstract: As a versatile polymer in many applications, synthesized polyethylenimine (PEI) is polydisperse with diverse branched structures that attain pH-dependent protonation states. Understanding the structure-function relationship of PEI is necessary for enhancing its efficacy in various applications. Coarse-grained (CG) simulations can be performed at length and time scales directly comparable with experimental data while maintaining the molecular perspective. However, manually developing CG forcefields for complex PEI structures is time-consuming and prone to human errors. This article presents a fully automated algorithm that can coarse-grain any branched architecture of PEI from its all-atom (AA) simulation trajectories and topology. The algorithm is demonstrated by coarse-graining a branched 2 kDa PEI, which can replicate the AA diffusion coefficient, radius of gyration, and end-to-end distance of the longest linear chain. Commercially available 25 and 2 kDa Millipore-Sigma PEIs are used for experimental validation. Specifically, branched PEI architectures are proposed, coarse-grained using the automated algorithm, and then simulated at different mass concentrations. The CG PEIs can reproduce existing experimental data on PEI's diffusion coefficient and Stokes-Einstein radius at infinite dilution as well as its intrinsic viscosity. This suggests a strategy where probable chemical structures of synthetic PEIs can be inferred computationally using the developed algorithm. The coarse-graining methodology presented here can also be extended to other polymers. read less USED (low confidence) J. Wu, Z. Rui, and Y. Dong, “Effect of substrate temperature on adhesion at liquid-aluminum/silica interface by phantom wall method,” Materials Today Communications. 2023. link Times cited: 0 USED (low confidence) D. Peng, N. Jin, E. Leng, Y. Liu, J. Ye, and P. Li, “Could an amorphous binder Co phase improve the mechanical properties of WC–Co? A study of molecular dynamics simulation,” RSC Advances. 2023. link Times cited: 0 Abstract: The trade-off effect between strength and fracture toughness… read moreAbstract: The trade-off effect between strength and fracture toughness typically observed in composites is challenging for the design and development of novel materials. An amorphous state can impede the trade-off effect of strength and fracture toughness, improving the mechanical properties of composites. Choosing the typical tungsten carbide–cobalt (WC–Co) cemented carbides as examples, where the amorphous binder phase was found, the impact of binder phase Co on the mechanical properties was further investigated by molecular dynamics (MD) simulations. The mechanical behavior and microstructure evolution of the WC–Co composite in the uniaxial compression and tensile processes were studied at different temperatures. The results showed that Young's modulus and ultimate compressive/tensile strengths were higher in WC–Co with amorphous Co, and the ultimate compressive/tensile strengths increased by about 11–27% compared to the samples with crystalline Co. Amorphous Co not only restricts the propagation of voids and cracks but also delays fractures. The relationship between temperatures and deformation mechanisms was also investigated, in which the tendency of strength to decrease with increasing temperature was clarified. read less USED (low confidence) Y. Qiao, S. Nie, W. Li, E. Liu, and X. Wang, “Diffusion during the Initial Stage of CVD Diamond Growth on Cemented Carbide – A Molecular Dynamics and Experimental Study,” Applied Surface Science. 2023. link Times cited: 0 USED (low confidence) D. Belashchenko, “Molecular Dynamic Modeling of Magnesium in the Scheme of the Embedded Atom Model,” Russian Journal of Physical Chemistry A. 2023. link Times cited: 0 USED (low confidence) S. Starikov and D. Smirnova, “Details of structure transformations in pure uranium and U-Mo alloys: insights from classical atomistic simulation,” Journal of Nuclear Materials. 2023. link Times cited: 1 USED (low confidence) P. Khan, R. Kaushik, and A. Jayaraj, “Approaches and Perspective of Coarse-Grained Modeling and Simulation for Polymer–Nanoparticle Hybrid Systems,” ACS Omega. 2022. link Times cited: 0 Abstract: Molecular modeling and simulations have emerged as effective… read moreAbstract: Molecular modeling and simulations have emerged as effective and indispensable tools to characterize polymeric systems. They provide fundamental and essential insights to design a product of the required properties and to improve the understanding of a phenomenon at the molecular level for a particular system. The polymer–nanoparticle hybrids are materials with outstanding properties and correspondingly large applications whose study has benefited from this new paradigm. However, despite the significant expansion of modern day computational powers, investigation of the long time and large length scale phenomenon in polymeric and polymer–nanoparticle systems is still a challenging task to complete through all-atom molecular dynamics (AA-MD) simulations. To circumvent this problem, a variety of coarse-grained (CG) models have been proposed, ranging from the generic CG models for qualitative properties predictions to more realistic chemically specific CG models for quantitative properties predictions. These CG models have already delivered some success stories in the study of several spatial and temporal evolutions of many processes. Some of these studies were beyond the feasibility of traditional atomistic resolution models due to either the size or the time constraints. This review captures the different types of popular CG approaches that are utilized in the investigation of the microscopic behavior of polymer–nanoparticle hybrid systems. The rationale of this article is to furnish an overview of the popular CG approaches and their applications, to review several important and most recent developments, and to delineate the perspectives on future directions in the field. read less USED (low confidence) G. Park, B. Beeler, and M. Okuniewski, “Computational determination of a primary diffusion mode in γU-10Mo under irradiation,” Journal of Nuclear Materials. 2022. link Times cited: 2 USED (low confidence) P. Canepa, “Pushing Forward Simulation Techniques of Ion Transport in Ion Conductors for Energy Materials,” ACS Materials Au. 2022. link Times cited: 2 Abstract: Simulation techniques are crucial to establish a firm link b… read moreAbstract: Simulation techniques are crucial to establish a firm link between phenomena occurring at the atomic scale and macroscopic observations of functional materials. Importantly, extensive sampling of space and time scales is paramount to ensure good convergence of physically relevant quantities to describe ion transport in energy materials. Here, a number of simulation methods to address ion transport in energy materials are discussed, with the pros and cons of each methodology put forward. Emphasis is given to the stochastic nature of results produced by kinetic Monte Carlo, which can adequately account for compositional disorder across multiple sublattices in solids. read less USED (low confidence) M. Dixit and T. Taniguchi, “Substantial Effect of Terminal Groups in cis-Polyisoprene: A Multiscale Molecular Dynamics Simulation Study,” Macromolecules. 2022. link Times cited: 3 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 USED (low confidence) E. Ricci, M. Minelli, and M. D. D. Angelis, “Modelling Sorption and Transport of Gases in Polymeric Membranes across Different Scales: A Review,” Membranes. 2022. link Times cited: 11 Abstract: Professor Giulio C. Sarti has provided outstanding contribut… read moreAbstract: Professor Giulio C. Sarti has provided outstanding contributions to the modelling of fluid sorption and transport in polymeric materials, with a special eye on industrial applications such as membrane separation, due to his Chemical Engineering background. He was the co-creator of innovative theories such as the Non-Equilibrium Theory for Glassy Polymers (NET-GP), a flexible tool to estimate the solubility of pure and mixed fluids in a wide range of polymers, and of the Standard Transport Model (STM) for estimating membrane permeability and selectivity. In this review, inspired by his rigorous and original approach to representing membrane fundamentals, we provide an overview of the most significant and up-to-date modeling tools available to estimate the main properties governing polymeric membranes in fluid separation, namely solubility and diffusivity. The paper is not meant to be comprehensive, but it focuses on those contributions that are most relevant or that show the potential to be relevant in the future. We do not restrict our view to the field of macroscopic modelling, which was the main playground of professor Sarti, but also devote our attention to Molecular and Multiscale Hierarchical Modeling. This work proposes a critical evaluation of the different approaches considered, along with their limitations and potentiality. read less USED (low confidence) E. Voyiatzis and A. Stroeks, “Atomistic Modeling of Hydrogen and Oxygen Solubility in Semicrystalline PA-6 and HDPE Materials.,” The journal of physical chemistry. B. 2022. link Times cited: 4 Abstract: Hydrogen is a clean and sustainable energy carrier which pla… read moreAbstract: Hydrogen is a clean and sustainable energy carrier which plays a major role in the transition of the global energy market to a less fossil fuel dependent future. Polymer-based materials are crucial in the production, storage, transportation, and energy extraction of hydrogen. More insights in the hydrogen-polymers interactions are required to guide material design and product development, especially for hydrogen solubility in polymers, which is crucial in many applications. The current study aims at rationalizing the determining factors of hydrogen solubility in two relevant polymers: polyamide-6 (PA-6) and high density polyethylene (HDPE). Based on atomistic molecular dynamics simulations and experimental data, we have reached several conclusions related to hydrogen and oxygen solubility in these two polymers. The crystal phases of PA-6 and HDPE are impenetrable to hydrogen and oxygen at elevated pressures, despite the small molecular size of hydrogen and oxygen. The practical implication for gas barrier applications is that polymer crystals act as impermeable obstacles and gas migration takes place primarily in the amorphous phase. Experimental hydrogen and oxygen solubilities in PA-6 and HDPE at elevated pressures can be predicted in a semiquantitative manner by molecular simulations. The discrepancies between experimental and predicted values could be attributed to neglect of the effect of crystal regions on the amorphous polymer domains. Although hydrogen is smaller than oxygen, it has been experimentally observed that hydrogen has a lower solubility in PA-6 and HDPE than oxygen. This observation has been confirmed by molecular simulations and attributed to the more favorable energetic interactions of oxygen with PA-6 and PE than of hydrogen. These interactions dominate the solubility behavior over the distribution of the accessible volume in the polymers. read less USED (low confidence) A. Hegde, E. Weiss, W. Windl, H. Najm, and C. Safta, “Bayesian calibration of interatomic potentials for binary alloys,” Computational Materials Science. 2022. link Times cited: 1 USED (low confidence) J. Hammons et al., “Processes Controlling Helium Bubble Dynamics at Varying Temperatures in Simulated Radioactive Materials,” Materialia. 2022. link Times cited: 0 USED (low confidence) P. Shamaprasad et al., “Using molecular simulation to understand the skin barrier,” Progress in lipid research. 2022. link Times cited: 11 USED (low confidence) Z. Sun, L. Zheng, K. Wang, Z. Huai, and Z. Liu, “Primary vs secondary: Directionalized guest coordination in β-cyclodextrin derivatives.,” Carbohydrate polymers. 2022. link Times cited: 12 USED (low confidence) Y. Hu and W. Curtin, “Modeling of precipitate strengthening with near-chemical accuracy: case study of Al-6xxx alloys,” Acta Materialia. 2022. link Times cited: 10 USED (low confidence) W. K. Kim, A. Kavalur, S. Whalen, and E. Tadmor, “Free energy calculation and ghost force correction for hot‐QC,” International Journal for Numerical Methods in Engineering. 2022. link Times cited: 0 Abstract: A new efficient variant of hot‐QC, the finite temperature ve… read moreAbstract: A new efficient variant of hot‐QC, the finite temperature version of the quasicontinuum (QC) method, is presented. In the original formulation of hot‐QC, a dynamically evolving atomistic region is coupled with either a dynamic (hot‐QC‐dynamic) or a static (hot‐QC‐static) continuum region. In the current work, a free energy minimization method is employed in which atom positions in both the atomistic and continuum regions always occupy equilibrium positions. The effect of ghost forces at the interface of the atomistic and continuum regions is discussed for all three variants of hot‐QC using two examples: a perfect cubic crystal and a Lomer dislocation dipole. Errors due to ghost forces and due to mesh entropy are considered and the efficacy of their correction terms are evaluated. It is shown that the proposed free energy minimization method has comparable accuracy to the other methods with significantly higher efficiency. read less USED (low confidence) Y. Kashyrina, A. S. Muratov, V. Kazimirov, and O. S. Roik, “X-ray diffraction study and molecular dynamic simulation of liquid Al-Cu alloys: a new data and interatomic potentials comparison,” Journal of Molecular Modeling. 2022. link Times cited: 0 USED (low confidence) R. D. Kamachali, “Melting upon Coalescence of Solid Nanoparticles,” Solids. 2022. link Times cited: 0 Abstract: The large surface-to-volume ratio of nanoparticles is unders… read moreAbstract: The large surface-to-volume ratio of nanoparticles is understood to be the source of many interesting phenomena. The melting temperature of nanoparticles is shown to dramatically reduce compared to bulk material. Yet, at temperatures below this reduced melting point, a liquid-like atomic arrangement on the surface of nanoparticles is still anticipated to influence its properties. To understand such surface effects, here, we study the coalescence of Au nanoparticles of various sizes using molecular dynamics simulations. Analysis of the potential energy and Lindemann index distribution across the nanoparticles reveals that high-energy, high-mobility surface atoms can enable the coalescence of nanoparticles at temperatures much lower than their corresponding melting point. The smaller the nanoparticles, the larger the difference between their melting and coalescence temperatures. For small enough particles and/or elevated enough temperatures, we found that the coalescence leads to a melting transition of the two nominally solid nanoparticles, here discussed in relation to the heat released due to the surface reduction upon the coalescence and the size dependence of latent heat. Such discontinuous melting transitions can lead to abrupt changes in the properties of nanoparticles, important for their applications at intermediate temperatures. read less USED (low confidence) T. Mahadevan, A. Baroni, M. Taron, S. Gin, J. Du, and J. Delaye, “Development of potentials for molecular dynamics simulations of dry and hydrated calcium aluminosilicate glasses by force matching and refinement,” Journal of Non-Crystalline Solids. 2022. link Times cited: 3 USED (low confidence) H. Gao, R. Shi, Y. Zhu, H. Qian, and Z.-yuan Lu, “Coarse-grained Dynamics Simulation in Polymer Systems: from Structures to Material Properties,” Chemical Research in Chinese Universities. 2022. link Times cited: 1 USED (low confidence) M. Zhou, B. Fu, Q. Hou, L. Wu, and R. Pan, “Determining the diffusion behavior of point defects in zirconium by a multiscale modelling approach,” Journal of Nuclear Materials. 2022. link Times cited: 3 USED (low confidence) Y. Gao, T. P. Mishra, S. H. Bo, G. Gautam, and P. Canepa, “Design and Characterization of Host Frameworks for Facile Magnesium Transport,” Annual Review of Materials Research. 2022. link Times cited: 9 Abstract: The development of inexpensive batteries based on magnesium … read moreAbstract: The development of inexpensive batteries based on magnesium (Mg) chemistry will contribute remarkably toward developing high-energy-density storage systems that can be used worldwide. Significant challenges remain in developing practical Mg batteries, the chief of which is designing materials that can provide facile transport of Mg. In this review, we cover the experimental and theoretical methods that can be used to quantify Mg mobility in a variety of host frameworks, the specific transport quantities that each technique is designed to measure or calculate, and some practical examples of their applications. We then list the unique challenges faced by different experimental and computational techniques in probing Mg ion transport in materials. This review concludes with an outlook on the directions that the scientific community could soon pursue as we strive to construct a pragmatic Mg battery. Expected final online publication date for the Annual Review of Materials Research, Volume 52 is July 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates. read less USED (low confidence) Z. Zhang, C. Wang, and Y. Ni, “Synergy Effect and Symmetry-Induced Enhancement Effect of Surface Multi-Defects on Nanohardness by Quasi-Continuum Method,” Materials. 2022. link Times cited: 0 Abstract: The quasicontinuum method has been applied to probe the thin… read moreAbstract: The quasicontinuum method has been applied to probe the thin film with surface multi-defects, which is commonly seen in nanoimprint technique and bulk micromachining. Three unilaterally distributed multi-defect models and six bilaterally distributed multi-defect models of Pt thin film have been carried out in nanoindentation. The results show that the nanohardness gradually decreases as the number of unilaterally distributed multi-defects increases, along with the increasingly low decline rate of the nanohardness. The synergy effect of the unilaterally distributed multi-defects has been highly evidenced by the critical load revision for dislocation emission of Pt thin film, and it is predicted into a universal form with the synergy coefficient among the existing multi-defects for FCC metals. Moreover, the nanohardness obviously increases when the bilaterally distributed multi-defects form into symmetrical couple, and it could be even greater than the one with defect-free surface, due to the symmetry-induced enhancement effect on nanohardness. The symmetry-induced enhancement coefficient has been brought out and has well explained the symmetry-induced enhancement effect of bilaterally distributed multi-defects on the nanohardness by a prediction formula. Furthermore, the characteristic length of symmetric relations has been brought out to calculate the symmetry-induced enhancement coefficient and it has been effectively predicted to equal to the sum of the adjacent distance between the surface defect and the indenter, the defect depth near the indenter, and the defect width for FCC metal. read less USED (low confidence) J. Wang, P. J. in ’t Veld, M. Robbins, and T. Ge, “Effects of Coarse-Graining on Molecular Simulation of Craze Formation in Polymer Glass,” Macromolecules. 2022. link Times cited: 3 USED (low confidence) M. Dewapriya and R. Miller, “Molecular dynamics study on the shock induced spallation of polyethylene,” Journal of Applied Physics. 2022. link Times cited: 3 USED (low confidence) X. Q. Tran et al., “Quantitative Characterization of the Thermally Driven Alloying State in Ternary Ir-Pd-Ru Nanoparticles.,” ACS nano. 2021. link Times cited: 3 Abstract: Compositional and structural arrangements of constituent ele… read moreAbstract: Compositional and structural arrangements of constituent elements, especially those at the surface and near-surface layers, are known to greatly influence the catalytic performance of alloyed nanoparticles (NPs). Although much research effort often focuses on the ability to tailor these important aspects in the design stage, their stability under realistic operating conditions remains a major technical challenge. Here, the compositional stability and associated structural evolution of a ternary iridium-palladium-ruthenium (Ir-Pd-Ru) nanoalloy at elevated temperatures have been studied using interrupted in situ scanning transmission electron microscopy and theoretical modeling. The results are based on a combinatory approach of statistical sampling at the sub-nanometer scale for large groups of NPs as well as tracking individual NPs. We find that the solid solution Ir-Pd-Ru NPs (∼5.6 nm) evolved into a Pd-enriched shell supported on an alloyed Ir-Ru-rich core, most notably when the temperature exceeds 500 °C, concurrently with the development of expansive atomic strain in the outer surface and subsurface layers with respect to the core regions. Theoretically, we identify the weak interatomic bonds, low surface energy, and large atomic sizes associated with Pd as the key factors responsible for such observed features. read less 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 USED (low confidence) J. A. Joseph et al., “Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy,” Nature Computational Science. 2021. link Times cited: 81 USED (low confidence) G. Yu and M. Wilson, “Molecular simulation studies of self-assembly for a chromonic perylene dye: all-atom studies and new approaches to coarse-graining,” Journal of Molecular Liquids. 2021. link Times cited: 5 USED (low confidence) Z. Sun, Q.-L. He, Z. Gong, P. Kalhor, Z. Huai, and Z. Liu, “A General Picture of Cucurbit[8]uril Host–Guest Binding: Recalibrating Bonded Interactions,” Molecules. 2021. link Times cited: 6 Abstract: Atomic-level understanding of the dynamic feature of host–gu… read moreAbstract: Atomic-level understanding of the dynamic feature of host–guest interactions remains a central challenge in supramolecular chemistry. The remarkable guest binding behavior of the Cucurbiturils family of supramolecular containers makes them promising drug carriers. Among Cucurbit[n]urils, Cucurbit[8]uril (CB8) has an intermediate portal size and cavity volume. It can exploit almost all host–guest recognition motifs formed by this host family. In our previous work, an extensive computational investigation of the binding of seven commonly abused and structurally diverse drugs to the CB8 host was performed, and a general dynamic binding picture of CB8-guest interactions was obtained. Further, two widely used fixed-charge models for drug-like molecules were investigated and compared in great detail, aiming at providing guidelines in choosing an appropriate charge scheme in host-guest modelling. Iterative refitting of atomic charges leads to improved binding thermodynamics and the best root-mean-squared deviation from the experimental reference is 2.6 kcal/mol. In this work, we focus on a thorough evaluation of the remaining parts of classical force fields, i.e., the bonded interactions. The widely used general Amber force fields are assessed and refitted with generalized force-matching to improve the intra-molecular conformational preference, and thus the description of inter-molecular host–guest interactions. The interaction pattern and binding thermodynamics show a significant dependence on the modelling parameters. The refitted system-specific parameter set improves the consistency of the modelling results and the experimental reference significantly. Finally, combining the previous charge-scheme comparison and the current force-field refitting, we provide general guidelines for the theoretical modelling of host–guest binding. read less USED (low confidence) Z. Sun and Q.-L. He, “Seeding the multi-dimensional nonequilibrium pulling for Hamiltonian variation: indirect nonequilibrium free energy simulations at QM levels.,” Physical chemistry chemical physics : PCCP. 2021. link Times cited: 9 Abstract: The combination of free energy simulations in the alchemical… read moreAbstract: The combination of free energy simulations in the alchemical and configurational spaces provides a feasible route to access the thermodynamic profiles under a computationally demanding target Hamiltonian. Normally, due to the significant differences between the computational cost of ab initio quantum mechanics (QM) calculations and those of semi-empirical quantum mechanics (SQM) and molecular mechanics (MM), this indirect method could be used to obtain the QM thermodynamics by combining the SQM or MM results and the SQM-to-QM or MM-to-QM corrections. In our previous work, a multi-dimensional nonequilibrium pulling framework for Hamiltonian variations was introduced based on bidirectional pulling and bidirectional reweighting. The method performs nonequilibrium free energy simulations in the configurational space to obtain the thermodynamic profile along the conformational change pathway under a selected computationally efficient Hamiltonian, and uses the nonequilibrium alchemical method to correct or perturb the thermodynamic profile to that under the target Hamiltonian. The BAR-based method is designed to achieve the best generality and transferability and thus leads to modest (∼20 fold) speedup. In this work, we explore the possibility of further accelerating the nonequilibrium free energy simulation by employing unidirectional pulling and using the selection criterion to obtain the initial configurations used to initiate nonequilibrium trajectories following the idea of adaptive steered molecular dynamics (ASMD). A single initial condition is used to seed the whole multi-dimensional nonequilibrium free energy simulation and the sampling is performed fully in the nonequilibrium ensemble. Introducing very short ps-length equilibrium sampling to grab more initial seeds could also be helpful. The ASMD scheme estimates the free energy difference with the unidirectional exponential average (EXP), but it does not follow exactly the requirements of the EXP estimator. Another deficiency of the seeding simulation is the inherently sequential or serial pulling due to the inter-segment dependency, which triggers some problems in the parallelizability of the simulation. Numerical tests are performed to grasp some insights and guidelines for using this selection-criterion-based ASMD scheme. The presented selection-criterion-based multi-dimensional ASMD scheme follows the same perturbation network of the BAR-based method, and thus could be used in various Hamiltonian-variation cases. read less USED (low confidence) M. U. Dad, A. Perveen, H. Liang, and Y. Yang, “Interface migration in Aluminum bicrystals via premelting,” Surfaces and Interfaces. 2021. link Times cited: 2 USED (low confidence) S. Forghani and N. Khaji, “An anisotropic multi-scale method for slipping dislocations,” International Journal of Plasticity. 2021. link Times cited: 4 USED (low confidence) A. P. Latham and B. Zhang, “Unifying coarse-grained force fields for folded and disordered proteins.,” Current opinion in structural biology. 2021. link Times cited: 21 USED (low confidence) Y. Yuan and F. Wang, “A comparison of three DFT exchange-correlation functionals and two basis sets for the prediction of the conformation distribution of hydrated polyglycine.,” The Journal of chemical physics. 2021. link Times cited: 4 Abstract: The performance of three density functional theory (DFT) exc… read moreAbstract: The performance of three density functional theory (DFT) exchange-correlation functionals, namely, Perdew-Burke-Ernzerhof (PBE), BP86, and B3LYP, in predicting conformational distributions of a hydrated glycine peptide is tested with two different basis sets in the framework of adaptive force matching (AFM). The conformational distributions yielded the free energy profiles of the DFT functional and basis set combinations. Unlike traditional validations of potential energy and structural parameters, our approach allows the free energy of DFT to be validated. When compared to experimental distributions, the def2-TZVP basis set provides better agreement than a slightly trimmed aug-cc-pVDZ basis set. B3LYP is shown to be better than BP86 and PBE. The glycine model fitted against B3LYP-D3(BJ) with the def2-TZVP basis set is the most accurate and named the AFM2021 model for glycine. The AFM2021 glycine model provides better agreement with experimental J-coupling constants than C36m and ff14SB, although the margin is very small when compared to C36m. Our previously published alanine model is also refitted with the slightly simplified AFM2021 energy expression. This work shows good promise of AFM for developing force fields for a range of proteinogenic peptides using only DFT as reference. read less USED (low confidence) S. Starikov and D. Smirnova, “Optimized interatomic potential for atomistic simulation of Zr-Nb alloy,” Computational Materials Science. 2021. link Times cited: 15 USED (low confidence) M. H. Pebdani and R. E. Miller, “Molecular dynamics simulation of pull-out Halloysite nanotube from polyurethane matrix,” Advances in Mechanical Engineering. 2021. link Times cited: 5 Abstract: Molecular dynamics (MD) simulation has been applied to study… read moreAbstract: Molecular dynamics (MD) simulation has been applied to study of pull-out of Halloysite nanotubes (HNTs) from a polyurethane (PU) matrix. First, the Machine learning (ML) particle swarm optimization (PSO) method was used to obtain force field parameters for MD from data of density functional theory (DFT) calculations. The current study shows the possibility of using a PSO technique to modify the force field with DFT data with less than 5 kcal/mol discrepancy. Second, we considered the influence of atomic interface on pulling out of HNT from PU. Energy variation has been proposed as the cohesion strength between matrix and nanoparticle. In addition, the best Lennard Jones parameters in the MD simulation make good agreement with an experimental sample stress-strain response. read less USED (low confidence) J. G. S. Canchaya et al., “Rheological properties of polymer chains at a copper oxide surface: Impact of the chain length, surface coverage, and grafted polymer shape.,” Physical review. E. 2021. link Times cited: 2 Abstract: We employ a recently derived semirealistic set of coarse-gra… read moreAbstract: We employ a recently derived semirealistic set of coarse-grained interactions to simulate polymer brushes of cis-1,4-polybutadiene grafted on a cuprous-oxide surface within the framework of dissipative particle dynamics. We consider two types of brushes, I and Y, that differ in the way they are connected to the surface. Our model explores the impact of free polymer chain length, grafting density of the brush, and imposed shear rate on the structural and dynamic properties of complex metal oxide polymer interfaces. read less USED (low confidence) D. Zheng and F. Wang, “Performing Molecular Dynamics Simulations and Computing Hydration Free Energies on the B3LYP-D3(BJ) Potential Energy Surface with Adaptive Force Matching: A Benchmark Study with Seven Alcohols and One Amine,” ACS Physical Chemistry Au. 2021. link Times cited: 7 Abstract: The potential energy surfaces at the B3LYP-D3(BJ) level for … read moreAbstract: The potential energy surfaces at the B3LYP-D3(BJ) level for eight solutes in dilute aqueous solutions were mapped into simple pairwise additive force field expressions using the adaptive force matching (AFM) method. The quality of the fits was validated by computing the hydration free energy (HFE), enthalpy of hydration, and diffusion constant for each solute. By force matching B3LYP-D3(BJ), the predictions from the models agree with the closest experimental HFE and enthalpy of hydration within chemical accuracy. The diffusion constants from the models are also in good agreement with experimental references. The good agreement provides confidence on the quality of B3LYP-D3(BJ) in producing potential energy surfaces for thermodynamic property calculations through AFM for the molecules studied. Accurate computational predictions could potentially provide validations to experimental measurements in cases where experimental measurements from different sources do not agree. read less USED (low confidence) N. M. de Los Santos-López, G. Pérez-Ángel, J. M. Méndez-Alcaraz, and R. Castañeda-Priego, “Competing interactions in the depletion forces of ternary colloidal mixtures.,” The Journal of chemical physics. 2021. link Times cited: 3 Abstract: Depletion interactions between colloidal particles surrounde… read moreAbstract: Depletion interactions between colloidal particles surrounded by smaller depletants are typically characterized by a strong attraction at contact and a moderately repulsive barrier in front of it that extends at distances similar to the size of the depletants; the appearance and height of the barrier basically depend on the concentration and, therefore, the correlation between depletants. From a thermodynamic point of view, the former can drive the system to phase separation or toward non-equilibrium states, such as gel-like states, but its effects on both local and global properties may be controlled by the latter, which acts as a kind of entropic gate. However, the latter has not been entirely analyzed and understood within the context of colloidal mixtures mainly driven by entropy. In this contribution, we present a systematic study of depletion forces in ternary mixtures of hard spherical particles with two species of depletants, in two and three dimensions. We focus the discussion on how the composition of the depletants becomes the main physical parameter that drives the competition between the attractive well and the repulsive barrier. Our results are obtained by means of the integral equation theory of depletion forces and techniques of contraction of the description adapted to molecular dynamics computer simulations. read less USED (low confidence) M. Dewapriya and R. E. Miller, “Energy absorption mechanisms of nanoscopic multilayer structures under ballistic impact loading,” Computational Materials Science. 2021. link Times cited: 22 USED (low confidence) K. M. Kidder, R. Szukalo, and W. Noid, “Energetic and entropic considerations for coarse-graining,” The European Physical Journal B. 2021. link Times cited: 9 USED (low confidence) S. Starikov et al., “Angular-dependent interatomic potential for large-scale atomistic simulation of iron: Development and comprehensive comparison with existing interatomic models,” Physical Review Materials. 2021. link Times cited: 16 Abstract: The development of classical interatomic potential for iron … read moreAbstract: The development of classical interatomic potential for iron is a quite demanding task with a long history background. A new interatomic potential for simulation of iron was created with a focus on description of crystal defects properties. In contrast with previous studies, here the potential development was based on force-matching method that requires only ab initio data as reference values. To verify our model, we studied various features of body-centered-cubic iron including the properties of point defects (vacancy and self-interstitial atom), the Peierls energy barrier for dislocations (screw and mix types), and the formation energies of planar defects (surfaces, grain boundaries, and stacking fault). The verification also implies thorough comparison of a potential with 11 other interatomic potentials reported in literature. This potential correctly reproduces the largest number of iron characteristics which ensures its advantage and wider applicability range compared to the other considered classical potentials. Here application of the model is illustrated by estimation of self-diffusion coefficients and the calculation of fcc lattice properties at high temperature. read less USED (low confidence) H. Song and M. Mendelev, “Molecular Dynamics Study of Mechanism of Solid–Liquid Interface Migration and Defect Formation in Al3Sm Alloy,” JOM. 2021. link Times cited: 2 USED (low confidence) B. Lan and D. Sun, “Breathing mode of nanoclusters: Definition and comparison to a continuous medium model,” Physical Review B. 2021. link Times cited: 4 Abstract: Breathing modes are closely related to many physical propert… read moreAbstract: Breathing modes are closely related to many physical properties of nanoclusters. Decades of research, however, failed to formulate a general and unambiguous definition. Here we present a straightforward and widely applicable definition of breathing modes based on power spectra of geometric quantities, namely, surface area, volume, etc. Applying group theory, normal-mode analysis, and molecular dynamics simulations, we have explored breathing modes of several ${\mathrm{Al}}_{n}$ clusters with high and low symmetries. The results suggest that our definition is able to cover not only common breathing modes but also some hidden modes. Our consistent definition also allows us to make a comprehensive and in-depth comparison with Lamb's continuous medium model, which reveals some high-frequency breathing modes are explicable only at the atomic level. read less USED (low confidence) S. Wang, L. Ma, J. Mead, S. Ju, G. Li, and H. Huang, “Catalyst-free synthesis and mechanical characterization of TaC nanowires,” Science China Physics, Mechanics & Astronomy. 2021. link Times cited: 7 USED (low confidence) Y.-F. Hu and W. Curtin, “Modeling peak-aged precipitate strengthening in Al–Mg–Si alloys,” Journal of The Mechanics and Physics of Solids. 2021. link Times cited: 21 USED (low confidence) T. Ge, J. Wang, and M. Robbins, “Effects of Coarse-Graining on Molecular Simulations of Mechanical Properties of Glassy Polymers,” Macromolecules. 2021. link Times cited: 2 Abstract: We simulate the mechanical response of polystyrene glasses u… read moreAbstract: We simulate the mechanical response of polystyrene glasses using the models with different levels of coarse-graining but the same structural correlations at thermal equilibrium. The stress level du... read less USED (low confidence) S. Attarian and S. Xiao, “Development of a 2NN-MEAM potential for boron.” 2021. link Times cited: 2 Abstract: In this paper, we present the first work in developing a sec… read moreAbstract: In this paper, we present the first work in developing a second nearest-neighbor modified embedded atom method (2NN-MEAM) potential function that can be used to model interatomic interactions in bo... read less USED (low confidence) Y. Yuan, Z. Ma, and F. Wang, “Development and Validation of a DFT-Based Force Field for a Hydrated Homoalanine Polypeptide,” The Journal of Physical Chemistry. B. 2021. link Times cited: 5 Abstract: A new force field has been created for simulating hydrated a… read moreAbstract: A new force field has been created for simulating hydrated alanine polypeptides using the adaptive force matching (AFM) method. Only density functional theory calculations using the Perdew–Burke–Ernzerhof exchange–correlation functional and the D3 dispersion correction were used to fit the force field. The new force field, AFM2020, predicts NMR scalar coupling constants for hydrated homopolymeric alanine in better agreements with experimental data than several other models including those fitted directly to such data. For Ala7, the new force field shows about 15% helical conformations, 20% conformation in the β basin, and 65% polyproline II. The predicted helical population of short hydrated alanine is higher than previous estimates based on the same experimental data. Gas-phase simulations indicate that the force field developed by AFM solution-phase data is likely to produce a reasonable conformation distribution when hydration water is no longer present, such as the interior of a protein. read less USED (low confidence) H. Wang, X. Gao, S. Chen, L. Yiming, Z.-wang Wu, and H. Ren, “Effects of Al on the precipitation of B2 Cu-rich particles in Fe–Cu ferritic alloy: Experimental and theoretical study,” Journal of Alloys and Compounds. 2020. link Times cited: 5 USED (low confidence) L. Stanek, R. Clay, M. Dharma-wardana, M. Wood, K. Beckwith, and M. Murillo, “Efficacy of the radial pair potential approximation for molecular dynamics simulations of dense plasmas,” arXiv: Plasma Physics. 2020. link Times cited: 12 Abstract: Macroscopic simulations of dense plasmas rely on detailed mi… read moreAbstract: Macroscopic simulations of dense plasmas rely on detailed microscopic information that can be computationally expensive and is difficult to verify experimentally. In this work, we delineate the accuracy boundary between microscale simulation methods by comparing Kohn-Sham density functional theory molecular dynamics (KS-MD) and radial pair potential molecular dynamics (RPP- MD) for a range of elements, temperature, and density. By extracting the optimal RPP from KS-MD data using force-matching, we constrain its functional form and dismiss classes of potentials that assume a constant power law for small interparticle distances. Our results show excellent agreement between RPP-MD and KS-MD for multiple metrics of accuracy at temperatures of only a few electron volts. The use of RPPs offers orders of magnitude decrease in computational cost and indicates that three-body potentials are not required beyond temperatures of a few eV. Due to its efficiency, the validated RPP-MD provides an avenue for reducing errors due to finite-size effects that can be on the order of $\sim20\%$. read less USED (low confidence) M. Dewapriya and R. E. Miller, “Superior Dynamic Penetration Resistance of Nanoscale Multilayer Polymer/Metal Films,” Journal of Applied Mechanics. 2020. link Times cited: 13 Abstract:
Recent advances in experimental techniques have enabled im… read moreAbstract:
Recent advances in experimental techniques have enabled impact tests of ultrathin films. For example, microprojectile impact tests of ultrathin polymer films have revealed that their specific penetration energy is about ten times more than that of the conventional armor materials. On the other hand, metallic nanostructures have demonstrated extraordinary mechanical properties. These observations suggest that multilayer arrangements of nanoscale polymer and metal films could possess superior ballistic impact resistance. In order to test this hypothesis, we simulated the impact tests of multilayer aluminum-polyurea nanostructures using molecular dynamics (MD). Our simulations demonstrate that the ballistic limit velocity (V50) and the specific penetration energy of the multilayers and aluminum nanofilms are significantly higher than the experimentally measured values for any material. In order to further investigate the mechanisms associated with the observed superior ballistic performance of multilayers, we computed their V50 using an existing membrane model and another analytical model reflecting a two-stage penetration process. Our results demonstrate a potential bottom-up design pathway for developing flexible barrier materials with superior dynamic penetration resistance. read less USED (low confidence) B. Lin, J. Li, Z. Wang, and J. Wang, “Dislocation nucleation from Zr–Nb bimetal interfaces cooperating with the dynamic evolution of interfacial dislocations,” International Journal of Plasticity. 2020. link Times cited: 13 USED (low confidence) G. V. Huerta and G. Raabe, “Genetic Parameterization of Interfacial Force Fields Based on Classical Bulk Force Fields and Ab Initio Data: Application to the Methanol-ZnO Interfaces,” Journal of chemical information and modeling. 2020. link Times cited: 2 Abstract: Despite the high advances of classical molecular simulation … read moreAbstract: Despite the high advances of classical molecular simulation to study bulk phases, classical force fields (FFs) to describe interactions at interfaces are rarely available in the literature. In this study, FFs to describe fluid | solid interfaces are developed by matching forces and energies from ab initio simulation and by using a newly developed genetic algorithm (GA). The interfacial FFs are parameterized to be combined with existing classical bulk FFs. Our procedure is tested on the methanol (CH3OH) | ZnO interface. The results for the forces, energies, and some structural adsorption properties calculated using an own parameterized interfacial FF are comparable with results from ab initio and experimental data. With this, we illustrate the potential of the proposed procedure to yield accurate models for interfacial systems to be combined with available bulk FFs. read less USED (low confidence) M. Dewapriya and R. E. Miller, “Molecular dynamics study of the mechanical behaviour of ultrathin polymer–metal multilayers under extreme dynamic conditions,” Computational Materials Science. 2020. link Times cited: 14 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 USED (low confidence) M. L. D. Reis, L. Proville, M. Marinica, and M. Sauzay, “Atomic scale simulations for the diffusion-assisted crossing of dislocation anchored by vacancy clusters,” Physical Review Materials. 2020. link Times cited: 3 Abstract: Nanosize vacancy clusters, characterized in metals after pla… read moreAbstract: Nanosize vacancy clusters, characterized in metals after plastic deformation, irradiation or specific heat treatments are suspected to participate in materials hardening through their interactions with mobile dislocations. Our numerical simulations made from combining three different simulation techniques, i.e., molecular statics, kinetic Monte Carlo and elastic line models allow us to compute the dislocations velocity in realistic conditions of applied shear stress, temperature, concentration, and size of the vacancy clusters, in face--centered-cubic aluminium. We show that the clusters behave as sources of vacancies that follow a reaction path along the dislocation line, which is recognized as a pipe diffusion process. The accumulation of vacancies in the dislocation stacking fault ribbon yields jogs that participate in the dislocation climb. Both vacancy leaks from clusters and climb of dislocation segments contribute to the dislocation crossing, which remains thermally activated. We integrated the ensemble of the thermally activated processes: Diffusion, emission, absorption processes, as well as dislocation-cluster crossing, into the same simulation allowing us to predict the dislocation mobility in good agreement with experimental deformation tests. read less USED (low confidence) D. Sun and X. Gong, “Nanocluster glass-formation: a potential energy landscape perspective,” New Journal of Physics. 2020. link Times cited: 4 Abstract: The intrinsic nature of glass states or glass transitions ha… read moreAbstract: The intrinsic nature of glass states or glass transitions has been a mystery for a long time. Recent studies have suggested that glass-formation versus crystallization occurs for potential energy landscapes (PEL) having a specific structure and the present work is an elaboration of this perspective. To explore how the flatness of the PEL related to glass transition, we develop a method to adjust the PEL in a controllable manner. We demonstrate that a relatively flat PEL is not only necessary but also sufficient for the formation of a nanoscale glass. We show that: (1) as long as a nanocluster is located in a region of PEL with local minimum deep enough, it can undergo an abrupt thermodynamic transition reminiscent of the first order transition of bulk materials; and (2) if a nanocluster is located in a relatively flat PEL, it can undergo a very broad transition in their dynamics and thermodynamics that resembles glass-formation in bulk materials in many ways. All these transitions are independent of its structure symmetry, order or disorder. Our simulations also uncover the direct transition from one potential energy minimum to another below the glass transition temperature, which is the consequence of flat PELs. read less USED (low confidence) T.-S. Lee et al., “Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery,” Journal of chemical information and modeling. 2020. link Times cited: 138 Abstract: Predicting protein-ligand binding affinities and the associa… read moreAbstract: Predicting protein-ligand binding affinities and the associated thermodynamics of biomolecular recognition is a primary objective of structure-based drug design. Alchemical free energy simulations offer a highly accurate and computationally efficient route to achieving this goal. While the AMBER molecular dynamics package has successfully been used for alchemical free energy simulations in academic research groups for decades, widespread impact in industrial drug discovery settings has been minimal because of the previous limitations within the AMBER alchemical code, coupled with challenges in system setup and postprocessing workflows. Through a close academia-industry collaboration we have addressed many of the previous limitations with an aim to improve accuracy, efficiency, and robustness of alchemical binding free energy simulations in industrial drug discovery applications. Here, we highlight some of the recent advances in AMBER20 with a focus on alchemical binding free energy (BFE) calculations, which are less computationally intensive than alternative binding free energy methods where full binding/unbinding paths are explored. In addition to scientific and technical advances in AMBER20, we also describe the essential practical aspects associated with running relative alchemical BFE calculations, along with recommendations for best practices, highlighting the importance not only of the alchemical simulation code but also the auxiliary functionalities and expertise required to obtain accurate and reliable results. This work is intended to provide a contemporary overview of the scientific, technical, and practical issues associated with running relative BFE simulations in AMBER20, with a focus on real-world drug discovery applications. read less USED (low confidence) R. Yan, S. Ma, W. Sun, T. Jing, and H. Dong, “The solid–liquid interface free energy of Al: A comparison between molecular dynamics calculations and experimental measurements,” Computational Materials Science. 2020. link Times cited: 8 USED (low confidence) P. Pandey, U. Hansmann, and F. Wang, “Altering the Solubility of the Antibiotic Candidate Nisin—A Computational Study,” ACS Omega. 2020. link Times cited: 9 Abstract: The growing bacterial resistance to available antibiotics ma… read moreAbstract: The growing bacterial resistance to available antibiotics makes it necessary to look for new drug candidates. An example is a lanthionine-containing nisin, which has a broad spectrum of antimicrobial activity. While nisin is widely utilized as a food preservative, its poor solubility and low stability at physiological pH hinder its use as an antibiotic. As the solubility of nisin is controlled by the residues of the hinge region, we have performed molecular dynamics simulations of various mutants and studied their effects on nisin’s solubility. These simulations are complicated by the presence of two uncommon residues (dehydroalanine and dehydrobutyrine) in the peptide. The primary goal of the present study is to derive rules for designing new mutants that will be more soluble at physiological pH and, therefore, may serve as a basis for the future antibiotic design. Another aim of our study is to evaluate whether existing force fields can model the solubility of these amino acids accurately, in order to motivate further developments of force fields to account for solubility information. read less USED (low confidence) R. Alexander et al., “Interatomic potentials for irradiation-induced defects in iron,” Journal of Nuclear Materials. 2020. link Times cited: 13 USED (low confidence) A. Bondarev, A. Fraile, T. Polcar, and D. Shtansky, “Mechanisms of friction and wear reduction by h-BN nanosheet and spherical W nanoparticle additives to base oil: Experimental study and molecular dynamics simulation,” Tribology International. 2020. link Times cited: 35 USED (low confidence) S. Starikov and V. Tseplyaev, “Two-scale simulation of plasticity in molybdenum: Combination of atomistic simulation and dislocation dynamics with non-linear mobility function,” Computational Materials Science. 2020. link Times cited: 9 USED (low confidence) Y. Liu, A. H. de Vries, J. Barnoud, W. Pezeshkian, J. Melcr, and S. Marrink, “Dual Resolution Membrane Simulations Using Virtual Sites,” The Journal of Physical Chemistry. B. 2020. link Times cited: 19 Abstract: All-atomistic (AA) and coarse-grain (CG) simulations have be… read moreAbstract: All-atomistic (AA) and coarse-grain (CG) simulations have been successfully applied to investigate a broad range of biomolecular processes. However, the accessible time and length scales of AA simulation are limited and the specific molecular details of CG simulation are simplified. Here, we propose a virtual site (VS) based hybrid scheme that can concurrently couple AA and CG resolutions in a single membrane simulation, mitigating the shortcomings of either representation. With some adjustments to make the AA and CG force fields compatible, we demonstrate that lipid bilayer properties are well kept in our hybrid approach. Our VS hybrid method was also applied to simulate a small lipid vesicle, with the inner leaflet and interior solvent represented in AA, and the outer leaflet together with exterior solvent at the CG level. Our multiscale method opens the way to investigate biomembrane properties at increased computational efficiency, in particular applications involving large solvent filled regions. read less USED (low confidence) M. Jahanshahi, M. Vokhshoori, and A. Khoei, “A coarse-graining approach for modeling nonlinear mechanical behavior of FCC nano-crystals,” Computational Materials Science. 2020. link Times cited: 3 USED (low confidence) E. Kirova, G. Norman, and V. Pisarev, “Dynamics of changes in stress autocorrelation functions of aluminum melt during ultrafast cooling,” Computational Materials Science. 2020. link Times cited: 8 USED (low confidence) J. Keupp, J. P. Dürholt, and R. Schmid, “Influence of flexible side-chains on the breathing phase transition of pillared layer MOFs: a force field investigation.,” Faraday discussions. 2020. link Times cited: 4 Abstract: The prototypical pillared layer MOFs, formed by a square lat… read moreAbstract: The prototypical pillared layer MOFs, formed by a square lattice of paddle-wheel units and connected by dinitrogen pillars, can undergo a breathing phase transition by a "wine-rack" type motion of the square lattice. We studied this behavior, which is not yet fully understood, using an accurate first principles parameterized force field (MOF-FF) for larger nanocrystallites on the example of Zn2(bdc)2(dabco) [bdc: benzenedicarboxylate, dabco: (1,4-diazabicyclo[2.2.2]octane)], and found clear indications for an interface between a closed and an open pore phase traveling through the system during the phase transformation [J. Keupp and R. Schmid, Adv. Theory Simul., 2019, 2, 1900117]. In conventional simulations in small supercells this mechanism is prevented by periodic boundary conditions (PBCs), enforcing a synchronous transformation of the entire crystal. Here, we extend this investigation to pillared layer MOFs with flexible side-chains, attached to the linker. Such functionalized (fu-)MOFs are experimentally known to have different properties with the side-chains acting as fixed guest molecules. First, in order to extend the parameterization for such flexible groups, a new parameterization strategy for MOF-FF had to be developed, using a multi-structure force based fit method. The resulting parameterization for a library of fu-MOFs is then validated with respect to a set of reference systems and shows very good accuracy. In the second step, a series of fu-MOFs with increasing side-chain length is studied with respect to the influence of the side-chains on the breathing behavior. For small supercells in PBCs a systematic trend of the closed pore volume with the chain length is observed. However, for a nanocrystallite model a distinct interface between a closed and an open pore phase is visible only for the short chain length, whereas for longer chains the interface broadens and a nearly concerted transformation is observed. Only by molecular dynamics simulations using accurate force fields can such complex phenomena can be studied on a molecular level. read less USED (low confidence) H. Chabba and D. Dafir, “Compression Behavior of Al-Mg Phases, Molecular Dynamics Simulation,” International Journal of Engineering Research in Africa. 2020. link Times cited: 2 Abstract: Aluminum alloys development always exit in the manufacturing… read moreAbstract: Aluminum alloys development always exit in the manufacturing process. Al/Mg alloys have been attracted significant attention because of their excellent mechanical properties. The microstructural evolution and deformation mechanisms are still challenging issues, and it is hard to observe directly by experimental methods. Accordingly, in this paper atomic simulations are performed to investigate the uniaxial compressive behavior of Al/Mg phases; with different ratio of Mg ranging from 31% to 56%. The compression is at the same strain rate (3.1010 s⁻¹), at the same temperature (300K) and pressure, using embedded atom method (EAM) potential to model the interactions and the deformation behavior between Al and Mg.From these simulations, we get the radial distribution function; the stress–strain responses to describe the elastic and plastic behaviors of β-Al3Mg2, ε-Al30Mg23, Al1Mg1 and γ-Al12Mg17 phases with 31, 41, 50 and 56% of Mg added to pure aluminum, respectively. The mechanical properties, such as Young’s modulus, elasticity limit and rupture pressure, are determined and presented. The engineering equation was used to plot the stress-strain curve for each phase.From the results obtained, the chemical composition has a significant effect on the properties of these phases. The stress-strain behavior comprised elastic, yield, strain softening and strain hardening regions that were qualitatively in agreement with previous simulations and experimental results. These stress-strain diagrams obtained show a rapid increase in stress up to a maximum followed by a gradual drop when the specimen fails by ductile fracture. Under compression, the deformation behavior of β-Al3Mg2 and γ-Al12Mg17 phases is slightly similar. From the results, it was found that ε-Al30Mg23 phase are brittle under uniaxial compressive loading and γ-Al12Mg17 phase is very ductile under the same compressive loading.The engineering stress-strain relationship suggests that β-Al3Mg2 and γ-Al12Mg17 phases have high elasticity limit, ability to resist deformation and also have the advantage of being highly malleable. From this simulation, we also find that the mechanical properties under compressive load of ε-Al30Mg23 phase are evidently less than other phases, which makes it the weakest phase. The obtained results were compared with the previous experimental studies, and generally, there is a good correlation.The Al-Mg system was built and simulated using molecular dynamics (MD) software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). read less USED (low confidence) D. Smirnova et al., “Atomistic description of self-diffusion in molybdenum: A comparative theoretical study of non-Arrhenius behavior,” Physical Review Materials. 2020. link Times cited: 16 Abstract: According to experimental observations, the temperature depe… read moreAbstract: According to experimental observations, the temperature dependence of self-diffusion coefficient in most body-centered cubic metals (bcc) exhibits non-Arrhenius behavior. The origin of this behavio ... read less USED (low confidence) A. Sobolev, O. Golovnia, and A. Popov, “Embedded atom potential for Sm–Co compounds obtained by force-matching,” Journal of Magnetism and Magnetic Materials. 2019. link Times cited: 3 USED (low confidence) D. Dubbeldam, K. S. Walton, T. Vlugt, and S. Calero, “Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials,” Advanced Theory and Simulations. 2019. link Times cited: 42 Abstract: Molecular simulations are an excellent tool to study adsorpt… read moreAbstract: Molecular simulations are an excellent tool to study adsorption and diffusion in nanoporous materials. Examples of nanoporous materials are zeolites, carbon nanotubes, clays, metal‐organic frameworks (MOFs), covalent organic frameworks (COFs) and zeolitic imidazolate frameworks (ZIFs). The molecular confinement these materials offer has been exploited in adsorption and catalysis for almost 50 years. Molecular simulations have provided understanding of the underlying shape selectivity, and adsorption and diffusion effects. Much of the reliability of the modeling predictions depends on the accuracy and transferability of the force field. However, flexibility and the chemical and structural diversity of MOFs add significant challenges for engineering force fields that are able to reproduce experimentally observed structural and dynamic properties. Recent developments in design, parameterization, and implementation of force fields for MOFs and zeolites are reviewed. read less USED (low confidence) H. Peng et al., “Chemical effect on the structural and dynamical properties in Zr-Ni-Al liquids,” Physical Review B. 2019. link Times cited: 9 Abstract: We develop an embedded-atom method (EAM) model to perform cl… read moreAbstract: We develop an embedded-atom method (EAM) model to perform classical molecular-dynamics computer simulations of a model of Zr-Ni-Al ternary melts, based on the existing binary ones. The EAM potential is validated against a broad range of experimental data for the liquid melt, including both static-structure factors and dynamical data on the mass-transport coefficients. We use our simulation model to address the structural and dynamical changes induced by a systematic replacement of Zr by Al in ${\mathrm{Zr}}_{75\ensuremath{-}x}{\mathrm{Ni}}_{25}{\mathrm{Al}}_{x}\phantom{\rule{4pt}{0ex}}(x=0--30)$ ternary alloys. We find strong chemical-ordering effects exhibited as the locally preferred structure when the Al-concentration ${c}_{\text{Al}}$ is increased. Along with the chemical effects, effective-power-law relations are found between the self-diffusion coefficients in the melts, with an exponent that monotonically decreases with increasing Al concentration. The associated Stokes-Einstein relation between diffusivity and viscosity breaks down at higher temperature upon Al addition. We also address the influence of Al admixture on the vibrational spectrum of the melt. With increasing ${c}_{\text{Al}}$, sound waves move faster, and an optical vibrational mode is found. read less USED (low confidence) X. Y. Li, D. Sun, and X. Gong, “Glass transition in disordered clusters,” Physics Letters A. 2019. link Times cited: 2 USED (low confidence) J. Li and F. Wang, “Surface Penetration without Enrichment: Simulations Show Ion Surface Propensities Consistent with Both Elevated Surface Tension and Surface Sensitive Spectroscopy.,” The journal of physical chemistry. B. 2019. link Times cited: 4 Abstract: Molecular dynamics was used to investigate ion surface prope… read moreAbstract: Molecular dynamics was used to investigate ion surface propensities in NaCl, KBr, and CsI solutions with an MP2 based force field. While NaCl is found to be strongly repelled from the liquid-vapor interface, softer ions, such as I-, penetrates closely to the interface. Despite the surface penetration, the concentration of CsI near the interface is still lower than that in the bulk, thus leading to no surface enrichment. Salt concentration is found to affect relative surface propensities of the ions. More significant surface penetration is observed at higher salt concentrations. Softer ions at higher concentrations form a complex multilayer arrangement that can not be characterized as a simple surface bilayer. The simulated ion distributions explain the spectroscopic evidence of surface perturbation by soft ions with a negative surface excess consistent with an increased surface tension of salt solutions. read less USED (low confidence) N. Mathur, T. Mane, and D. Sundaram, “Atomistically informed melting models for aluminum nanocrystals,” Chemical Physics. 2019. link Times cited: 3 USED (low confidence) D. Rosenberger and N. V. D. van der Vegt, “Relative entropy indicates an ideal concentration for structure-based coarse graining of binary mixtures.,” Physical review. E. 2019. link Times cited: 2 Abstract: Many methodological approaches have been proposed to improve… read moreAbstract: Many methodological approaches have been proposed to improve systematic or bottom-up coarse-graining techniques to enhance the representability and transferability of the derived interaction potentials. Transferability describes the ability of a coarse-grained (CG) model to be predictive, i.e., to describe a system at state points different from those chosen for parametrization. Whereas the representability characterizes the accuracy of a CG model to reproduce target properties of the underlying reference or fine-grained model at a given state point. In this article, we shift the focus away from methodological aspects and rather raise the question whether we can overcome the disadvantages of a given method in terms of representability and transferability by systematically selecting the state point at which the CG model gets parametrized. We answer this question by applying the inverse Monte Carlo (IMC) approach-a structure-based coarse-graining method-to derive effective interactions for binary mixtures of simple Lennard-Jones (LJ) particles, which are different in size. For such simple systems we indeed can identify a concentration where the derived potentials show the best performance in terms of structural representability and transferability. This specific concentration is identified by computing the relative entropy which quantifies the information loss between different IMC models and the reference LJ model at varying mixture compositions. Further, we show that an IMC model for mixtures of n-hexane and n-perfluorohexane shows the same trend in transferability as the IMC models for the LJ system. All derived models are more transferable in the direction of increasing concentration of the larger-sized compound. read less USED (low confidence) J. Dai, Q. Chen, T. Glossmann, and W. Lai, “Comparison of interatomic potential models on the molecular dynamics simulation of fast-ion conductors: A case study of a Li garnet oxide Li7La3Zr2O12,” Computational Materials Science. 2019. link Times cited: 6 USED (low confidence) T. Mahadevan, W. Sun, and J. Du, “Development of Water Reactive Potentials for Sodium Silicate Glasses.,” The journal of physical chemistry. B. 2019. link Times cited: 22 Abstract: Molecular dynamics (MD) simulations provide important insigh… read moreAbstract: Molecular dynamics (MD) simulations provide important insights into atomistic phenomena and are complement to experimental methods of studying glass-water interaction and glass corrosion. For simulations of glass-water systems using MD, there is a need to for a reactive potential that is capable not only to describe the bulk and surface glass structures but also reactions between glass and water. An important aspect of the glass water interaction is the dissociation of water and its interaction with glass components that can result in the dissolution and alteration in the structure of glass. These phenomena can be efficiently simulated using "Reactive" potentials that allow for the dissociation of water while properly describing the bulk physical properties of water. We demonstrate a method to develop parameters for simulations of sodium silicate glasses and their interactions with bulk water. The developed parameter set was used to simulate sodium silicate glasses of different compositions, and the local structure of the simulated glass is in good compliance with experimentally obtained structural information. We also demonstrate that the parameter set predicts an accurate value for the hydration number and dissociation reactions of NaOH in water. Based on these results, we posit that these simple and computationally efficient reactive potentials can be used for further studies of water-induced structural modifications in sodium silicate glasses. read less USED (low confidence) K. Dang, D. Bamney, K. Bootsita, L. Capolungo, and D. Spearot, “Mobility of dislocations in Aluminum: Faceting and asymmetry during nanoscale dislocation shear loop expansion,” Acta Materialia. 2019. link Times cited: 33 USED (low confidence) C. Yang and L. Qi, “Modified embedded-atom method potential of niobium for studies on mechanical properties,” Computational Materials Science. 2019. link Times cited: 17 USED (low confidence) Z. Liu et al., “Development of interatomic potentials for Fe-Cr-Al alloy with the particle swarm optimization method,” Journal of Alloys and Compounds. 2019. link Times cited: 20 USED (low confidence) K. Kempfer, J. Devémy, A. Dequidt, M. Couty, and P. Malfreyt, “Development of Coarse-Grained Models for Polymers by Trajectory Matching,” ACS Omega. 2019. link Times cited: 26 Abstract: Coarse-grained (CG) models allow for simulating the necessar… read moreAbstract: Coarse-grained (CG) models allow for simulating the necessary time and length scales relevant to polymers. However, developing realistic force fields at the CG level is still a challenge because there is no guarantee that the CG model reproduces all the properties of the atomistic model. A recent promising method was proposed for small molecules using statistical trajectory matching. Here, we extend this method to the case of polymeric systems. As the quality of the final model crucially depends on the model design, we study and discuss the effect of the modeling choices on the structure and dynamics of bulk polymers before a quantitative comparison is made between CG methods on different properties and polymers. read less USED (low confidence) J. Fang, X. Liu, H. Lu, X. Liu, and X. Song, “Crystal defects responsible for mechanical behaviors of a WC-Co composite at room and high temperatures - a simulation study.,” Acta crystallographica Section B, Structural science, crystal engineering and materials. 2019. link Times cited: 11 Abstract: The microstructure evolution and changes in the structures o… read moreAbstract: The microstructure evolution and changes in the structures of crystal defects of the nanocrystalline WC-Co composite in the process of uniaxial compression were studied by simulations at both room and high temperatures. The deformation processes were demonstrated as a function of stress and temperature for the stages prior to and after yielding of the composite. The Peierls stresses were evaluated for Co and WC dislocations with increasing temperature. The deformation mechanisms for each stage of the stress-strain curve were disclosed, in which the effect of temperature was clarified. It was found that with the increase of stress, from elastic deformation to plastic deformation then to yielding of the composite, the dominant mechanisms are grain boundary migration, formation and motion of dislocations in Co, concurrent motion and reaction of dislocations in Co and WC, and then rotation of WC grains in combination with motion of Co and WC dislocations. At the yielding stage, sliding of WC grain boundaries plays an increasingly important role in the contribution to plastic deformation at high temperatures. With strain the proportion of mobile dislocations decreases, and dislocations pile up at triple junctions of WC grains, WC/WC grain boundaries and WC/Co phase boundaries in priority order, leading to the nucleation and propagation of microcracks in these regions. read less USED (low confidence) A. Lopez-Cazalilla, A. Ilinov, K. Nordlund, F. Djurabekova, and F. Djurabekova, “Modeling of high-fluence irradiation of amorphous Si and crystalline Al by linearly focused Ar ions,” Journal of Physics: Condensed Matter. 2019. link Times cited: 5 Abstract: Long time ion irradiation of surfaces under tilted incidence… read moreAbstract: Long time ion irradiation of surfaces under tilted incidence causes formation of regular nanostructures known as surface ripples. The nature of mechanisms leading to ripples is still not clear, this is why computational methods can shed the light on such a complex phenomenon and help to understand which surface processes are mainly responsible for it. In this work, we analyse the surface response of two materials, a semiconductor (silicon) and a metal (aluminium) under irradiation with the 250 eV and 1000 eV Ar ions focused at 70° from the normal to the surface. We simulate consecutive ion impacts by the means of molecular dynamics to investigate the effect on ripple formation. We find that the redistribution mechanism seems to be the main creator of ripples in amorphous materials, while the erosion mechanism is the leading origin for the pattern formation in crystalline metals. read less USED (low confidence) D. Smirnova, S. Starikov, and A. Vlasova, “New interatomic potential for simulation of pure magnesium and magnesium hydrides,” Computational Materials Science. 2018. link Times cited: 17 USED (low confidence) S. Starikov and M. Korneva, “Description of phase transitions through accumulation of point defects: UN, UO2 and UC,” Journal of Nuclear Materials. 2018. link Times cited: 14 USED (low confidence) V. Borovikov, M. Mendelev, and A. King, “Effects of Ag and Zr solutes on dislocation emission from Σ11(332)[110] symmetric tilt grain boundaries in Cu: Bigger is not always better,” International Journal of Plasticity. 2018. link Times cited: 22 USED (low confidence) K. Machado, D. Zanghi, M. Salanne, V. Stabrowski, and C. Bessada, “Anionic Structure in Molten Cryolite–Alumina Systems,” The Journal of Physical Chemistry C. 2018. link Times cited: 10 Abstract: For aluminum production, the alumina (Al2O3) dissolution in … read moreAbstract: For aluminum production, the alumina (Al2O3) dissolution in the electrolyte is one of the important step in the industrial process. The electrolyte is a cryolitic bath containing mainly NaF and AlF3 at around 1000 °C. In this liquid, the main anionic species are fluoroaluminates ions such as [AlF6]3–, [AlF5]2–, [AlF4]−, and F–. During the Al2O3 dissolution, different kinds of oxyfluoroaluminates species are formed. However, due to the difficult experimental conditions and the large number of potential ions, no quantitative speciation could be made up to now. Here, we propose a speciation of alumina–cryolite melts combining in situ NMR experiments, classical molecular dynamics simulations, and electronic structure calculations. This allows us to establish the nature and quantities of each species, depending on the Al2O3 concentration, for two different initial cryolitic compositions. In particular, we show that the O atoms are always linked to at least two Al atoms, leading to the formation of polymeric ox... read less USED (low confidence) M. Widom, “Modeling the structure and thermodynamics of high-entropy alloys,” Journal of Materials Research. 2018. link Times cited: 72 Abstract: High-entropy and multiprincipal element alloys present excit… read moreAbstract: High-entropy and multiprincipal element alloys present exciting opportunities and challenges for computational modeling of their structure and phase stability. Recent interest has catalyzed rapid development of techniques and equally rapid growth of new results. This review surveys the essential concepts of thermodynamics and total energy calculation, and the bridge between them provided by statistical mechanics. Specifically, we review the electronic density functional theory of alloy total energy as applied to supercells and special quasirandom structures. We contrast these with the coherent potential approximation and semi-empirical approximations. Statistical mechanical approaches include cluster expansions, hybrid Monte Carlo/molecular dynamics simulations, and extraction of entropy from correlation functions. We also compare first-principles approaches with Calculation of Phase Diagrams (CALPHAD) and highlight the need to augment experimental databases with first-principles derived data. Numerous example applications are given highlighting recent progress utilizing the concepts and methods that are introduced. read less USED (low confidence) Y. Lei, X. Sun, R. Zhou, and B. Zhang, “Embedded atom method potentials for Ce-Ni binary alloy,” Computational Materials Science. 2018. link Times cited: 4 USED (low confidence) J. Zhou et al., “Bond−Energy−Electron Relaxation of BeN Nanoclusters and BeX Alloys,” Advanced Theory and Simulations. 2018. link Times cited: 3 Abstract: By combining bond order‐length‐strength (BOLS) notion and de… read moreAbstract: By combining bond order‐length‐strength (BOLS) notion and density functional theory (DFT) calculations, the bond−energy−electron relaxtion of BeN nanoclusters and BeX (C, S, B, Cl, Cu, Co, Te) alloys are studied. The results show that the size and shape of the Be nanoclusters will cause the binding energy (BE) shift, the local densification of electrons and quantum entrapment. Actions exemplified the atomic coordination ratio and the BE of BeX alloys can predict the quantitative information regarding the change of the bond length, local bond strain, bond energy density and atomic cohesive energy. read less USED (low confidence) M. Childers and V. Daggett, “Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles.,” The journal of physical chemistry. B. 2018. link Times cited: 59 Abstract: Far from the static, idealized conformations deposited into … read moreAbstract: Far from the static, idealized conformations deposited into structural databases, proteins are highly dynamic molecules that undergo conformational changes on temporal and spatial scales that may span several orders of magnitude. These conformational changes, often intimately connected to the functional roles that proteins play, may be obscured by traditional biophysical techniques. Over the past 40 years, molecular dynamics (MD) simulations have complemented these techniques by providing the "hidden" atomistic details that underlie protein dynamics. However, there are limitations of the degree to which molecular simulations accurately and quantitatively describe protein motions. Here we show that although four molecular dynamics simulation packages (AMBER, GROMACS, NAMD, and ilmm) reproduced a variety of experimental observables for two different proteins (engrailed homeodomain and RNase H) equally well overall at room temperature, there were subtle differences in the underlying conformational distributions and the extent of conformational sampling obtained. This leads to ambiguity about which results are correct, as experiment cannot always provide the necessary detailed information to distinguish between the underlying conformational ensembles. However, the results with different packages diverged more when considering larger amplitude motion, for example, the thermal unfolding process and conformational states sampled, with some packages failing to allow the protein to unfold at high temperature or providing results at odds with experiment. While most differences between MD simulations performed with different packages are attributed to the force fields themselves, there are many other factors that influence the outcome, including the water model, algorithms that constrain motion, how atomic interactions are handled, and the simulation ensemble employed. Here four different MD packages were tested each using best practices as established by the developers, utilizing three different protein force fields and three different water models. Differences between the simulated protein behavior using two different packages but the same force field, as well as two different packages with different force fields but the same water models and approaches to restraining motion, show how other factors can influence the behavior, and it is incorrect to place all the blame for deviations and errors on force fields or to expect improvements in force fields alone to solve such problems. read less USED (low confidence) R. Béjaud, J. Durinck, and S. Brochard, “The effect of surface step and twin boundary on deformation twinning in nanoscale metallic systems,” Computational Materials Science. 2018. link Times cited: 8 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) S. Starikov, L. Kolotova, A. Kuksin, D. Smirnova, and V. Tseplyaev, “Atomistic simulation of cubic and tetragonal phases of U-Mo alloy: Structure and thermodynamic properties,” Journal of Nuclear Materials. 2018. link Times cited: 46 USED (low confidence) G. Kacar, “Dissipative particle dynamics parameterization and simulations to predict negative volume excess and structure of PEG and water mixtures,” Chemical Physics Letters. 2017. link Times cited: 8 USED (low confidence) Y. Hu, J. Schuler, and T. Rupert, “Identifying interatomic potentials for the accurate modeling of interfacial segregation and structural transitions,” Computational Materials Science. 2017. link Times cited: 16 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) L. Kolotova and S. Starikov, “Atomistic simulation of defect formation and structure transitions in U-Mo alloys in swift heavy ion irradiation,” Journal of Nuclear Materials. 2017. link Times cited: 8 USED (low confidence) T. C. Moore, C. Iacovella, A. C. Leonhard, A. Bunge, and C. McCabe, “Molecular dynamics simulations of stratum corneum lipid mixtures: A multiscale perspective.,” Biochemical and biophysical research communications. 2017. link Times cited: 16 USED (low confidence) T. Wejrzanowski and K. Kurzydłowski, “Modeling of Size Effects in Diffusion Driven Processes at Nanoscale - Large Atomic and Mesoscale Methods,” Diffusion Foundations. 2017. link Times cited: 1 Abstract: The results of the studies presented here are devoted to und… read moreAbstract: The results of the studies presented here are devoted to understanding of microstructure effect on the processes and properties driven by diffusion. The role of various interfaces (intergranular, phase, free surface), as the high-energy defects, is underlined and investigated with special attention. The methodology relevant to analyses of the microstructural processes is first briefly presented. The capability and limitations of classical molecular dynamics, mesoscale Monte Carlo and cellular automaton techniques are described. Two examples of the diffusion driven processes analyzed at various length and time scale are shown: namely, grain growth in nanometallic materials and melting of thin embedded films. The modeling results are also accompanied with experimental studies. Thanks to application of numerical methods, models of relevant processes were proposed, which enabled to provide quantitative relationships between microstructure and the process kinetics. Such relationships can be later used for design of optimized materials for wide range of applications. read less USED (low confidence) H. Zhang, H. Zhang, F. Liu, Y. Yang, and D. Sun, “The Molecular Dynamics Study of Vacancy Formation During Solidification of Pure Metals,” Scientific Reports. 2017. link Times cited: 24 USED (low confidence) J. Zhong, D. J. Siegel, L. Hector, and J. B. Adams, “Atomistic Simulations of Adhesion, Indentation and Wear at the Nanoscale.” 2017. link Times cited: 0 USED (low confidence) Q. Feng, X. Song, H. Xie, H. Wang, X. Liu, and F. Yin, “Deformation and plastic coordination in WC-Co composite — Molecular dynamics simulation of nanoindentation,” Materials & Design. 2017. link Times cited: 53 USED (low confidence) P. M. Tailor, R. Wheatley, and N. Besley, “An empirical force field for the simulation of the vibrational spectroscopy of carbon nanomaterials,” Carbon. 2017. link Times cited: 12 USED (low confidence) D. Smirnova and S. Starikov, “An interatomic potential for simulation of Zr-Nb system,” Computational Materials Science. 2017. link Times cited: 37 USED (low confidence) P. Pokatashkin, P. Korotaev, and A. Yanilkin, “Amorphization in .ALPHA.-boron: A molecular dynamics study,” Physical Review B. 2017. link Times cited: 3 USED (low confidence) B. N. Galimzyanov and A. Mokshin, “Three-particle correlations in liquid and amorphous aluminium,” Physica A-statistical Mechanics and Its Applications. 2017. link Times cited: 2 USED (low confidence) A. Carré, S. Ispas, J. Horbach, and W. Kob, “Developing empirical potentials from ab initio simulations: The case of amorphous silica,” Computational Materials Science. 2016. link Times cited: 24 USED (low confidence) L. Kolotova, A. Kuksin, D. Smirnova, S. Starikov, and V. Tseplyaev, “Features of structure and phase transitions in pure uranium and U–Mo alloys: atomistic simulation,” Journal of Physics: Conference Series. 2016. link Times cited: 2 Abstract: We study structural properties of cubic and tetragonal phase… read moreAbstract: We study structural properties of cubic and tetragonal phases of U-Mo alloys using atomistic simulations: molecular dynamics and density functional theory. For pure uranium and U-Mo alloys at low temperatures we observe body-centered tetragonal (bct) structure, which is similar to the metastable γ°-phase found in the experiments. At higher temperatures bct structure transforms to a quasi body-centered cubic (q-bcc) phase that exhibits cubic symmetry just on the scale of several interatomic spacings or when averaged over time. Instantaneous pair distribution function (PDF) differs from PDF for the time-averaged atomic coordinates corresponding to the bcc lattice. The local positions of uranium atoms in q-bcc lattice correspond to the bct structure, which is energetically favourable due to formation of short U-U bonds. Transition from bct to q-bcc could be considered as ferro-to paraelastic transition of order-disorder type. The temperature of transition depends on Mo concentration. For pure uranium it is equal to about 700 K, which is well below than the upper boundary of the stability region of the α-U phase. Due to this reason, bct phase is observed only in uranium alloys containing metals with low solubility in α-U. read less USED (low confidence) N. Burbery, R. Das, and W. Ferguson, “Thermo-kinetic mechanisms for grain boundary structure multiplicity, thermal instability and defect interactions,” Materials Chemistry and Physics. 2016. link Times cited: 9 USED (low confidence) J. Li and F. Wang, “The Effect of Core Correlation on the MP2 Hydration Free Energies of Li(+), Na(+), and K(.).,” The journal of physical chemistry. B. 2016. link Times cited: 4 Abstract: Simple nonpolarizable molecular mechanics potentials were de… read moreAbstract: Simple nonpolarizable molecular mechanics potentials were developed for Li(+), Na(+), and K(+) with the adaptive force matching (AFM) method using the second order Møller-Plesset perturbation theory (MP2) with the frozen core approximation as reference. The effects of different choices of core orbitals and basis sets in the MP2 calculations were investigated for Na(+) and Li(+). For Na(+), correlating the 2s2p electrons in MP2 changes its hydration free energy by 18 kJ/mol, which is surprisingly large, constituting to about 5% of the intrinsic hydration free energy of the ion. Whereas correlating the 2s2p electrons with the aug-cc-pCVTZ basis set leads to the best agreement with experiments, with the aug-cc-pVTZ basis set, a better hydration free energy will be obtained if the 2s2p are kept as frozen core orbitals. Even with nonpolarizable energy expressions, the AFM derived ion potentials predict the experimental hydration free energies of the various salts within 2% of experimental values, suggesting the robustness of the fitting procedure. However, the 2% agreement can only be achieved if the core correlation is modeled appropriately in the MP2 reference calculations. read less USED (low confidence) J. Wahlers, K. D. Fulfer, D. P. Harding, D. Kuroda, R. Kumar, and R. Jorn, “Solvation Structure and Concentration in Glyme-Based Sodium Electrolytes: A Combined Spectroscopic and Computational Study,” Journal of Physical Chemistry C. 2016. link Times cited: 31 Abstract: The optimal salt concentration used in metal-ion energy stor… read moreAbstract: The optimal salt concentration used in metal-ion energy storage devices has long focused heavily on 1 M electrolytes; however, recent evidence suggests taking a deeper look at electrolyte properties as a function of salt concentration. Toward that goal, the effect of concentration on solvation properties for a prototype sodium electrolyte is considered with potential applications for sodium-ion and sodium–air technologies. An empirical force field for sodium triflate in digylme, an electrolyte already in use with sodium–air systems, was developed from ab initio molecular dynamics simulations in conjunction with the variational force-matching method. Atomistic simulations of this electrolyte along with Fourier transform infrared (FTIR) experimental studies validate the qualitative accuracy of the model and demonstrate its transferability across different concentrations. The solvation structure and the extent of ion pairing effects in the electrolyte were considered for concentrations ranging from 0.25 to 2... read less USED (low confidence) N. Korolev, L. Nordenskiöld, and A. Lyubartsev, “Multiscale coarse-grained modelling of chromatin components: DNA and the nucleosome.,” Advances in colloid and interface science. 2016. link Times cited: 20 USED (low confidence) M. Uranagase and R. Matsumoto, “Tension–compression asymmetry in uniaxial deformation of a magnesium bicrystal with [1¯100] symmetric tilt grain boundary,” Computational Materials Science. 2016. link Times cited: 7 USED (low confidence) C. Fang, X. Meng, Y. Xie, and B. Zhao, “Quasicontinuum investigation of the feedback effects on friction behavior of an abrasive particle over a single crystal aluminum substrate,” Tribology International. 2016. link Times cited: 5 USED (low confidence) S. Starikov and L. Kolotova, “Features of cubic and tetragonal structures of U–Mo alloys: Atomistic simulation,” Scripta Materialia. 2016. link Times cited: 8 USED (low confidence) M. Uranagase and R. Matsumoto, “Effects of normal stresses on the homogeneous nucleation of a basal dislocation in magnesium,” Computational Materials Science. 2016. link Times cited: 2 USED (low confidence) A. Kuksin, S. Starikov, D. Smirnova, and V. Tseplyaev, “The diffusion of point defects in uranium mononitride: Combination of DFT and atomistic simulation with novel potential,” Journal of Alloys and Compounds. 2016. link Times cited: 24 USED (low confidence) X. Qian, X. Gu, and R. Yang, “Lattice Thermal Conductivity of Organic-Inorganic Hybrid Perovskite CH3NH3PbI3,” arXiv: Materials Science. 2015. link Times cited: 92 Abstract: Great success has been achieved in improving the photovoltai… read moreAbstract: Great success has been achieved in improving the photovoltaic energy conversion efficiency of the organic-inorganic perovskite-based solar cells, but with very limited knowledge on the thermal transport in hybrid perovskites, which would affect the device lifetime and stability. Based on the potential developed from the density functional theory calculations, we studied the lattice thermal conductivity of the hybrid halide perovskite CH3NH3PbI3 using equilibrium molecular dynamics simulations. Temperature-dependent thermal conductivity is reported from 160 K to 400 K, which covers the tetragonal phase (160-330 K) and the pseudocubic phase (>330K). A very low thermal conductivity (0.50 W/mK) is found in the tetragonal phase at room temperature, whereas a much higher thermal conductivity is found in the pseudocubic phase (1.80 W/mK at 330 K). The low group velocity of acoustic phonons and the strong anharmonicity are found responsible for the relatively low thermal conductivity of the tetragonal CH3NH3PbI3. read less USED (low confidence) P. Gao and H. Guo, “Transferability of the coarse-grained potentials for trans-1,4-polybutadiene.,” Physical chemistry chemical physics : PCCP. 2015. link Times cited: 12 Abstract: In this paper, we evaluate the transferability of the coarse… read moreAbstract: In this paper, we evaluate the transferability of the coarse-grained (CG) force field (FF) of trans-1,4-polybutadiene which was built via a combined structure-based and thermodynamic quantity-based CG method at 413 K and 1 atm by systematically examining CG simulated structural and thermodynamic properties against the underlying atomistic simulation results at different temperatures. Interestingly, the derived CG force field exhibits good "state-point transferability" to some extent. For example, when applying this CG FF to the nearby state point (e.g., amorphous phase at 500 K), the resulting local conformation statistics, chain size, and local packing properties as well as density values for the CG models closely match the atomistic simulated data. When further applying this CG force field to the crystalline state at 300 K, the structural and thermodynamic properties of the crystalline phase formed for these CG and atomistic MD simulations still match within a certain level of accuracy. Furthermore, the CG torsion potential has a dual effect: for the amorphous state, the presence of an intramolecular energy barrier against rotation improves the capability of CG models to more precisely reproduce the structural properties, while in the crystalline state this CG torsion barrier suppresses the formation of the more fully stretched chain with a higher trans content. As a result, in the crystalline phase the CG model chains without torsion potentials possess a more stretched chain conformation, pack more efficiently, and have a higher crystallinity degree than its counterpart with CG torsion potentials as well as its underlying atomistic model. However, the dual effect of CG torsion potentials does not mean that we have to use different dihedral parameters to describe different state points. Both CG FFs, one with and another without torsion potentials, are able to represent the melt and the crystalline states. Overall, the phase and its structural consistency between the CG and atomistic models over other state points (e.g., crystalline phase) for which CG FFs were not explicitly parameterized very encouraging such that the combined structure-based and thermodynamic quantity-based CG method can be used to derive an optimized CG FF for multi-scale simulation of polymer systems under different thermodynamic conditions. read less USED (low confidence) V. Tseplyaev and S. Starikov, “The atomistic simulation of pressure-induced phase transition in uranium mononitride,” Journal of Physics: Conference Series. 2015. link Times cited: 12 Abstract: Phase transition in uranium mononitride (UN) at high pressur… read moreAbstract: Phase transition in uranium mononitride (UN) at high pressure has been studied using molecular dynamics. At low pressure, UN has the cubic structure like NaCl (with the space group Fm3̅m). The research based on Gibbs energy calculation shows that cubic UN turns into rhombohedral face-centered structure (with the space group R3̅m) at pressure about 32 GPa. It is shown that parameters of R3̅m-structure change at increasing of the pressure. At various pressures, the parameters of structures with isotropic stress tensor are different. read less 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 USED (low confidence) R. J. Zamora, K. L. Baker, and D. Warner, “Illuminating the chemo-mechanics of hydrogen enhanced fatigue crack growth in aluminum alloys,” Acta Materialia. 2015. link Times cited: 17 USED (low confidence) D. Yang and Q. Wang, “Systematic and simulation-free coarse graining of homopolymer melts: a relative-entropy-based study.,” Soft matter. 2015. link Times cited: 10 Abstract: We applied the systematic and simulation-free strategy propo… read moreAbstract: We applied the systematic and simulation-free strategy proposed in our previous work (D. Yang and Q. Wang, J. Chem. Phys., 2015, 142, 054905) to the relative-entropy-based (RE-based) coarse graining of homopolymer melts. RE-based coarse graining provides a quantitative measure of the coarse-graining performance and can be used to select the appropriate analytic functional forms of the pair potentials between coarse-grained (CG) segments, which are more convenient to use than the tabulated (numerical) CG potentials obtained from structure-based coarse graining. In our general coarse-graining strategy for homopolymer melts using the RE framework proposed here, the bonding and non-bonded CG potentials are coupled and need to be solved simultaneously. Taking the hard-core Gaussian thread model (K. S. Schweizer and J. G. Curro, Chem. Phys., 1990, 149, 105) as the original system, we performed RE-based coarse graining using the polymer reference interaction site model theory under the assumption that the intrachain segment pair correlation functions of CG systems are the same as those in the original system, which de-couples the bonding and non-bonded CG potentials and simplifies our calculations (that is, we only calculated the latter). We compared the performance of various analytic functional forms of non-bonded CG pair potential and closures for CG systems in RE-based coarse graining, as well as the structural and thermodynamic properties of original and CG systems at various coarse-graining levels. Our results obtained from RE-based coarse graining are also compared with those from structure-based coarse graining. read less USED (low confidence) M. Alam and S. Groh, “Dislocation modeling in bcc lithium: A comparison between continuum and atomistic predictions in the modified embedded atoms method,” Journal of Physics and Chemistry of Solids. 2015. link Times cited: 19 USED (low confidence) D. D. Hsu, W. Xia, S. G. Arturo, and S. Keten, “Thermomechanically consistent and temperature transferable coarse-graining of atactic polystyrene,” Macromolecules. 2015. link Times cited: 74 Abstract: We present a systematic, two-bead per monomer coarse-grainin… read moreAbstract: We present a systematic, two-bead per monomer coarse-graining strategy allowing for the prediction of the thermomechanical behavior of polystyrene. Analytical bonded potentials optimized to match atomistic bonded distributions for different stereochemistries emulate local structure. Alternatively, the backbone torsional potential is leveraged to match the chain stiffness in a direct approach. Nonbonded potentials using a temperature-dependent density correction term demonstrate transferability of the temperature-dependent modulus. Flory–Fox constants of the Tg-optimized CG model are commensurate with all-atomistic and experimental results. The thermomechanically consistent coarse-graining (TCCG) procedure is demonstrated using polystyrene as a benchmark system to be a robust and effective technique to extend the computational prediction of the thermomechanical behavior of polymers to the mesoscale. read less USED (low confidence) M. Petisme, M. Gren, and G. Wahnström, “Molecular dynamics simulation of WC/WC grain boundary sliding resistance in WC–Co cemented carbides at high temperature,” International Journal of Refractory Metals & Hard Materials. 2015. link Times cited: 29 USED (low confidence) D. Smirnova, A. Kuksin, and S. Starikov, “Investigation of point defects diffusion in bcc uranium and U–Mo alloys,” Journal of Nuclear Materials. 2015. link Times cited: 47 USED (low confidence) Y. Xu and J. Chen, “Atomistic potentials based energy flux integral criterion for dynamic adiabatic shear banding,” Journal of The Mechanics and Physics of Solids. 2015. link Times cited: 7 USED (low confidence) R. Hoagland and S. Valone, “Emission of dislocations from grain boundaries by grain boundary dissociation,” Philosophical Magazine. 2015. link Times cited: 17 Abstract: In this article, we examine the conditions that favour the e… read moreAbstract: In this article, we examine the conditions that favour the emission of Shockley partial dislocations (SPDs) that standoff from a grain boundary (GB) plane by a few lattice parameters as part of the atomic structure of some GBs. To do so, we consider GBs to be formed by the operation of arrays of intrinsic grain boundary dislocations (GBDs) that create the tilt and twist misorientation, and the lattice mismatch between the two crystal grains adjoining the GB. The conditions to be considered that favour SPDs are the following: (1) Frank’s rule, (2) the proper sequential arrangement of partial dislocations to bound an intrinsic stacking fault and (3) the equilibrium stand-off distance (ESD). We apply an isotropic elasticity analysis to compute the ESD, in the absence of an applied stress, for SPDs emerging from asymmetric tilt GBs in two FCC metals, Cu and Al. The ESD is shown to be dependent on the glide plane orientation relative to the GB plane and on the position of the glide planes, relative to the position of the GBDs. An applied stress increases the ESD up to a critical stress that removes the SPDs without limit from the GB. We examine the effect of the stacking fault energy on the ESD and critical stress. The critical stress is effectively linearly dependent on the stacking fault energy. Finally, we present results of atomistic simulations of asymmetric tilt Σ11[1 0 1]{4 1 4}||{2 5 2} GBs in Cu bicrystal models subject to shock loading that behave in a manner similar to the elasticity predictions. The atomistic simulations reveal additional behaviour associated with elastic incompatibility between the two grains in the bicrystal models. read less USED (low confidence) J. Hernández-Rojas and D. Wales, “The effect of dispersion damping functions on the structure of water clusters,” Chemical Physics. 2014. link Times cited: 15 USED (low confidence) I. Shin and E. Carter, “Simulations of dislocation mobility in magnesium from first principles,” International Journal of Plasticity. 2014. link Times cited: 47 USED (low confidence) Y. Xu, J. Chen, and H. Li, “Finite hyperelastic–plastic constitutive equations for atomistic simulation of dynamic ductile fracture,” International Journal of Plasticity. 2014. link Times cited: 11 USED (low confidence) T. Heinemann, K. Palczynski, J. Dzubiella, and S. Klapp, “Angle-resolved effective potentials for disk-shaped molecules.,” The Journal of chemical physics. 2014. link Times cited: 16 Abstract: We present an approach for calculating coarse-grained angle-… read moreAbstract: We present an approach for calculating coarse-grained angle-resolved effective pair potentials for uniaxial molecules. For integrating out the intramolecular degrees of freedom we apply umbrella sampling and steered dynamics techniques in atomistically-resolved molecular dynamics (MD) computer simulations. Throughout this study we focus on disk-like molecules such as coronene. To develop the methods we focus on integrating out the van der Waals and intramolecular interactions, while electrostatic charge contributions are neglected. The resulting coarse-grained pair potential reveals a strong temperature and angle dependence. In the next step we fit the numerical data with various Gay-Berne-like potentials to be used in more efficient simulations on larger scales. The quality of the resulting coarse-grained results is evaluated by comparing their pair and many-body structure as well as some thermodynamic quantities self-consistently to the outcome of atomistic MD simulations of many-particle systems. We find that angle-resolved potentials are essential not only to accurately describe crystal structures but also for fluid systems where simple isotropic potentials start to fail already for low to moderate packing fractions. Further, in describing these states it is crucial to take into account the pronounced temperature dependence arising in selected pair configurations due to bending fluctuations. read less USED (low confidence) D. Schopf, H. Euchner, and H. Trebin, “Effective potentials for simulations of the thermal conductivity of type-I semiconductor clathrate systems,” Physical Review B. 2014. link Times cited: 13 USED (low confidence) K. Farrell and J. Oden, “Calibration and validation of coarse-grained models of atomic systems: application to semiconductor manufacturing,” Computational Mechanics. 2014. link Times cited: 0 USED (low confidence) J. Roth, A. Krauß, J. Lotze, and H. Trebin, “Simulation of laser ablation in aluminum: the effectivity of double pulses,” Applied Physics A. 2014. link Times cited: 21 USED (low confidence) A. Agrawal, D. Aryal, D. Perahia, T. Ge, and G. Grest, “Coarse-Graining Atactic Polystyrene and Its Analogues,” Macromolecules. 2014. link Times cited: 8 Abstract: Capturing large length scales in polymers and soft matter wh… read moreAbstract: Capturing large length scales in polymers and soft matter while retaining atomistic properties is imperative to computational studies of dynamic systems. Here we present the results for a coarse-grained model based on atomistic simulation of atactic polystyrene (PS). Similar to previous work by Harmandaris et al. and Fritz et al., each monomer is described by two coarse-grained beads. In contrast to these early studies in which intramolecular potentials were based on Monte Carlo simulations of isotactic and syndiotactic single PS molecules to capture stereochemistry, we obtained intramolecular interactions from a single molecular dynamics simulation of an all-atom atactic PS melt. The nonbonded interactions are obtained using the iterative Boltzmann inversion (IBI) scheme. This methodology has been extended to coarse graining of poly(4-tert-butylstyrene) (PtBS) in which an additional type of coarse-grained bead is used to describe the tert-butyl group. Similar to the process for PS, the intramolecular int... read less USED (low confidence) C. Fang and X. J. Yang, “Study of nanocontact and incipient nanoscratch process using the quasicontinuum method,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2014. link Times cited: 7 USED (low confidence) S. Ju, H.-H. Huang, and J. Huang, “Predicted atomic arrangement of Mg67Zn28Ca5 and Ca50Zn30Mg20 bulk metallic glasses by atomic simulation,” Journal of Non-crystalline Solids. 2014. link Times cited: 15 USED (low confidence) J. Chen, P. Ming, and J. Yang, “A Constrained Cauchy-Born Elasticity Accelerated Multigrid Method for Nanoindentation,” Communications in Computational Physics. 2014. link Times cited: 5 Abstract: We introduce a new multigrid method to study the lattice sta… read moreAbstract: We introduce a new multigrid method to study the lattice statics model arising from nanoindentation. A constrained Cauchy-Born elasticity model is used as the coarse-grid operator. This method accelerates the relaxation process and considerably reduces the computational cost. In particular, it saves quite a bit when dislocations nucleate and move, as demonstrated by the simulation results. read less USED (low confidence) M. Bhattacharya, A. Dutta, and P. Barat, “Stick Slip Response of Dislocation Core.” 2014. link Times cited: 0 USED (low confidence) M. C. Nguyen, J.-H. Choi, X. Zhao, C. Wang, Z. Zhang, and K. Ho, “New layered structures of cuprous chalcogenides as thin film solar cell materials: Cu2Te and Cu2Se.,” Physical review letters. 2013. link Times cited: 79 Abstract: The stable crystal structures of two cuprous chalcogenides o… read moreAbstract: The stable crystal structures of two cuprous chalcogenides of Cu2X (X=Te or Se) are predicted using an adaptive genetic algorithm in combination with first-principles density functional theory calculations. Both systems are found to prefer a unique and previously unrecognized layered structure, with the total energies much lower than all structures proposed in the literature so far. The newly discovered structures are further shown to be dynamically and mechanically stable, and possess electronic properties consistent with existing experimental observations. In particular, their layered nature is expected to prevail over other structural forms at the interfaces of thin-film solar cells, and knowledge about the precise atomic structures of the interfaces is a prerequisite for achieving long-term stability and high efficiency of CdTe and Cu(In,Ga)Se2 solar cells. read less USED (low confidence) W. Li et al., “Force distribution analysis of mechanochemically reactive dimethylcyclobutene.,” Chemphyschem : a European journal of chemical physics and physical chemistry. 2013. link Times cited: 14 Abstract: Internal molecular forces can guide chemical reactions, yet … read moreAbstract: Internal molecular forces can guide chemical reactions, yet are not straightforwardly accessible within a quantum mechanical description of the reacting molecules. Here, we present a force-matching force distribution analysis (FM-FDA) to analyze internal forces in molecules. We simulated the ring opening of trans-3,4-dimethylcyclobutene (tDCB) with on-the-fly semiempirical molecular dynamics. The self-consistent density functional tight binding (SCC-DFTB) method accurately described the force-dependent ring-opening kinetics of tDCB, showing quantitative agreement with both experimental and computational data at higher levels. Mechanical force was applied in two different ways, namely, externally by a constant pulling force and internally by embedding tDCB within a strained macrocycle-containing stiff stilbene. We analyzed the distribution of tDCB internal forces in the two different cases by FM-FDA and found that external force gave rise to a symmetric force distribution in the cyclobutene ring, which also scaled linearly with the external force, indicating that the force distribution was uniquely determined by the symmetric architecture of tDCB. In contrast, internal forces due to stiff stilbene resulted in an asymmetric force distribution within tDCB, which indicated a different geometry of force application and supported the important role of linkers in the mechanochemical reactivity of tDCB. In addition, three coordinates were identified through which the distributed forces contributed most to rate acceleration. These coordinates are mostly parallel to the coordinate connecting the two CH3 termini of tDCB. Our results confirm previous observations that the linker outside of the reactive moiety, such as a stretched polymer or a macrocycle, affects its mechanochemical reactivity. We expect FM-FDA to be of wide use to understand and quantitatively predict mechanochemical reactivity, including the challenging cases of systems within strained macrocycles. read less USED (low confidence) M. Fermeglia, P. Posocco, and S. Pricl, “Nano tools for macro problems: multiscale molecular modeling of nanostructured polymer systems,” Composite Interfaces. 2013. link Times cited: 6 Abstract: A current challenge of physical, chemical, and engineering s… read moreAbstract: A current challenge of physical, chemical, and engineering sciences is to develop theoretical tools for predicting structure and properties of complex materials from the knowledge of a few input parameters. In this work, we present a general multiscale molecular simulation protocol for predicting morphologies and properties of nanostructured polymer systems and we apply it to three examples of industrial relevance. The first example is of general importance for the polymer industry and is related to the enhancement of mechanical and barrier properties, if a nanofiller is dispersed into a polymer matrix: the role of multiscale modeling for the development of the material in the stage of screening, the best design is evidenced. The second example, important for the optoelectronic industry, is related to the prediction of the dispersion of gold nanoparticles into a diblock copolymer system forming different nanostructures (lamellae, cylinders, …). In this case, it is relevant to understand how it is possible to influence the self-assembly of the nanoparticles in different regions of the diblock copolymer structure. The third example is of interest to automotive and polymer industries and involves inorganic nanoparticles grafted with organic side chains. The assembly is dispersed in a polymeric matrix and it is interesting to predict the effect of the chain length and grafting density on the nanostructure. read less USED (low confidence) J. Vorberger and D. Gericke, “Effective ion–ion potentials in warm dense matter,” High Energy Density Physics. 2013. link Times cited: 13 USED (low confidence) S. Sukhomlinov and K. Smirnov, “Structure-dependent interatomic dispersion coefficients in oxides with maximally localized Wannier functions,” Journal of Physics: Condensed Matter. 2012. link Times cited: 3 Abstract: The interatomic C6 dispersion coefficients in crystalline an… read moreAbstract: The interatomic C6 dispersion coefficients in crystalline and amorphous SiO2 and ZrO2 structures were obtained with the approach proposed by Silvestrelli (2008 Phys. Rev. Lett. 100 053002) and based on the use of maximally localized Wannier functions (MLWFs) for partitioning the electron density. Localization of Wannier functions close to the nuclei in oxide systems makes it possible to assign the MLWFs to the atoms in an unambiguous way and then to compute the C6 coefficients in an atom pairwise manner. A modification of the method is suggested in which the MLWFs are condensed to effective orbitals centred on the atoms and parameters of these effective orbitals are used for computing the interatomic dispersion coefficients. The obtained values of the dispersion coefficients were found to vary not only from one oxide to another, but also between different modifications of the same compound. The oxygen–oxygen coefficient C 6 OO ?> reveals the largest variation and its value in ZrO2 structures is twice as large as that in SiO2 ones. Atomic characteristics obtained in the frame of the effective orbital method, such as the self-atom dispersion coefficient, and the oxide ion polarizability were found to correlate with the metal–oxygen bond length and the oxygen coordination number in the systems. This behaviour is attributed to the confinement of electrons by the electrostatic potential. The values of the coefficient and of the polarizability were related to charges of the oxygen atoms. In all studied systems the oxygen atoms having larger absolute values of charge were found to be less polarizable because of a stronger confinement effect. The obtained results can be used in the development of polarizable force fields for the atomistic modelling of oxide materials. read less USED (low confidence) P. White, “Molecular dynamic modelling of fatigue crack growth in aluminium using LEFM boundary conditions,” International Journal of Fatigue. 2012. link Times cited: 27 USED (low confidence) L. Proville, D. Rodney, and M. Marinica, “Quantum effect on thermally activated glide of dislocations.,” Nature materials. 2012. link Times cited: 192 USED (low confidence) Y. Yang, D. Olmsted, M. Asta, and B. Laird, “Atomistic characterization of the chemically heterogeneous Al–Pb solid–liquid interface,” Acta Materialia. 2012. link Times cited: 50 USED (low confidence) S. Peláez, P. García-Mochales, and P. Serena, “Edge energy calculations in Al and Ni ultra-thin nanowires by molecular dynamics simulations,” Computational Materials Science. 2012. link Times cited: 3 USED (low confidence) H. Lu, Y. Ni, J. Mei, J. Li, and H. Wang, “Anisotropic plastic deformation beneath surface step during nanoindentation of FCC Al by multiscale analysis,” Computational Materials Science. 2012. link Times cited: 16 USED (low confidence) H. Lu and Y. Ni, “Effect of surface step on nanoindentation of thin films by multiscale analysis,” Thin Solid Films. 2012. link Times cited: 11 USED (low confidence) D. Cereceda et al., “Assessment of interatomic potentials for atomistic analysis of static and dynamic properties of screw dislocations in W,” Journal of Physics: Condensed Matter. 2012. link Times cited: 50 Abstract: Screw dislocations in bcc metals display non-planar cores at… read moreAbstract: Screw dislocations in bcc metals display non-planar cores at zero temperature which result in high lattice friction and thermally-activated strain rate behavior. In bcc W, electronic structure molecular statics calculations reveal a compact, non-degenerate core with an associated Peierls stress between 1.7 and 2.8 GPa. However, a full picture of the dynamic behavior of dislocations can only be gained by using more efficient atomistic simulations based on semiempirical interatomic potentials. In this paper we assess the suitability of five different potentials in terms of static properties relevant to screw dislocations in pure W. Moreover, we perform molecular dynamics simulations of stress-assisted glide using all five potentials to study the dynamic behavior of screw dislocations under shear stress. Dislocations are seen to display thermally-activated motion in most of the applied stress range, with a gradual transition to a viscous damping regime at high stresses. We find that one potential predicts a core transformation from compact to dissociated at finite temperature that affects the energetics of kink-pair production and impacts the mechanism of motion. We conclude that a modified embedded-atom potential achieves the best compromise in terms of static and dynamic screw dislocation properties, although at an expense of about ten-fold compared to central potentials. read less 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 USED (low confidence) B. Arman, A. Reddy, and G. Arya, “Viscoelastic Properties and Shock Response of Coarse-Grained Models of Multiblock versus Diblock Copolymers: Insights into Dissipative Properties of Polyurea,” Macromolecules. 2012. link Times cited: 59 Abstract: We compare and contrast the microstructure, viscoelastic pro… read moreAbstract: We compare and contrast the microstructure, viscoelastic properties, and shock response of coarse-grained models of multiblock copolymer and diblock copolymers using molecular dynamics simulations. This study is motivated by the excellent dissipative and shock-mitigating properties of polyurea, speculated to arise from its multiblock chain architecture. Our microstructural analyses reveal that the multiblock copolymer microphase-separates into small, interconnected, rod-shaped, hard domains surrounded by a soft matrix, whereas the diblock copolymer forms larger, unconnected, hard domains. Our viscoelastic analyses indicate that compared with the diblock copolymer, the multiblock copolymer is not only more elastic but also more dissipative, as signified by its larger storage and loss modulus at low to intermediate frequencies. Our shock simulations and slip analyses reveal that shock waves propagate slower in the multiblock copolymer in comparison with the diblock copolymer, most likely due to the more def... read less USED (low 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 USED (low confidence) D. E. Smirnova, S. Starikov, S. Starikov, V. Stegailov, and V. Stegailov, “Interatomic potential for uranium in a wide range of pressures and temperatures,” Journal of Physics: Condensed Matter. 2012. link Times cited: 3 Abstract: Using the force-matching method we develop an interatomic po… read moreAbstract: Using the force-matching method we develop an interatomic potential that allows us to study the structure and properties of α-U, γ-U and liquid uranium. The potential is fitted to the forces, energies and stresses obtained from ab initio calculations. The model gives a good comparison with the experimental and ab initio data for the lattice constants of α-U and γ-U, the elastic constants, the room-temperature isotherm, the normal density isochore, the bond-angle distribution functions and the vacancy formation energies. The calculated melting line of uranium at pressures up to 80 GPa and the temperature of the α–γ transition at 3 GPa agree well with the experimental phase diagram of uranium. read less USED (low confidence) M. Gill-Comeau and L. J. Lewis, “Ultrashort-pulse laser ablation of nanocrystalline aluminum,” Physical Review B. 2011. link Times cited: 29 Abstract: Molecular-dynamics simulations of the ablation of nanocrysta… read moreAbstract: Molecular-dynamics simulations of the ablation of nanocrystalline Al films by ultrashort laser pulses in the low-fluence (no-ionization) regime (0-2.5 times the ablation threshold, F{sub th}) are reported. The simulations employ an embedded-atom method potential for the dynamics of the ions and a realistic two-temperature model for the electron gas (and its interactions with the ion gas), which confers different electronic properties to the monocrystalline solid, nanocrystalline solid, and liquid regions of the targets. The ablation dynamics in three nanocrystalline structures is studied: two dense targets with different crystallite sizes (d=3.1 and 6.2 nm on average) and a d=6.2 nm porous sample. The results are compared to the ablation of monocrystalline Al. Significant differences are observed, the nanocrystalline targets showing, in particular, a lower ablation threshold and a larger melting depth, and yielding pressure waves of higher amplitude than the monocrystalline targets. Furthermore, it is shown that nanocrystalline targets experience no residual stress associated with thermal expansion and lateral constraints, and that little crystal growth occurs in the solid during and after ablation. Laser-induced spallation of the back surface of the films is also investigated; we find, in particular, that the high-strain fracture resistance of nanocrystalline samples is significantly reduced inmore » comparison to the crystalline material.« less read less USED (low confidence) A. Nair, D. Warner, and R. Hennig, “Coupled quantum–continuum analysis of crack tip processes in aluminum,” Journal of The Mechanics and Physics of Solids. 2011. link Times cited: 20 USED (low confidence) Y. D. Li, Q. Cao, C. Wang, and C. S. Liu, “Molecular dynamics study of structural evolution of aluminum during rapid quenching under different pressures,” Physica B-condensed Matter. 2011. link Times cited: 11 USED (low confidence) M. Liao, Y.-C. Wang, S. Ju, T.-W. Lien, and L.-F. Huang, “Deformation behaviors of an armchair boron-nitride nanotube under axial tensile strains,” Journal of Applied Physics. 2011. link Times cited: 49 Abstract: Deformation behaviors of an (8,8) boron-nitride nanotube (BN… read moreAbstract: Deformation behaviors of an (8,8) boron-nitride nanotube (BNNT) under axial tensile strains were investigated via molecular dynamics (MD) simulations. The Tersoff potential was employed in the simulations with potential parameters determined by fitting the MD simulations results to those obtained from density functional theory calculations for BNNTs with the aid of the force-matching method. Variations in the axial stress, bond lengths, bond angles, radial buckling, and slip vectors with tensile strain were all examined. The axial, the radial, and tangential components of the slip vector were employed to monitor the local elongation, the local necking, and the local twisting deformations, respectively, near the tensile failure of the BNNT. From this study, it was noted that the BNNT started to fail at the failure strain of 26.7%. The components of the slip vector grew abruptly and rapidly after the failure strain, especially for the axial component. This implies that the local elongation dominates the ten... read less USED (low confidence) M. Malik, T. Shi, Z. Tang, and P. Peng, “Al-Film/Si-Substrate System Nanoscratching Response Based upon Molecular Dynamics Simulation in NEMS,” Defect and Diffusion Forum. 2011. link Times cited: 0 Abstract: A growing scientific effort is being devoted to the study of… read moreAbstract: A growing scientific effort is being devoted to the study of nanoscale interface aspects such as thin-film adhesion, abrasive wear and nanofriction at surfaces by using the nanoscratching technique but there remain immense challenges. In this paper, a three-dimensional (3D) model is suggested for the molecular dynamics (MD) simulation and experimental verification of nanoscratching initiated from nano-indentation, carried out using atomic force microscope (AFM) indenters on Al-film/Si-substrate systems. Hybrid potentials such as Morse and Tersoff, and embedded atom methods (EAM) are taken into account together for the first time in this MD simulation (for three scratching conditions: e.g. orientation, depth and speed, and the relationship between forces and related parameters) in order to determine the mechanisms of nanoscratching phenomena. Salient features such as nanoscratching velocity, direction and depth - as well as indenter shape- and size-dependent functions such as scratch hardness, wear and coefficient of friction - are also examined. A remarkable conclusion is that the coefficient of friction clearly depends upon the tool rake-angle and therefore increases sharply for a large negative angle. read less USED (low confidence) M. Muzyk, Z. Pakieła, and K. Kurzydłowski, “Ab initio calculations of the generalized stacking fault energy in aluminium alloys,” Scripta Materialia. 2011. link Times cited: 95 USED (low confidence) J. Wax, M. R. Johnson, L. Bove, and M. Mihalkovič, “Multiscale study of the influence of chemical order on the properties of liquid Li-Bi alloys,” Physical Review B. 2011. link Times cited: 7 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 USED (low confidence) E. Holm, D. Olmsted, and S. Foiles, “Comparing grain boundary energies in face-centered cubic metals: Al, Au, Cu and Ni,” Scripta Materialia. 2010. link Times cited: 124 USED (low confidence) N. Jakse and A. Pasturel, “Dynamical properties of deeply undercooled and amorphous systems: Combined classical and ab initio molecular dynamics simulations approaches,” Computational Materials Science. 2010. link Times cited: 0 USED (low confidence) J. Song, W. Curtin, T. Bhandakkar, and H. Gao, “Dislocation shielding and crack tip decohesion at the atomic scale,” Acta Materialia. 2010. link Times cited: 20 USED (low confidence) D. Irving, “Understanding Metal/Metal Electrical Contact Conductance from the Atomic to Continuum Scales.” 2010. link Times cited: 2 USED (low confidence) S. Brochard, P. Hirel, L. Pizzagalli, and J. Godet, “Elastic limit for surface step dislocation nucleation in face-centered cubic metals: Temperature and step height dependence,” Acta Materialia. 2010. link Times cited: 56 USED (low confidence) G. Kimminau, P. Erhart, E. Bringa, B. Remington, and J. Wark, “Phonon instabilities in uniaxially compressed fcc metals as seen in molecular dynamics simulations,” Physical Review B. 2010. link Times cited: 19 Abstract: We show that the generation of stacking faults in perfect fa… read moreAbstract: We show that the generation of stacking faults in perfect face-centered-cubic (fcc) crystals, uniaxially compressed along [001], is due to transverse-acoustic phonon instabilities. The position in reciprocal space where the instability first manifests itself is not a point of high symmetry in the Brillouin zone. This model provides a useful explanation for the magnitude of the elastic limit, in addition to the affects of box size, temperature, and compression on the time scale for the generation of stacking faults. We observe this phenomenon in both simulations that use the Lennard-Jones potential and embedded atom potentials. Not only does this work provide fundamental insight into the microscopic response of the material but it also describes certain behavior seen in previous molecular dynamics simulations of single-crystal fcc metals shock compressed along the principal axis. read less USED (low confidence) L. Li, J. Shao, S. Duan, and J. Q. Liang, “Atomistic simulation of the fcc–hcp transition in single-crystal Al under uniaxial loading,” New Journal of Physics. 2010. link Times cited: 8 Abstract: The dynamic behavior of the single-crystal Al under [001] un… read moreAbstract: The dynamic behavior of the single-crystal Al under [001] uniaxial strain is simulated by classic molecular dynamics. The fcc–hcp structural transition is successfully observed when the loading pressure reaches about 90 GPa, and the reverse transition is also found with hysteresis. The mechanism and morphology evolution of both the forward and backward transitions are analyzed in detail. It is found in the process of the structural transition that the (010)fcc or (100)fcc planes transit into (0001)hcp planes, and the twins of the hcp phase along the (112)-plane appear, whose boundaries finally become along the (110)-plane. Besides, we find the twinning (along the (110)fcc planes) in the hcp phase prior to the back transition (hcp–fcc). Our simulations show the coexistence of fcc and hcp phases over a wide range of pressures, and finally, the phase transition is evaluated by using the radial distribution functions. read less USED (low confidence) J. Wan and W. Carter, “Self-ordering mechanism of nanocluster-chain on the functional vicinal surfaces,” Applied Physics Letters. 2009. link Times cited: 2 Abstract: An energy model of nanoclusters-chain self-organized on the … read moreAbstract: An energy model of nanoclusters-chain self-organized on the functional vicinal surfaces is established to investigate the self-ordering processes, which provides a promising and challenging nanomaterial-design method by means of the energy minimum principle and entropy change principle. The cluster-chain structure can be predicted through controlling the linear coverage of nanoclusters (PM) and the step width (L). The different interactions including the steps and terraces will perform a positive influence on the self-ordering due to their long-range forces. read less USED (low confidence) I. Shin, A. Ramasubramaniam, C. Huang, L. Hung, and E. Carter, “Orbital-free density functional theory simulations of dislocations in aluminum,” Philosophical Magazine. 2009. link Times cited: 29 Abstract: The core structure of screw and edge dislocations in fcc Al … read moreAbstract: The core structure of screw and edge dislocations in fcc Al was investigated using orbital-free density functional theory (OF-DFT). Detailed calibrations of kinetic energy density functionals (KEDFs) and local pseudopotentials were performed to reproduce accurately the energies of several phases of bulk Al, as well as the elastic moduli and stacking fault energies of fcc Al. Thereafter, dislocations were modeled with both periodic and non-periodic cells containing a few thousand atoms, and the widths of the dissociated cores were extracted. The results are in good agreement with previous estimates from experiment and theory, further validating OF-DFT with non-local KEDFs as a seamless and accurate tool for simulating large features in main group, nearly-free-electron-like metals at the mesoscale. read less USED (low confidence) R. Janisch and C. Elsässer, “Interstitial impurities at grain boundaries in metals: insight from atomistic calculations,” International Journal of Materials Research. 2009. link Times cited: 12 Abstract: The investigation of segregation and embrittlement at grain … read moreAbstract: The investigation of segregation and embrittlement at grain boundaries in metals is a research area with a long tradition. In recent times, the feasibility of computational studies on the atomic scale gave a new impetus to the community. In this feature article we summarize our contributions to the understanding of segregation of interstitial impurities and embrittlement at grain boundaries in the bcc transition metals against the background of research activities in the field. We mainly discuss the benefits and limitations of ab-initio electronic structure calculations. read less USED (low confidence) S.-G. Kim et al., “Semi-Empirical Potential Methods for Atomistic Simulations of Metals and Their Construction Procedures,” Journal of Engineering Materials and Technology-transactions of The Asme. 2009. link Times cited: 20 Abstract: General theory of semi-empirical potential methods including… read moreAbstract: General theory of semi-empirical potential methods including embedded-atom method and modified-embedded-atom method (MEAM) is reviewed. The procedures to construct these potentials are also reviewed. A multi-objective optimization (MOO) procedure has been developed to construct MEAM potentials with minimal manual fitting. This procedure has been applied successfully to develop a new MEAM potential for magnesium. The MOO procedure is designed to optimally reproduce multiple target values that consist of important material properties obtained from experiments and first-principle calculations based on density-functional theory. The optimized target quantities include elastic constants, cohesive energies, surface energies, vacancy-formation energies, and the forces on atoms in a variety of structures. The accuracy of the present potential is assessed by computing several material properties of Mg including their thermal properties. We found that the new MEAM potential shows a significant improvement over previously published potentials, especially for the atomic forces and melting temperature calculations. read less USED (low confidence) S. Sonntag, J. Roth, F. Gaehler, and H. Trebin, “Femtosecond laser ablation of aluminium,” Applied Surface Science. 2009. link Times cited: 43 USED (low confidence) J. Zhong and H. Shuai, “Quasicontinuum study of nanoindentation into nanocrystalline aluminum thin film.” 2009. link Times cited: 0 Abstract: Quasicontinuum simulations are performed to examine the mech… read moreAbstract: Quasicontinuum simulations are performed to examine the mechanical response of nanocrystalline aluminum thin film under nanoindentation. The simulations are conducted by driving the flat indenter into the (111) face of one grain in the aluminum film, two load drops have been found during the indentation process, evidence indicates that these load drops are related to the stacking fault emitted from the grain boundary. The effect of indenter width on nanoindentation response is also studied through three simulations with different indenter sizes. A rule is discovered that larger load is needed to initiate the first load drop for the wider indenter; however, this rule is not followed by the second load drop. read less USED (low confidence) D. Warner and W. Curtin, “Origins and implications of temperature-dependent activation energy barriers for dislocation nucleation in face-centered cubic metals,” Acta Materialia. 2009. link Times cited: 92 USED (low confidence) D. Olmsted, S. Foiles, and E. Holm, “Survey of computed grain boundary properties in face-centered cubic metals: I. Grain boundary energy,” Acta Materialia. 2009. link Times cited: 632 USED (low confidence) L. Hung and E. Carter, “Accurate simulations of metals at the mesoscale: Explicit treatment of 1 million atoms with quantum mechanics,” Chemical Physics Letters. 2009. link Times cited: 97 USED (low confidence) E. Vamvakopoulos and D. Tanguy, “Equilibrium vacancy concentrations in Al-Σ=33(554)[110] by grand canonical Monte Carlo simulations,” Physical Review B. 2009. link Times cited: 7 USED (low confidence) D. Rodney and L. Proville, “Stress-dependent Peierls potential: Influence on kink-pair activation,” Physical Review B. 2009. link Times cited: 67 Abstract: Atomistic calculations based on the nudged elastic band meth… read moreAbstract: Atomistic calculations based on the nudged elastic band method for a Lomer dislocation in aluminum evidence a dependence of the Peierls potential on the applied shear stress in such a way that the Peierls stress predicted from the zero-stress potential is half its true value for the case considered here. Stress-dependent Peierls potentials that are extracted are then introduced as substrate potentials in a string model with a line tension (LT) adjusted to match the dislocation kink width obtained from atomistic simulations. The LT model is found to predict accurately dislocation saddle configurations and corresponding kink-pair activation enthalpies for a wide range of stresses. In particular, it is shown that the stress dependence of the Peierls potential is required to model with accuracy the nonlinearity of the enthalpy-stress curve. read less USED (low confidence) S. Hendy, D. Schebarchov, and A. Awasthi, “Molecular dynamics simulations of nanoparticles,” International Journal of Nanotechnology. 2009. link Times cited: 18 Abstract: Nanoparticles are becoming increasingly important in many ar… read moreAbstract: Nanoparticles are becoming increasingly important in many areas of nanotechnology. Here we use classical molecular dynamics simulations to investigate the competition between surface and volumetric effects in metal nanoparticles. In particular, we review work on the melting of isolated nanoparticles, solid-solid transitions in nanoparticles and the deposition of nanoparticles on substrates. In all these examples the delicate balance between surface and volumetric effects can lead to a complex dependence of behaviour on size, from non-monoticity to more exotic phenomena that have no counterpart in bulk materials. In melting, we find that the nature of the wetting of the solid by the melt is important in determining both the melting temperature and the nature of the melting transition. Furthermore, we find that the preference of the melt to wet certain facets can induce solid-solid transitions in partially melted particles. Finally, we observe a re-entrant adhesion transition in nanoparticle deposition as the collision switches from elastic to plastic and the particle begins to spread on the surface. These examples provide an interesting insight into nanoparticle physics. read less USED (low confidence) Y. D. Li, Q.-H. Hao, Q. Cao, and C. S. Liu, “Two-order-parameter description of liquid Al under five different pressures,” Physical Review B. 2008. link Times cited: 5 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 USED (low confidence) W. Jiang, J. Su, and X.-Q. Feng, “Effect of surface roughness on nanoindentation test of thin films,” Engineering Fracture Mechanics. 2008. link Times cited: 172 USED (low confidence) A. Franchini, V. Bortolani, G. Santoro, and M. Brigazzi, “Thermal effects in static friction: thermolubricity.,” Physical review. E, Statistical, nonlinear, and soft matter physics. 2008. link Times cited: 5 Abstract: We present a molecular dynamics analysis of the static frict… read moreAbstract: We present a molecular dynamics analysis of the static friction between two thick slabs. The upper block is formed by N2 molecules and the lower block by Pb atoms. We study the effects of the temperature as well as the effects produced by the structure of the surface of the lower block on the static friction. To put in evidence the temperature effects we will compare the results obtained with the lower block formed by still atoms with those obtained when the atoms are allowed to vibrate (e.g., with phonons). To investigate the importance of the geometry of the surface of the lower block we apply the external force in different directions, with respect to a chosen crystallographic direction of the substrate. We show that the interaction between the lattice dynamics of the two blocks is responsible for the strong dependence of the static friction on the temperature. The lattice dynamics interaction between the two blocks strongly reduces the static friction, with respect to the case of the rigid substrate. This is due to the large momentum transfer between atoms and the N2 molecules which disorders the molecules of the interface layer. A further disorder is introduced by the temperature. We perform calculations at T = 20K which is a temperature below the melting, which for our slab is at 50K . We found that because of the disorder the static friction becomes independent of the direction of the external applied force. The very low value of the static friction seems to indicate that we are in a regime of thermolubricity similar to that observed in dynamical friction. read less USED (low confidence) Y. Cheng, A. Cao, H. Sheng, and E. Ma, “Local order influences initiation of plastic flow in metallic glass: Effects of alloy composition and sample cooling history,” Acta Materialia. 2008. link Times cited: 365 USED (low confidence) H. Wang, D. Xu, R.-fu Yang, and P. Veyssiére, “The transformation of edge dislocation dipoles in aluminium,” Acta Materialia. 2008. link Times cited: 39 USED (low confidence) H.-tao Wang, Z. Qin, Y. Ni, and W. Zhang, “Quasicontinuum simulation of indentation on FCC metals,” Transactions of Nonferrous Metals Society of China. 2008. link Times cited: 9 USED (low confidence) M. Karttunen, T. Murtola, and I. Vattulainen, “Systematic Approach to Coarse-Graining of Molecular Descriptions and Interactions with Applications to Lipid Membranes.” 2008. link Times cited: 1 USED (low confidence) J. Jin, S. Shevlin, and Z. Guo, “Multiscale simulation of onset plasticity during nanoindentation of Al (001) surface,” Acta Materialia. 2008. link Times cited: 59 USED (low confidence) Y. Cheng and E. Ma, “Indicators of internal structural states for metallic glasses: Local order, free volume, and configurational potential energy,” Applied Physics Letters. 2008. link Times cited: 110 Abstract: The structural states of metallic glasses (MGs) have been de… read moreAbstract: The structural states of metallic glasses (MGs) have been described previously using concepts such as free volume and configurational potential energy. Here we discuss the inadequacy of these indicators by examining a Cu–Zr–Al MG model experiencing different cooling and relaxation history. The results identify the local (icosahedral) ordering as a fundamental process underlying structural relaxation, and the degree of order as a more sensitive and revealing structural indicator. read less USED (low confidence) Y. Cheng, H. Sheng, and E. Ma, “Relationship between structure, dynamics, and mechanical properties in metallic glass-forming alloys,” Physical Review B. 2008. link Times cited: 362 USED (low confidence) A. Upadhyay, N. Inogamov, B. Rethfeld, and H. Urbassek, “Ablation by ultrashort laser pulses: Atomistic and thermodynamic analysis of the processes at the ablation threshold,” Physical Review B. 2008. link Times cited: 88 Abstract: Ultrafast laser irradiation of solids may ablate material of… read moreAbstract: Ultrafast laser irradiation of solids may ablate material off the surface. We study this process for thin films using molecular-dynamics simulation and thermodynamic analysis. Both metals and Lennard-Jones (LJ) materials are studied. We find that despite the large difference in thermodynamical properties between these two classes of materials--e.g., for aluminum versus LJ the ratio T{sub c}/T{sub tr} of critical to triple-point temperature differs by more than a factor of 4--the values of the ablation threshold energy E{sub abl} normalized to the cohesion energy, {epsilon}{sub abl}=E{sub abl}/E{sub coh}, are surprisingly universal: all are near 0.3 with {+-}30% scattering. The difference in the ratio T{sub c}/T{sub tr} means that for metals the melting threshold {epsilon}{sub m} is low, {epsilon}{sub m} {epsilon}{sub abl}. This thermodynamical consideration gives a simple explanation for the difference between metals and LJ. It explains why despite the universality in {epsilon}{sub abl}, metals thermomechanically ablate always from the liquid state. This is opposite to LJ materials, which (near threshold) ablate from the solid state. Furthermore, we find that immediately below the ablation threshold, the formation of large voids (cavitation) in the irradiated material leads to a strong temporary expansion on amore » very slow time scale. This feature is easily distinguished from the acoustic oscillations governing the material response at smaller intensities, on the one hand, and the ablation occurring at larger intensities, on the other hand. This finding allows us to explain the puzzle of huge surface excursions found in experiments at near-threshold laser irradiation.« less read less USED (low confidence) M. Wilson, B. K. Sharma, and C. Massobrio, “Ionicity in disordered GeSe2: a comparison of first-principles and atomistic potential models.,” The Journal of chemical physics. 2008. link Times cited: 9 Abstract: The structural properties of liquid GeSe(2), generated using… read moreAbstract: The structural properties of liquid GeSe(2), generated using two distinct computational methodologies, are compared. The results of molecular dynamics simulations, utilizing both first-principles density functional and a potential model which account for aspects of many-body interactions, are considered. The potential model favors ionic character in the bonding, resulting in a structure with very little chemical disorder and no homopolar bonds, in contrast to experimental observation. The use of a relatively simple potential model is shown to be useful in order to understand differences between the observed experimental structure and those obtained from the first-principles approach, the latter being affected by insufficient account of ionic character in the bonding. Both computational schemes are able to predict the appearance of the first sharp diffraction peak in the total neutron structure factor and in some of the partial structure factors as well as the concomitant presence of corner- and edge-sharing tetrahedral connections. For the potential model, this holds true provided the system temperatures are set to values high enough to allow for diffusion properties typical of a liquid. Structural properties obtained for the two sets of configurations are in closer agreement when the potential model is applied at very high temperatures. read less USED (low confidence) D. Stewart and K. Cheong, “Molecular dynamics simulations of dislocations and nanocrystals,” Current Applied Physics. 2008. link Times cited: 13 USED (low confidence) R. E. Miller and D. Rodney, “On the nonlocal nature of dislocation nucleation during nanoindentation,” Journal of The Mechanics and Physics of Solids. 2008. link Times cited: 65 USED (low confidence) D. Rodney, “Atomic modeling of irradiation-induced hardening,” Comptes Rendus Physique. 2008. link Times cited: 18 USED (low confidence) K. Nordlund and S. Dudarev, “Interatomic potentials for simulating radiation damage effects in metals,” Comptes Rendus Physique. 2008. link Times cited: 29 USED (low confidence) A. Perron, O. Politano, and V. Vignal, “Grain size, stress and surface roughness,” Surface and Interface Analysis. 2008. link Times cited: 17 Abstract: In this article, we report molecular dynamics (MD) simulatio… read moreAbstract: In this article, we report molecular dynamics (MD) simulations on the formation of roughness at the surface of strained polycrystalline aluminum samples at 300 K. The computed roughness increases as a function of applied strain but does not follow a linear law for all applied strains. A linear relationship with a small slope is obtained in the elastic domain. Then, the roughness increases rapidly with the applied strain in the plastic domain studied. Moreover, the surface roughness increases as a function of grain size (between 5 and 20 nm) in the plastic domain (<6%). Copyright © 2008 John Wiley & Sons, Ltd. read less USED (low confidence) A. Perron, O. Politano, and V. Vignal, “Quenched molecular dynamics studies on the extraction energy of aluminum atoms,” Surface and Interface Analysis. 2008. link Times cited: 1 Abstract: The extraction energy of an aluminum atom is calculated at 0… read moreAbstract: The extraction energy of an aluminum atom is calculated at 0 K as a function of coordination number and defect depth for three surface orientations [(100), (110) and (111)]. For each orientation, atoms are selected and extracted one by one. A linear relationship is obtained between the extraction energy of surface atoms and their coordination numbers (with slight variations due to the geometrical configuration of the atoms). However, the study of the influence of the defect depth on the extraction energy highlights the role played by intrinsic stress on the extraction energy. Copyright © 2008 John Wiley & Sons, Ltd. read less USED (low confidence) N. Negulyaev, V. Stepanyuk, W. Hergert, P. Bruno, and J. Kirschner, “Atomic-scale self-organization of Fe nanostripes on stepped Cu(111) surfaces: Molecular dynamics and kinetic Monte Carlo simulations,” Physical Review B. 2008. link Times cited: 24 Abstract: Growth of Fe nanostripes on a vicinal Cu(111) surface is inv… read moreAbstract: Growth of Fe nanostripes on a vicinal Cu(111) surface is investigated on the atomic scale by performing molecular dynamics and kinetic Monte Carlo simulations. We involve in our study the kinetic mechanisms of atomic incorporation recently reported by Mo et al. [Phys. Rev. Lett. 94, 155503 (2005)]. The atomistic processes responsible for the interlayer mass transport and the formation of Fe stripes of 1 ML height are identified. We demonstrate that strain relaxations at steps have a strong impact on the self-assembly of one-dimensional Fe atomic structures on vicinal Cu(111). read less USED (low confidence) Y. S. Mitrokhin, J. Kovneristy, and V. Shudegov, “Molecular dynamic simulation of the melting process in Ni3Al alloy.” 2008. link Times cited: 0 Abstract: The melting process for an intermetallic compound Ni3Al is m… read moreAbstract: The melting process for an intermetallic compound Ni3Al is modeled with the use of two molecular dynamics (MD) methods, i.e., classical MD and ab initio MD. In the first case, we have a good statistics; however the results of modeling significantly depend on the choice of an interatomic interaction potential model. In the second case, any fitting parameters are not necessary, but a great computational power is required. The ab initio MD results are in better agreement with experiment. However, using this method, it is impossible to receive good statistics because of a small number of atoms. The two methods are mutually complimentary and allow to obtain valid results in the modeling of new materials as well. read less USED (low confidence) C. Woodward, D. Trinkle, L. G. Hector, and D. Olmsted, “Prediction of dislocation cores in aluminum from density functional theory.,” Physical review letters. 2008. link Times cited: 151 Abstract: The strain field of isolated screw and edge dislocation core… read moreAbstract: The strain field of isolated screw and edge dislocation cores in aluminum are calculated using density-functional theory and a flexible boundary condition method. Nye tensor density contours and differential displacement fields are used to accurately bound Shockley partial separation distances. Our results of 5-7.5 A (screw) and 7.0-9.5 A (edge) eliminate uncertainties resulting from the wide range of previous results based on Peierls-Nabarro and atomistic methods. Favorable agreement of the predicted cores with limited experimental measurements demonstrates the need for quantum mechanical treatment of dislocation cores. read less USED (low confidence) M. Mendelev, S. Han, W. Son, G. Ackland, and D. Srolovitz, “Simulation of the interaction between Fe impurities and point defects in V,” Physical Review B. 2007. link Times cited: 56 Abstract: We report improved results of atomistic modeling of V-Fe all… read moreAbstract: We report improved results of atomistic modeling of V-Fe alloys. We introduced an electronic structure embedding approach to improve the description of the point defects in first-principles calculations, by including the semicore electrons in some V atoms those near the interstitial where the semicore levels are broadened but not those further from the point defect. This enables us to combine good accuracy for the defect within large supercells and to expand the data set of first-principles point defect calculations in vanadium with and without small amounts of iron. Based on these data, previous first-principles work, and new calculations on the alloy liquid, we fitted an interatomic potential for the V-Fe system which describes the important configurations likely to arise when such alloys are exposed to radiation. This potential is in a form suitable for molecular dynamics MD simulations of large systems. Using the potential, we have calculated the migration barriers of vacancies in the presence of iron, showing that these are broadly similar. On the other hand, MD simulations show that V self-diffusion at high temperatures and Fe diffusion are greatly enhanced by the presence of interstitials. read less USED (low confidence) B. Shiari, R. E. Miller, and D. Klug, “Multiscale simulation of material removal processes at the nanoscale,” Journal of The Mechanics and Physics of Solids. 2007. link Times cited: 70 USED (low confidence) D. Warner, W. Curtin, and S. Qu, “Rate dependence of crack-tip processes predicts twinning trends in f.c.c. metals.,” Nature materials. 2007. link Times cited: 202 USED (low confidence) E. B. E. Mendoub, R. Albaki, I. Charpentier, J. Bretonnet, J. Wax, and N. Jakse, “Molecular dynamics and integral equation study of the structure and thermodynamics of polyvalent liquid metals,” Journal of Non-crystalline Solids. 2007. link Times cited: 6 USED (low confidence) J. R. Morris, M. Mendelev, and D. Srolovitz, “A comparison of crystal-melt interfacial free energies using different Al potentials,” Journal of Non-crystalline Solids. 2007. link Times cited: 23 USED (low confidence) S. Peláez and P. Serena, “Equation of state of ultra-narrow metallic nanowires,” Surface Science. 2007. link Times cited: 3 USED (low confidence) P. Puri and V. Yang, “Molecular Dynamics Simulations of Effects of Pressure and Void Size on Melting of Aluminum.” 2007. link Times cited: 2 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 USED (low confidence) A. Upadhyay and H. Urbassek, “Response of ultrathin metal films to ultrafast laser irradiation: A comparative molecular-dynamics study.” 2007. link Times cited: 10 Abstract: Using molecular-dynamics computer simulation, we study the m… read moreAbstract: Using molecular-dynamics computer simulation, we study the materials processes in ultrathin metal films induced by ultrafast laser irradiation. We investigate four different metals (Al, Cu, Ti, W), which vary widely in their cohesive energy, melting temperature, bulk modulus, and crystal structure. Despite these variations, we find that the same materials processes are induced in these films: With increasing laser fluence, the film melts, voids are formed, the film tears (spallation), and finally fragments to form a multitude of clusters. When the energy transfer starting the process is scaled to the cohesive energy of the material, the thresholds of these processes adopt similar – but not identical – values. read less USED (low confidence) J.-W. Moon, G. Richter, W. Sigle, and M. Rühle, “Bridging grain boundary volume to segregation at symmetric grain boundaries,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2007. link Times cited: 0 USED (low confidence) Y. Qi and R. Mishra, “Ab Initio Study of the Effect of Solute Atoms on Stacking Fault Energy in Aluminum,” Bulletin of the American Physical Society. 2007. link Times cited: 78 Abstract: Received 11 December 2006; revised manuscript received 16 Fe… read moreAbstract: Received 11 December 2006; revised manuscript received 16 February 2007; published 6 June 2007The stacking fault energy SFE in binary and ternary alloys of Al with common alloying elements wasstudied using density functional theory. Among these alloying elements, Fe further increases the SFE and Gereduces the SFE of Al. The alloying elements increase the SFE by increasing the directional inhomogeneity inthe electronic charge distribution of Al. The maximum value of charge difference on the fault plane, Max ,is used to characterize how many electrons have been redistributed due to the stacking fault formation, and theSFE increases with Max .DOI: 10.1103/PhysRevB.75.224105 PACS number s : 61.72.Nn, 62.20.Fe, 71.15.Nc read less USED (low confidence) Y. Qi and P. Krajewski, “Molecular dynamics simulations of grain boundary sliding: The effect of stress and boundary misorientation,” Acta Materialia. 2007. link Times cited: 95 USED (low confidence) T. Murtola, E. Falck, M. Karttunen, and I. Vattulainen, “Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints.,” The Journal of chemical physics. 2007. link Times cited: 66 Abstract: The authors introduce a coarse-grained (CG) model for a lipi… read moreAbstract: The authors introduce a coarse-grained (CG) model for a lipid membrane comprised of phospholipids and cholesterol at different molar concentrations, which allows them to study systems that are approximately 100 nm in linear size. The systems are studied in the fluid phase above the main transition temperature. The effective interactions for the CG model are extracted from atomic-scale molecular dynamics simulations using the inverse Monte Carlo (IMC) technique, an approach similar to the one the authors used earlier to construct another CG bilayer model [T. Murtola et al., J. Chem. Phys. 121, 9156 (2004)]. Here, the authors improve their original CG model by employing a more accurate description of the molecular structure for the phospholipid molecules. Further, they include a thermodynamic constraint in the IMC procedure to yield area compressibilities in line with experimental data. The more realistic description of the molecular structure of phospholipids and a more accurate representation of the interaction between cholesterols and phospholipid tails are shown to improve the behavior of the model significantly. In particular, the new model predicts the formation of denser transient regions in a pure phospholipid system, a finding that the authors have verified through large scale atomistic simulations. They also find that the model predicts the formation of cholesterol-rich and cholesterol-poor domains at intermediate cholesterol concentrations, in agreement with the original model and the experimental phase diagram. However, the domains observed here are much more distinct compared to the previous model. Finally, the authors also explore the limitations of the model, discussing its advantages and disadvantages. read less USED (low confidence) P. Puri and V. Yang, “Molecular Dynamics Study of Melting of Nano Aluminum Particles.” 2007. link Times cited: 3 Abstract: Molecular dynamics simulations are performed using isobaric-… read moreAbstract: Molecular dynamics simulations are performed using isobaric-isoenthalpic (NPH) ensembles to predict the melting of nano-sized aluminum particles in the range of 2-9 nm and to investigate the effect of charge development on the melting. Five different potential functions (i.e., the Lennard-Jones, Glue, Embedded Atom, Streitz-Mintmire, and SuttonChen potentials are employed, and the results are compared using the size dependence of melting phenomenon as a benchmark. A combination of structural and thermodynamic parameters such as the potential energy, Lindemann index, translational-order parameter, and radial-distribution functions are employed to characterize the melting process. Both bulk and particle melting are considered. The former is characterized by a sharp increase in structural and thermodynamic properties, whereas the latter involves surface pre-melting. The effect of surface charges on the melting point is found to be insignificant for nano-sized aluminum particles. The melting point of a nano particle increases monotonically with increasing size and approaches the bulk melting point at approximately 8 nm. Two-body potentials like the Lennard-Jones potential fail to capture the thermodynamic melting phenomenon. The Sutton-Chen potential, fitted to match structural properties, also fails to capture the size dependence of the particle melting point. Many-body potentials like the Glue and Streitz-Mintmire potentials result in accurate melting temperature as a function of particle size. read less USED (low confidence) A. Mokshin, R. Yulmetyev, R. Khusnutdinoff, and P. Hänggi, “Analysis of the dynamics of liquid aluminium: recurrent relation approach,” Journal of Physics: Condensed Matter. 2006. link Times cited: 26 Abstract: By use of the recurrent relation approach (RRA) we study the… read moreAbstract: By use of the recurrent relation approach (RRA) we study the microscopic dynamics of liquid aluminium at T = 973 K and develop a theoretical model which satisfies all the corresponding sum rules. The investigation covers the inelastic features as well as the crossover of our theory into the hydrodynamical and the free-particle regimes. A comparison between our theoretical results with those following from a generalized hydrodynamical approach is also presented. In addition to this we report the results of our molecular dynamics simulations for liquid aluminium, which are also discussed and compared to experimental data. The results obtained reveal (i) that the microscopical dynamics of density fluctuations is defined mainly by the first four even frequency moments of the dynamic structure factor, and (ii) the inherent relation of the high-frequency collective excitations observed in experimental spectra of dynamic structure factor S(k,ω) with the two-, three- and four-particle correlations. read less USED (low confidence) N. Zhou and L. Zhou, “Structure and nucleation mechanisms of misfit dislocations in epitaxial FCC thin films with positive and negative mismatches,” Materials Chemistry and Physics. 2006. link Times cited: 9 USED (low confidence) N. Ooi, L. Hector, J. B. Adams, and D. Stanzione, “First Principles Study of the Aluminum–Cubic Boron Nitride Interface,” The Journal of Adhesion. 2006. link Times cited: 7 Abstract: A plane wave density functional methodology, with the local … read moreAbstract: A plane wave density functional methodology, with the local density approximation for the elemental constituents, was used to investigate the structure, bonding, and adhesion of atomic-scale interfaces between aluminum and cubic-boron nitride (c-BN). Two fully periodic interfaces, Al(110)–c-BN(110) and Al(001)–c-BN(110), were constructed for this purpose. Interfacial bonding, examined with contours of the charge density difference and electron localization function, was found to be stronger between Al–N pairs than Al–B pairs. The computed work of separation ( Ws ) values were 2.25 J/m2 for Al(110)–c-BN(110) and 2.65 J/m2 for Al(001)–c-BN(110). The higher adhesion in the latter interface is attributed to a higher planar density of interfacial Al atoms. The computed Ws values were compared with values from first principles calculations on other aluminum–ceramic interfaces. The possibility of adhesive transfer during tensile debonding was qualitatively investigated. read less USED (low confidence) D. Olmsted, L. Hector, and W. Curtin, “Molecular dynamics study of solute strengthening in Al/Mg alloys,” Journal of The Mechanics and Physics of Solids. 2006. link Times cited: 99 USED (low confidence) L. Wang and H. Liu, “The microstructural evolution of Al12Mg17 alloy during the quenching processes,” Journal of Non-crystalline Solids. 2006. link Times cited: 14 USED (low confidence) K. Moriguchi and M. Igarashi, “Correlation between lattice-strain energetics and melting properties: Molecular dynamics and lattice dynamics using EAM models of Al,” Physical Review B. 2006. link Times cited: 14 USED (low confidence) W. Kaplan and Y. Kauffmann, “STRUCTURAL ORDER IN LIQUIDS INDUCED BY INTERFACES WITH CRYSTALS,” Annual Review of Materials Research. 2006. link Times cited: 135 Abstract: ▪ Abstract Interfaces between solids and liquids are importa… read moreAbstract: ▪ Abstract Interfaces between solids and liquids are important for a range of materials processes, including soldering and brazing, liquid-phase sintering, crystal growth, and lubrication. There is a wealth of fundamental studies on solid-liquid interfaces in materials, primarily focused on thermodynamics (relative interface energies and segregation effects) from high-temperature wetting experiments, which is often applied to processing design. Less is known about the atomistic structure at solid-liquid interfaces, mainly because of the difficulty involved in obtaining such information experimentally. This work reviews both theoretical and experimental studies of atomistic configurations at solid-liquid interfaces, focusing on the issue of ordering in the liquid adjacent to crystalline solids. read less USED (low confidence) Y. Zhang, L. Wang, W. Wang, and J. Zhou, “Structural transition of sheared-liquid metal in quenching state,” Physics Letters A. 2006. link Times cited: 16 USED (low confidence) K. Spiegel and A. Magistrato, “Modeling anticancer drug-DNA interactions via mixed QM/MM molecular dynamics simulations.,” Organic & biomolecular chemistry. 2006. link Times cited: 75 Abstract: The development of anticancer drugs started over four decade… read moreAbstract: The development of anticancer drugs started over four decades ago, with the serendipitous discovery of the antitumor activity of cisplatin and its successful use in the treatment of various cancer types. Despite the efforts made in unraveling the mechanism of the action of cisplatin, as well as in the rational design of new anticancer compounds, in many cases detailed structural and mechanistic information is still lacking. Many of these drugs exert their anticancer activity by covalently binding to DNA inducing a distortion or simply impeding replication, thus triggering a cellular response, which eventually leads to cell death. A detailed understanding of the structural and electronic properties of drug-DNA complexes and their mechanism of binding is the key step in elucidating the principles of their anticancer activity. At the theoretical level, the description of covalent drug-DNA complexes requires the use of state-of-the-art computer simulation techniques such as hybrid quantum/classical molecular dynamics simulations. In this review we provide a general overview on: drugs which covalently bind to DNA duplexes, the basic concepts of quantum mechanics/molecular mechanics (QM/MM), molecular dynamics methods and a list of selected applications of these simulations to the study of drug-DNA adducts. Finally, the potential and the limitations of this approach to the study of such systems are critically evaluated. read less USED (low confidence) J. Yang and X. Li, “Comparative study of boundary conditions for molecular dynamics simulations of solids at low temperature,” Physical Review B. 2006. link Times cited: 17 USED (low confidence) C. Anders, S. Messlinger, and H. Urbassek, “Deformation of slow liquid and solid clusters upon deposition : A molecular-dynamics study of Al cluster impact on an Al surface,” Surface Science. 2006. link Times cited: 9 USED (low confidence) M. Černý, R. Boyer, M. Šob, and S. Yip, “Higher-energy Structures and Stability of Cu and Al Crystals Along Displacive Transformation Paths,” Journal of Computer-Aided Materials Design. 2006. link Times cited: 11 USED (low confidence) N. Zhou and L. Zhou, “A fusion-crystalization mechanism for nucleation of misfit dislocations in FCC epitaxial films,” Journal of Crystal Growth. 2006. link Times cited: 10 USED (low confidence) D. Sun et al., “Crystal-melt interfacial free energies in hcp metals: A molecular dynamics study of Mg,” Physical Review B. 2006. link Times cited: 327 Abstract: Crystal-melt interfacial free energies $(\ensuremath{\gamma}… read moreAbstract: Crystal-melt interfacial free energies $(\ensuremath{\gamma})$ are computed for hcp Mg by employing equilibrium molecular-dynamics (MD) simulations and the capillary-fluctuation method (CFM). This work makes use of a newly developed embedded-atom-method (EAM) interatomic potential for Mg fit to crystal, liquid, and melting properties. We describe how the CFM, which has previously been applied to cubic systems only, can be generalized for studies of hcp metals by employing a parametrization for the orientation dependence of $\ensuremath{\gamma}$ in terms of hexagonal harmonics. The method is applied in the calculation of the Turnbull coefficient $(\ensuremath{\alpha})$ and crystalline anisotropies of $\ensuremath{\gamma}$. We obtain a value of $\ensuremath{\alpha}=0.48$, with interfacial free energies for different high-symmetry orientations differing by approximately 1%. These results are compared to those obtained in previous MD-CFM studies for cubic EAM metals as well as experimental studies of solid-liquid interfaces in hcp alloys. In addition, the implications of our results for the prediction of dendrite growth directions in hcp metals are discussed. read less USED (low confidence) E. Jannot, V. Mohles, G. Gottstein, and B. Thijsse, “Atomistic Simulation of Pipe Diffusion in AlCu Alloys,” Defect and Diffusion Forum. 2006. link Times cited: 11 Abstract: Activation energies for solute diffusion along dislocations … read moreAbstract: Activation energies for solute diffusion along dislocations are difficult to measure experimentally. The aim of this work is to provide insight into pipe diffusion with the help of atomistic simulations. The distribution of vacancy formation energy and the activation energy for copper migration are determined in the core of an edge dislocation in aluminum. The Dimer method is used to find activation energies for vacancy migration. The activated region around the dislocation where a very high diffusivity is observed and the activation energy for copper diffusion associated with this region are interpreted with regard to the contribution of the dislocation and the contribution of the alloying. read less USED (low confidence) D. Tanguy and M. Mareschal, “Superabundant vacancies in a metal-hydrogen system: Monte Carlo simulations,” Physical Review B. 2005. link Times cited: 25 Abstract: An equilibrium Monte Carlo simulation capable of treating su… read moreAbstract: An equilibrium Monte Carlo simulation capable of treating superabundant vacancy formation and ordering in metal-hydrogen systems (M-H) is developed. It combines lattice site occupations and continuous degrees of freedom which enables one to perform insertion/removal moves and hydrogen-vacancy cluster moves while the position of the particles are sampled. The bulk phase diagram in (μM,NH,V,T) ensemble is estimated for concentrations lower than 1 at. %. Within the framework of an EAM Al-H potential, ordering of superabundant vacancies in the shape of chains and platelets is reported at room temperature. read less USED (low confidence) S. Pathak and V. Shenoy, “Size dependence of thermal expansion of nanostructures,” Physical Review B. 2005. link Times cited: 41 Abstract: A theory for the size dependence of the coefficient of therm… read moreAbstract: A theory for the size dependence of the coefficient of thermal expansion (CTE) of nanostructures is developed. The theory predicts that the fractional change in the CTE from the bulk value scales inversely with the size of the nanostructure. An explicit relation for the intrinsic length scale that governs the size dependence is derived.The theory is tested against full-scale molecular dynamics simulations and excellent agreement is found. Further, it is shown that the CTE can rise or fall with size depending on the properties of the bounding surfaces of the nanostructure. The theory has the potential to be used as part of a predictive tool for the design of nanostructures. read less USED (low confidence) M. Forsblom and G. Grimvall, “Homogeneous melting of superheated crystals: Molecular dynamics simulations,” Physical Review B. 2005. link Times cited: 30 Abstract: Mechanical properties of solids are governed by crystal impe… read moreAbstract: Mechanical properties of solids are governed by crystal imperfections. Computational materials science is largely concerned with the modelling of such defects, e.g. their formation, migration, and interaction energies. Atomistic simulations of systems containing lattice defects are inherently difficult because of the generally complicated geometrical structure of the defects, the need for large simulation cells, etc. In this thesis, the role of lattice defects in the mechanism behind homogeneous melting is demonstrated. Also, a generic calculational scheme for studying atomic vibrations close to extended defects (applied to a dislocation) has been considered. Furthermore, heat capacities in the solid and liquid phases of aluminium have been calculated, as well as various thermophysical defect properties. The work was carried out using classical atomistic simulations, mainly molecular dynamics, of aluminium and copper. The interatomic forces were modelled with effective interactions of the embedded-atom type. The main results of this thesis are the following: • The thermal fluctuation initiating melting is an aggregate typically with 6-7 interstitials and 3-4 vacancies. • In the initial stage of melting, no signs of a shear modulus melting mechanism, or the presence of line-like defects (dislocations), can be seen. • The typical time interval from when melting initiates to the time at which the liquid phase is fully developed is of the order of 1000τ, where the period τ corresponds to the maximum vibrational frequency in the solid. • The solid-liquid boundary advances at a pace comparable to that of thermal transport by vibrating atoms in the crystal at high temperatures. • The seemingly small anharmonic effect in the heat capacity of aluminium is caused by a partial cancellation of the low-order term linear in the temperature and anharmonic terms of higher order in the temperature. • The core region of an edge dislocation in face-centred cubic aluminium has compressed and expanded regions. The excess volume associated with the dislocation core is small, about 6 percent of the atomic volume, as a result of a partial cancellation between the volume changes of the compressed and expanded regions. • The compressed and expanded regions of the edge dislocation core give negative and positive contributions, respectively, to the excess vibrational entropy. The overall effect is a positive vibrational excess entropy of the dislocation core which is about 2kB per atomic repeat length along the dislocation core. • The atomic vibrations near the dislocation core are modelled by considering an atomic cluster with about 500-1000 atoms containing the core of dislocation, embedded in a large discrete, but relaxed, lattice of about 23 000 atoms. An atomic region that is four atomic layers thick and about 18 atomic diameters long in the direction parallel to the Burgers vector, accounts for most of the excess entropy. • The constant-pressure heat capacity of aluminium shows a minimum as a function of temperature in the liquid phase. read less USED (low confidence) M. Slabanja and G. Wahnström, “Kinetic Monte Carlo study of Al–Mg precipitation,” Acta Materialia. 2005. link Times cited: 20 USED (low confidence) A. Kubota and W. Wolfer, “Transition pathways in the unfaulting of dislocation loops,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2005. link Times cited: 9 USED (low confidence) P. Süle, “Substrate induced enhancement of atomic layer growth on Al(1 1 1): The effect of the mass anisotropy,” Surface Science. 2005. link Times cited: 4 USED (low confidence) Y. Qi, L. Hector, N. Ooi, and J. B. Adams, “A first principles study of adhesion and adhesive transfer at Al(1 1 1)/graphite(0 0 0 1),” Surface Science. 2005. link Times cited: 40 USED (low confidence) T. Iwasaki, “Molecular-dynamics study of interfacial diffusion between high-permittivity gate dielectrics and germanium substrates,” Journal of Materials Research. 2005. link Times cited: 4 Abstract: The stability of interfaces with germanium, which has recent… read moreAbstract: The stability of interfaces with germanium, which has recently been discussed as a replacement for silicon in ultra-large-scale integrated circuits (ULSIs), was studied. Interfacial oxygen diffusion from high-permittivity gate dielectrics (ZrO_2 and HfO_2) into germanium substrates must be suppressed to prevent the formation of interfacial layers between the gate dielectrics and the germanium substrates. Oxygen diffusion was simulated through a molecular-dynamics technique that takes into account many-body interactions and charge transfer between different elements. The simulation results show that the addition of yttrium is effective in suppressing interfacial oxygen diffusion at the ZrO_2/germanium interfaces. On the other hand, the addition of yttrium is not effective in suppressing interfacial oxygen diffusion at the HfO_2/germanium interfaces. The results also show that the diffusion at the ZrO_2/Ge(111) and HfO_2/Ge(111) interfaces is much more suppressed than the diffusion at the ZrO_2/Ge(001) and HfO_2/Ge(001) interfaces. read less USED (low confidence) M. Forsblom and G. Grimvall, “How superheated crystals melt,” Nature Materials. 2005. link Times cited: 96 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 USED (low confidence) V. Shenoy, “Atomistic calculations of elastic properties of metallic fcc crystal surfaces,” Physical Review B. 2005. link Times cited: 674 Abstract: Elastic properties of crystal surfaces are useful in underst… read moreAbstract: Elastic properties of crystal surfaces are useful in understanding mechanical properties of nanostructures. This paper presents a fully nonlinear treatment of surface stress and surface elastic constants. A method for the determination of surface elastic properties from atomistic simulations is developed. This method is illustrated with examples of several crystal faces of some fcc metals modeled with embedded atom potentials. The key finding in this study is the importance of accounting for the additional relaxations of atoms at the crystal surface due to strain. Although these relaxations do not affect the values of surface stress (as had been determined in previousworks), they have a profound effect on the surface elastic constants.Failure to account for these relaxations can lead to values of elastic constants that are incorrect not only in magnitude but also in sign. A possible method for the experimental determination of the surface elastic constants is outlined. read less USED (low confidence) Y. Kauffmann, A. Rečnik, and W. Kaplan, “The accuracy of quantitative image matching for HRTEM applications,” Materials Characterization. 2005. link Times cited: 14 USED (low confidence) D. Wolf, V. Yamakov, S. Phillpot, A. Mukherjee, and H. Gleiter, “Deformation of nanocrystalline materials by molecular-dynamics simulation: relationship to experiments?,” Acta Materialia. 2005. link Times cited: 636 USED (low confidence) H. Zhang, M. Upmanyu, and D. Srolovitz, “Curvature driven grain boundary migration in aluminum: molecular dynamics simulations,” Acta Materialia. 2005. link Times cited: 107 USED (low confidence) Š. Pick et al., “Magnetism and structure on the atomic scale: Small cobalt clusters in Cu(001),” Physical Review B. 2004. link Times cited: 48 Abstract: The interplay between structure and magnetic properties of s… read moreAbstract: The interplay between structure and magnetic properties of small cobalt clusters embedded in a Cu(001) surface is studied performing ab initio and tight-binding calculations in a fully relaxed geometry. We reveal that, despite the small macroscopic mismatch between Co and Cu, the strain relaxations at the interface have a profound effect on the structure of the clusters and the substrate. The physical mechanism responsible for the strain relaxations in embedded clusters is related to the size-dependent mesoscopic mismatch which has been recently introduced to understand homo- and heteroepitaxial growth at the mesoscale [O. V. Lysenko et al., Phys. Rev. Lett. 89, 126102 (2002)]. We show that the atomic relaxations strongly reduce the magnetic anisotropy energy (MAE) and the orbital magnetic moments of embedded clusters. The largest MAE of about 1.8 meV is found for a single Co atom in the Cu(001) surface. A strong enhancement of the spin magnetic moments in embedded clusters as compared to a single atom of Co incorporated in the Cu(001) surface is found. Magnetic properties of embedded and supported clusters are compared. While in supported clusters the MAE is strongly enhanced at the edge atoms, the immersion of the cluster into the surface and atomic relaxations make the distribution of the local MAE contributions and orbital-moment values almost homogeneous. read less USED (low confidence) O. Politano, S. Garruchet, and J. Salazar, “Numerical and theoretical considerations on the surface energy for pure solids under strain,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2004. link Times cited: 8 USED (low confidence) D. Olmsted, L. Hector, W. Curtin, and R. Clifton, “Atomistic simulations of dislocation mobility in Al, Ni and Al/Mg alloys,” Modelling and Simulation in Materials Science and Engineering. 2004. link Times cited: 271 Abstract: Dislocation velocities and mobilities are studied using mole… read moreAbstract: Dislocation velocities and mobilities are studied using molecular dynamics simulations for edge and screw dislocations in pure aluminium and nickel, and edge dislocations in Al–2.5%Mg and Al–5.0%Mg random substitutional alloys using EAM potentials. In the pure materials, the velocities of all dislocations are close to linear with the ratio of (applied stress)/(temperature) at low velocities consistent with phonon drag models, and quantitative agreement with the experiment is obtained for the mobility in Al. At higher velocities, different behaviour is observed. The edge dislocation velocity remains dependent solely on (applied stress)/(temperature) up to approximately 1.0 MPa K−1, and approaches a plateau velocity that is lower than the smallest ‘forbidden’ speed predicted by continuum models. In contrast, above a velocity around half of the smallest continuum wave speed, the screw dislocation damping has a contribution dependent solely on stress with a functional form close to that predicted by a radiation damping model of Eshelby. At the highest applied stresses, there are several regimes of nearly constant (transonic) velocity separated by velocity gaps in the vicinity of forbidden velocities; various modes of dislocation disintegration and destabilization were also encountered in this regime. In the alloy systems, there is a temperature- and concentration-dependent pinning regime where the velocity drops sharply below the pure metal velocity. Above the pinning regime but at moderate stresses, the velocity is again linear in (applied stress)/(temperature) but with a lower mobility than in the pure metal. read less USED (low confidence) L. Guang-xu, L. Chang-song, and Z. Zhen-gang, “Universal Scaling Law for Atomic Diffusion and Viscosity in Liquid Metals,” Chinese Physics Letters. 2004. link Times cited: 13 Abstract: The recently proposed scaling law relating the diffusion coe… read moreAbstract: The recently proposed scaling law relating the diffusion coefficient and the excess entropy of liquid [Samanta A et al. 2004 Phys. Rev. Lett. 92 145901; Dzugutov M 1996 Nature 381 137], and a quasi-universal relationship between the transport coefficients and excess entropy of dense fluids [Rosenfeld Y 1977 Phys. Rev. A 15 2545], are tested for diverse liquid metals using molecular dynamics simulations. Interatomic potentials derived from the glue potential and second-moment approximation of tight-binding scheme are used to study liquid metals. Our simulation results give sound support to the above-mentioned universal scaling laws. Following Dzugutov, we have also reached a new universal scaling relationship between the viscosity coefficient and excess entropy. The simulation results suggest that the reduced transport coefficients can be expressed approximately in terms of the corresponding packing density. read less USED (low confidence) J. Hoyt et al., “Crystal–Melt Interfaces and Solidification Morphologies in Metals and Alloys,” MRS Bulletin. 2004. link Times cited: 100 Abstract: When liquids solidify, the interface between a crystal and i… read moreAbstract: When liquids solidify, the interface between a crystal and its melt often forms branching structures (dendrites), just as frost spreads across a window.The development of a quantitative understanding of dendritic evolution continues to present a major theoretical and experimental challenge within the metallurgical community. This article looks at key parameters that describe the interface—excess free energy and mobility—and discusses how these important properties relate to our understanding of crystal growth and other interfacial phenomena such as wetting and spreading of droplets and nucleation of the solid phase from the melt. In particular, two new simulation methods have emerged for computing the interfacial free energy and its anisotropy: the cleaving technique and the capillary fluctuation method. These are presented, along with methods for extracting the kinetic coefficient and a comparison of the results to several theories of crystal growth rates. read less USED (low confidence) E. Tadmor and N. Bernstein, “A first-principles measure for the twinnability of FCC metals,” Journal of The Mechanics and Physics of Solids. 2004. link Times cited: 218 USED (low confidence) H. Gong and B. Liu, “Influence of interfacial texture on solid-state amorphization and associated asymmetric growth in immiscible Cu-Ta multilayers,” Physical Review B. 2004. link Times cited: 8 Abstract: For the immiscible Cu-Ta system, a Finnis-Sinclair potential… read moreAbstract: For the immiscible Cu-Ta system, a Finnis-Sinclair potential is constructed and proven to be realistic in reproducing some static properties of the system. Applying the potential, molecular dynamics simulations reveal that among the nine $\mathrm{Cu}∕\mathrm{Ta}$ interfaces stacked by possible combinations of the (100), (110), and (111) atomic planes, the Ta (110) plane could remain stable up to a temperature of $600\phantom{\rule{0.2em}{0ex}}\ifmmode^\circ\else\textdegree\fi{}\mathrm{C}$, while the Cu (111) plane could remain unchanged only if combined with the Ta (100) and (110) planes. Simulations also show that for the other $\mathrm{Cu}∕\mathrm{Ta}$ interfaces, the interface energy serves as the driving force for interdiffusion of the Cu and Ta atoms across the interface, resulting in solid-state amorphization. Interestingly, it is calculated that the amorphization energy of Cu is smaller than that of Ta, thus resulting in an asymmetric growth behavior of the amorphous interlayer, i.e., amorphization of the Cu lattice is easier and faster than that of the Ta lattice. In general, the agreement between the simulation results and experimental observations is fairly good. read less USED (low confidence) S. L. Frederiksen, K. Jacobsen, and J. Schiøtz, “Simulations of intergranular fracture in nanocrystalline molybdenum,” Acta Materialia. 2004. link Times cited: 72 USED (low confidence) E. Rodary, D. Rodney, L. Proville, Y. Bréchet, and G. Martin, “Dislocation glide in model Ni ( Al ) solid solutions by molecular dynamics,” Physical Review B. 2004. link Times cited: 69 Abstract: d tothe glide velocity. We also find that the obstacles are m… read moreAbstract: d tothe glide velocity. We also find that the obstacles are made of specific configurations of the Al atoms, which arebrought in positions of strong mutual repulsion in course of the glide process. The solute-solute short rangerepulsion, rather than the usually assumed dislocation-solute interaction, is thus argued to be the main mecha-nism responsible for chemical hardening in the present concentrated random solid solution. The use of theabove results in the frame of multi-scale modeling is exemplified.DOI: 10.1103/PhysRevB.70.054111 PACS number(s): 62.20.FeI. INTRODUCTION read less USED (low confidence) L. Zhou, X. Wei, and N. Zhou, “Lattice distortion and thermal stability of nano-crystalline copper,” Computational Materials Science. 2004. link Times cited: 11 USED (low confidence) R. E. Miller and A. Acharya, “A stress-gradient based criterion for dislocation nucleation in crystals,” Journal of The Mechanics and Physics of Solids. 2004. link Times cited: 62 USED (low confidence) G. Grochola, S. Russo, and I. Snook, “On computer simulation methods for calculating ‘exact’ surface formation free energies of steps and (1 × 2) missing row reconstructions,” Surface Science. 2004. link Times cited: 7 USED (low confidence) D. Walgraef, “Texture evolution in adsorbed monoatomic layers,” Physica E-low-dimensional Systems & Nanostructures. 2004. link Times cited: 0 USED (low confidence) H. Swygenhoven, P. Derlet, and A. Frøseth, “Stacking fault energies and slip in nanocrystalline metals,” Nature Materials. 2004. link Times cited: 853 USED (low confidence) Y.-M. Kim and B.-J. Lee, “A modified embedded-atom method interatomic potential for the Cu–Zr system,” Journal of Materials Research. 2004. link Times cited: 65 USED (low confidence) J. D. Torre, G. Gilmer, and M. Rouhani, “Imperfect wetting of vapor-deposited thin films: Monte Carlo simulations and nucleation model,” Physical Review B. 2004. link Times cited: 4 USED (low confidence) Z. Shi, P. Wynblatt, and S. G. Srinivasan, “Melting behavior of nanosized lead particles embedded in an aluminum matrix,” Acta Materialia. 2004. link Times cited: 24 USED (low confidence) A. Frøseth, H. Swygenhoven, and P. Derlet, “The influence of twins on the mechanical properties of nc-Al,” Acta Materialia. 2004. link Times cited: 145 USED (low confidence) Y. Mishin, “Atomistic modeling of the γ and γ’-phases of the Ni-Al system,” Acta Materialia. 2004. link Times cited: 395 USED (low confidence) M. Forsblom, N. Sandberg, and G. Grimvall, “Anharmonic effects in the heat capacity of Al,” Physical Review B. 2004. link Times cited: 30 Abstract: Mechanical properties of solids are governed by crystal impe… read moreAbstract: Mechanical properties of solids are governed by crystal imperfections. Computational materials science is largely concerned with the modelling of such defects, e.g. their formation, migration, and interaction energies. Atomistic simulations of systems containing lattice defects are inherently difficult because of the generally complicated geometrical structure of the defects, the need for large simulation cells, etc. In this thesis, the role of lattice defects in the mechanism behind homogeneous melting is demonstrated. Also, a generic calculational scheme for studying atomic vibrations close to extended defects (applied to a dislocation) has been considered. Furthermore, heat capacities in the solid and liquid phases of aluminium have been calculated, as well as various thermophysical defect properties. The work was carried out using classical atomistic simulations, mainly molecular dynamics, of aluminium and copper. The interatomic forces were modelled with effective interactions of the embedded-atom type. The main results of this thesis are the following: • The thermal fluctuation initiating melting is an aggregate typically with 6-7 interstitials and 3-4 vacancies. • In the initial stage of melting, no signs of a shear modulus melting mechanism, or the presence of line-like defects (dislocations), can be seen. • The typical time interval from when melting initiates to the time at which the liquid phase is fully developed is of the order of 1000τ, where the period τ corresponds to the maximum vibrational frequency in the solid. • The solid-liquid boundary advances at a pace comparable to that of thermal transport by vibrating atoms in the crystal at high temperatures. • The seemingly small anharmonic effect in the heat capacity of aluminium is caused by a partial cancellation of the low-order term linear in the temperature and anharmonic terms of higher order in the temperature. • The core region of an edge dislocation in face-centred cubic aluminium has compressed and expanded regions. The excess volume associated with the dislocation core is small, about 6 percent of the atomic volume, as a result of a partial cancellation between the volume changes of the compressed and expanded regions. • The compressed and expanded regions of the edge dislocation core give negative and positive contributions, respectively, to the excess vibrational entropy. The overall effect is a positive vibrational excess entropy of the dislocation core which is about 2kB per atomic repeat length along the dislocation core. • The atomic vibrations near the dislocation core are modelled by considering an atomic cluster with about 500-1000 atoms containing the core of dislocation, embedded in a large discrete, but relaxed, lattice of about 23 000 atoms. An atomic region that is four atomic layers thick and about 18 atomic diameters long in the direction parallel to the Burgers vector, accounts for most of the excess entropy. • The constant-pressure heat capacity of aluminium shows a minimum as a function of temperature in the liquid phase. read less USED (low confidence) L. Shilkrot, R. E. Miller, and W. Curtin, “Multiscale plasticity modeling: coupled atomistics and discrete dislocation mechanics,” Journal of The Mechanics and Physics of Solids. 2004. link Times cited: 278 USED (low confidence) S. Jun, Y. M. Lee, S. Y. Kim, and S. Im, “Atomistic Simulations of Dislocation-Loop Glidings in Al(111) Nanoindentation,” Key Engineering Materials. 2004. link Times cited: 0 Abstract: Molecular dynamics simulation of nanoindentation on Al(111) … read moreAbstract: Molecular dynamics simulation of nanoindentation on Al(111) surface is presented. The simulation is performed using the Ercolessi-Adams glue potential and the Berendsen thermostat. Boundary conditions of 'pseudo' thin film are imposed in order to focus on the dislocation motion in ultra-thin film. Nucleation and development of defects underneath the indenter tip are visualized, and the gliding patterns of dislocation loops are investigated with particular emphasis on the effect of film thickness. Simulation results show that the early emission of dislocation loop is highly dependent on the film thickness. read less USED (low confidence) J. Peltola and K. Nordlund, “Ion beam induced coherent displacement in Al on Au system,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2004. link Times cited: 4 USED (low confidence) N. Chandra and S. Namilae, “Multi-Scale Modeling of Nanocrystalline Materials,” Materials Science Forum. 2004. link Times cited: 1 Abstract: Spatial and temporal limitations of atomic scale simulations… read moreAbstract: Spatial and temporal limitations of atomic scale simulations necessitate the development of multi scale methodologies linking atomic and continuum scales. In this paper, we present formulations to evaluate continuum quantities of stress, strain and local elastic moduli of grain boundaries in a molecular dynamics setting. Energetics and deformation of symmetric tilt grain boundaries of Aluminum are studied using the stress strain measures. The atomistic simulation studies of grain boundary sliding show a clear dependence of magnitude of sliding on grain boundary energy. Asymptotic expansion homogenization (AEH) is a mathematically rigorous approach for homogenization of periodic structures, which has been used extensively in composites and porous media. We propose a methodology and demonstrate the applicability of AEH to link atomic scale effects in much larger scale systems. read less USED (low confidence) R. E. Miller, L. Shilkrot, and W. Curtin, “A coupled atomistics and discrete dislocation plasticity simulation of nanoindentation into single crystal thin films,” Acta Materialia. 2004. link Times cited: 123 USED (low confidence) H. Gong, L. Kong, and B. Liu, “Metastability of an immiscible Cu-Mo system calculated from first-principles and a derived n -body potential,” Physical Review B. 2004. link Times cited: 17 Abstract: An ab initio calculation is performed to predict the structu… read moreAbstract: An ab initio calculation is performed to predict the structures, lattice constants, and cohesive energies of the metastable ${\mathrm{Cu}}_{75}{\mathrm{Mo}}_{25},$ ${\mathrm{Cu}}_{50}{\mathrm{Mo}}_{50},$ and ${\mathrm{Cu}}_{25}{\mathrm{Mo}}_{75}$ phases. With the aid of an ab initio calculation, an n-body Cu-Mo potential is derived and proven to be realistic in reproducing some intrinsic properties of the metastable Cu-Mo phases. Based on the Cu-Mo potential, a molecular dynamics simulation reveals that a crystal-to-amorphous transition takes place in a Cu-rich fcc solid solution when the solute concentration reaches/exceeds a critical value of 25 at. % Mo. Moreover, a molecular dynamics simulation also predicts the formation of metastable fcc and bcc Cu-Mo phases and determines the heats of formation of both crystalline and amorphous phases, thus constructing an energy diagram of the Cu-Mo system over the entire composition range. The calculation/simulation results are compared with the experimental observations, and the agreements between them are fairly good. read less USED (low confidence) R. C. Picu and D. Zhang, “Atomistic study of pipe diffusion in Al–Mg alloys,” Acta Materialia. 2004. link Times cited: 149 USED (low confidence) M. de Koning, S. R. de Debiaggi, and A. M. Monti, “Vacancy-Formation Thermodynamics in Aluminium and Nickel: a Computational Study,” Defect and Diffusion Forum. 2003. link Times cited: 12 Abstract: Although anharmonic effects on the properties of point defec… read moreAbstract: Although anharmonic effects on the properties of point defects have been considered in the past, only recent progress in simulation techniques have come to show their importance. Using molecular dynamics and nonequilibrium free-energy techniques we investigate such effects on the formation free energies of vacancies and divacancies in aluminium and nickel represented by many-body interatomic potentials. Furthermore, we discuss the applicability of the harmonic approximation to compute defect formation entropies for the used potentials. It is found that the harmonic approximation may fail to give a correct description of defect-formation entropies, even at low temperatures. Using the results of the calculations including all anharmonic effects, we analyze the stability of point defects and interpret the results in terms of the curvature that some fcc metals exhibit in the high temperature range of the equilibrium vacancy concentration Arrhenius plots. read less USED (low confidence) D. Tanguy and T. Magnin, “Atomic-scale simulation of intergranular segregation of H in Al–Mg: implications for H-induced damage,” Philosophical Magazine. 2003. link Times cited: 15 Abstract: The goal of this work is to make a contribution to the under… read moreAbstract: The goal of this work is to make a contribution to the understanding of the microscopic mechanisms of H-induced intergranular damage. We develop an embedded-atom method interatomic potential for H in the Al–Mg system with the main aim of reproducing the current understanding of H trapping to vacancies. This model is used to investigate the effect of the Mg–H affinity on the segregation of H on the Σ =5 (310) [001] grain boundary. Monte Carlo simulations in the grand canonical ensemble are used to estimate equilibrium H concentrations at this boundary at T=300 K. A large structure change, associated with the H enrichment of the grain boundary, is reported. The implications on damage to the interface are discussed. read less USED (low confidence) P. Wynblatt, “Comparison between modeling and experimental measurements of interfacial properties,” Applied Surface Science. 2003. link Times cited: 2 USED (low confidence) H. Gong, L. Kong, W. Lai, and B. Liu, “Glass-forming ability determined by an n-body potential in a highly immiscible Cu-W system through molecular dynamics simulations,” Physical Review B. 2003. link Times cited: 16 Abstract: With an important aid from ab initio calculations, an n-body… read moreAbstract: With an important aid from ab initio calculations, an n-body potential is constructed under the embedded atom method for a highly immiscible Cu-W system characterized by a positive heat of formation of +33 kJ/mol. The obtained potential is capable of reproducing some realistic physical properties, such as cohesive energies and lattice constants, etc., of Cu and W, as well as two nonequilibrium ${\mathrm{Cu}}_{3}\mathrm{W}$ and CuW compounds. Applying the potential, molecular dynamics simulations using solid solution models are conducted to calculate the critical solid solubility, at which a metallic glass transition takes place, thus determining the glass-forming range of the Cu-W system to be from 20 to 65 at. % of W, which is in good agreement with the experimental results. Interestingly, an abnormally large volume expansion in association with the transition is found to be within 6.9\char21{}13.1% in the Cu-W system and it is much greater than the typical value of 1\char21{}2% frequently observed in the systems with negative heats of formation. read less USED (low confidence) B. Godwal, R. Rao, A. Verma, M. Shukla, H. C. Pant, and S. Sikka, “Equation of state of condensed matter in laser-induced high-pressure regime,” Laser and Particle Beams. 2003. link Times cited: 10 Abstract: We have simulated the shock Hugoniot of copper and uranium b… read moreAbstract: We have simulated the shock Hugoniot of copper and uranium based on the results of first principles electronic structure calculations. The room temperature isotherm has been obtained by evaluating the accurate ground state total energies at various compressions, and the thermal and electronic excitation contributions were obtained by adopting isotropic models using the results obtained by the band structure calculations. Our calculations ensure smooth consideration of pressure ionization effects as the relevant core states are treated in the semi-core form at the ambient pressure. The pressure variation of the electronic Gruneisen parameter was estimated for copper using the band structure results, which leads to good agreement of the simulated shock Hugoniot with the measured shock data. The simulation results obtained for U are also compared with the experimental data available in literature and with our own data. read less 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 USED (low confidence) J. Zhong, J. B. Adams, and L. Hector, “Molecular dynamics simulations of asperity shear in aluminum,” Journal of Applied Physics. 2003. link Times cited: 26 Abstract: One important wear mechanism involves the shear of asperitie… read moreAbstract: One important wear mechanism involves the shear of asperities by other asperities. Molecular dynamics is used to simulate the shearing of aluminum asperities by a “hard” (Lennard-Jones) asperity. These simulations involve the use of a reliable interatomic potential based on the embedded atom method for aluminum that was developed by fitting a large database of density functional calculated forces and experimental data. The simulations are repeated for a wide range of conditions, including velocities, temperatures, asperity shapes, degree of intersection, crystal orientations and adhesive strengths, to determine their effects on the wear process. The design-of-experiment approach is used to analyze the relative importance of each factor and its interactions. Thermal distributions and mechanical deformation in the residual aluminum substrate during asperity shear are analyzed. The final results show that the most significant factor in determining the wear process is the interasperity bonding. The degree of overlap between two asperities is also important. The temperature, the translational velocity, and the crystal orientation play smaller roles. read less USED (low confidence) V. Yamakov, D. Wolf, S. Phillpot, and H. Gleiter, “Dislocation–dislocation and dislocation–twin reactions in nanocrystalline Al by molecular dynamics simulation,” Acta Materialia. 2003. link Times cited: 235 USED (low confidence) H. Ohkubo, Y. Shimomura, I. Mukouda, K. Sugio, and M. Kiritani, “Formation of vacancy clusters in deformed thin films of Al–Mg and Al–Cu dilute alloys,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2003. link Times cited: 29 USED (low confidence) R. Zope and Y. Mishin, “Interatomic potentials for atomistic simulations of the Ti-Al system,” Physical Review B. 2003. link Times cited: 477 Abstract: Semiempirical interatomic potentials have been developed for… read moreAbstract: Semiempirical interatomic potentials have been developed for Al, $\ensuremath{\alpha}\ensuremath{-}\mathrm{Ti},$ and $\ensuremath{\gamma}\ensuremath{-}\mathrm{TiAl}$ within the embedded atom method (EAM) formalism by fitting to a large database of experimental as well as ab initio data. The ab initio calculations were performed by the linearized augmented plane wave (LAPW) method within the density functional theory to obtain the equations of state for a number of crystal structures of the Ti-Al system. Some of the calculated LAPW energies were used for fitting the potentials while others for examining their quality. The potentials correctly predict the equilibrium crystal structures of the phases and accurately reproduce their basic lattice properties. The potentials are applied to calculate the energies of point defects, surfaces, and planar faults in the equilibrium structures. Unlike earlier EAM potentials for the Ti-Al system, the proposed potentials provide a reasonable description of the lattice thermal expansion, demonstrating their usefulness for molecular-dynamics and Monte Carlo simulations at high temperatures. The energy along the tetragonal deformation path (Bain transformation) in $\ensuremath{\gamma}\ensuremath{-}\mathrm{TiAl}$ calculated with the EAM potential is in fairly good agreement with LAPW calculations. Equilibrium point defect concentrations in $\ensuremath{\gamma}\ensuremath{-}\mathrm{TiAl}$ are studied using the EAM potential. It is found that antisite defects strongly dominate over vacancies at all compositions around stoichiometry, indicating that $\ensuremath{\gamma}\ensuremath{-}\mathrm{TiAl}$ is an antisite disorder compound, in agreement with experimental data. read less USED (low confidence) E. Tadmor and S. Hai, “A Peierls criterion for the onset of deformation twinning at a crack tip,” Journal of The Mechanics and Physics of Solids. 2003. link Times cited: 247 USED (low confidence) F. Gao and W. J. Weber, “Atomic simulation of ion-solid interaction in ceramics,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2003. link Times cited: 10 USED (low confidence) K. M. Carling, G. Wahnström, T. Mattsson, N. Sandberg, and G. Grimvall, “Vacancy concentration in Al from combined first-principles and model potential calculations,” Physical Review B. 2003. link Times cited: 63 Abstract: We present a comprehensive study of vacancy formation enthal… read moreAbstract: We present a comprehensive study of vacancy formation enthalpies and entropies in aluminum. The calculations are done in the framework of the local-density and generalized-gradient approximations in the density-functional formalism. To assess anharmonic contributions to the formation free energies, we use an interatomic potential with parameters determined from density-functional-theory calculations. We find that the binding energy for the nearest-neighbor divacancy is negative, i.e., it is energetically unstable. The entropy contributions slightly stabilize the divacancy but also the binding free energy at the melting temperature is found to be negative. We show that the anharmonic atomic vibrations explain the non-Arrhenius temperature dependence of the vacancy concentration in contrast to the commonly accepted interpretation of the experimental data in terms of the monovacancy-divacancy model. read less USED (low confidence) Chantrenne, Raynaud, and Barrat, “STUDY OF PHONON HEAT TRANSFER IN METALLIC SOLIDS FROM MOLECULAR DYNAMIC SIMULATIONS,” Microscale Thermophysical Engineering. 2003. link Times cited: 37 Abstract: Heat transfer in solids is analyzed in order to show that th… read moreAbstract: Heat transfer in solids is analyzed in order to show that the total phonon thermal conductivity in metal can be estimated from the knowledge of phonon-phonon interactions. Nonequilibrium molecular dynamics (NEMD) is used to simulate heat transfer due to phonon-phonon interactions in an aluminum slab. The influence of the many simulation parameters on the slab conductance is studied. The thermal conductivity due to phonon-phonon interactions of the slab is calculated for different thicknesses (from 2–20 nm). The curve is extrapolated to infinite thickness to estimate the bulk value of the thermal conductivity due to phonon-phonon interactions. To decrease the uncertainty due to the extrapolation, the phonon radiative transfer equation (PRTE) is solved to simulate 1D phonon heat transfer in a slab. The extinction coefficient of phonons is estimated by comparing the thermal conductance of the slab obtained by NEMD and PRTE. It is then possible to calculate the phonon-phonon mean free path, the thermal conductivity due to phonon-phonon interactions, and the total phonon thermal conductivity with a much better accuracy. read less USED (low confidence) V. Yamakov, D. Wolf, S. Phillpot, and H. Gleiter, “Deformation twinning in nanocrystalline Al by molecular-dynamics simulation,” Acta Materialia. 2002. link Times cited: 403 USED (low confidence) M. Ortega, S. Debiaggi, and A. M. Monti, “Self‐Diffusion in FCC Metals: Static and Dynamic Simulations in Aluminium and Nickel,” Physica Status Solidi B-basic Solid State Physics. 2002. link Times cited: 26 Abstract: Self-diffusion in model Al and Ni has been studied by molecu… read moreAbstract: Self-diffusion in model Al and Ni has been studied by molecular static and molecular dynamic techniques. The structure of defect-lattice configurations has been obtained with the former technique. With the latter, the vacancy diffusion mechanism has been analysed over a wide temperature range, and particular attention has been paid to multiple jumps in the high temperature region. The possible contribution of divacancies, within the limits imposed by the interatomic potentials used, has also been considered. read less 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 USED (low confidence) L. Shilkrot, W. Curtin, and R. E. Miller, “A coupled atomistic/continuum model of defects in solids,” Journal of The Mechanics and Physics of Solids. 2002. link Times cited: 156 USED (low confidence) H. Gong, L. Kong, W. Lai, and B. Liu, “Atomistic modeling of solid-state amorphization in an immiscible Cu-Ta system,” Physical Review B. 2002. link Times cited: 48 Abstract: An embedded-atom potential for the equilibrium immiscible Cu… read moreAbstract: An embedded-atom potential for the equilibrium immiscible Cu-Ta system is constructed with an important aid of first principles calculation, which provides some physical properties of two nonequilibrium CuTa and ${\mathrm{Cu}}_{3}\mathrm{Ta}$ alloy phases for fitting the potential. Applying the constructed potential, molecular dynamics simulations with a Cu-based solid solution model reveal that when the Ta solute atoms exceed a critical value of 30 at. % in Cu, the enthalpy of the model is elevated up to a high level, thus triggering first a fcc-to-orthorhombic martensitic transition and second a diffusion-controlled orthorhombic-to-disordered transition. Surprisingly, an anomalously large volume expansion of the Cu-based solid solution upon amorphization transition is observed and is calculated to be around 10%, which is much greater than the value of 2% usually observed in the binary metal systems characterized by a negative heat of formation. The simulation results are compared with the experimental observations and the agreement between them is fairly good. Besides, the physical meaning as well as the implication of the simulation results are also discussed. read less USED (low confidence) V. Yamakov, D. Wolf, S. Phillpot, A. Mukherjee, and H. Gleiter, “Dislocation processes in the deformation of nanocrystalline aluminium by molecular-dynamics simulation,” Nature Materials. 2002. link Times cited: 843 USED (low confidence) J. Adler, A. Hashibon, N. Schreiber, A. Sorkin, S. Sorkin, and G. Wagner, “Visualization of MD and MC simulations for atomistic modeling,” Computer Physics Communications. 2002. link Times cited: 17 USED (low confidence) A. Strachan, T. Çagin, O. Gulseren, S. Mukherjee, R. E. Cohen, and W. A. Goddard, “First principles force field for metallic tantalum,” Modelling and Simulation in Materials Science and Engineering. 2002. link Times cited: 32 Abstract: We develop a many-body force field (FF) for tantalum based o… read moreAbstract: We develop a many-body force field (FF) for tantalum based on extensive ab initio quantum mechanical (QM) calculations and illustrate its application with molecular dynamics (MD). As input data to the FF we use ab initio methods (LAPW-GGA) to calculate: (i) the zero temperature equation of state (EOS) of Ta for bcc, fcc, and hcp crystal structures for pressures up to ∼500 GPa, and (ii) elastic constants. We use a mixed-basis pseudopotential code to calculate: (iii) volume-relaxed vacancy formation energy also as a function of pressure. In developing the Ta FF we also use previous QM calculations of: (iv) the EOS for the A15 structure; (v) the surface energy bcc (100); (vi) energetics for shear twinning of the bcc crystal. We find that, with appropriate parameters, an embedded atom model FF (denoted as qEAM FF) is able to reproduce all this QM data. We illustrate the use of the qEAM FF with MD to calculate such finite temperature properties as the melting curve up to 300 GPa and thermal expansivity in a wide temperature range. Both our predictions agree well with experimental values. read less USED (low confidence) P. Szelestey, M. Patriarca, L. Perondi, and K. Kaski, “MODIFIED EAM POTENTIALS FOR MODELLING STACKING–FAULT BEHAVIOR IN Cu, Al, Au, AND Ni,” International Journal of Modern Physics B. 2002. link Times cited: 10 Abstract: In this paper we have developed empirical Embedded Atom Mode… read moreAbstract: In this paper we have developed empirical Embedded Atom Model potentials, following the fitting scheme proposed by Chantasiriwan and Milstein, in order to describe the stacking fault behaviour of copper, gold, nickel and aluminium. We show that the potentials based on this scheme can be modified to provide reasonable stacking-fault energy values and consequently a better description of the plastic properties. Modifications were done by changing the cut-off distance in case of aluminium and nickel, and in case of gold and copper by also modifying the functional form of the pair-potential. In order to validate these modified potentials we have tested them by studying various properties, such as structural, defect, and surface energies, and phonon spectra and comparing results with those from experiments and other model potentials. read less USED (low confidence) N. Sandberg, B. Magyari-Köpe, and T. Mattsson, “Self-diffusion rates in Al from combined first-principles and model-potential calculations.,” Physical review letters. 2002. link Times cited: 60 Abstract: Monovacancy diffusion alone dominates over diffusion due to … read moreAbstract: Monovacancy diffusion alone dominates over diffusion due to divacancies and interstitials in Al for all temperatures up to the melting point. Deviations from a single Arrhenius dependence are due to anharmonicity. The conclusion is based on a combination of theoretical methods, from density functional theory to thermodynamic integration, without fitting to experimental data. The calculated diffusion rate agrees with experimental data over 11 orders of magnitude. read less USED (low confidence) J. Li, K. Vliet, T. Zhu, S. Yip, and S. Suresh, “Atomistic mechanisms governing elastic limit and incipient plasticity in crystals,” Nature. 2002. link Times cited: 612 USED (low confidence) A. Sagy, Z. Reches, and J. Fineberg, “Dynamic fracture by large extraterrestrial impacts as the origin of shatter cones,” Nature. 2002. link Times cited: 64 USED (low confidence) T. Fujita, Z. Horita, and T. Langdon, “Characteristics of diffusion in Al-Mg alloys with ultrafine grain sizes,” Philosophical Magazine A. 2002. link Times cited: 64 Abstract: Equal-channel angular pressing (ECAP) was used to refine the… read moreAbstract: Equal-channel angular pressing (ECAP) was used to refine the grain sizes of pure Al and an Al-3 wt% Mg alloy containing minor additions of either Sc or Zr. Following ECAP, the grain sizes were in the ultrafine submicrometre range. Diffusion couples were prepared from the fine-grained material produced by ECAP and from the coarse-grained material without ECAP and these couples were used to measure the interdiffusion coefficients for Mg in an Al lattice. The results show the interdiffusion coefficient is larger in the fine-grained material and the experimental data from this couple agree with predictions from molecular dynamic simulations using the embedded-atom method. An activation energy of about 87 kJ mol−1 is estimated for grain-boundary diffusion of Mg in Al where this value is consistent with the expectations from measurements of the activation energy for lattice diffusion of Mg in Al. There is no evidence for enhanced diffusion in the boundaries produced by ECAP due, it is suggested, to the rapid equilibration of these non-equilibrium boundaries at elevated temperatures. read less USED (low confidence) G. Campbell, M. Kumar, W. King, J. Belak, J. Moriarty, and S. Foiles, “The rigid-body displacement observed at the Σ = 5, (310)-[001] symmetric tilt grain boundary in central transition bcc metals,” Philosophical Magazine. 2002. link Times cited: 17 Abstract: The identical ∑ = 5, (310)-[001] symmetric tilt grain bounda… read moreAbstract: The identical ∑ = 5, (310)-[001] symmetric tilt grain boundary (STGB) was fabricated in three different bcc metals (Nb, Mo and Ta) by ultrahigh-vacuum diffusion bonding and the atomic structure was observed by high-resolution transmission electron microscopy. We report the results of quantitative measures of the rigid-body shift of the ∑ = 5, (310)-[001] STGB for all three metals. The atomic structures of these boundaries were also predicted by atomistic simulations using potentials developed within the framework of the model generalized pseudopotential theory for these same three metals. These potentials are an example of a new class of interatomic potentials that incorporate angularly dependent d-state interactions. These models of interatomic interactions should have applicability to simulations of the central transition bcc metals owing to the directional nature of the d bonding. To test these new models, methods were developed for quantitative measurement of the grain-boundary structure from... read less USED (low confidence) P. Vogl, U. Hansen, and V. Fiorentini, “Multiscale approaches for metal thin film growth,” Computational Materials Science. 2002. link Times cited: 10 USED (low confidence) M. Bockstedte, S. J. Liu, O. Pankratov, C. Woo, and H.-C. Huang, “Diffusion of clusters down (111) aluminum islands,” Computational Materials Science. 2002. link Times cited: 8 USED (low confidence) R. Hoagland and R. Kurtz, “The relation between grain-boundary structure and sliding resistance,” Philosophical Magazine A. 2002. link Times cited: 37 Abstract: During sliding, the grain-boundary (GB) energy depends on th… read moreAbstract: During sliding, the grain-boundary (GB) energy depends on the atomic structures produced during relative translation of the two grains. The variation in the GB energy within the two-dimensional boundary unit cell (BUC) constitutes the GB-γ surface. Maxima in the slope of the γ surface determines the sliding resistance, that is the stress required to move the system over the lowest saddle points along a particular path within the BUC. In this paper we present the results of an atomistic study of the γ surfaces for two types of boundaries in a fcc metal. One of the boundaries is a Σg = 11, <110 > {131} which is a low-energy boundary and has a simple γ surface with a single stable configuration located at the corners and centre of the BUC. The resistance to sliding was determined by chain-of-states methods along four shear vectors connecting equivalent states within the BUC and is found to be very high in all cases. The asymmetric, Σ = 11, <110 > {252}-{414} GB, has a higher GB energy and its γ surface is much more complex, with distinctly different structures appearing at various locations in the BUC. At certain locations, more than one structure is found for the asymmetric GB. Although complex, a chain-of-states calculation along one path across the BUC suggests that the shear strength of this GB is also quite high. Extrinsic GB dislocations are found to lower the resistance to shear considerably and, therefore, to perform the same role in shear of GBs as do glide dislocations in slip of the lattice. The existence of multiple configurations has significant implications for the interaction of lattice dislocations with GBs, the core structure of GB dislocations, the temperature dependence of GB properties, and the GB sliding resistance, which we discuss. read less USED (low confidence) S. Namilae, N. Chandra, and T. Nieh, “Atomistic simulation of grain boundary sliding in pure and magnesium doped aluminum bicrystals,” Scripta Materialia. 2002. link Times cited: 58 USED (low confidence) S. Foiles and D. Medlin, “Structure and climb of twin dislocations in aluminum,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2001. link Times cited: 13 USED (low confidence) V. Yamakov, D. Wolf, M. Salazar, S. Phillpot, and H. Gleiter, “Length-scale effects in the nucleation of extended dislocations in nanocrystalline Al by molecular-dynamics simulation,” Acta Materialia. 2001. link Times cited: 359 USED (low confidence) C. Busse, C. Engin, H. Hansen, U. Linke, T. Michely, and H. Urbassek, “Adatom formation and atomic layer growth on Al(1 1 1) by ion bombardment: experiments and molecular dynamics simulations,” Surface Science. 2001. link Times cited: 29 USED (low confidence) S. Nishitani, S. Ohgushi, Y. Inoue, and H. Adachi, “Grain boundary energies of Al simulated by environment-dependent embedded atom method,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 2001. link Times cited: 11 USED (low confidence) O. Trushin, P. Salo, M. Alatalo, and T. Ala‐Nissila, “Atomic mechanisms of cluster diffusion on metal fcc(100) surfaces,” Surface Science. 2001. link Times cited: 19 USED (low confidence) V. Shenoy, “Size-dependent rigidities of nanosized torsional elements,” International Journal of Solids and Structures. 2001. link Times cited: 159 USED (low confidence) O. Trushin et al., “Adatom island diffusion on metal fcc(100) surfaces.” 2001. link Times cited: 1 USED (low confidence) R. Schäublin, P. Almeida, A. Almazouzi, and M. Victoria, “Correlation of simulated TEM images with irradiation induced damage,” Journal of Nuclear Materials. 2000. link Times cited: 7 USED (low confidence) C.-S. Liu and Z.-G. Zhu, “Comparison between Cooling Rate Dependence of Macroscopic and Microscopic Quantities in Simulated Aluminium Glass,” Chinese Physics Letters. 2000. link Times cited: 2 Abstract: Constant-pressure molecular dynamics simulations and an anal… read moreAbstract: Constant-pressure molecular dynamics simulations and an analysis of the local atomic structures have been performed to study the cooling rate dependence of some macroscopic and microscopic quantities in aluminium glass. Macroscopic quantities, enthalpy and density, see an observable but small dependence on the cooling rate. Icosahedral ordering units exhibit strong cooling rate dependence, which is responsible for the dependence of the enthalpy and the density on the cooling rate; while the almost independence of some microstructural units such as the 1541, 1431 and 1421 pairs of the cooling rate may lead to a small dependence of the enthalpy and the density on the cooling rate. read less USED (low confidence) D. Olmsted, K. Hardikar, and R. Phillips, “Lattice resistance and Peierls stress in finite size atomistic dislocation simulations,” Modelling and Simulation in Materials Science and Engineering. 2000. link Times cited: 33 Abstract: Atomistic computations of the Peierls stress in fcc metals a… read moreAbstract: Atomistic computations of the Peierls stress in fcc metals are relatively scarce. By way of contrast, there are many more atomistic computations for bcc metals, as well as mixed discrete-continuum computations of the Peierls-Nabarro type for fcc metals. One of the reasons for this is the low Peierls stresses in fcc metals. Because atomistic computations of the Peierls stress take place in finite simulation cells, image forces caused by boundaries must either be relaxed or corrected for if system size-independent results are to be obtained. One of the approaches that has been developed for treating such boundary forces is by computing them directly and subsequently subtracting their effects, as developed in (Shenoy V B and Phillips R 1997 Phil. Mag. A 76 367). That work was primarily analytic, and limited to screw dislocations and special symmetric geometries. We extend that work to edge and mixed dislocations, and to arbitrary two-dimensional geometries, through a numerical finite element computation. We also describe a method for estimating the boundary forces directly on the basis of atomistic calculations. We apply these methods to the numerical measurement of the Peierls stress and lattice resistance curves for a model aluminium (fcc) system using an embedded-atom potential. read less USED (low confidence) R. Wang and F. Qianfeng, “Core structure and mobility of an edge dislocation in aluminum,” Journal of Alloys and Compounds. 2000. link Times cited: 15 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 USED (low confidence) J. Jaffe, R. Kurtz, and M. Gutowski, “Comparison of embedded-atom models and first-principles calculations for Al phase equilibrium,” Computational Materials Science. 2000. link Times cited: 7 USED (low confidence) A. Lyubartsev and A. Laaksonen, “Determination of effective pair potentials from ab initio simulations: application to liquid water,” Chemical Physics Letters. 2000. link Times cited: 30 USED (low confidence) A. Landa, P. Wynblatt, E. Johnson, and U. Dahmen, “Computer simulation of Pb/Al interfaces,” Acta Materialia. 2000. link Times cited: 24 USED (low confidence) R. Hugo and R. Hoagland, “The kinetics of gallium penetration into aluminum grain boundaries—in situ TEM observations and atomistic models,” Acta Materialia. 2000. link Times cited: 95 USED (low confidence) G. Gilmer, H.-C. Huang, T. D. Rubia, J. D. Torre, and F. Baumann, “Lattice Monte Carlo models of thin film deposition,” Thin Solid Films. 2000. link Times cited: 122 USED (low confidence) M. Sarychev, Y. Zhitnikov, L. Borucki, C. Liu, and T. Makhviladze, “A new, general model for mechanical stress evolution during electromigration,” Thin Solid Films. 2000. link Times cited: 14 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) V. Bulatov, O. Richmond, and M. Glazov, “An atomistic dislocation mechanism of pressure-dependent plastic flow in aluminum,” Acta Materialia. 1999. link Times cited: 90 USED (low confidence) X.-Y. Liu, C.-L. Liu, and L. J. Borucki, “A new investigation of copper’s role in enhancing Al-Cu interconnect electromigration resistance from an atomistic view,” Acta Materialia. 1999. link Times cited: 44 USED (low confidence) W. Fan, Y.-zhen He, and X. Gong, “Molecular dynamics study on the structural changes of the tilt grain boundary in aluminium,” Philosophical Magazine. 1999. link Times cited: 12 Abstract: The structure and physical properties of two Al tilt grain b… read moreAbstract: The structure and physical properties of two Al tilt grain boundaries (GBs) at different temperatures have been studied using the molecular dynamics method. We find that, with increasing temperature, the GB structure changes by steps. Three characteristic temperatures T 0, T 1 and T 2 have been identified for the changes in the GB structure. A comparison with available experimental data has also been made. read less USED (low confidence) A. Bilić, B. King, and D. J. O’connor, “EMBEDDED ATOM METHOD STUDY OF SURFACE ALLOYING OF Al ON Pd(001),” Surface Review and Letters. 1999. link Times cited: 0 Abstract: We have simulated the structure and energetics of thin films… read moreAbstract: We have simulated the structure and energetics of thin films created by the deposition of Al onto Pd(001). The study has been carried out within the semiempirical embedded atom method (EAM), utilizing a Pd–Al potential from the literature and two other alloy potentials generated from elemental potentials. Only one of the potentials reproduces the experimentally observed reconstruction. Problems with the construction and validity of the alloy potentials are highlighted. read less USED (low confidence) A. Almazouzi, M. Caturla, M. Alurralde, T. D. Rubia, and M. Victoria, “Defect production and damage evolution in Al: a molecular dynamics and Monte Carlo computer simulation,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 1999. link Times cited: 18 USED (low confidence) R. Kurtz, R. Hoagland, and J. Hirth, “Computer simulation of extrinsic grain-boundary defects in the ∑11, 〈101〉131 symmetric tilt boundary,” Philosophical Magazine. 1999. link Times cited: 38 Abstract: A computer simulation was performed to investigate the struc… read moreAbstract: A computer simulation was performed to investigate the structure and properties of extrinsic grain-boundary (GB) defects in the {11, 〈101〉 {131} symmetric tilt boundary. An embedded-atom method potential was employed to represent aluminium. Standard molecular dynamics relaxation techniques were used to compute low-temperature (about 0 K) equilibrium structures. Extrinsic GB dislocations were introduced into the models by application of the exact anisotropic elastic displacement field for a bicrystal interface. Some dislocations were accompanied by geometrically necessary steps (in which case the pair form a disconnection) to avoid formation of GB faults. The structure and properties of the equilibrium GB were compared with GBs containing steps, dislocations and disconnections. A broad range of GB defects was studied in order to characterize their potential effect on GB sliding resistance. read less USED (low confidence) P. Gumbsch, “Atomistic modelling of diffusion-controlled interfacial decohesion,” Materials Science and Engineering A-structural Materials Properties Microstructure and Processing. 1999. link Times cited: 12 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 USED (low confidence) J. Hirth and R. Hoagland, “Extrinsically dissociated dislocations in simulated aluminium,” Philosophical Magazine. 1998. link Times cited: 10 Abstract: The dissociation of dislocations into partials bounding an e… read moreAbstract: The dissociation of dislocations into partials bounding an extrinsic stacking fault is studied in an atomistic simulation of aluminium. An embedded-atom-type potential is employed. Of two possible extended configurations, one retains an extrinsic stacking fault in a stable array while the other converts to an array with an intrinsic stacking fault. The results are related to interaction forces among the partial dislocations in the arrays. read less USED (low confidence) R. Kurtz and R. Hoagland, “Effect of grain boundary dislocations on the sliding resistance of Σ11 grain boundaries in aluminum,” Scripta Materialia. 1998. link Times cited: 15 USED (low confidence) R. Hoagland, A. Voter, and S. Foiles, “Self-diffusion within the cores of a dissociated glide dislocation in an fcc solid,” Scripta Materialia. 1998. link Times cited: 11 USED (low confidence) H. Heinisch, R. Hoagland, R. Kurtz, and J. Hirth, “Computer simulation of a [110] edge dislocation intersecting a σ11 〈101〉 131 grain boundary in aluminum,” Scripta Materialia. 1998. link Times cited: 5 USED (low confidence) X. Liu and J. B. Adams, “GRAIN-BOUNDARY SEGREGATION IN Al-10%Mg ALLOYS AT HOT WORKING TEMPERATURES,” Acta Materialia. 1998. link Times cited: 102 USED (low confidence) G. Odette and G. Lucas, “Recent progress in understanding reactor pressure vessel steel embrittlement,” Radiation Effects and Defects in Solids. 1998. link Times cited: 334 Abstract: This paper reviews the current understanding of the basic me… read moreAbstract: This paper reviews the current understanding of the basic mechanisms of irradiation embrittlement in reactor pressure vessel steels. Radiation enhanced diffusiona at operating temperatures around 290°C leads to the formation of various ultrafine scale hardening phases, including copper rich and copper catalysed manganese-nickel rich precipitates. Other nanofeatures that do not require copper, so-called matrix defects, include alloy phosphides and carbonitrides as well as defect cluster-solute complexes. Matrix defects that are thermally unstable (anneal) under irradiation play a very important role in mediating flux and temperature effects. The balance of features depends on the composition of the steel and the irradiation conditions. Copper enriched phases, which are the dominant embrittling feature in alloys containing significant trace quantities of this element, are fairly well understood. In contrast, the detailed identity and etiology of the matrix defects and manganese-nickel rich phases t... read less USED (low confidence) Y. Shimomura and R. Nishiguchi, “Vacancy clustering to faulted loop, stacking fault tetrahedron and void in fcc metals,” Radiation Effects and Defects in Solids. 1997. link Times cited: 16 Abstract: An atomistic step of growth to a faulted loop, a stacking fa… read moreAbstract: An atomistic step of growth to a faulted loop, a stacking fault tetrahedron (sft) and a void by clustering of vacancies in fcc metals was studied by molecular dynamics computer simulation with an isotropic EAM potential due to Daw and Baskes [1]. In aluminum, a tri-vacancy relaxes to the Damask-Dienes-Weizer structure (3v-sft). A penta-vacancy relaxes to an octahedral 6v in which an atom is included. The relaxed 5v is stable so that a 6v grows to doubly linked relaxed 5v. This is a critical step of faulted loop formation. By further absorption of vacancy, a cluster grows to an array of relaxed 5vs on a (111) plane and finally collapses to a faulted loop. In gold, a stable structure of vacancy cluster below 15v is a void. A tri-vacancy in gold does not relax to the Damask-Dienes-Weizer structure. Above the size of 6v, partial relaxation of 3v-sft type was observed. The relaxation of a micro-void to a sft is the thermal activated process. In nickel, a void is the most stable cluster below 20v and a... read less USED (low confidence) X. Liu, P. Ohotnicky, J. B. Adams, C. L. Rohrer, and R. Hyland, “Anisotropic surface segregation in AlMg alloys,” Surface Science. 1997. link Times cited: 165 USED (low confidence) H. Cox, R. Johnston, and J. Murrell, “Modelling of surface relaxation and melting of aluminium,” Surface Science. 1997. link Times cited: 23 USED (low confidence) E. Tadmor, M. Ortiz, and R. Phillips, “Quasicontinuum analysis of defects in solids,” Philosophical Magazine. 1996. link Times cited: 1472 Abstract: We develop a method which permits the analysis of problems r… read moreAbstract: We develop a method which permits the analysis of problems requiring the simultaneous resolution of continuum and atomistic length scales-and associated deformation processes-in a unified manner. A finite element methodology furnishes a continuum statement of the problem of interest and provides the requisite multiple-scale analysis capability by adaptively refining the mesh near lattice defects and other highly energetic regions. The method differs from conventional finite element analyses in that interatomic interactions are incorporated into the model through a crystal calculation based on the local state of deformation. This procedure endows the model with crucial properties, such as slip invariance, which enable the emergence of dislocations and other lattice defects. We assess the accuracy of the theory in the atomistic limit by way of three examples: a stacking fault on the (111) plane, and edge dislocations residing on (111) and (100) planes of an aluminium single crystal. The method correctly predicts the splitting of the (111) edge dislocation into Shockley partials. The computed separation of these partials is consistent with results obtained by direct atomistic simulations. The method predicts no splitting of the Al Lomer dislocation, in keeping with observation and the results of direct atomistic simulation. In both cases, the core structures are found to be in good agreement with direct lattice statics calculations, which attests to the accuracy of the method at the atomistic scale. read less USED (low confidence) R. E. Miller and R. Phillips, “Critical analysis of local constitutive models for slip and decohesion,” Philosophical Magazine. 1996. link Times cited: 30 Abstract: Many problems in the modelling of materials call for a synth… read moreAbstract: Many problems in the modelling of materials call for a synthesis of approaches used at both the atomistic and the continuum levels. One notable implementation of this type of strategy is in the construction of local constitutive relations which serve to provide a microscopic underpinning for the energetics of phenomena ranging from interfacial debonding to dislocation nucleation. The need for atomistics in the formulation of such local constitutive approaches is twofold; first, atomistics can serve as the basis of the constitutive phenomenology itself; secondly, atomistics can be used to make quantitative tests of the assumptions which underlie the continuum framework. The present work demonstrates this strategy through the examples of two types of continuum models: the Peierls framework used in the analysis of dislocation nucleation in solids and the type of model used to describe interfacial debonding. Using atomistics within the framework of the embedded-atom method, we test each of the centra... read less USED (low confidence) A. Voter and G. Editor, “Interatomic Potentials for Atomistic Simulations,” MRS Bulletin. 1996. link Times cited: 28 Abstract: Atomistic simulations are playing an increasingly prominent … read moreAbstract: Atomistic simulations are playing an increasingly prominent role in materials science. From relatively conventional studies of point and planar defects to large-scale simulations of fracture and machining, atomistic simulations offer a microscopic view of the physics that cannot be obtained from experiment. Predictions resulting from this atomic-level understanding are proving increasingly accurate and useful. Consequently, the field of atomistic simulation is gaining ground as an indispensable partner in materials research, a trend that can only continue. Each year, computers gain roughly a factor of two in speed. With the same effort one can then simulate a system with twice as many atoms or integrate a molecular-dynamics trajectory for twice as long. Perhaps even more important, however, are the theoretical advances occurring in the description of the atomic interactions, the so-called “interatomic potential” function. The interatomic potential underpins any atomistic simulation. The accuracy of the potential dictates the quality of the simulation results, and its functional complexity determines the amount of computer time required. Recent developments that fit more physics into a compact potential form are increasing the accuracy available per simulation dollar. This issue of MRS Bulletin offers an introductory survey of interatomic potentials in use today, as well as the types of problems to which they can be applied. This is by no means a comprehensive review. It would be impractical here to attempt to present all the potentials that have been developed in recent years. Rather, this collection of articles focuses on a few important forms of potential spanning the major classes of materials bonding: covalent, metallic, and ionic. read less USED (low confidence) C.-L. Liu and S. Plimpton, “Molecular dynamics simulations of grain boundary diffusion in Al using embedded atom method potentials,” Journal of Materials Research. 1995. link Times cited: 9 Abstract: Molecular dynamics (MD) simulations of diffusion in a Σ5(310… read moreAbstract: Molecular dynamics (MD) simulations of diffusion in a Σ5(310) [001] Al tilt grain boundary were performed using for the first time three different potentials based on the embedded atom method (EAM). The EAM potentials that produce more accurate melting temperatures also yield activation energies in better agreement with experimental data. Compared to pair potentials, the EAM potentials also give more accurate results. read less USED (low confidence) Y. Oh, W. Ko, N.-W. Kwak, J. Jang, T. Ohmura, and H. Han, “Small-scale analysis of brittle-to-ductile transition behavior in pure tungsten,” Journal of Materials Science & Technology. 2022. link Times cited: 12 USED (low confidence) S. Urata, N. Nakamura, K. Aiba, T. Tada, and H. Hosono, “How fluorine minimizes density fluctuations of silica glass: Molecular dynamics study with machine-learning assisted force-matching potential,” Materials & Design. 2021. link Times cited: 14 USED (low confidence) W. Li, “Mechanophores in polymer mechanochemistry: Insights from single-molecule experiments and computer simulations.” 2021. link Times cited: 0 USED (low confidence) B. Bauerhenne, “Empirical MD Simulations of Laser-Excited Matter,” Materials Interaction with Femtosecond Lasers. 2021. link Times cited: 0 USED (low confidence) W. Rangubpit, P. Sompornpisut, and R. Pandey, “Structure and dynamics of aquaporin-1.,” Vitamins and hormones. 2020. link Times cited: 0 USED (low confidence) R. Devanathan, “Interatomic Potentials for Nuclear Materials,” Handbook of Materials Modeling. 2020. link Times cited: 1 USED (low confidence) E. Laurini, P. Posocco, M. Fermeglia, and S. Pricl, “Multiscale Molecular Modeling of Clay–Polymer Nanocomposites.” 2017. link Times cited: 5 USED (low confidence) S. Starikov, A. Kuksin, and D. Smirnova, “Multi-scale model for point defects behaviour in uranium mononitride,” Journal of Physics: Conference Series. 2017. link Times cited: 1 Abstract: A multiscale approach was used to study the properties of po… read moreAbstract: A multiscale approach was used to study the properties of point defects in uranium mononitride (UN). In this work we used combination of several methods: ab initio calculations; molecular dynamics simulations with a new interatomic potential; thermodynamic model. Density functional theory (DFT) calculations are used for fitting of the parameters of the angular-dependent interatomic potential, as well as for evaluation of the defects formation and migration energies. Molecular dynamics (MD) simulations are applied to analyze what migration/formation mechanisms are activated at finite temperatures and to calculate diffusion coefficients of point defects. The thermodynamic model for description of concentrations and diffusivities for point defects in non-stoichiometric UN1+x is proposed. read less USED (low confidence) L. Kolotova and S. Starikov, “Atomistic simulation of defects formation and structure transitions in U-Mo alloys at swift heavy ion irradiation,” Journal of Physics: Conference Series. 2017. link Times cited: 1 Abstract: At irradiation of swift heavy ions, the track formation freq… read moreAbstract: At irradiation of swift heavy ions, the track formation frequently takes place in nuclear materials. There is a large interest to understanding of the mechanisms of defects/track formation at this phenomenon. In this work, the atomistic simulation of defects formation and melting in U-Mo alloys at irradiation of swift heavy ions has been carried out. We use the two-temperature atomistic model with explicit account of electron pressure and electron thermal conductivity. This two-temperature model describes ionic subsystem by means of molecular dynamics while the electron subsystem is considered in the continuum approach. The various mechanisms of structure changes at irradiation are examined. In particular, the simulation results indicate that the defects formation may be produced without melting and subsequent crystallization. Threshold stopping power of swift ions for the defects formation at irradiation in the various conditions are calculated. read less USED (low confidence) C. Pinilla, M. Acuña-Rojas, N. Seriani, and S. Scandolo, “An atomistic model of MgSiO3 perovskite and post-perovskite phases,” Computational Materials Science. 2017. link Times cited: 2 USED (low confidence) O. Alizadeh, G. T. Eshlaghi, and S. Mohammadi, “Nanoindentation simulation of coated aluminum thin film using quasicontinuum method,” Computational Materials Science. 2016. link Times cited: 12 USED (low confidence) S. Genheden, “Coarse-grained bond and angle distributions from atomistic simulations: On the systematic parameterisation of lipid models.,” Journal of molecular graphics & modelling. 2016. link Times cited: 3 USED (low confidence) D. T. Allen and C. Lorenz, “Molecular Scale Simulations of the Self–Assembly of Amphiphilic Molecules: Current State-of-the-Art and Future Directions.” 2016. link Times cited: 5 Abstract: Gaining an understanding of the self–assembly of amphiphilic… read moreAbstract: Gaining an understanding of the self–assembly of amphiphilic molecules has been a goal for experimental, theoretical and computational research in the field of soft matter for approximately a century. In the field of materials modelling, understanding the self–assembly of amphiphilic molecules at experimental conditions has proven to be a challenging problem and has led to several developments that have driven the entire field of computational materials science forward. In this review, we present the current-state-ofthe-art in terms of applying all-atom and coarse–grain molecular dynamics simulations in order to study the self–assembly process and the structure that results. Additionally, we present a few of the challenges that still exist with some ideas as to future directions that may be used to overcome them. read less USED (low confidence) S. Lu and X. Zhou, “Construction of Coarse-Grained Models by Reproducing Equilibrium Probability Density Function,” Communications in Theoretical Physics. 2015. link Times cited: 4 Abstract: The present work proposes a novel methodology for constructi… read moreAbstract: The present work proposes a novel methodology for constructing coarse-grained (CG) models, which aims at minimizing the difference between CG model and the corresponding original system. The difference is defined as a functional of their equilibrium conformational probability densities, then is estimated from equilibrium averages of many independent physical quantities denoted as basis functions. An orthonormalization strategy is adopted to get the independent basis functions from sufficiently preselected interesting physical quantities of the system. Thus the current method is named as probability density matching coarse-graining (PMCG) scheme, which effectively takes into account the overall characteristics of the original systems to construct CG model, and it is a natural improvement of the usual CG scheme wherein some physical quantities are intuitively chosen without considering their correlations. We verify the general PMCG framework in constructing a one-site CG water model from TIP3P model. Both structure of liquids and pressure of the TIP3P water system are found to be well reproduced at the same time in the constructed CG model. read less USED (low confidence) R. J. Gowers and P. Carbone, “Coarse-Grained and Hybrid Simulations of Nanostructures.” 2015. link Times cited: 0 USED (low confidence) R. Khanna and V. Sahajwalla, “Atomistic Simulations of Properties and Phenomena at High Temperatures.” 2014. link Times cited: 3 USED (low confidence) S. Lu, D. Li, and D. Brenner, “Molecular Dynamics Simulations of Plastic Damage in Metals.” 2014. link Times cited: 6 USED (low confidence) P. Rico and P. Antonio, “Relaxation processes in Cu-Zr metallic glasses by molecular dynamics simulations.” 2014. link Times cited: 0 Abstract: Παρουσιάζουμε αποτελέσματα προσομοιώσεων Μοριακής Δυναμικής … read moreAbstract: Παρουσιάζουμε αποτελέσματα προσομοιώσεων Μοριακής Δυναμικής σχετικά με τις διαδικασίες εφησυχασμών που συμβαίνουν στη Μεταλλική Ύαλο Cu₆₅Zr₃₅ σε κατάσταση ηρεμίας, κατά τη διάρκεια της εφελκυστικής τάσης, καθώς και την απελευθέρωση τάσης που λαμβάνει χώρα όταν το υλικό αυτό είναι υπό σταθερή πίεση. Η μελέτη περιλαμβάνει μια διεξοδική ανάλυση των θερμοδυναμικών, δομικών και δυναμικών ιδιοτήτων αυτού του συστήματος. Βρήκαμε έναν δονητικό τρόπο των ατομικών κινήσεων που λαμβάνει χώρα σε ιδιαίτερα τοπικές περιοχές που χαρακτηρίζονται από την υψηλή τους κινητικότητα και τη χαμηλή τοπική πυκνότητα και αποτελούνται κυρίως από χαλαρά συσσωρευμένες ομάδες ατόμων. Ο δονητικός αυτός τρόπος έχει μια συχνότητα που ουσιαστικά είναι ανεξάρτητη τόσο από τη θερμοκρασία όσο και από την εφαρμοζόμενη ένταση. Ωστόσο, οι περιοχές όπου εντοπίζονται τα ταλαντευόμενα άτομα αυξάνονται με τη θερμοκρασία και την εφαρμοζόμενη ένταση. Υποστηρίζεται ότι οι κινήσεις αυτές αποτελούν τις «γρήγορες διαδικασίες» που βρίσκονται μεταξύ της χαλάρωσης β και της κορυφής του Boson στο χαρακτηριστικό φάσμα των δυναμικών τρόπων λειτουργίας στα γυαλιά. Επιπλέον, διαπιστώσαμε ότι η ύαλος αυτή παρουσίασε μια χαρακτηριστική ενδοθερμική απόκριση κατά τον εφελκυσμό η οποία δεν έχει αναφερθεί προηγουμένως. Η μελέτη αυτής της απόκρισης και η εξέλιξή της κατά τη διέγερση δείχνει την παρουσία διαδικασιών γήρανσης και αναζωογόνησης και οριοθετεί τα διαφορετικά στάδια στα οποία κυριαρχεί η καθεμία από αυτές τις διεργασίες στο γυαλί μας. Συμπεραίνεται ότι οι γρήγορες διεργασίες είναι πρόδρομοι του τρόπου β και θα μπορούσαν να θεωρηθούν ως παράγοντες πρόβλεψης της χωρικής προέλευσης των ζωνών μετασχηματισμού διάτμησης που διέπουν την έναρξη της πλαστικής ροής. Περαιτέρω, κατά την διάρκεια της διαδικασίας χαλάρωσης του στρες που συμβαίνει όταν το γυαλί υποβάλλεται σε σταθερή τάση, η θέση των ταλαντευόμενων ατόμων συμπίπτει με τις ετερογενείς περιοχές όπου απελευθερώνεται το μεγαλύτερο μέρος του στρες και της ενέργειας του συστήματος και επομένως δρουν ως διαμεσολαβητές στρες των μεταλλικών γυαλιών. Αυτά τα αποτελέσματα θα μπορούσαν να είναι χρήσιμα για την κατανόηση του σύνθετου φάσματος χαλάρωσης των μεταλλικών γυαλιών και να παρέχουν μια καλύτερη εικόνα της περίπλοκης δυναμικής χαλάρωσης που χαρακτηρίζει αυτά τα υλικά, ειδικά στην περιοχή υψηλότερων συχνοτήτων. Επιπλέον, τα αποτελέσματα που παρουσιάζονται εδώ έχουν σημαντικές συνέπειες στις μακροσκοπικές ιδιότητες των μεταλλικών γυαλιών, όπως η ολκιμότητα, η ευθραυστότητα και το κάταγμα της σκληρότητας. Αποδεικνύεται λοιπόν ότι η κατανόηση της δομικής και δυναμικής συμπεριφοράς των MG κατά τη διάρκεια αυτών των διαδικασιών χαλάρωσης είναι ζωτικής σημασίας για τον ενδεχόμενο έλεγχο και βελτίωση των ιδιοτήτων τους. read less USED (low confidence) G. Fiorin, M. Klein, R. Devane, and W. Shinoda, “Computer Simulation of Self-Assembling Macromolecules.” 2013. link Times cited: 5 USED (low confidence) A. Iskandarov, S. Dmitriev, and Y. Umeno, “On Accurate Approach for Molecular Dynamics Study of Ideal Strength at Elevated Temperature,” Journal of Solid Mechanics and Materials Engineering. 2012. link Times cited: 3 Abstract: Influence of temperature on ideal shear strength (ISS), τc, … read moreAbstract: Influence of temperature on ideal shear strength (ISS), τc, of two fcc metals (Al and Cu) was studied by means of molecular dynamics simulations. To get reliable results we investigated influence of parameters of the applied Parrinello-Rahman stress control method and implemented damping of simulation cell fluctuations to avoid occurrence of structural instability assisted by too high fluctuations. The damping successfully reduces strain and stress fluctuations during simulations if the damping factor is specified properly. We also investigated simulation cell size effect to evaluate minimal number of atoms providing reliable results in order to reduce computational efforts and estimate the possibility of applying ab initio calculations. Recently developed embedded atom method (EAM) interatomic potentials for both metals were also examined to find most appropriate for our study. EAM potential developed by Zope et al. and Mishin et al. were revealed to be most suitable for Al and Cu, respectively. It is essential to choose appropriate simulation parameters and interatomic potentials for the valid evaluation of ISS at elevated temperatures. We find almost linear decrease in ideal strength with increasing temperature for [112](111) shear deformation, while critical strain decreases in a nonlinear manner. At room temperature, reduction of shear strength for Al(Cu) is less than 35%(25%) compared to that at 0 K. read less USED (low confidence) L. Pahlevani and H. Shodja, “Surface and Interface Effects on Torsion of Eccentrically Two-Phase fcc Circular Nanorods: Determination of the Surface/Interface Elastic Properties via an Atomistic Approach,” Journal of Applied Mechanics. 2011. link Times cited: 36 Abstract: The effect of surface and interface elasticity in the analys… read moreAbstract: The effect of surface and interface elasticity in the analysis of the Saint–Venant torsion problem of an eccentrically two-phase fcc circular nanorod is considered; description of the behavior of such a small structure via usual classical theories cease to hold. In this work, the problem is formulated in the context of the surface/interface elasticity. For a rigorous solution of the proposed problem, conformal mapping with a Laurent series expansion are employed together. The numerical results well illustrate that the torsional rigidity and stress distribution corresponding to such nanosized structural elements are significantly affected by the size. In order to employ surface and interface elasticity, several key properties such as surface energy, surface stresses, and surface elastic constants of several fcc materials as well as interface properties of the noncoherent fcc bicrystals are derived in terms of Rafii-Tabar and Sutton interatomic potential function. For determination of the surface/interface parameters a molecular dynamics program, which uses the above-mentioned potential function, is developed. The calculated surface and interface properties are in reasonable agreement with the corresponding results in literature. Some applications of the given results can be contemplated in the design of micro-/nano-electromechanical systems. read less USED (low confidence) T. Luther and C. Könke, “COUPLED COHESIVE ZONE REPRESENTATIONS FROM 3D QUASICONTINUUM SIMULATION ON BRITTLE GRAIN BOUNDARIES,” International Journal for Multiscale Computational Engineering. 2011. link Times cited: 2 USED (low confidence) C. Lorenz and N. Doltsinis, “Molecular Dynamics Simulation: From ‘Ab Initio’ to ‘Coarse Grained.’” 2011. link Times cited: 12 USED (low confidence) F. Gao, “Computer Simulation Methods for Defect Configurations and Nanoscale Structures.” 2009. link Times cited: 2 USED (low confidence) J. Zhong and H. Shuai, “Quasicontinuum study of nanoindentation into nanocrystalline aluminum thin film,” Journal of Physics: Conference Series. 2009. link Times cited: 0 Abstract: Quasicontinuum simulations are performed to examine the mech… read moreAbstract: Quasicontinuum simulations are performed to examine the mechanical response of nanocrystalline aluminum thin film under nanoindentation. The simulations are conducted by driving the flat indenter into the (111) face of one grain in the aluminum film, two load drops have been found during the indentation process, evidence indicates that these load drops are related to the stacking fault emitted from the grain boundary. The effect of indenter width on nanoindentation response is also studied through three simulations with different indenter sizes. A rule is discovered that larger load is needed to initiate the first load drop for the wider indenter; however, this rule is not followed by the second load drop. read less USED (low confidence) H. Trebin et al., “Simulating structure and physical properties of complex metallic alloys.” 2008. link Times cited: 3 Abstract: An introduction is presented to numerical methods, by which … read moreAbstract: An introduction is presented to numerical methods, by which the behavior of complex metallic alloys can be simulated. We primarily consider the molecular dynamics (MD) technique as implemented in our software package IMD, where Newton’s equations of motion are solved for all atoms in a solid. After a short discourse on integration algorithms, some possible types of interactions are addressed. Already simple model potentials, as for example the Lennard-Jones-Gauss potential, can give rise to complex structures, where the characteristic length scales of the order by far exceed the range of the pair interaction. Realistic interactions are modelled by highly parametrized effective potentials, like the EAM (Embedded Atom Method) potential. Our program potfit allows to fit the parameters such that data from experiment or from ab-initio calculations are well reproduced. Several applications of the methods are outlined, notably the simulation of aluminium diffusion in quasicrystalline d-Al-Ni-Co, the computation of the phonon dispersion via the dynamical structure factor of MgZn2, the propagation of cracks in NbCr2, and an order-disorder phase transition in CaCd6. read less USED (low confidence) F. Rösch, “Atomistic dynamics of crack propagation in complex metallic alloys.” 2008. link Times cited: 0 Abstract: The failure of solid matter is familiar to us from everyday … read moreAbstract: The failure of solid matter is familiar to us from everyday life. A broken dish or a shattered glass is annoying. The breakage of a ship or an airplane hull, however, can cost human lives. Nevertheless, insight into the fundamental mechanisms leading to fracture has been gained only within the last couple of years. One reason for this is that fracture is a multi-scale phenomenon. A macroscopic external strain is directed to the crack tip, where it breaks atomic bonds. Thus, to understand fracture mechanisms in macroscopic devices, one also has to know the processes on the atomic scale. These are hardly accessible by experiments, in particular when dynamic aspects are the center of interest. They are also not included in the classical elastic theory of fracture. Computer simulations have proven to be a useful tool to examine fracture processes on an atomic level. In molecular dynamics simulations the trajectories of the atoms are calculated by integration of Newtons equations of motion. Numerical experiments with simple crystal structures and model interactions reveal phenomena that are related to the discrete nature of matter and therefore cannot be explained by continuum theories. In more complex systems the mechanisms are not yet clear.
In the current work two extreme cases of complex metallic alloys are investigated. The model quasicrystal is built-up mainly from atomic clusters. Due to the aperiodic long-range order, no unit cell exists. A major building block of the quasicrystal can also be used to obtain a periodic Friauf-Laves compound. The Friauf-Laves phases are topologically close-packed binary structures and form a huge class of intermetallic compounds. Among them are many candidates for high-temperature use. However, their brittleness at low and ambient temperature limits applications. Molecular dynamics simulations are performed to examine this brittle behavior at low temperature. First, model potentials are applied to qualitatively probe the influence of the underlying structure on crack propagation. In a second step, a specific Friauf-Laves compound is chosen. Interatomic potentials are constructed, which reproduce quantities obtained by quantum-mechanical calculations. Systematic fracture simulations then are performed.
Der Bruch fester Materie geschieht durch die Ausbreitung von Rissen und ist uns aus dem Alltag vertraut. Ein zerbrochener Teller oder ein zerschlagenes Glas ist lastig. Versagt dagegen der Rumpf eines Schiffes oder der eines Flugzeuges, kann dies Menschen das Leben kosten. Gleichwohl wurde erst in den letzten Jahren Einblick in die grundlegenden Mechanismen gewonnen, die zum Versagen von Festkorpern durch Rissbildung fuhren. Ein Grund hierfur ist, dass Bruch ein Multi-Skalen-Phanomen darstellt. Eine makroskopisch von ausen angelegte Spannung wird an der Rissspitze verstarkt. Daraufhin werden atomare Bindungen gebrochen. Um Bruchmechanismen makroskopischer Bauteile zu verstehen, wird somit die Kenntnis von Prozessen auf atomarer Ebene benotigt. Diese sind durch heutige experimentelle Techniken kaum zuganglich, insbesondere dann nicht, wenn dynamische Aspekte im Mittelpunkt des Interesses stehen. Solche Prozesse sind auch in der klassischen Elastizitatstheorie des Bruchs nicht berucksichtigt. Computersimulationen haben sich als nutzliches Hilfsmittel zur Untersuchung atomarer Vorgange erwiesen. In Molekulardynamik-Simulationen werden die Bahnen der Atome durch Integration der Newton'schen Bewegungsgleichungen berechnet. Numerische Experimente mit einfachen Kristallstrukturen und Modellwechselwirkungen lassen Effekte erkennen, fur die der diskrete Aufbau der Materie verantwortlich ist. Kontinuumstheorien sind daher nicht geeignet, die erwahnten Phanomene zu erklaren. Die Vorgange in komplexeren Festkorpern sind bis heute noch nicht vollstandig verstanden. Um einen Einblick in die grundlegenden Mechanismen zu erhalten, wird in der vorliegende Arbeit das Bruchverhalten komplexer metallischer Verbindungen bei tiefen Temperaturen mit Hilfe der Molekulardynamik untersucht. read less 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 USED (low confidence) M. Buehler, “Hierarchical Nanomechanics of Collagen Fibrils: Atomistic and Molecular Modeling.” 2008. link Times cited: 26 USED (low confidence) R. Aga and J. R. Morris, “Modeling: The Role Of Atomistic Simulations.” 2008. link Times cited: 1 USED (low confidence) R. Miller, “7 – Coupled atomistic/continuum modelling of plasticity in materials.” 2007. link Times cited: 0 USED (low confidence) W. Andreoni, A. Curioni, D. Fischer, S. Billeter, and C. Pignedoli, “STUDYING THE EFFECTS OF NITROGEN AND HAFNIUM INCORPORATION INTO THE SIO2/SI(100) INTERFACE WITH REPLICA-EXCHANGE MOLECULAR DYNAMICS AND DENSITYFUNCTIONAL- THEORY CALCULATIONS.” 2006. link Times cited: 0 USED (low confidence) R. Hayes, M. Fago, M. Ortiz, and E. Carter, “Prediction of Dislocation Nucleation During Nanoindentation by the Orbital-Free Density Functional Theory Local Quasi-continuum Method,” Multiscale Model. Simul. 2005. link Times cited: 41 Abstract: We introduce the orbital-free density functional theory loca… read moreAbstract: We introduce the orbital-free density functional theory local quasi-continuum\linebreak (OFDFT-LQC) method: a first-principles-based multiscale material model that embeds OFDFT unit cells at the subgrid level of a finite element computation. Although this method cannot address intermediate length scales such as grain boundary evolution or microtexture, it is well suited to study material phenomena such as continuum level prediction of dislocation nucleation and the effects of varying alloy composition. The model is illustrated with the simulation of dislocation nucleation during indentation into the $(111)$ and $(\overline{1}10)$ surfaces of aluminum and compared against results obtained using an embedded atom method interatomic potential. None of the traditional dislocation nucleation criteria (Hertzian principal shear stress, actual principal shear stress, von Mises strain, or resolved shear stress) correlates with a previously proposed local elastic stability criterion, $\Lambda$. Discrepancies in dislocation nucleation predictions between OFDFT-LQC and other simulations highlight the need for accurate, atomistic constitutive models and the use of realistically sized indenters in the simulations. read less USED (low confidence) Y. Mishin, “Interatomic Potentials for Metals.” 2005. link Times cited: 41 USED (low confidence) Y. Mishin, “Atomistic Computer Simulation of Diffusion.” 2005. link Times cited: 7 USED (low confidence) T. Tsuru and Y. Shibutani, “Formation of Prismatic Dislocation Loop of Single Crystalline Aluminum under Nanoindentation.” 2004. link Times cited: 1 USED (low confidence) V. Yamakov et al., “Deformation-mechanism map for nanocrystalline metals by molecular-dynamics simulation,” Nature Materials. 2004. link Times cited: 726 USED (low confidence) E. Tadmor, “A Peierls Criterion for Deformation Twinning at a Mode II Crack.” 2004. link Times cited: 2 USED (low confidence) D. Walgraef, “Reaction-diffusion approach to nanostructure formation and texture evolution in adsorbed monoatomic layers,” International Journal of Quantum Chemistry. 2004. link Times cited: 22 Abstract: It is shown that coverage evolution, during atomic depositio… read moreAbstract: It is shown that coverage evolution, during atomic deposition on a substrate, may be described, on mesoscopic scales, by dynamical models of the reaction–diffusion type. The models combine reaction terms representing adsorption–desorption processes and nonlinear diffusion terms of the Cahn–Hilliard type. The combination may lead, below a critical temperature, to the instability of uniform deposited layers. The instability induces to the formation of nanostructures that correspond to regular spatial variations of atomic coverage. Such models also may describe texture evolution during the deposition of polycrystalline films. In this case, grains with different orientations with respect to the substrate may coexist. Grains with lower surface energy usually dominate, except at high temperatures, where grains with faster lateral diffusion may override energetically favored ones. Furthermore, at sufficiently low temperatures, uniform grain distributions may become unstable versus regular spatial variations of grain orientations. The relevance of this approach to the deposition of Al or Cu on TiN or Ta substrates is discussed. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004 read less USED (low confidence) N. Ooi and J. B. Adams, “Density Functional Study of the Aluminum—Graphite Interface,” Journal of Computational Electronics. 2004. link Times cited: 5 USED (low confidence) V. Yamakov, D. Wolf, and S. Phillpot, “Nanostructured Polycrystals: Molecular-Dynamics Simulation of Plastic Deformation.” 2003. link Times cited: 2 USED (low confidence) M. Asta, D. Sun, and J. Hoyt, “Role of Atomic-Scale Simulation in the Modeling of Solidification Microstructure.” 2003. link Times cited: 0 USED (low confidence) W. Liu, Y. X. Wang, C. Woo, and H.-C. Huang, “Dislocation Nucleation and Propagation During Deposition of Cubic Metal Thin Films,” MRS Proceedings. 2001. link Times cited: 0 Abstract: In this paper we present three-dimensional molecular dynamic… read moreAbstract: In this paper we present three-dimensional molecular dynamics simulations of dislocation nucleation and propagation during thin film deposition. Aiming to identify mechanisms of dislocation nucleation in polycrystalline thin films, we choose the film material to be the same as the substrate – which is stressed. Tungsten and aluminum are taken as representatives of BCC and FCC metals, respectively, in the molecular dynamics simulations. Our studies show that both glissile and sessile dislocations are nucleated during the deposition, and surface steps are preferential nucleation sites of dislocations. Further, the results indicate that dislocations nucleated on slip systems with large Schmid factors more likely survive and propagate into the film. When a glissile dislocation is nucleated, it propagates much faster horizontally than vertically into the film. The mechanisms and criteria of dislocation nucleation are essential to the implementation of the atomistic simulator ADEPT. read less USED (low confidence) J. Adams, “Bonding Energy Models.” 2001. link Times cited: 7 USED (low confidence) C. S. Liu, Z.-G. Zhu, J. Xia, and D. Sun, “Different Cooling Rate Dependences of Different Microstructure Units in Aluminium Glass by Molecular Dynamics Simulation,” Chinese Physics Letters. 2000. link Times cited: 14 Abstract: Constant-pressure molecular dynamics simulation and the pair… read moreAbstract: Constant-pressure molecular dynamics simulation and the pair analysis technique have been performed to study the microstructural evolution of aluminium during rapid solidification. The microstructure characteristics of icosahedral ordering increase with decrease of the cooling rate, whereas the microstructure unit characteristics of hcp crystalline structure decrease. There are two kinds of microstructure units which are similar to those in the fcc crystal containing interstitialcies. These two kinds of microscopic units are nearly independent of the cooling rate. The microscopic structural unit characteristics of fcc crystalline structure do not depend on the cooling rate either. These results may help us understand the microstructure of glass and its stability. read less 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 USED (low confidence) K. Hardikar and R. Phillips, “The Energetics of Dislocation-Obstacle Interactions by 3-D Quasicontinuum Simulations,” MRS Proceedings. 1999. link Times cited: 1 USED (low confidence) X.-Y. Liu and C.-L. Liu, “Stress Effects on Al and Al(Cu) Thin Film Grain-Boundary Diffusion,” MRS Proceedings. 1999. link Times cited: 0 USED (low confidence) C.-L. Liu, X.-Y. Liu, and L. Borucki, “Defect Generation and Diffusion Mechanisms in Al and Al-Cu,” MRS Proceedings. 1998. link Times cited: 6 Abstract: We describe a newly-developed defect generation mechanism, n… read moreAbstract: We describe a newly-developed defect generation mechanism, namely the grain boundary Frenkel pair (GBFP) model, and corresponding diffusion mechanisms during electromigration developed using atomic molecular statics (MS), Monte Carlo (MC), and molecular dynamics (MD) simulation techniques in Al and Al-Cu. We contend that large numbers of interstitials and vacancies exist at grain boundaries and both contribute to mass transport. Cu preferentially segregates to the interstitial sites at grain boundaries via a Frenkel pair generation process and reduces the overall grain boundary diffusivity due to the strong binding in the Al-Cu dimer. Predictions from our models are in excellent agreement with available experimental data and observations. read less USED (low confidence) Y. Mishin, D. Farkas, M. Mehl, and D. Papaconstantopoulos, “Interatomic Potentials for Al and Ni From Experimental Data and AB Initio Calculations,” MRS Proceedings. 1998. link Times cited: 43 Abstract: New embedded-atom potentials for Al and Ni have been develop… read moreAbstract: New embedded-atom potentials for Al and Ni have been developed by fitting to both experimental data and the results of ab initio calculations. The ab initio data were obtained in the form of energies of different alternative computer-generated crystalline structures of these metals. The potentials accurately reproduce basic equilibrium properties of Al and Ni such as the elastic constants, phonon dispersion curves, vacancy formation and migration energies, stacking fault energies, and surface energies. The equilibrium energies of various alternative structures not included in the fitting database are calculated with these potentials. The results are compared with predictions of total-energy tight-binding calculations for the same structures. The embedded-atom potentials correctly reproduce the structural stability trends, which suggests that they are transferable to different local environments encountered in atomistic simulations of lattice defects. read less USED (low confidence) D. N. Pawaskar, R. E. Miller, R. Bai, A. Schwartzman, R. Phillips, and C. Briant, “Atomistic Studies of Generic Tilt Grain Boundary Structures,” MRS Proceedings. 1998. link Times cited: 1 Abstract: We investigate the atomic-scale structures of high-sigma (Σ)… read moreAbstract: We investigate the atomic-scale structures of high-sigma (Σ) tilt grain boundaries in aluminum using lattice statics calculations. In particular, we examine the efficacy of the structural unit model (SUM) in the context of long-period boundaries. Our investigation of both the equilibrium and metastable structures for certain high Σ boundaries may necessitate a revision of the SUM formalism. We also consider further departures from high symmetry boundaries by considering the structural rearrangements induced by steps on boundaries. read less USED (low confidence) R. Hugo and R. Hoagland, “Influence of Aluminum Grain Boundary Misorientation on Penetration by Gallium,” MRS Proceedings. 1997. link Times cited: 0 Abstract: Materials that undergo intergranular degradation processes, … read moreAbstract: Materials that undergo intergranular degradation processes, such as Stress Corrosioi Cracking (SCC) or certain types of Liquid Metal Embrittlement (LME), show variations in sus ceptibility with grain boundary character Samples with high fractions of “special” boundaries i.e. highly periodic boundaries with low-S Coincidence Site Lattices (CSL), exhibit higher resis tance to these types of attack[l,2]. Very useful comparisons have been drawn between low periodicity boundaries and high-periodicity boundaries; however, few attempts have been mad to date to explain variations in behavior between various “general” boundaries. The presen study employs the LME of aluminum by liquid gallium in an attempt to elucidate the variation in structure and properties of general grain boundaries. read less USED (low confidence) D. Medlin, S. Foiles, and C. B. Carter, “Grain Boundary Dislocation Structure and Motion in an Aluminum Σ=3 [0 1 1] Bicrystal,” MRS Proceedings. 1996. link Times cited: 2 USED (low confidence) H. Huang, T. D. Rubia, and M. Fluss, “A Molecular Dynamics Study of Cu Segregation to the Σ11 Grain Boundary In Al,” MRS Proceedings. 1996. link Times cited: 3 USED (low confidence) M. Payne, I. Robertson, D. I. Thomson, and V. Heine, “Ab initio databases for fitting and testing interatomic potentials,” Philosophical Magazine Part B. 1996. link Times cited: 17 Abstract: We describe the construction of ab initio databases that can… read moreAbstract: We describe the construction of ab initio databases that can be used for fitting and testing empirical atomistic potentials. In particular, we show how the use of a large ab initio database can overcome the problem of overfitting an empirical potential to a limited set of data. read less USED (low confidence) V. Shenoy and R. Phillips, “Critical evaluation of atomistic simulations of 3D dislocation configurations,” MRS Proceedings. 1995. link Times cited: 0 Abstract: Though atomistic simulation of 3D dislocation configurations… read moreAbstract: Though atomistic simulation of 3D dislocation configurations is an important objective for the analysis of problems ranging from point defect condensation to the operation of Frank-Read sources, such calculations pose new challenges. In particular, use of finite sized simulation cells produce additional stresses due to the presence of fixed boundaries in the far field which can contaminate the interpretation of these simulations. This paper discusses an approximate scheme for accounting for such boundary stresses, and is illustrated via consideration of the lattice resistance encountered by straight dislocations and simulations of 3D bow out of pinned dislocation segments. These results allow for a reevaluation of the concepts of the Peierls stress and the line tension from the atomistic perspective. read less USED (low confidence) G. Odette, “Radiation Induced Microstructural Evolution in Reactor Pressure Vessel Steels,” MRS Proceedings. 1994. link Times cited: 74 Abstract: The evolution of the fine scale microstructural features lea… read moreAbstract: The evolution of the fine scale microstructural features leading to irradiation embrittlement of reactor pressure vessel steels is described. Copper rich phases undergo accelerated precipitation from supersaturated solution due to radiation enhanced diffusion. In steels with significant trace quantities of copper the precipitates, characterized by high concentrations and small sizes, are the dominant embrittling feature. Precipitate concentrations, sizes, volume fractions and compositions are consistent with thermodynamic and kinetic models that rationalize the effects of a number of irradiation and metallurgical variables. Phosphide and carbonitride phases may also develop along with new manganese nickel rich precipitates, promoted by high nickel contents. These features may lead to severe embrittlement at high fluence even in low copper steels. While their detailed identity and characteristics are not known, defect cluster-solute complexes with a range of thermal stability are important both directly and indirectly; for example, in mediating flux and temperature effects. In conjunction with the application of state-of-the-art characterization methods, development of advanced modeling tools will be needed to address a number of outstanding issues. read less NOT USED (low confidence) M. Hodapp, “Machine learning is funny but physics makes the money: How machine-learning potentials can advance computer-aided materials design in metallurgy,” Computational Materials Science. 2024. link Times cited: 0 NOT USED (low confidence) J. Airas, X. Ding, and B. Zhang, “Transferable Implicit Solvation via Contrastive Learning of Graph Neural Networks,” ACS Central Science. 2023. link Times cited: 1 NOT USED (low confidence) J. C. Verduzco, E. Holbrook, and A. Strachan, “GPT-4 as an interface between researchers and computational software: improving usability and reproducibility,” ArXiv. 2023. link Times cited: 0 Abstract: Large language models (LLMs) are playing an increasingly imp… read moreAbstract: Large language models (LLMs) are playing an increasingly important role in science and engineering. For example, their ability to parse and understand human and computer languages makes them powerful interpreters and their use in applications like code generation are well-documented. We explore the ability of the GPT-4 LLM to ameliorate two major challenges in computational materials science: i) the high barriers for adoption of scientific software associated with the use of custom input languages, and ii) the poor reproducibility of published results due to insufficient details in the description of simulation methods. We focus on a widely used software for molecular dynamics simulations, the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), and quantify the usefulness of input files generated by GPT-4 from task descriptions in English and its ability to generate detailed descriptions of computational tasks from input files. We find that GPT-4 can generate correct and ready-to-use input files for relatively simple tasks and useful starting points for more complex, multi-step simulations. In addition, GPT-4's description of computational tasks from input files can be tuned from a detailed set of step-by-step instructions to a summary description appropriate for publications. Our results show that GPT-4 can reduce the number of routine tasks performed by researchers, accelerate the training of new users, and enhance reproducibility. read less NOT USED (low confidence) H. Na and G. Song, “Coarse-Graining Waters: Unveiling The Effective Hydrophilicity/Hydrophobicity of Individual Protein Atoms and The Roles of Waters’ Hydrogens.,” Journal of chemical theory and computation. 2023. link Times cited: 0 Abstract: There have been many coarse-graining methods developed that … read moreAbstract: There have been many coarse-graining methods developed that aim to reduce the sizes of simulated systems and their computational costs. In this work, we develop a new coarse-graining method, called coarse-graining-delta (or δ-CG in short), that reduces the degrees of freedom of the potential energy surface by coarse-graining relative locations of atoms from their unit centers. Our method extends and generalizes the methods used in the coarse-grained normal mode analysis and enables us to study the roles of the individual removed atoms in a system, which have been difficult to study in molecular dynamics simulations. By applying δ-CG to coarse-grain three-point water molecules into single-point solvent particles, we successfully identify the effective hydrophilicity and hydrophobicity of all the individual protein atom types, which collectively correlate well with the known hydrophilic, hydrophobic, and amphipathic characteristics of amino acids. Moreover, our investigation shows that water's hydrogens have two roles in interacting with protein atoms. First, water molecules adjust their poses around different amino acids and their atoms, and the statistical preferences of the hydrogen poses near the atoms determine the effective hydrophilicity and hydrophobicity of the atoms, which have not been successfully addressed before. Second, the collective dynamics of the hydrogens assist the water molecules in escaping from the potential energy wells of the hydrophilic atoms. Our method also shows that coarse-graining a system mathematically leads to breaking antisymmetry of the nonbonded interactions; as a result, two interacting coarse-grained units exert different forces on each other. Our study indicates that the accuracy of coarse-grained force fields, such as the MARTINI force field and the UNRES force field, can be improved in two ways: (i) refining their potential energy functions and coefficients by analyzing the coarse-grained potential energy surface using δ-CG, and (ii) introducing non-antisymmetric interactions. read less NOT USED (low confidence) Z. Zhang et al., “Learning coarse-grained force fields for fibrogenesis modeling,” Computer Physics Communications. 2023. link Times cited: 0 NOT USED (low confidence) M. Ivanov, M. Posysoev, and A. Lyubartsev, “Coarse-Grained Modeling Using Neural Networks Trained on Structural Data,” Journal of Chemical Theory and Computation. 2023. link Times cited: 0 Abstract: We propose a method of bottom-up coarse-graining, in which i… read moreAbstract: We propose a method of bottom-up coarse-graining, in which interactions within a coarse-grained model are determined by an artificial neural network trained on structural data obtained from multiple atomistic simulations. The method uses ideas of the inverse Monte Carlo approach, relating changes in the neural network weights with changes in average structural properties, such as radial distribution functions. As a proof of concept, we demonstrate the method on a system interacting by a Lennard–Jones potential modeled by a simple linear network and a single-site coarse-grained model of methanol–water solutions. In the latter case, we implement a nonlinear neural network with intermediate layers trained by atomistic simulations carried out at different methanol concentrations. We show that such a network acts as a transferable potential at the coarse-grained resolution for a wide range of methanol concentrations, including those not included in the training set. read less NOT USED (low confidence) J. Decayeux, J. Fries, V. Dahirel, M. Jardat, and P. Illien, “Isotropic active colloids: explicit vs. implicit descriptions of propulsion mechanisms.,” Soft matter. 2023. link Times cited: 1 Abstract: Modeling the couplings between active particles often neglec… read moreAbstract: Modeling the couplings between active particles often neglects the possible many-body effects that control the propulsion mechanism. Accounting for such effects requires the explicit modeling of the molecular details at the origin of activity. Here, we take advantage of a recent two-dimensional model of isotropic active particles whose propulsion originates from the interactions between solute particles in the bath. The colloid catalyzes a chemical reaction in its vicinity, which results in a local phase separation of solute particles, and the density fluctuations of solute particles cause the enhanced diffusion of the colloid. In this paper, we investigate an assembly of such active particles, using (i) an explicit model, where the microscopic dynamics of the solute particles is accounted for; and (ii) an implicit model, whose parameters are inferred from the explicit model at infinite dilution. In the explicit solute model, the long-time diffusion coefficient of the active colloids strongly decreases with density, an effect which is not captured by the derived implicit model. This suggests that classical models, which usually decouple pair interactions from activity, fail to describe collective dynamics in active colloidal systems driven by solute-solute interactions. read less NOT USED (low confidence) J. Airas, X. Ding, and B. Zhang, “Transferable Coarse Graining via Contrastive Learning of Graph Neural Networks,” bioRxiv. 2023. link Times cited: 1 Abstract: Coarse-grained (CG) force fields are essential for molecular… read moreAbstract: Coarse-grained (CG) force fields are essential for molecular dynamics simulations of biomolecules, striking a balance between computational efficiency and biological realism. These simulations employ simplified models grouping atoms into interaction sites, enabling the study of complex biomolecular systems over biologically relevant timescales. Efforts are underway to develop accurate and transferable CG force fields, guided by a bottom-up approach that matches the CG energy function with the potential of mean force (PMF) defined by the finer system. However, practical challenges arise due to many-body effects, lack of analytical expressions for the PMF, and limitations in parameterizing CG force fields. To address these challenges, a machine learning-based approach is proposed, utilizing graph neural networks (GNNs) to represent CG force fields and potential contrasting for parameterization from atomistic simulation data. We demonstrate the effectiveness of the approach by deriving a transferable GNN implicit solvent model using 600,000 atomistic configurations of six proteins obtained from explicit solvent simulations. The GNN model provides solvation free energy estimations much more accurately than state-of-the-art implicit solvent models, reproducing configurational distributions of explicit solvent simulations. We also demonstrate the reasonable transferability of the GNN model outside the training data. Our study offers valuable insights for building accurate coarse-grained models bottom-up. read less NOT USED (low confidence) M. Dixit and T. Taniguchi, “Role of Terminal Groups of cis-1,4-Polyisoprene Chains in the Formation of Physical Junction Points in Natural Rubber.,” Biomacromolecules. 2023. link Times cited: 1 Abstract: The terminal structures of cis-1,4-polyisoprene (PI) chains … read moreAbstract: The terminal structures of cis-1,4-polyisoprene (PI) chains play a vital role in the excellent comprehensive performance of Hevea natural rubber (NR) with properties such as high toughness, tear-resistance, and wet skid resistance. The cis-1,4-polyisoprene chain constituting NR exhibits a distinct composition of terminal groups comprising two distinct types, namely, the ω and α terminal groups. The structures of the ω terminal [dimethyl allyl (DMA)-(trans-1,4-isoprene)2] and six kinds of α end groups of the polymer chain of NR have been explored by utilizing a newly developed 2D NMR method. In the present work, we examine different kinds of PI melt systems, and we choose various combinations of terminal groups: Hydrogen, one DMA unit with two trans isoprene units as ω end groups and ester-terminated isopentene (α1), hydroxy-terminated isopentene (α2), ester-terminated isobutane (α3), hydroxy-terminated isobutane (α4), ester-terminated 1,4-cis-isoprene (α5), and hydroxy-terminated 1,4-cis-isoprene (α6), i.e., HPIH (PI0)-pure PI (Hydrogen terminal), ωPIα1 (PII), ωPIα2 (PIII), ωPIα3 (PIIII), ωPIα4 (PIIV), ωPIα5 (PIV), and ωPIα6 (PIVI). We evaluated dynamic and static properties of PI chains such as the end-to-end vector autocorrelation function (C(t)), its average relaxation time (τ), end-to-end distance (Ree), and radius of gyration (Rg). We also estimated the diffusion coefficients of polyisoprene chains and pair correlation functions [radial distribution functions (RDFs)], potentials of mean force (PMFs) in between end residues, and survival probability (P(τ)) of end groups around the end group by analyzing the equilibrated trajectories of full-atom MD simulations. As per the examination of C(t), rotational relaxation time τ, and RDFs, we discovered that the existence of a strong hydrogen bond in α2-α2, α4-α4, and α6-α6 residues makes the dynamics of hydroxy-terminated polyisoprene chains in ωPIα2,α4,α6 melt systems slower. From the analyses of RDFs and PMFs (W(r)), the association between [α2]-[α2], [α4]-[α4], and [α6]-[α6] terminals in ωPIα2,α4,α6 melt systems is significantly stronger than in [ISO]-[ISO] [Hydrogen terminated 1,4-cis-isoprene:(ISO)] in HPIH and ω-ω, [α1]-[α1], [α3]-[α3], and [α5]-[α5] in ωPIα1,α3,α5 systems. We quantified the fraction of cluster formation of terminal groups of a given size in the seven PI melt systems by employing the criteria of PMFs. It is revealed that no stable cluster exists in the HPIH, ωPIα1, ωPIα3, and ωPIα5 melt systems. Conversely, in the ωPIα2, ωPIα4, and ωPIα6 systems, we perceived stable clusters of [(α2)p] [(α4)p] and [(α6)p] end groups where p (2 ≤ x ≤ 6). These stable clusters validate the presence of physical junction points in between hydroxy-terminated polyisoprene chains through their α2, α4, and α6 terminals. These physical junction points might be crucial for superior properties of NR such as high toughness, crack growth resistance, and strain-induced crystallization. read less NOT USED (low confidence) X. Wang, Z. Huai, and Z. Sun, “Host Dynamics under General-Purpose Force Fields,” Molecules. 2023. link Times cited: 1 Abstract: Macrocyclic hosts as prototypical receptors to gaseous and d… read moreAbstract: Macrocyclic hosts as prototypical receptors to gaseous and drug-like guests are crucial components in pharmaceutical research. The external guests are often coordinated at the center of these macromolecular containers. The formation of host–guest coordination is accompanied by the broken of host–water and host–ion interactions and sometimes also involves some conformational rearrangements of the host. A balanced description of various components of interacting terms is indispensable. However, up to now, the modeling community still lacks a general yet detailed understanding of commonly employed general-purpose force fields and the host dynamics produced by these popular selections. To fill this critical gap, in this paper, we profile the energetics and dynamics of four types of popular macrocycles, including cucurbiturils, pillararenes, cyclodextrins, and octa acids. The presented investigations of force field definitions, refitting, and evaluations are unprecedently detailed. Based on the valuable observations and insightful explanations, we finally summarize some general guidelines on force field parametrization and selection in host–guest modeling. read less NOT USED (low confidence) V. Bhat, C. P. Callaway, and C. Risko, “Computational Approaches for Organic Semiconductors: From Chemical and Physical Understanding to Predicting New Materials.,” Chemical reviews. 2023. link Times cited: 7 Abstract: While a complete understanding of organic semiconductor (OSC… read moreAbstract: While a complete understanding of organic semiconductor (OSC) design principles remains elusive, computational methods─ranging from techniques based in classical and quantum mechanics to more recent data-enabled models─can complement experimental observations and provide deep physicochemical insights into OSC structure-processing-property relationships, offering new capabilities for in silico OSC discovery and design. In this Review, we trace the evolution of these computational methods and their application to OSCs, beginning with early quantum-chemical methods to investigate resonance in benzene and building to recent machine-learning (ML) techniques and their application to ever more sophisticated OSC scientific and engineering challenges. Along the way, we highlight the limitations of the methods and how sophisticated physical and mathematical frameworks have been created to overcome those limitations. We illustrate applications of these methods to a range of specific challenges in OSCs derived from π-conjugated polymers and molecules, including predicting charge-carrier transport, modeling chain conformations and bulk morphology, estimating thermomechanical properties, and describing phonons and thermal transport, to name a few. Through these examples, we demonstrate how advances in computational methods accelerate the deployment of OSCsin wide-ranging technologies, such as organic photovoltaics (OPVs), organic light-emitting diodes (OLEDs), organic thermoelectrics, organic batteries, and organic (bio)sensors. We conclude by providing an outlook for the future development of computational techniques to discover and assess the properties of high-performing OSCs with greater accuracy. read less NOT USED (low confidence) E. Ricci and N. Vergadou, “Integrating Machine Learning in the Coarse-Grained Molecular Simulation of Polymers.,” The journal of physical chemistry. B. 2023. link Times cited: 2 Abstract: Machine learning (ML) is having an increasing impact on the … read moreAbstract: Machine learning (ML) is having an increasing impact on the physical sciences, engineering, and technology and its integration into molecular simulation frameworks holds great potential to expand their scope of applicability to complex materials and facilitate fundamental knowledge and reliable property predictions, contributing to the development of efficient materials design routes. The application of ML in materials informatics in general, and polymer informatics in particular, has led to interesting results, however great untapped potential lies in the integration of ML techniques into the multiscale molecular simulation methods for the study of macromolecular systems, specifically in the context of Coarse Grained (CG) simulations. In this Perspective, we aim at presenting the pioneering recent research efforts in this direction and discussing how these new ML-based techniques can contribute to critical aspects of the development of multiscale molecular simulation methods for bulk complex chemical systems, especially polymers. Prerequisites for the implementation of such ML-integrated methods and open challenges that need to be met toward the development of general systematic ML-based coarse graining schemes for polymers are discussed. read less NOT USED (low confidence) M. DeLuca, S. Sensale, P.-A. Lin, and G. Arya, “Prediction and Control in DNA Nanotechnology.,” ACS applied bio materials. 2023. link Times cited: 5 Abstract: DNA nanotechnology is a rapidly developing field that uses D… read moreAbstract: DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeling techniques. In this Review, we present various aspects of prediction and control in DNA nanotechnology, including the various scales of molecular simulation, statistical mechanics, kinetic modeling, continuum mechanics, and other prediction methods. We also address the current uses of artificial intelligence and machine learning in DNA nanotechnology. We discuss how experiments and modeling are synergistically combined to provide control over device behavior, allowing scientists to design molecular structures and dynamic devices with confidence that they will function as intended. Finally, we identify processes and scenarios where DNA nanotechnology lacks sufficient prediction ability and suggest possible solutions to these weak areas. read less NOT USED (low confidence) B. Zhou, Y. Zhou, and D. Xie, “Accelerated Quantum Mechanics/Molecular Mechanics Simulations via Neural Networks Incorporated with Mechanical Embedding Scheme.,” Journal of chemical theory and computation. 2023. link Times cited: 0 Abstract: A powerful tool to study the mechanism of reactions in solut… read moreAbstract: A powerful tool to study the mechanism of reactions in solutions or enzymes is to perform the ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations. However, the computational cost is too high due to the explicit electronic structure calculations at every time step of the simulation. A neural network (NN) method can accelerate the QM/MM-MD simulations, but it has long been a problem to accurately describe the QM/MM electrostatic coupling by NN in the electrostatic embedding (EE) scheme. In this work, we developed a new method to accelerate QM/MM calculations in the mechanic embedding (ME) scheme. The potentials and partial point charges of QM atoms are first learned in vacuo by the embedded atom neural networks (EANN) approach. MD simulations are then performed on this EANN/MM potential energy surface (PES) to obtain free energy (FE) profiles for reactions, in which the QM/MM electrostatic coupling is treated in the mechanic embedding (ME) scheme. Finally, a weighted thermodynamic perturbation (wTP) corrects the FE profiles in the ME scheme to the EE scheme. For two reactions in water and one in methanol, our simulations reproduced the B3LYP/MM free energy profiles within 0.5 kcal/mol with a speed-up of 30-60-fold. The results show that the strategy of combining EANN potential in the ME scheme with the wTP correction is efficient and reliable for chemical reaction simulations in liquid. Another advantage of our method is that the QM PES is independent of the MM subsystem, so it can be applied to various MM environments as demonstrated by an SN2 reaction studied in water and methanol individually, which used the same EANN PES. The free energy profiles are in excellent accordance with the results obtained from B3LYP/MM-MD simulations. In future, this method will be applied to the reactions of enzymes and their variants. read less NOT USED (low confidence) J. Wang, A. A. Panchal, and P. Canepa, “Strategies for fitting accurate machine-learned inter-atomic potentials for solid electrolytes,” Materials Futures. 2023. link Times cited: 3 Abstract: Ion transport in materials is routinely probed through sever… read moreAbstract: Ion transport in materials is routinely probed through several experimental techniques, which introduce variability in reported ionic diffusivities and conductivities. The computational prediction of ionic diffusivities and conductivities helps in identifying good ionic conductors, and suitable solid electrolytes (SEs), thus establishing firm structure-property relationships. Machine-learned potentials are an attractive strategy to extend the capabilities of accurate ab initio molecular dynamics (AIMD) to longer simulations for larger systems, enabling the study of ion transport at lower temperatures. However, machine-learned potentials being in their infancy, critical assessments of their predicting capabilities are rare. Here, we identified the main factors controlling the quality of a machine-learning potential based on the moment tensor potential formulation, when applied to the properties of ion transport in ionic conductors, such as SEs. Our results underline the importance of high-quality and diverse training sets required to fit moment tensor potentials. We highlight the importance of considering intrinsic defects which may occur in SEs. We demonstrate the limitations posed by short-timescale and high-temperature AIMD simulations to predict the room-temperature properties of materials. read less NOT USED (low confidence) N. Goldman, L. Fried, R. Lindsey, C. Pham, and R. Dettori, “Enhancing the accuracy of density functional tight binding models through ChIMES many-body interaction potentials.,” The Journal of chemical physics. 2023. link Times cited: 2 Abstract: Semi-empirical quantum models such as Density Functional Tig… read moreAbstract: Semi-empirical quantum models such as Density Functional Tight Binding (DFTB) are attractive methods for obtaining quantum simulation data at longer time and length scales than possible with standard approaches. However, application of these models can require lengthy effort due to the lack of a systematic approach for their development. In this work, we discuss the use of the Chebyshev Interaction Model for Efficient Simulation (ChIMES) to create rapidly parameterized DFTB models, which exhibit strong transferability due to the inclusion of many-body interactions that might otherwise be inaccurate. We apply our modeling approach to silicon polymorphs and review previous work on titanium hydride. We also review the creation of a general purpose DFTB/ChIMES model for organic molecules and compounds that approaches hybrid functional and coupled cluster accuracy with two orders of magnitude fewer parameters than similar neural network approaches. In all cases, DFTB/ChIMES yields similar accuracy to the underlying quantum method with orders of magnitude improvement in computational cost. Our developments provide a way to create computationally efficient and highly accurate simulations over varying extreme thermodynamic conditions, where physical and chemical properties can be difficult to interrogate directly, and there is historically a significant reliance on theoretical approaches for interpretation and validation of experimental results. read less NOT USED (low confidence) S. Hu et al., “RLEKF: An Optimizer for Deep Potential with Ab Initio Accuracy,” AAAI Conference on Artificial Intelligence. 2022. link Times cited: 0 Abstract: It is imperative to accelerate the training of neural networ… read moreAbstract: It is imperative to accelerate the training of neural network force field such as Deep Potential, which usually requires thousands of images based on first-principles calculation and a couple of days to generate an accurate potential energy surface. To this end, we propose a novel optimizer named reorganized layer extended Kalman filtering (RLEKF), an optimized version of global extended Kalman filtering (GEKF) with a strategy of splitting big and gathering small layers to overcome the O(N^2) computational cost of GEKF. This strategy provides an approximation of the dense weights error covariance matrix with a sparse diagonal block matrix for GEKF. We implement both RLEKF and the baseline Adam in our alphaDynamics package and numerical experiments are performed on 13 unbiased datasets. Overall, RLEKF converges faster with slightly better accuracy. For example, a test on a typical system, bulk copper, shows that RLEKF converges faster by both the number of training epochs (x11.67) and wall-clock time (x1.19). Besides, we theoretically prove that the updates of weights converge and thus are against the gradient exploding problem. Experimental results verify that RLEKF is not sensitive to the initialization of weights. The RLEKF sheds light on other AI-for-science applications where training a large neural network (with tons of thousands parameters) is a bottleneck. read less 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) R. L. N. Mbitou et al., “Consistent and Transferable Force Fields for Statistical Copolymer Systems at the Mesoscale.,” Journal of chemical theory and computation. 2022. link Times cited: 2 Abstract: The statistical trajectory matching (STM) method was applied… read moreAbstract: The statistical trajectory matching (STM) method was applied successfully to derive coarse grain (CG) models for bulk properties of homopolymers. The extension of the methodology for building CG models for statistical copolymer systems is much more challenging. We present here the strategy for developing CG models for styrene-butadiene-rubber, and we compare the quality of the resulting CG force fields on the structure and thermodynamics at different chemical compositions. The CG models are used through the use of a genuine mesoscopic method called the dissipative particle dynamics method and compared to high-resolution molecular dynamics simulations. We conclude that the STM method is able to produce coarse-grained potentials that are transferable in composition by using only a few reference systems. Additionally, this methodology can be applied on any copolymer system. read less NOT USED (low confidence) N. Medvedev et al., “Frontiers, challenges, and solutions in modeling of swift heavy ion effects in materials,” Journal of Applied Physics. 2022. link Times cited: 5 Abstract: Since a few breakthroughs in the fundamental understanding o… read moreAbstract: Since a few breakthroughs in the fundamental understanding of the effects of swift heavy ions (SHIs) decelerating in the electronic stopping regime in the matter have been achieved in the last decade, it motivated us to review the state-of-the-art approaches in the modeling of SHI effects. The SHI track kinetics occurs via several well-separated stages and spans many orders of magnitude in time: from attoseconds in ion-impact ionization depositing an extreme amount of energy in a target to femtoseconds of electron transport and hole cascades, to picoseconds of lattice excitation and response, to nanoseconds of atomic relaxation, and even longer times of the final macroscopic reaction. Each stage requires its own approaches for quantitative description. We discuss that understanding the links between the stages makes it possible to describe the entire track kinetics within a hybrid multiscale model without fitting procedures. The review focuses on the underlying physical mechanisms of each process, the dominant effects they produce, and the limitations of the existing approaches, as well as various numerical techniques implementing these models. It provides an overview of the ab initio-based modeling of the evolution of the electronic properties, Monte Carlo simulations of nonequilibrium electronic transport, molecular dynamics modeling of atomic reaction including phase transformations and damage on the surface and in the bulk, kinetic Mote Carlo of atomic defect kinetics, and finite-difference methods of track interaction with chemical solvents describing etching kinetics. We outline the modern methods that couple these approaches into multiscale and combined multidisciplinary models and point to their bottlenecks, strengths, and weaknesses. The analysis is accompanied by examples of important results, improving the understanding of track formation in various materials. Summarizing the most recent advances in the field of the track formation process, the review delivers a comprehensive picture and detailed understanding of the phenomenon. Important future directions of research and model development are also outlined. read less NOT USED (low confidence) W. Wang, Z. Wu, and R. G’omez-Bombarelli, “Learning Pair Potentials using Differentiable Simulations,” The Journal of chemical physics. 2022. link Times cited: 9 Abstract: Learning pair interactions from experimental or simulation d… read moreAbstract: Learning pair interactions from experimental or simulation data is of great interest for molecular simulations. We propose a general stochastic method for learning pair interactions from data using differentiable simulations (DiffSim). DiffSim defines a loss function based on structural observables, such as the radial distribution function, through molecular dynamics (MD) simulations. The interaction potentials are then learned directly by stochastic gradient descent, using backpropagation to calculate the gradient of the structural loss metric with respect to the interaction potential through the MD simulation. This gradient-based method is flexible and can be configured to simulate and optimize multiple systems simultaneously. For example, it is possible to simultaneously learn potentials for different temperatures or for different compositions. We demonstrate the approach by recovering simple pair potentials, such as Lennard-Jones systems, from radial distribution functions. We find that DiffSim can be used to probe a wider functional space of pair potentials compared with traditional methods like iterative Boltzmann inversion. We show that our methods can be used to simultaneously fit potentials for simulations at different compositions and temperatures to improve the transferability of the learned potentials. read less 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) X. Ding and B. W. Zhang, “Contrastive Learning of Coarse-Grained Force Fields,” Journal of chemical theory and computation. 2022. link Times cited: 11 Abstract: Coarse-grained models have proven helpful for simulating com… read moreAbstract: Coarse-grained models have proven helpful for simulating complex systems over long time scales to provide molecular insights into various processes. Methodologies for systematic parametrization of the underlying energy function or force field that describes the interactions among different components of the system are of great interest for ensuring simulation accuracy. We present a new method, potential contrasting, to enable efficient learning of force fields that can accurately reproduce the conformational distribution produced with all-atom simulations. Potential contrasting generalizes the noise contrastive estimation method with umbrella sampling to better learn the complex energy landscape of molecular systems. When applied to the Trp-cage protein, we found that the technique produces force fields that thoroughly capture the thermodynamics of the folding process despite the use of only α-carbons in the coarse-grained model. We further showed that potential contrasting could be applied over large data sets that combine the conformational ensembles of many proteins to improve force field transferability. We anticipate potential contrasting as a powerful tool for building general-purpose coarse-grained force fields. read less NOT USED (low confidence) I. Toda-Caraballo, J. Wróbel, and D. Nguyen-Manh, “Generalized universal equation of states for magnetic materials: A novel formulation for an interatomic potential in Fe,” Physical Review Materials. 2022. link Times cited: 0 NOT USED (low confidence) M. Müser, S. Sukhomlinov, and L. Pastewka, “Interatomic potentials: achievements and challenges,” Advances in Physics: X. 2022. link Times cited: 12 Abstract: ABSTRACT Interatomic potentials approximate the potential en… read moreAbstract: ABSTRACT Interatomic potentials approximate the potential energy of atoms as a function of their coordinates. Their main application is the effective simulation of many-atom systems. Here, we review empirical interatomic potentials designed to reproduce elastic properties, defect energies, bond breaking, bond formation, and even redox reactions. We discuss popular two-body potentials, embedded-atom models for metals, bond-order potentials for covalently bonded systems, polarizable potentials including charge-transfer approaches for ionic systems and quantum-Drude oscillator models mimicking higher-order and many-body dispersion. Particular emphasis is laid on the question what constraints ensue from the functional form of a potential, e.g., in what way Cauchy relations for elastic tensor elements can be violated and what this entails for the ratio of defect and cohesive energies, or why the ratio of boiling to melting temperature tends to be large for potentials describing metals but small for short-ranged pair potentials. The review is meant to be pedagogical rather than encyclopedic. This is why we highlight potentials with functional forms sufficiently simple to remain amenable to analytical treatments. Our main objective is to provide a stimulus for how existing approaches can be advanced or meaningfully combined to extent the scope of simulations based on empirical potentials. Graphical abstract read less NOT USED (low confidence) R. Lindsey, C. H. Pham, N. Goldman, S. Bastea, and L. Fried, “Machine‐Learning a Solution for Reactive Atomistic Simulations of Energetic Materials,” Propellants, Explosives, Pyrotechnics. 2022. link Times cited: 3 NOT USED (low confidence) H. Kulik et al., “Roadmap on Machine learning in electronic structure,” Electronic Structure. 2022. link Times cited: 60 Abstract: In recent years, we have been witnessing a paradigm shift in… read moreAbstract: In recent years, we have been witnessing a paradigm shift in computational materials science. In fact, traditional methods, mostly developed in the second half of the XXth century, are being complemented, extended, and sometimes even completely replaced by faster, simpler, and often more accurate approaches. The new approaches, that we collectively label by machine learning, have their origins in the fields of informatics and artificial intelligence, but are making rapid inroads in all other branches of science. With this in mind, this Roadmap article, consisting of multiple contributions from experts across the field, discusses the use of machine learning in materials science, and share perspectives on current and future challenges in problems as diverse as the prediction of materials properties, the construction of force-fields, the development of exchange correlation functionals for density-functional theory, the solution of the many-body problem, and more. In spite of the already numerous and exciting success stories, we are just at the beginning of a long path that will reshape materials science for the many challenges of the XXIth century. read less NOT USED (low confidence) Z. Wei, C. Zhang, Y. Kan, Y. Zhang, and Y. Chen, “Developing machine learning potential for classical molecular dynamics simulation with superior phonon properties,” Computational Materials Science. 2022. link Times cited: 1 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) M. Dettmann et al., “Comparing the Expense and Accuracy of Methods to Simulate Atomic Vibrations in Rubrene.,” Journal of chemical theory and computation. 2021. link Times cited: 3 Abstract: Atomic vibrations can inform about materials properties from… read moreAbstract: Atomic vibrations can inform about materials properties from hole transport in organic semiconductors to correlated disorder in metal-organic frameworks. Currently, there are several methods for predicting these vibrations using simulations, but the accuracy-efficiency tradeoffs have not been examined in depth. In this study, rubrene is used as a model system to predict atomic vibrational properties using six different simulation methods: density functional theory, density functional tight binding, density functional tight binding with a Chebyshev polynomial-based correction, a trained machine learning model, a pretrained machine learning model called ANI-1, and a classical forcefield model. The accuracy of each method is evaluated by comparison to the experimental inelastic neutron scattering spectrum. All methods discussed here show some accuracy across a wide energy region, though the Chebyshev-corrected tight-binding method showed the optimal combination of high accuracy with low expense. We then offer broad simulation guidelines to yield efficient, accurate results for inelastic neutron scattering spectrum prediction. read less NOT USED (low confidence) J. Gao, X. Luo, F. Fang, and J. Sun, “Fundamentals of atomic and close-to-atomic scale manufacturing:A review,” International Journal of Extreme Manufacturing. 2021. link Times cited: 42 Abstract:
Atomic and Close-to-atomic Scale Manufacturing (ACSM) repr… read moreAbstract:
Atomic and Close-to-atomic Scale Manufacturing (ACSM) represents techniques for manufacturing high-end products in various fields, including future-generation computing, communication, energy and medical devices and materials. In this paper, the theoretical boundary between ACSM and classical manufacturing is identified after a thorough discussion of quantum mechanics and their effects on manufacturing. The physical origins of atomic interactions and energy beams-matter interactions are revealed from the point view of quantum mechanics. The mechanisms that dominate several key ACSM processes are introduced, and a current numerical study on these processes is reviewed. A comparison of current ACSM processes is performed in terms of dominant interactions, representative processes, resolution and modelling methods. Future fundamental research is proposed for establishing new approaches for modelling ACSM, material selection or preparation and control of manufacturing tools and environments. This paper is by no means comprehensive, but provides a starting point for further systematic investigation of ACSM fundamentals to support and accelerate its industrial scale implementation in the near future. read less NOT USED (low confidence) S. Dhamankar and M. A. Webb, “Chemically specific coarse‐graining of polymers: Methods and prospects,” Journal of Polymer Science. 2021. link Times cited: 42 NOT USED (low confidence) H. Yang, Y. Zhu, E. Dong, Y. Wu, J. Yang, and W. Zhang, “Dual adaptive sampling and machine learning interatomic potentials for modeling materials with chemical bond hierarchy,” Physical Review B. 2021. link Times cited: 4 Abstract: The development of reliable and flexible machine learning ba… read moreAbstract: The development of reliable and flexible machine learning based interatomic potentials (ML-IPs) is becoming increasingly important in studying the physical properties of complex condensed matter systems. Besides the structure descriptor model for total energy decomposition, the trial-and-error approach used in the design of the training dataset makes the ML-IP hardly improvable and reliable for modeling materials with chemical bond hierarchy. In this work, a dual adaptive sampling (DAS) method with an on the fly ambiguity threshold was developed to automatically generate an effective training dataset covering a wide temperature range or a wide spectrum of thermodynamic conditions. The DAS method consists of an inner loop for exploring the local configuration space and an outer loop for covering a wide temperature range. We validated the developed DAS method by simulating thermal transport of complex materials. The simulation results show that even with a substantially small dataset, our approach not only accurately reproduces the energies and forces but also predicts reliably effective high-order force constants to at least fourth order. The lattice thermal conductivity and its temperature dependence were evaluated using the Green-Kubo simulations with ML-IP for $\mathrm{Co}{\mathrm{Sb}}_{3}$ with up to third-order phonon scattering, and those for ${\mathrm{Mg}}_{3}{\mathrm{Sb}}_{2}$ with up to fourth-order phonon scattering, and all show good agreements with experiments. Our work provides an avenue to effectively construct a training dataset for ML-IP of complex materials with chemical bond hierarchy. 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) C. Wu, K. Li, X. Ning, and L. Zhang, “An Enhanced Scheme for Multiscale Modeling of Thermomechanical Properties of Polymer Bulks.,” The journal of physical chemistry. B. 2021. link Times cited: 2 Abstract: While multiscale modeling significantly enhances the capabil… read moreAbstract: While multiscale modeling significantly enhances the capability of molecular simulations of polymer systems, it is well realized that the systematically derived coarse-grained (CG) models generally underestimate the thermomechanical properties. In this work, a charge-based mapping scheme has been adopted to include explicit electrostatic interactions and benchmarked against two typical polymers, atactic poly(methyl methacrylate) (PMMA) and polystyrene (PS). The CG potentials are parameterized against the oligomer bulks of nine monomers per chain to match the essential structural features and the two basic pressure-volume-temperature (PVT) properties, which are obtained from the all-atomistic (AA) molecular dynamics (MD) simulations at a single elevated temperature. The so-parameterized CG potentials are extended with the MD method to simulate the two polymer bulks of one hundred monomers per chain over a wide temperature range. Without any scaling, all the simulated results, including mass densities and bulk moduli at room temperature, thermal expansion coefficients at rubbery and glassy states, and glass transition temperatures (Tg), compare well with the corresponding experimental data. The proposed scheme not only contributes to realistically simulating various thermomechanical properties of both apolar and polar polymers but also allows for directly simulating their electrical properties. read less NOT USED (low confidence) B. Kim et al., “Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force.,” Journal of chemical theory and computation. 2021. link Times cited: 14 Abstract: First-principles determination of free energy profiles for c… read moreAbstract: First-principles determination of free energy profiles for condensed-phase chemical reactions is hampered by the daunting costs associated with configurational sampling on ab initio quantum mechanical/molecular mechanical (AI/MM) potential energy surfaces. Here, we report a new method that enables efficient AI/MM free energy simulations through mean force fitting. In this method, a free energy path in collective variables (CVs) is first determined on an efficient reactive aiding potential. Based on the configurations sampled along the free energy path, correcting forces to reproduce the AI/MM forces on the CVs are determined through force matching. The AI/MM free energy profile is then predicted from simulations on the aiding potential in conjunction with the correcting forces. Such cycles of correction-prediction are repeated until convergence is established. As the instantaneous forces on the CVs sampled in equilibrium ensembles along the free energy path are fitted, this procedure faithfully restores the target free energy profile by reproducing the free energy mean forces. Due to its close connection with the reaction path-force matching (RP-FM) framework recently introduced by us, we designate the new method as RP-FM in collective variables (RP-FM-CV). We demonstrate the effectiveness of this method on a type-II solution-phase SN2 reaction, NH3 + CH3Cl (the Menshutkin reaction), simulated with an explicit water solvent. To obtain the AI/MM free energy profiles, we employed the semiempirical AM1/MM Hamiltonian as the base level for determining the string minimum free energy pathway, along which the free energy mean forces are fitted to various target AI/MM levels using the Hartree-Fock (HF) theory, density functional theory (DFT), and the second-order Møller-Plesset perturbation (MP2) theory as the AI method. The forces on the bond-breaking and bond-forming CVs at both the base and target levels are obtained by force transformation from Cartesian to redundant internal coordinates under the Wilson B-matrix formalism, where the linearized FM is facilitated by the use of spline functions. For the Menshutkin reaction tested, our FM treatment greatly reduces the deviations on the CV forces, originally in the range of 12-33 to ∼2 kcal/mol/Å. Comparisons with the experimental and benchmark AI/MM results, tests of the new method under a variety of simulation protocols, and analyses of the solute-solvent radial distribution functions suggest that RP-FM-CV can be used as an efficient, accurate, and robust method for simulating solution-phase chemical reactions. read less NOT USED (low confidence) J. Wang, N. Charron, B. Husic, S. Olsson, F. Noé, and C. Clementi, “Multi-body effects in a coarse-grained protein force field.,” The Journal of chemical physics. 2021. link Times cited: 25 Abstract: The use of coarse-grained (CG) models is a popular approach … read moreAbstract: The use of coarse-grained (CG) models is a popular approach to study complex biomolecular systems. By reducing the number of degrees of freedom, a CG model can explore long time- and length-scales inaccessible to computational models at higher resolution. If a CG model is designed by formally integrating out some of the system's degrees of freedom, one expects multi-body interactions to emerge in the effective CG model's energy function. In practice, it has been shown that the inclusion of multi-body terms indeed improves the accuracy of a CG model. However, no general approach has been proposed to systematically construct a CG effective energy that includes arbitrary orders of multi-body terms. In this work, we propose a neural network based approach to address this point and construct a CG model as a multi-body expansion. By applying this approach to a small protein, we evaluate the relative importance of the different multi-body terms in the definition of an accurate model. We observe a slow convergence in the multi-body expansion, where up to five-body interactions are needed to reproduce the free energy of an atomistic model. read less NOT USED (low confidence) M. R. DeLyser and W. Noid, “Bottom-up coarse-grained models for external fields and interfaces.,” The Journal of chemical physics. 2020. link Times cited: 12 Abstract: Bottom-up coarse-grained (CG) models accurately describe the… read moreAbstract: Bottom-up coarse-grained (CG) models accurately describe the structure of homogeneous systems but sometimes provide limited transferability and a poor description of thermodynamic properties. Consequently, inhomogeneous systems present a severe challenge for bottom-up models. In this work, we examine bottom-up CG models for interfaces and inhomogeneous systems. We first analyze the effect of external fields upon the many-body potential of mean force. We also demonstrate that the multiscale CG (MS-CG) variational principle for modeling the external field corresponds to a generalization of the first Yvon-Born-Green equation. This provides an important connection with liquid state theory, as well as physical insight into the structure of interfaces and the resulting MS-CG models. We then develop and assess MS-CG models for a film of liquid methanol that is adsorbed on an attractive wall and in coexistence with its vapor phase. While pair-additive potentials provide unsatisfactory accuracy and transferability, the inclusion of local-density (LD) potentials dramatically improves the accuracy and transferability of the MS-CG model. The MS-CG model with LD potentials quite accurately describes the wall-liquid interface, the bulk liquid density, and the liquid-vapor interface while simultaneously providing a much improved description of the vapor phase. This model also provides an excellent description of the pair structure and pressure-density equation of state for the bulk liquid. Thus, LD potentials hold considerable promise for transferable bottom-up models that accurately describe the structure and thermodynamic properties of both bulk and interfacial systems. read less NOT USED (low confidence) G. Jenness, C. G. Bresnahan, and M. Shukla, “Adventures in DFTB: Toward an Automatic Parameterization Scheme.,” Journal of chemical theory and computation. 2020. link Times cited: 3 Abstract: As we push forward on understanding the fate of chemicals in… read moreAbstract: As we push forward on understanding the fate of chemicals in the environment, we need a method that will allow for the simulation of the inherent heterogeneity. Density functional tight binding (DFTB) is a methodology that allows for a detailed electronic description and would be ideal for this problem. While many parameters can be derived directly from DFT, empirical parameters still exist in the confinement and repulsion potentials. In this manuscript, we examine these potentials and present solutions that will minimize the degree of empiricism. Our results show that it is possible to construct confinement potentials from examining the atomic radial wavefunctions. Moreover, we found that the heterogeneous repulsion potentials can be derived from using only homogeneous repulsion curves. read less 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) L. Jiang, D. Rogers, J. Hirst, and H. Do, “Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene.,” Journal of chemical theory and computation. 2020. link Times cited: 8 Abstract: Utilising a force matching procedure, we parameterise new fo… read moreAbstract: Utilising a force matching procedure, we parameterise new force fields systematically for large conjugated systems. We model both conjugated polymers and molecular crystals that contain diketopyrrolopyrrole, thiophene, and thieno[3,2-b]thiophene units. These systems have recently been found to have low band gaps, which exhibit high efficiency for photovoltaic devices. The equilibrium structures, forces and energies of the building block chromophores: diketopyrrolopyrrole thiophene, and thieno[3,2- b]thiophene computed using our parameters are comparable to those computed using the reference electronic structure method. We assess the suitability of this new force field for electronic property calculations by comparing the electronic excitation properties computed along classical and ab initio molecular dynamics trajectories. For both trajectories, we find similar distributions of TDDFT calculated excitation energies and oscillator strengths for the building block chromophore diketopyrrolopyrrole-thieno[3,2- b]thiophene. The structural, dynamical, and electronic properties of the macromolecular assemblies built upon these chromophores are characterised. For both polymers and molecular crystals, pronounced peaks around 0 degree or 180 degree are observed for the torsions between chromophores under ambient conditions. The high planarity in these systems can promote local ordering and π-π stacking, thereby potentially facilitating charge transport across these materials. For the model conducting polymers, we found that the fluctuations in the density of states per chain per monomer is negligibly small and does not vary significantly with chains comprising 20 to 40 monomers. Analysis of the electron-hole distributions and the transition density matrices indicates that the delocalised length is approximately four to six monomers, which is in good agreement with other theoretical and experimental studies of different conducting polymers. For the molecular crystals, our investigation of the characteristic timescale of the fluctuation in the excitonic couplings shows that low frequency vibration below 10 cm-1 is observed for the nearest neighbours. These observations are in line with previous studies on other molecular crystals, in which low frequency vibrations are believed to be responsible for the large modulation of the excitonic coupling. Thus, our approach and the new force fields provide a direct route for studying the structure-property relations and the molecular level origins of the high-efficiency of these classes of materials. read less NOT USED (low confidence) J. Roel-Touris and A. Bonvin, “Coarse-grained (hybrid) integrative modeling of biomolecular interactions,” Computational and Structural Biotechnology Journal. 2020. link Times cited: 15 NOT USED (low confidence) V. Dantanarayana et al., “Predictive model of charge carrier mobilities in organic semiconductor small molecules with force-matched potentials.,” Journal of chemical theory and computation. 2020. link Times cited: 12 Abstract: Charge mobility of crystalline organic semiconductors (OSC) … read moreAbstract: Charge mobility of crystalline organic semiconductors (OSC) is limited by local dynamic disorder. Recently, the charge mobility for several high mobility organic semiconductors, including TIPS-Pentacene, were accurately predicted from a density functional theory (DFT) simulation constrained by the crystal structure and the inelastic neutron scattering spectrum, which provide direct measures of the structure and the dynamic disorder in the length scale and energy range of interest. However, the computational expense required for calculating all of the atomic and molecular forces is prohibitive. Here we demonstrate the use of density functional tight binding (DFTB), a semi-empirical quantum mechanical method that is two to three orders of magnitude more efficient than DFT. We show that force matching a many-body interaction potential to DFT derived forces yields highly accurate DFTB models capable of reproducing the low-frequency intricacies of experimental INS spectra and accurately predicting charge mobility. We subsequently predicted charge mobilities from our DFTB model of a number of previously unstudied structural analogs to TIPS-pentacene using dynamic disorder from DFTB and transient localization theory. The approach we establish here could provide a truely rapid simulation pathway for accurate materials properties prediction, in our vision applied to new OSCs with tailored properties. read less NOT USED (low confidence) K. Kempfer, J. Devémy, A. Dequidt, M. Couty, and P. Malfreyt, “Multi-scale modeling of the polymer-filler interaction.,” Soft matter. 2020. link Times cited: 8 Abstract: We report mesoscopic simulations of the interaction between … read moreAbstract: We report mesoscopic simulations of the interaction between a silica nanoparticle and cis-1,4-polybutadiene chains with realistic coarse-(CG) grained models. The CG models are obtained with a bottom-up Bayesian method based on trajectory matching of atomistic configurations of the system. We then investigate the structural properties of the interfacial region as a function of the grafting density and polymer chain length. We take advantage of the realistic CG models to explore the dynamics of the nanoparticle over a period of 10 microseconds. We show that the dynamics of the nanoparticle is affected by the grafting density and the polymer chain length of the grafted chains. read less NOT USED (low confidence) T. T. Duignan, C. Mundy, G. Schenter, and X. S. Zhao, “A method for accurately predicting solvation structure.,” Journal of chemical theory and computation. 2019. link Times cited: 8 Abstract: Accurately predicting the molecular structure of solutions i… read moreAbstract: Accurately predicting the molecular structure of solutions is a fundamental scientific challenge. Using quantum mechanical density functional theory (DFT) to make these predictions is hindered by significant variation depending on which DFT functional is used. Here, we present a simple metric that can determine the reliability of a DFT functional for predicting solvation structure. We then show that including a simple interaction term to correct this metric leads to quantitative agreement with experimental measurements of liquid structure. We demonstrate the utility of this method by using it to accurately describe the hydration structure around the Na+ and K+ ions as well as the structural properties of pure water with a computationally cheap functional. read less NOT USED (low confidence) Y. Hong, B. Hou, H. Jiang, and J. Zhang, “Machine learning and artificial neural network accelerated computational discoveries in materials science,” Wiley Interdisciplinary Reviews: Computational Molecular Science. 2019. link Times cited: 55 Abstract: Artificial intelligence (AI) has been referred to as the “fo… read moreAbstract: Artificial intelligence (AI) has been referred to as the “fourth paradigm of science,” and as part of a coherent toolbox of data‐driven approaches, machine learning (ML) dramatically accelerates the computational discoveries. As the machinery for ML algorithms matures, significant advances have been made not only by the mainstream AI researchers, but also those work in computational materials science. The number of ML and artificial neural network (ANN) applications in the computational materials science is growing at an astounding rate. This perspective briefly reviews the state‐of‐the‐art progress in some supervised and unsupervised methods with their respective applications. The characteristics of primary ML and ANN algorithms are first described. Then, the most critical applications of AI in computational materials science such as empirical interatomic potential development, ML‐based potential, property predictions, and molecular discoveries using generative adversarial networks (GAN) are comprehensively reviewed. The central ideas underlying these ML applications are discussed, and future directions for integrating ML with computational materials science are given. Finally, a discussion on the applicability and limitations of current ML techniques and the remaining challenges are summarized. read less NOT USED (low confidence) C. Nowak, M. Misra, and F. Escobedo, “Framework for Inverse Mapping Chemistry-Agnostic Coarse-Grained Simulation Models into Chemistry-Specific Models,” Journal of chemical information and modeling. 2019. link Times cited: 3 Abstract: Coarse-grained (CG) models have allowed molecular simulation… read moreAbstract: Coarse-grained (CG) models have allowed molecular simulations to access large enough time and length scales to elucidate relationships between macroscale properties and microscale molecular interactions. However, an unaddressed inverse-design problem concerns the identification of an optimal chemistry-specific (CS) molecule that the generic CG model represents. This has been addressed here by introducing new tools for automatically generating and refining the mapping of CS-molecule candidates to the constraints of a CG model, based on representative optimization criteria. With these tools, for each CS-molecule from a candidate group, the best mapping of that molecule onto the CG model is found and their fit assessed by an objective function designed to emphasize matching key properties of the CG model. We employ this methodology to a range of CG models from small solvent molecules up to block copolymer systems to show its ability to find optimal candidates, and to uncover the underlying length scale of some of the CG models. For instances where the identity of the CG model is known a priori, the methodology identifies the correct AA chemistry. For instances where the identity is unknown and a pool of candidates is provided, the method selects a chemistry that aligns well with physical intuition. The best candidate chemistry is also found to be sensitive to changes to the CG model. read less NOT USED (low confidence) T. Giese and D. York, “Development of a Robust Indirect Approach for MM→QM Free Energy Calculations that Combines Force-matched Reference Potential and Bennett’s Acceptance Ratio Methods.,” Journal of chemical theory and computation. 2019. link Times cited: 52 Abstract: We use the PBE0/6-31G* density functional method to perform … read moreAbstract: We use the PBE0/6-31G* density functional method to perform ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations under periodic boundary conditions with rigorous electrostatics using the ambient potential composite Ewald method in order to test the convergence of MM→QM/MM free energy corrections for the prediction of 17 small-molecule solvation free energies and 8 ligand binding free energies to T4 lysozyme. The ``indirect'' thermodynamic cycle for calculating free energies is used to explore whether a series of reference potentials improve the statistical quality of the predictions. Specifically, we construct a series of reference potentials that optimizes a molecular mechanical (MM) force field's parameters to reproduce the ab initio QM/MM forces from a QM/MM simulation. The optimizations form a systematic progression of successively expanded parameters that include bond, angle, dihedral and charge parameters. For each reference potential, we calculate benchmark quality reference values for the MM→QM/MM correction by performing the mixed MM and QM/MM Hamiltonians at 11 intermediate states, each for 200 ps. We then compare forward and reverse application of Zwanzig's relation, thermodynamic integration, and Bennett's acceptance ratio (BAR) methods as a function of reference potential, simulation time, and the number of simulated intermediate states. We find that Zwanzig's equation is inadequate unless a large number of intermediate states are explicitly simulated. The TI and BAR mean signed errors are very small even when only the end-state simulations are considered, and the standard deviation of the TI and BAR errors are decreased by choosing a reference potential that optimizes the bond and angle parameters. We find a robust approach for the data sets of fairly rigid molecules considered here is to use bond+angle reference potential together with the end-state-only BAR analysis. This requires a QM/MM simulations to be performed in order to generate reference data to parameterize the bond+angle reference potential, and then this same simulation serves a dual purpose as the full QM/MM end-state. The convergence of the results with respect to time suggests that computational resources may be used more efficiently by running multiple simulations for no more than 50 ps, rather than running one long simulation. read less NOT USED (low confidence) J. D. Schneible, A. Singhal, R. L. Lilova, C. Hall, A. Grafmueller, and S. Menegatti, “Tailoring the Chemical Modification of Chitosan Hydrogels to Fine Tune the Release of a Synergistic Combination of Chemotherapeutics.,” Biomacromolecules. 2019. link Times cited: 20 Abstract: Combination chemotherapy with defined ratio and sequence of … read moreAbstract: Combination chemotherapy with defined ratio and sequence of drug release is a clinically established and effective route to treat advanced solid tumors. In this context, a growing body of literature demonstrates the potential of hydrogels constructed with chemically modified polysaccharides as depots for controlled release of chemotherapeutics. Identifying the appropriate modification in terms of physicochemical properties of the functional group and its degree of substitution (χ) to achieve the desired release profile for multiple drugs is, however, a complex multivariate problem. To address this issue, we have developed a computational toolbox that models the migration of a drug pair through a hydrated network of polysaccharide chains modified with hydrophobic moieties. In this study, we chose Doxorubicin (DOX) and Gemcitabine (GEM) as model drugs, as their synergistic effect against breast cancer has been thoroughly investigated, and chitosan as model polymer. Our model describes how the modification of chitosan chains with acetyl, butanoyl, and heptanoyl moieties at different values χ governs both the structure of the hydrogel network and drug migration through it. Our experimental data confirm the in silico predictions for both single and dual-drug release, and, most notably, the counterintuitive inversion of release vs. χ that occurs when switching from a single to a dual-drug system. Consensus between predicted and experimental data indicates that acetyl modifications (χ = 32-42%) and butanoyl-modifications (χ = 19-24%) provide synergistic GEM/DOX release molar ratios (5-10 i.e.,). Collectively, these results demonstrate the potential of this model in guiding the design of chemotherapeutic hydrogels to combat cancer. read less NOT USED (low confidence) H. Liu, Z. Fu, Y. Li, N. F. A. Sabri, and M. Bauchy, “Parameterization of empirical forcefields for glassy silica using machine learning,” MRS Communications. 2019. link Times cited: 16 Abstract: The development of reliable, yet computationally efficient i… read moreAbstract: The development of reliable, yet computationally efficient interatomic forcefields is key to facilitate the modeling of glasses. However, the parameterization of novel forcefields is challenging as the high number of parameters renders traditional optimization methods inefficient or subject to bias. Here, we present a new parameterization method based on machine learning, which combines ab initio molecular dynamics simulations and Bayesian optimization. By taking the example of glassy silica, we show that our method yields a new interatomic forcefield that offers an unprecedented agreement with ab initio simulations. This method offers a new route to efficiently parameterize new interatomic forcefields for disordered solids in a non-biased fashion. read less NOT USED (low confidence) A. Mirzoev, L. Nordenskiöld, and A. Lyubartsev, “Magic v.3: An integrated software package for systematic structure-based coarse-graining,” Comput. Phys. Commun. 2019. link Times cited: 18 NOT USED (low confidence) D. Rosenberger, T. Sanyal, M. Shell, and N. V. D. van der Vegt, “Transferability of Local Density-Assisted Implicit Solvation Models for Homogeneous Fluid Mixtures.,” Journal of chemical theory and computation. 2019. link Times cited: 16 Abstract: The application of bottom-up coarse grained (CG) models to s… read moreAbstract: The application of bottom-up coarse grained (CG) models to study the equilibrium mixing behavior of liquids is rather challenging, since these models can be significantly influenced by the density or the concentration of the state chosen during parametrization. This dependency leads to low transferability in density/concentration space and has been one of the major limitations in bottom-up coarse graining. Recent approaches proposed to tackle this shortcoming range from the addition of thermodynamic constraints, to an extended ensemble parametrization, to the addition of supplementary terms to the system's Hamiltonian. To study fluid phase equilibria with bottom-up CG models, the application of local density (LD) potentials appears to be a promising approach, as shown in previous work by Sanyal and Shell [T. Sanyal, M. S. Shell, J. Phys. Chem. B, 2018, 122, 5678]. Here, we want to further explore this method and test its ability to model a system which contains structural inhomogeneities only on the molecular scale, namely, solutions of methanol and water. We find that a water-water LD potential improves the transferability of an implicit-methanol CG model toward high water concentration. Conversely, a methanol-methanol LD potential does not significantly improve the transferability of an implicit-water CG model toward high methanol concentration. These differences appear due to the presence of cooperative interactions in water at high concentrations that the LD potentials can capture. In addition, we compare two different approaches to derive our CG models, namely, relative entropy optimization and the Inverse Monte Carlo method, and formally demonstrate under which analytical and numerical assumptions these two methods yield equivalent results. read less NOT USED (low confidence) K. Claridge and A. Troisi, “Developing Consistent Molecular Dynamics Force Fields for Biological Chromophores via Force Matching.,” The journal of physical chemistry. B. 2019. link Times cited: 20 Abstract: The role of the environment in excitation energy transport i… read moreAbstract: The role of the environment in excitation energy transport in the pigment-protein complexes (PPCs) of photosynthetic organisms is a widely investigated topic. The spectral density is a key component in understanding this protein-pigment interaction; however, the typical approach for calculating spectral density, combining molecular dynamics with quantum chemistry (QC) calculations, suffers from the geometry mismatch problem, arising from the structural inconsistency between the force field (FF) and the QC calculation. Existing parameterization methods demand much time-consuming manual inputs, limiting the number of systems that can be studied. We present a method, utilizing force matching for the autoparameterization of new pigment FFs for the use in spectral density calculations of PPCs, and apply the method to three pigments. The use of these optimized FFs in spectral density computation results in a notable difference in comparison to the original FF. read less NOT USED (low confidence) A. Kavalur and W. K. Kim, “A hybrid quasicontinuum method,” International Journal for Numerical Methods in Engineering. 2018. link Times cited: 2 Abstract: Quasicontinuum (QC) is a partitioned‐domain multiscale metho… read moreAbstract: Quasicontinuum (QC) is a partitioned‐domain multiscale method where the full‐atomistic description is retained in highly deformable subdomains while the energy in the remaining region is approximated using a continuum constitutive relation called the Cauchy‐Born (CB) rule. While the CB rule can capture the full nonlinearity of the strain energy, its computational cost is one or two orders of magnitude higher than the linear elasticity (LE) constitutive relation. In this paper, we propose an extension to the QC method, referred to as “hybrid QC,” where both the CB and LE relations are combined to increase the efficiency of the original QC method. This extension is summed up to a two‐step process. First, the continuum region is further divided into subregions with CB being restricted to subregions adjoining the atomistic region while LE is adopted in the remaining subregions. Second, a corrective scheme is applied to the LE subregion to recover the higher‐order accuracy. The hybrid QC method is validated through two examples: (i) a crystal containing a dipole of Lomer dislocations and (ii) a nanoindentation system. The simulation results show that the proposed hybrid QC method is numerically more efficient than the original QC method while maintaining virtually the same accuracy. read less NOT USED (low confidence) S. Bore, H. B. Kolli, T. Kawakatsu, G. Milano, and M. Cascella, “Mesoscale Electrostatics Driving Particle Dynamics in Nonhomogeneous Dielectrics.,” Journal of chemical theory and computation. 2018. link Times cited: 16 Abstract: We introduce a density functional-based formalism to compute… read moreAbstract: We introduce a density functional-based formalism to compute the electrostatic energy and forces for a mesoscopic system in the condensed phase, described with molecular resolution. The dielectric permittivity is variable in space, and it is dependent on the density fields of the individual particles present in the system. The electrostatic potential is obtained from standard numerical solutions of the generalized Poisson equation. The presence of a particle-dependent varying dielectrics produces the appearance of mesoscopic polarization forces, which are dependent on the local fluctuations of the permittivity, as well as of the electrostatic field. The proposed implementation is numerically robust, with an error on the Coulomb forces that can be systematically controlled by the mesh of spatial grid used for solving the generalized Poisson equation. We show that the method presented here is able to reproduce the concentration-dependent partitioning of an ideal salt in water/oil mixtures, in particular, reproducing the ∝ 1/ϵ dependency of the partition coefficient for the free ions predicted by Born theory. Moreover, this approach reproduces the correct electrostatic features of both dipolar and charged lipid bilayers, with positive membrane and dipole potentials. The sum of both Coulomb and polarization interactions inside the membrane yields a globally repulsive potential of mean force for the ions, independently on their charge. The computational efficiency of the method makes it particularly suitable for the description of large-scale polyelectrolyte soft-matter systems. read less NOT USED (low confidence) P. S. Hudson, S. Boresch, D. Rogers, and H. Woodcock, “Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching.,” Journal of chemical theory and computation. 2018. link Times cited: 42 Abstract: The calculation of free energy differences between levels of… read moreAbstract: The calculation of free energy differences between levels of theory has numerous potential pitfalls. Chief among them is the lack of overlap, i.e., ensembles generated at one level of theory (e.g., "low") not being good approximations of ensembles at the other (e.g., "high"). Numerous strategies have been devised to mitigate this issue. However, the most straightforward approach is to ensure that the "low" level ensemble more closely resembles that of the "high". Ideally, this is done without increasing computational cost. Herein, we demonstrate that by reparametrizing classical intramolecular potentials to reproduce high level forces (i.e., force matching) configurational overlap between a "low" (i.e., classical) and "high" (i.e., quantum) level can be significantly improved. This procedure is validated on two test cases and results in vastly improved convergence of free energy simulations. read less NOT USED (low confidence) J. M. Ortiz-Roldán et al., “Fitting electron density as a physically sound basis for the development of interatomic potentials of complex alloys.,” Physical chemistry chemical physics : PCCP. 2018. link Times cited: 2 Abstract: The development of new interatomic potentials to model metal… read moreAbstract: The development of new interatomic potentials to model metallic systems is a difficult task, due in part to the dependence between the parameters that describe the electron density and the short-range interactions. Parameter search methods are prone to false convergence. To solve this problem, we have developed a methodology for obtaining the electron density parameters independently of the short-range interactions, so that physically sound parameters can be obtained to describe the electron density, after which the short-range parameters can be fitted, thus reducing the complexity of the process and yielding better interatomic potentials. With the new method we can develop self-consistent, accurate force fields, using solely calculations, without the need to fit to experimental data. Density functional theory calculations are used to compute the observables with which the potential is fit. We applied the method to a Ni-based Inconel 625 superalloy (IN625), modelled here as Ni, Cr, Mo and Fe solid solution alloys. The capability of the force fields developed using this new method is validated, by comparing the structural and thermo-elastic properties predicted with the force fields, with the corresponding experimental data, both for single crystals and polycrystalline alloys. read less NOT USED (low confidence) T. Jiang, S. Simko, and R. E. Bulo, “Accurate Quantum Mechanics/Molecular Mechanics Simulation of Aqueous Solutions with Tailored Molecular Mechanics Models.,” Journal of chemical theory and computation. 2018. link Times cited: 6 Abstract: In recent years, quantum mechanical/molecular mechanical (QM… read moreAbstract: In recent years, quantum mechanical/molecular mechanical (QM/MM) methods have emerged that are designed specifically for chemical reactions in water. Despite the many advances, a remaining problem is that the patchwork of QM and MM descriptions changes the solvent structure. In a solvent as intricately connected as water, such structural changes can alter a chemical process even across large distances. Examples of structural artifacts in QM/MM water include density accumulation at the QM/MM boundary, decreased order, and density differences between regions. These issues are mostly apparent if the difference between the QM and the MM model is very large, which is often the case with water models. Here, we assess the QM/MM performance of simple MM models that are specifically parametrized to match selected data from a QM simulation of bulk water. To this end, we introduce a novel MM model (PM6-(DH+)-EFF) that reproduces PM6-DH+ water properties. We also assess a recent PBE-DFT-based MM model (PBE-EFF) that reproduces structural properties of bulk water simulated with PBE-DFT. Both models consist solely of tabulated potential energy terms for interactions between atom pairs. We compare the matched QM/MM results (PBE-DFT/PBE-EFF and PM6-DH+/PM6(-DH+)-EFF) with those from mismatched QM/MM simulations (PM6-DH+/PBE-EFF). The mismatched simulations reflect issues similar to those reported for other mismatched QM/MM pairs. The matched simulations yield very good results with water structures that barely deviate from the QM reference. In view of these findings, we strongly recommend adoption of specifically parametrized MM models in the QM/MM simulation of chemical processes in water. read less NOT USED (low confidence) S. Bore, G. Milano, and M. Cascella, “Hybrid Particle-Field Model for Conformational Dynamics of Peptide Chains.,” Journal of chemical theory and computation. 2018. link Times cited: 21 Abstract: We propose the first model of a polypeptide chain based on a… read moreAbstract: We propose the first model of a polypeptide chain based on a hybrid-particle field approach. The intramolecular potential is built on a two-bead coarse grain mapping for each amino acid. We employ a combined potential for the bending and the torsional degrees of freedom that ensures the stabilization of secondary structure elements in the conformational space of the polypeptide. The electrostatic dipoles associated with the peptide bonds of the main chain are reconstructed by a topological procedure. The intermolecular interactions comprising both the solute and the explicit solvent are treated by a density functional-based mean-field potential. Molecular dynamics simulations on a series of test systems show how the model here introduced is able to capture all the main features of polypeptides. In particular, homopolymers of different lengths yield a complex folding phase diagram, covering from the collapsed to swollen state. Moreover, simulations on models of a four-helix bundle and of an alpha + beta peptide evidence how the collapse of the hydrophobic core drives the appearance of both folded motifs and the stabilization of tertiary or quaternary assemblies. Finally, the polypeptide model is able to structurally respond to the environmental changes caused by the presence of a lipid bilayer. read less NOT USED (low confidence) J. A. Martinez, T. Liang, S. Sinnott, and S. Phillpot, “A third-generation charge optimized many body (COMB3) potential for nitrogen-containing organic molecules,” Computational Materials Science. 2017. link Times cited: 11 NOT USED (low confidence) A. Lyubartsev, “Inverse Monte Carlo Methods.” 2017. link Times cited: 2 Abstract: Modeling ofmany important biomolecular and so matter systems… read moreAbstract: Modeling ofmany important biomolecular and so matter systems requires consideration of length and time scales not reachable by atomistic simulations. An evident solution of this problem is introducing simplified models with lower spacial resolution, which have received a commonname: coarsegrained (CG)models. In CGmodels, atoms of (macro)molecules are united into CG sites and solvent atoms are o en not considered explicitly. This reduces greatly the number of degrees of freedom of the studied system and allows simulations of much larger systems which are not feasible to read less NOT USED (low confidence) K. Kreis, K. Kremer, R. Potestio, and M. Tuckerman, “From classical to quantum and back: Hamiltonian adaptive resolution path integral, ring polymer, and centroid molecular dynamics.,” The Journal of chemical physics. 2017. link Times cited: 15 Abstract: Path integral-based methodologies play a crucial role for th… read moreAbstract: Path integral-based methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical simulations. To reduce this numerical effort, we recently proposed a method, based on a rigorous Hamiltonian formulation, which restricts the quantum modeling to a small but relevant spatial region within a larger reservoir where particles are treated classically. In this work, we extend this idea and show how it can be implemented along with state-of-the-art path integral simulation techniques, including path-integral molecular dynamics, which allows for the calculation of quantum statistical properties, and ring-polymer and centroid molecular dynamics, which allow the calculation of approximate quantum dynamical properties. To this end, we derive a new integration algorithm that also makes use of multiple time-stepping. The scheme is validated via adaptive classical-path-integral simulations of liquid water. Potential applications of the proposed multiresolution method are diverse and include efficient quantum simulations of interfaces as well as complex biomolecular systems such as membranes and proteins. read less NOT USED (low confidence) K. Dong, X. Liu, H. Dong, X. Zhang, and S. Zhang, “Multiscale Studies on Ionic Liquids.,” Chemical reviews. 2017. link Times cited: 479 Abstract: Ionic liquids (ILs) offer a wide range of promising applicat… read moreAbstract: Ionic liquids (ILs) offer a wide range of promising applications because of their much enhanced properties. However, further development of such materials depends on the fundamental understanding of their hierarchical structures and behaviors, which requires multiscale strategies to provide coupling among various length scales. In this review, we first introduce the structures and properties of these typical ILs. Then, we introduce the multiscale modeling methods that have been applied to the ILs, covering from molecular scale (QM/MM), to mesoscale (CG, DPD), to macroscale (CFD for unit scale and thermodynamics COSMO-RS model and environmental assessment GD method for process scale). In the following section, we discuss in some detail their applications to the four scales of ILs, including molecular scale structures, mesoscale aggregates and dynamics, and unit scale reactor design and process design and optimization of typical IL applications. Finally, we address the concluding remarks of multiscale strategies in the understanding and predictive capabilities of ILs. The present review aims to summarize the recent advances in the fundamental and application understanding of ILs. read less NOT USED (low confidence) J. F. Rudzinski, K. Lu, S. Milner, J. K. Maranas, and W. Noid, “Extended Ensemble Approach to Transferable Potentials for Low-Resolution Coarse-Grained Models of Ionomers.,” Journal of chemical theory and computation. 2017. link Times cited: 11 Abstract: We develop an extended ensemble method for constructing tran… read moreAbstract: We develop an extended ensemble method for constructing transferable, low-resolution coarse-grained (CG) models of polyethylene-oxide (PEO)-based ionomer chains with varying composition at multiple temperatures. In particular, we consider ionomer chains consisting of 4 isophthalate groups, which may be neutral or sulfonated, that are linked by 13 PEO repeat units. The CG models represent each isophthalate group with a single CG site and also explicitly represent the diffusing sodium counterions but do not explicitly represent the PEO backbone. We define the extended ensemble as a collection of equilibrium ensembles that are obtained from united atom (UA) simulations at 2 different temperatures for 7 chemically distinct ionomers with varying degrees of sulfonation. We employ a global force-matching method to determine the set of interaction potentials that, when appropriately combined, provide an optimal approximation to the many-body potential of mean force for each system in the extended ensemble. This optimized xn force field employs long-ranged Coulomb potentials with system-specific dielectric constants that systematically decrease with increasing sulfonation and temperature. An empirical exponential model reasonably describes the sensitivity of the dielectric to sulfonation, but we find it more challenging to model the temperature-dependence of the dielectrics. Nevertheless, given appropriate dielectric constants, the transferable xn force field reasonably describes the ion pairing that is observed in the UA simulations as a function of sulfonation and temperature. Remarkably, despite eliminating any explicit description of the PEO backbone, the CG model predicts string-like ion aggregates that appear qualitatively consistent with the ionomer peak observed in X-ray scattering experiments and, moreover, with the temperature dependence of this peak. read less NOT USED (low confidence) N. V. Plotnikov, “Using Empirical Valence Bond Constructs as Reference Potentials For High‐Level Quantum Mechanical Calculations.” 2017. link Times cited: 0 NOT USED (low confidence) M. Molinari, A. Brukhno, S. C. Parker, and D. Spagnoli, “Force Field Application and Development.” 2016. link Times cited: 1 NOT USED (low confidence) Z. Li, X. Bian, X. Yang, and G. Karniadakis, “A comparative study of coarse-graining methods for polymeric fluids: Mori-Zwanzig vs. iterative Boltzmann inversion vs. stochastic parametric optimization.,” The Journal of chemical physics. 2016. link Times cited: 46 Abstract: We construct effective coarse-grained (CG) models for polyme… read moreAbstract: We construct effective coarse-grained (CG) models for polymeric fluids by employing two coarse-graining strategies. The first one is a forward-coarse-graining procedure by the Mori-Zwanzig (MZ) projection while the other one applies a reverse-coarse-graining procedure, such as the iterative Boltzmann inversion (IBI) and the stochastic parametric optimization (SPO). More specifically, we perform molecular dynamics (MD) simulations of star polymer melts to provide the atomistic fields to be coarse-grained. Each molecule of a star polymer with internal degrees of freedom is coarsened into a single CG particle and the effective interactions between CG particles can be either evaluated directly from microscopic dynamics based on the MZ formalism, or obtained by the reverse methods, i.e., IBI and SPO. The forward procedure has no free parameters to tune and recovers the MD system faithfully. For the reverse procedure, we find that the parameters in CG models cannot be selected arbitrarily. If the free parameters are properly defined, the reverse CG procedure also yields an accurate effective potential. Moreover, we explain how an aggressive coarse-graining procedure introduces the many-body effect, which makes the pairwise potential invalid for the same system at densities away from the training point. From this work, general guidelines for coarse-graining of polymeric fluids can be drawn. read less NOT USED (low confidence) S. Kmiecik, D. Gront, M. Koliński, L. Wieteska, A. Dawid, and A. Kolinski, “Coarse-Grained Protein Models and Their Applications.,” Chemical reviews. 2016. link Times cited: 671 Abstract: The traditional computational modeling of protein structure,… read moreAbstract: The traditional computational modeling of protein structure, dynamics, and interactions remains difficult for many protein systems. It is mostly due to the size of protein conformational spaces and required simulation time scales that are still too large to be studied in atomistic detail. Lowering the level of protein representation from all-atom to coarse-grained opens up new possibilities for studying protein systems. In this review we provide an overview of coarse-grained models focusing on their design, including choices of representation, models of energy functions, sampling of conformational space, and applications in the modeling of protein structure, dynamics, and interactions. A more detailed description is given for applications of coarse-grained models suitable for efficient combinations with all-atom simulations in multiscale modeling strategies. read less NOT USED (low confidence) T. E. de Oliveira, P. Netz, K. Kremer, C. Junghans, and D. Mukherji, “C-IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids.,” The Journal of chemical physics. 2016. link Times cited: 22 Abstract: We present a coarse-graining strategy that we test for aqueo… read moreAbstract: We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion (C-IBI). While the underlying coarse-grained model is still structure based and, thus, preserves pair-wise solution structure, our method also reproduces solvation thermodynamics of binary and/or ternary mixtures. Additionally, we observe much faster convergence within C-IBI compared to IBI. To validate the robustness, we apply C-IBI to study test cases of solvation thermodynamics of aqueous urea and a triglycine solvation in aqueous urea. read less NOT USED (low confidence) N. Goldman, L. Fried, and L. Koziol, “Using force-matched potentials to improve the accuracy of density functional tight binding for reactive conditions.,” Journal of chemical theory and computation. 2015. link Times cited: 24 Abstract: We show that force matching can be used to determine accurat… read moreAbstract: We show that force matching can be used to determine accurate empirical repulsive energies for the density functional tight binding method (DFTB) for chemical reactivity in condensed phases. Our approach yields improved results over previous parametrizations for molten liquid carbon and a phenolic polymer under combustion conditions. The method we present here allows for predictions of chemical properties over longer time periods than accessible via Kohn-Sham density functional theory while retaining its accuracy. read less NOT USED (low confidence) F. Cao and H. Sun, “Transferability and nonbond functional form of coarse grained force field - tested on linear alkanes.,” Journal of chemical theory and computation. 2015. link Times cited: 32 Abstract: Whether or not a coarse grained force field (CGFF) can be ma… read moreAbstract: Whether or not a coarse grained force field (CGFF) can be made to be transferrable is an important question to be addressed. By comparing potential energy with potential of mean force (PMF) of a molecular dimer, we proposed to use a free energy function (FE-12-6) with the parameters in entropic and energetic terms explicitly to represent the nonbond interactions in CGFF. Although the FE-12-6 function cannot accurately describe the PMF curves, a cancelation of short radii and strong repulsion makes the function a good approximation. For nonpolar molecules represented by linear alkanes, FE-12-6 is demonstrated to be highly effective in representing the nonbond interactions in CGFF. The force field parameters are well transferrable among different alkane molecules, in different thermodynamic states and for predicting various thermodynamic properties including heats of vaporization, vapor-liquid-equilibrium coexistence curves, surface tensions, and liquid densities. read less NOT USED (low confidence) I. C. Jenkins, J. Crocker, and T. Sinno, “Interaction potentials from arbitrary multi-particle trajectory data.,” Soft matter. 2015. link Times cited: 7 Abstract: Understanding the complex physics of particle-based systems … read moreAbstract: Understanding the complex physics of particle-based systems at the nanoscale and mesoscale increasingly relies on simulation methods, empowered by exponential advances in computing speed. A major impediment to progress lies in reliably obtaining the interaction potential functions that control system behavior - which are key inputs for any simulation approach - and which are often difficult or impossible to obtain directly using traditional experimental methods. Here, we present a straightforward methodology for generating pair potential functions from large multi-particle trajectory datasets, with no operational constraints regarding their state of equilibration, degree of damping or presence of hydrodynamic interactions. Using simulated datasets, we demonstrate that the method is highly robust against trajectory perturbations from Brownian motion and common errors introduced by particle tracking algorithms. Given the recent rapid pace of advancement in high-speed and three-dimensional microscopy and associated particle tracking algorithms, we anticipate a near future experimental regime where easily collected high-dimensional trajectory sets can be rapidly converted to the detailed interaction and hydrodynamic force fields required to replicate the system's physics in simulation. read less NOT USED (low confidence) K. Farrell, J. T. Oden, and D. Faghihi, “A Bayesian framework for adaptive selection, calibration, and validation of coarse-grained models of atomistic systems,” J. Comput. Phys. 2015. link Times cited: 23 NOT USED (low confidence) J. Wagner, J. Dama, and G. Voth, “Predicting the Sensitivity of Multiscale Coarse-Grained Models to their Underlying Fine-Grained Model Parameters.,” Journal of chemical theory and computation. 2015. link Times cited: 11 Abstract: The sensitivity of a coarse-grained (CG) force field to chan… read moreAbstract: The sensitivity of a coarse-grained (CG) force field to changes in the underlying fine-grained (FG) model from which it was derived provides modeling insight for improving transferability across interaction parameters, transferability across temperature, and the calculation of thermodynamic derivatives. Methods in the literature, such as multi-trajectory finite differences and reweighted finite differences, are either too computationally demanding to calculate within acceptable noise tolerances or are too biased for practical accuracy. This work presents a new reweighting-free, single-simulation formula that allows for practical, high signal-to-noise calculations of CG model sensitivity with respect to FG model interaction parameters and thermodynamic state points. This formula, the self-consistent basis (SCB) single point formula, determines the many-body sensitivity in a single step by approximating the derivative of the many-body potential projected onto the same set of trial functions as the sensitivity. A related diagnostic formula also derived in this paper is the self-consistent iterative (SCI) single point formula, which is useful for identifying the importance of many-body sources of error and verifying CG representability of observables. The SCI formula determines the many-body sensitivity iteratively via a series of partially self-consistent, variational approximations to the complete many-body sensitivity. The new, computationally efficient SCB formula shows substantially less noise than previous methods when applied to single site methanol and solvent-free sodium chloride CG models, though bias can remain a problem. It represents a novel method for calculating alchemical transferability across interaction parameters at low computational cost and with high fidelity, and the results point to new understanding of the current limits of CG model transferability. read less NOT USED (low confidence) M. L. Laury, L. P. Wang, V. Pande, T. Head‐Gordon, and J. Ponder, “Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.,” The journal of physical chemistry. B. 2015. link Times cited: 180 Abstract: A set of improved parameters for the AMOEBA polarizable atom… read moreAbstract: A set of improved parameters for the AMOEBA polarizable atomic multipole water model is developed. An automated procedure, ForceBalance, is used to adjust model parameters to enforce agreement with ab initio-derived results for water clusters and experimental data for a variety of liquid phase properties across a broad temperature range. The values reported here for the new AMOEBA14 water model represent a substantial improvement over the previous AMOEBA03 model. The AMOEBA14 model accurately predicts the temperature of maximum density and qualitatively matches the experimental density curve across temperatures from 249 to 373 K. Excellent agreement is observed for the AMOEBA14 model in comparison to experimental properties as a function of temperature, including the second virial coefficient, enthalpy of vaporization, isothermal compressibility, thermal expansion coefficient, and dielectric constant. The viscosity, self-diffusion constant, and surface tension are also well reproduced. In comparison to high-level ab initio results for clusters of 2-20 water molecules, the AMOEBA14 model yields results similar to AMOEBA03 and the direct polarization iAMOEBA models. With advances in computing power, calibration data, and optimization techniques, we recommend the use of the AMOEBA14 water model for future studies employing a polarizable water model. read less NOT USED (low confidence) P. Brommer, A. Kiselev, D. Schopf, P. Beck, J. Roth, and H. Trebin, “Classical interaction potentials for diverse materials from ab initio data: a review of potfit,” Modelling and Simulation in Materials Science and Engineering. 2014. link Times cited: 76 Abstract: Force matching is an established technique to generate effec… read moreAbstract: Force matching is an established technique to generate effective potentials for molecular dynamics simulations from first-principles data. This method has been implemented in the open source code potfit. Here, we present a review of the method and describe the main features of the code. Particular emphasis is placed on the features added since the initial release: interactions represented by analytical functions, differential evolution as optimization method, and a greatly extended set of interaction models. Beyond the initially present pair and embedded-atom method potentials, potfit can now also optimize angular dependent potentials, charge and dipolar interactions, and electron-temperature-dependent potentials. We demonstrate the functionality of these interaction models using three example systems: phonons in type I clathrates, fracture of α-alumina, and laser-irradiated silicon. read less NOT USED (low confidence) V. H. Rusu, R. Baron, and R. Lins, “PITOMBA: Parameter Interface for Oligosaccharide Molecules Based on Atoms.,” Journal of chemical theory and computation. 2014. link Times cited: 15 Abstract: A novel four-bead coarse-grained (CG) model for carbohydrate… read moreAbstract: A novel four-bead coarse-grained (CG) model for carbohydrates denoted PITOMBA was devised using a bottom-up approach based on the atomistic GROMOS 53A6GLYC force field and on experimental thermodynamical data. The model was developed to be used in conjunction with the SPC CG water model (J. Chem. Phys. 2011, 134, 084110) and the GROMOS force field functional form. Explicit electrostatic interactions are considered by assigning point charges to each CG bead. Validation of the model is presented to a variety of structural and thermodynamic properties for mono- and oligosaccharides in solution. In addition, the model development philosophy allows for prompt extensions to include hexopyranose chains with diverse glycosidic linkages and branches. read less NOT USED (low confidence) A. E. Kobryn, D. D. Nikolic, O. Lyubimova, S. Gusarov, and A. Kovalenko, “Dissipative particle dynamics with an effective pair potential from integral equation theory of molecular liquids.,” The journal of physical chemistry. B. 2014. link Times cited: 8 Abstract: We present a method of DPD simulation based on a coarse-grai… read moreAbstract: We present a method of DPD simulation based on a coarse-grained effective pair potential obtained from the DRISM-KH molecular theory of solvation. The theory is first used to calculate the radial distribution functions of all-atom solute monomers in all-atom solvent and then to invert them into an effective pair potential between coarse-grained beads such that their fluid without solvent accounts for molecular specificities and solvation effects in the all-atom system. Bonded interactions are sampled in relatively short MD of the all-atom system and modeled with best multi-Gaussian fit. Replacing the heuristically defined conservative force potential in DPD, the coarse-grained effective pair potential is free from the artificial restrictions on potential range and shape and on equal volume of solute and solvent blobs inherent in standard DPD. The procedure is flexible in specifying coarse-grained mapping and enormously increases computational efficiency by eliminating solvent. The method is validated on polystyrene chains of various length in toluene at finite concentrations for room and polystyrene glass transition temperature. It yields the chain elastic properties and diffusion coefficient in good agreement with experiment and all-atom MD simulations. DPD with coarse-grained effective pair potential is capable of predicting both structural and dynamic properties of polymer solutions and soft matter with high accuracy and computational efficiency. read less NOT USED (low confidence) Z. Li, X. Bian, B. Caswell, and G. Karniadakis, “Construction of dissipative particle dynamics models for complex fluids via the Mori-Zwanzig formulation.,” Soft matter. 2014. link Times cited: 89 Abstract: We present a bottom-up coarse-graining procedure to construc… read moreAbstract: We present a bottom-up coarse-graining procedure to construct mesoscopic force fields directly from microscopic dynamics. By grouping many bonded atoms in the molecular dynamics (MD) system into a single cluster, we compute both the conservative and non-conservative interactions between neighboring clusters. In particular, we perform MD simulations of polymer melts to provide microscopic trajectories for evaluating coarse-grained (CG) interactions. Subsequently, dissipative particle dynamics (DPD) is considered as the effective dynamics resulting from the Mori-Zwanzig (MZ) projection of the underlying atomistic dynamics. The forces between finite-size clusters have, in general, both radial and transverse components and hence we employ four different DPD models to account differently for such interactions. Quantitative comparisons between these DPD models indicate that the DPD models with MZ-guided force fields yield much better static and dynamics properties, which are consistent with the underlying MD system, compared to standard DPD with empirical formulae. When the rotational motion of the particle is properly taken into account, the entire velocity autocorrelation function of the MD system as well as the pair correlation function can be accurately reproduced by the MD-informed DPD model. Since this coarse-graining procedure is performed on an unconstrained MD system, our framework is general and can be used in other soft matter systems in which the clusters can be faithfully defined as CG particles. read less NOT USED (low confidence) A. Gabrieli, M. Sant, P. Demontis, and G. B. Suffritti, “Fast and efficient optimization of Molecular Dynamics force fields for microporous materials: Bonded interactions via force matching,” Microporous and Mesoporous Materials. 2014. link Times cited: 11 NOT USED (low confidence) Y. Zhou and J. Pu, “Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations.,” Journal of chemical theory and computation. 2014. link Times cited: 39 Abstract: We present a general strategy of reparametrizing semiempiric… read moreAbstract: We present a general strategy of reparametrizing semiempirical (SE) methods against ab initio (AI) methods for combined quantum mechanical and molecular mechanical (QM/MM) simulations of specific chemical reactions in condensed phases. The resulting approach, designated Reaction Path Force Matching (RP-FM), features cycles of sampling configurations along a reaction path on an efficient SE/MM potential energy surface (PES) and adjusting specific reaction parameters (SRPs) in the SE method such that the atomic forces computed at the target AI/MM level are reproduced. Iterative applications of the RP-FM cycle make possible achieving the accuracy of AI/MM simulations without explicitly sampling the computationally expensive AI/MM PES. The bypassed sampling, nevertheless, is implicitly accomplished through the aid of the efficient SE-SRP/MM PES, on which the target-level reaction path is expected to be obtained upon convergence. We demonstrate the effectiveness of the RP-FM procedure for a symmetric proton transfer reaction in the gas phase and in solution. The remarkable agreements between the RP-FM optimized SE-SRP methods and the target AI method on various properties, including energy profiles, potential of mean force free energy profiles, atomic forces, charge populations, and solvation effects, suggest that RP-FM can be used as an efficient and reliable strategy for simulating condensed-phase chemical reactions. read less NOT USED (low confidence) E. Lyman and S. Patel, “Molecular Dynamics of Lipid Bilayers: Standards, Successes, and Works in Progress.” 2014. link Times cited: 1 NOT USED (low confidence) S. Fritsch, R. Potestio, D. Donadio, and K. Kremer, “Nuclear Quantum Effects in Water: A Multiscale Study.,” Journal of chemical theory and computation. 2014. link Times cited: 44 Abstract: We outline a method to investigate the role of nuclear quant… read moreAbstract: We outline a method to investigate the role of nuclear quantum effects in liquid water making use of a force field derived from ab initio simulations. Starting from a first-principles molecular dynamics simulation, we obtain an effective force field for bulk liquid water using the force-matching technique. After validating that our effective model reproduces the key structural and dynamic properties of the reference system, we use it to perform path integral simulations to investigate the role played by nuclear quantum effects on bulk water, probing radial distribution functions, vibrational spectra, and hydrogen bond fluctuations. Our approach offers a practical route to derive ab initio quality molecular models to study quantum effects at a low computational cost. read less NOT USED (low confidence) M. Doemer, P. Maurer, P. Campomanes, I. Tavernelli, and U. Rothlisberger, “Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin.,” Journal of chemical theory and computation. 2014. link Times cited: 20 Abstract: We extended a previously developed force matching approach t… read moreAbstract: We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the retinal protonated Schiff base in dark state bovine rhodopsin. We were able to develop a highly accurate force field that is able to capture subtle structural changes within the chromophore that have a pronounced influence on the optical properties. The optical absorption spectrum calculated from configurations extracted from a MD trajectory using the new force field is in excellent agreement with QM/MM and experimental references. read less NOT USED (low confidence) J. A. Martinez, D. E. Yilmaz, D. E. Yilmaz, T. Liang, S. Sinnott, and S. Phillpot, “Fitting empirical potentials: Challenges and methodologies,” Current Opinion in Solid State & Materials Science. 2013. link Times cited: 45 NOT USED (low confidence) P. Nicolini, E. Guàrdia, and M. Masia, “Shortcomings of the standard Lennard-Jones dispersion term in water models, studied with force matching.,” The Journal of chemical physics. 2013. link Times cited: 8 Abstract: In this work, ab initio parametrization of water force field… read moreAbstract: In this work, ab initio parametrization of water force field is used to get insights into the functional form of empirical potentials to properly model the physics underlying dispersion interactions. We exploited the force matching algorithm to fit the interaction forces obtained with dispersion corrected density functional theory based molecular dynamics simulations. We found that the standard Lennard-Jones interaction potentials poorly reproduce the attractive character of dispersion forces. This drawback can be resolved by accounting for the distinctive short range behavior of dispersion interactions, multiplying the r(-6) term by a damping function. We propose two novel parametrizations of the force field using different damping functions. Structural and dynamical properties of the new models are computed and compared with the ones obtained from the non-damped force field, showing an improved agreement with reference first principle calculations. read less NOT USED (low confidence) F. Leonarski, F. Trovato, V. Tozzini, A. Leś, and J. Trylska, “Evolutionary Algorithm in the Optimization of a Coarse-Grained Force Field.,” Journal of chemical theory and computation. 2013. link Times cited: 29 Abstract: Simulations using residue-scale coarse-grained models of bio… read moreAbstract: Simulations using residue-scale coarse-grained models of biomolecules are less computationally demanding than simulations employing full-atomistic force fields. However, the coarse-grained models are often difficult and tedious to parametrize for certain applications. Therefore, a systematic and objective method to help develop or adapt the coarse-grained models is needed. We present an automatic method that implements an evolutionary algorithm to find a set of optimal force field parameters for a one-bead coarse-grained model. In addition to an optimized force field, parameter correlations and significance of the potential energy terms can be determined. The method is applied to two classes of problems: the dynamics of an RNA helix and the RNA structure prediction. 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) L. P. Wang et al., “Systematic improvement of a classical molecular model of water.,” The journal of physical chemistry. B. 2013. link Times cited: 279 Abstract: We report the iAMOEBA ("inexpensive AMOEBA") class… read moreAbstract: We report the iAMOEBA ("inexpensive AMOEBA") classical polarizable water model. The iAMOEBA model uses a direct approximation to describe electronic polarizability, in which the induced dipoles are determined directly from the permanent multipole electric fields and do not interact with one another. The direct approximation reduces the computational cost relative to a fully self-consistent polarizable model such as AMOEBA. The model is parameterized using ForceBalance, a systematic optimization method that simultaneously utilizes training data from experimental measurements and high-level ab initio calculations. We show that iAMOEBA is a highly accurate model for water in the solid, liquid, and gas phases, with the ability to fully capture the effects of electronic polarization and predict a comprehensive set of water properties beyond the training data set including the phase diagram. The increased accuracy of iAMOEBA over the fully polarizable AMOEBA model demonstrates ForceBalance as a method that allows the researcher to systematically improve empirical models by efficiently utilizing the available data. read less NOT USED (low confidence) B. Ni and A. Baumketner, “Reduced atomic pair-interaction design (RAPID) model for simulations of proteins.,” The Journal of chemical physics. 2013. link Times cited: 9 Abstract: Increasingly, theoretical studies of proteins focus on large… read moreAbstract: Increasingly, theoretical studies of proteins focus on large systems. This trend demands the development of computational models that are fast, to overcome the growing complexity, and accurate, to capture the physically relevant features. To address this demand, we introduce a protein model that uses all-atom architecture to ensure the highest level of chemical detail while employing effective pair potentials to represent the effect of solvent to achieve the maximum speed. The effective potentials are derived for amino acid residues based on the condition that the solvent-free model matches the relevant pair-distribution functions observed in explicit solvent simulations. As a test, the model is applied to alanine polypeptides. For the chain with 10 amino acid residues, the model is found to reproduce properly the native state and its population. Small discrepancies are observed for other folding properties and can be attributed to the approximations inherent in the model. The transferability of the generated effective potentials is investigated in simulations of a longer peptide with 25 residues. A minimal set of potentials is identified that leads to qualitatively correct results in comparison with the explicit solvent simulations. Further tests, conducted for multiple peptide chains, show that the transferable model correctly reproduces the experimentally observed tendency of polyalanines to aggregate into β-sheets more strongly with the growing length of the peptide chain. Taken together, the reported results suggest that the proposed model could be used to succesfully simulate folding and aggregation of small peptides in atomic detail. Further tests are needed to assess the strengths and limitations of the model more thoroughly. read less NOT USED (low confidence) P. Posocco, S. Pricl, and M. Fermeglia, “Multiscale Modeling Approach for Polymeric Nanocomposites.” 2013. link Times cited: 3 NOT USED (low confidence) L. P. Wang, J. Chen, and T. V. Voorhis, “Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data.,” Journal of chemical theory and computation. 2013. link Times cited: 166 Abstract: We introduce ForceBalance, a method and free software packag… read moreAbstract: We introduce ForceBalance, a method and free software package for systematic force field optimization with the ability to parametrize a wide variety of functional forms using flexible combinations of reference data. We outline several important challenges in force field development and how they are addressed in ForceBalance, and present an example calculation where these methods are applied to develop a highly accurate polarizable water model. ForceBalance is available for free download at https://simtk.org/home/forcebalance. read less NOT USED (low confidence) L. Vanduyfhuys, T. Verstraelen, M. Vandichel, M. Waroquier, and V. Speybroeck, “Ab Initio Parametrized Force Field for the Flexible Metal-Organic Framework MIL-53(Al).,” Journal of chemical theory and computation. 2012. link Times cited: 62 Abstract: A force field is proposed for the flexible metal-organic fra… read moreAbstract: A force field is proposed for the flexible metal-organic framework MIL-53(Al), which is calibrated using density functional theory calculations on nonperiodic clusters. The force field has three main contributions: an electrostatic term based on atomic charges derived with a modified Hirshfeld-I method, a van der Waals (vdW) term with parameters taken from the MM3 model, and a valence force field whose parameters were estimated with a new methodology that uses the gradients and Hessian matrix elements retrieved from nonperiodic cluster calculations. The new force field predicts geometries and cell parameters that compare well with the experimental values both for the large and narrow pore phases. The energy profile along the breathing mode of the empty material reveals the existence of two minima, which confirms the intrinsic bistable behavior of the MIL-53. Even without the stimulus of external guest molecules, the material may transform from the large pore (lp) to the narrow pore (np) phase [Liu et al. J. Am. Chem. Soc.2008, 120, 11813]. The relative stability of the two phases critically depends on the vdW parameters, and the MM3 dispersion interaction has the tendency to overstabilize the np phase. read less NOT USED (low confidence) X. Li, “An atomistic-based boundary element method for the reduction of molecular statics models,” Computer Methods in Applied Mechanics and Engineering. 2012. link Times cited: 17 NOT USED (low confidence) M. Horstemeyer, “Atomistic Modeling Methods.” 2012. link Times cited: 0 NOT USED (low confidence) M. Horstemeyer, “An Introduction to Integrated Computational Materials Engineering (ICME).” 2012. link Times cited: 3 Abstract: The concept of Integrated Computational Materials Engineerin… read moreAbstract: The concept of Integrated Computational Materials Engineering (ICME) arises from the new simulation-based design paradigm that employs a hierarchical multiscale modeling methodology for optimizing load-bearing structures. The methodology integrates material models, structure – property relationships that are observed from experiments, and simulations starting at the quantum level. At the structural level, heterogeneous microstructures are embedded in the fi nite element analysis. Because these microstructures are included, the paradigm shift from safety factors to predicting failure is fundamental. ICME ' s opportunity has emerged because of the recent confl uence of smaller desktop computers with enhanced computing power coupled with the advent of physically based material models. Furthermore, the clear trend in modeling and simulation is to integrate more knowledge into materials processing and product performance. I propose that ICME is the appropriate means to garner the required accuracy for a simulation-based design and manufacturing paradigm , and this book is a means for engineers to realize that goal. This fi rst chapter includes Horstemeyer's [1] review of the various multiscale method-ologies related to solid materials and the associated experimental infl uences, the various infl uences of multiscale modeling on different disciplines, and some examples of multiscale modeling in design of structural components. 1.1 BACKGROUND Although computational multiscale modeling methodologies were developed in the very late 20th century, the fundamental notions of multiscale modeling have been around since da Vinci studied different sizes of ropes. The recent rapid growth in multiscale modeling arose from the confl uence of parallel computing power, experimental capabilities that characterize structure – property relations down to the atomic level, and theories that admit multiple length scales. The ubiquitous research focused on multiscale modeling has since broached different disciplines (solid mechanics, fl uid mechanics, mate rials science, physics, mathematics, biological, and chemistry), different regions of the world (most continents), and different length scales (from atoms to autos). With the advent of accurate modeling and simulation and signifi cant increases in economical computing power, virtual design and manufacturing provides the means to reduce product development time and cost while improving overall quality and manufacturing effi ciency. However, the quality of the end product depends on the quality of the modeling with respect to the particular conditions involved and the computational effi ciency of the simulations (e.g., plasticity and fracture of specifi c materials under extremely rapid stress conditions). Several case studies are later shown to demonstrate the important … read less NOT USED (low confidence) L. Lu and G. Voth, “The Multiscale Coarse‐Graining Method.” 2012. link Times cited: 102 NOT USED (low confidence) C. Knight and G. Voth, “The curious case of the hydrated proton.,” Accounts of chemical research. 2012. link Times cited: 259 Abstract: Understanding the hydrated proton is a critically important … read moreAbstract: Understanding the hydrated proton is a critically important problem that continues to engage the research efforts of chemists, physicists, and biologists because of its involvement in a wide array of phenomena. Only recently have several unique properties of the hydrated proton been unraveled through computer simulations. One such process is the detailed molecular mechanism by which protons hop between neighboring water molecules, thus giving rise to the anomalously high diffusion of protons relative to other simple cations. Termed Grotthuss shuttling, this process occurs over multiple time and length scales, presenting unique challenges for computer modeling and simulation. Because the hydrated proton is in reality a dynamical electronic charge defect that spans multiple water molecules, the simulation methodology must be able to dynamically readjust the chemical bonding topology. This reactive nature of the chemical process is automatically captured with ab initio molecular dynamics (AIMD) simulation methods, where the electronic degrees of freedom are treated explicitly. Unfortunately, these calculations can be prohibitively expensive for more complex proton solvation and transport phenomena in the condensed phase. These AIMD simulations remain extremely valuable, however, in validating empirical models, verifying results, and providing insight into molecular mechanisms. In this Account, we discuss recent progress in understanding the solvation and transport properties of the hydrated excess proton. The advances are based on results obtained from reactive molecular dynamics simulations using the multistate empirical valence bond (MS-EVB) methodology. This approach relies on a dynamic linear combination of chemical bond topologies to model charge delocalization and dynamic bonding environments. When parametrized via a variational force-matching algorithm from AIMD trajectories, the MS-EVB method can be viewed as a multiscale bridging of ab initio simulation results to a simpler and more efficient representation. The process allows sampling of longer time and length scales, which would normally be too computationally expensive with AIMD alone. With the MS-EVB methodology, the statistically important components of the excess proton solvation and hopping mechanisms in liquid water have been identified. The most likely solvation structure for the hydrated proton is a distorted Eigen-type complex (H(9)O(4)(+)). In this state, the excess proton charge defect rapidly resonates between three possible distorted Eigen-type structures until a successful proton hop occurs. This process, termed the "special-pair dance", serves as a kind of preparatory phase for the proton hopping while the neighboring water hydrogen-bonding network fluctuates and ultimately rearranges to facilitate a proton hop. The modifications of the solvation structure and transport properties of the excess proton in concentrated acid solutions were further investigated. The Eigen-type solvation structure also possesses both "hydrophilic" and "hydrophobic" sides, which accounts for the affinity of the hydrated proton for the air-water interface. This unusual "amphiphilic" character of the hydrated proton further leads to the metastable formation of contact ion pairs between two hydrated protons. It also engenders a surprisingly constant degree of solubility of hydrophobic species as a function of acid concentration, which contrasts with a markedly variable solubility as a function of salt (such as NaCl or KCl) concentration. read less 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) J. Sala, E. Guàrdia, and M. Masia, “Improving the force matching algorithm: Application to a simple point charge flexible model of water,” Comput. Phys. Commun. 2011. link Times cited: 11 NOT USED (low confidence) J. Chen and P. Ming, “An Efficient Multigrid Method for Molecular Mechanics Modeling in Atomic Solids,” Communications in Computational Physics. 2011. link Times cited: 14 Abstract: We propose a multigrid method to solve the molecular mechani… read moreAbstract: We propose a multigrid method to solve the molecular mechanics model (molecular dynamics at zero temperature). The Cauchy-Born elasticity model is employed as the coarse grid operator and the elastically deformed state as the initial guess of the molecular mechanics model. The efficiency of the algorithm is demonstrated by three examples with homogeneous deformation, namely, one dimensional chain under tensile deformation and aluminum under tension and shear deformations. The method exhibits linear-scaling computational complexity, and is insensitive to parameters arising from iterative solvers. In addition, we study two examples with inhomogeneous deformation: vacancy and nanoindentation of aluminum. The results are still satisfactory while the linear-scaling property is lost for the latter example. read less NOT USED (low confidence) N. Chennamsetty, H. Bock, M. Lísal, and J. Brennan, “An introduction to coarse-graining approaches: linking atomistic and mesoscales.” 2011. link Times cited: 7 NOT USED (low confidence) P. Kowalczyk, P. A. Gauden, and A. Ciach, “Optimization of coarse-grained interaction potential: inside inherent limitations of coarse-graining methods.,” The journal of physical chemistry. B. 2011. link Times cited: 8 Abstract: We studied the inherent limitations of coarse-grained (CG) p… read moreAbstract: We studied the inherent limitations of coarse-grained (CG) potentials within the recently developed approach (Kowalczyk et al. J. Phys. Chem. B2009, 113, 12988-12998). For all studied fluids, the spherically symmetric CG potential constructed according to our scheme modified in this work balances the reproduction of various equilibrium properties (i.e., structural and thermodynamic) measured in CG simulations. The inherent loss of atomistic information at the CG level correlates with the contribution from short-range directional interactions. The highest loss of atomistic information at 298 K and 1 bar is reported for protic liquids (i.e., methanol and acetamide), while the best description at the CG level was obtained for molecular hydrogen and carbon dioxide. The investigated aprotic liquids (i.e., benzene, toluene, and acetone) can be CG into spherically symmetric interaction potentials with some loss of atomistic details. Interestingly, we show that the proposed optimal CG potential reproduces also the interfacial properties of vapor-liquid coexistence for aprotic benzene at 298 K. For all studied fluids, we find that one can easily reproduce structural properties without preserving their cohesive properties or vice versa. However, a general conclusion from our study is the following: an increase in the protic character of a fluid leads to an increase of inherent loss of atomistic details at the CG level. read less NOT USED (low confidence) I. Fukuda, Y. Yonezawa, and H. Nakamura, “Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle.,” The Journal of chemical physics. 2011. link Times cited: 72 Abstract: We propose a novel idea, zero-dipole summation, for evaluati… read moreAbstract: We propose a novel idea, zero-dipole summation, for evaluating the electrostatic energy of a classical particle system, and have composed an algorithm for effectively utilizing the idea for molecular dynamics. It conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple cutoff truncation. The resulting energy formula is nevertheless represented by a simple pairwise function sum, which enables facile application to high-performance computation. By following a heuristic approach to derive the current electrostatic energy formula, we developed an axiomatic approach to construct the method consistently. Explorations of the theoretical details of our method revealed the structure of the generated error, and we analyzed it by comparisons with other methods. A numerical simulation using liquid sodium chloride confirmed that the current method with a small damping factor yielded sufficient accuracy with a practical cutoff distance region. The current energy function also conducts stable numerical integration in a liquid MD simulation. Our method is an extension of the charge neutralized summation developed by Wolf et al. [J. Chem. Phys. 110, 8254 (1999)]. Furthermore, we found that the current method becomes a generalization of the preaveraged potential method proposed by Yakub and Ronchi [J. Chem. Phys. 119, 11556 (2003)], which is based on a viewpoint different from the neutrality. The current study presents these relationships and suggests possibilities for their further applications. read less NOT USED (low confidence) T. Morrow, “Overcoming Large Time- and Length-Scale Challenges in Molecular Modeling: A Review of Atomistic to Mesoscale Coarse-Graining Methods.” 2010. link Times cited: 1 NOT USED (low confidence) W. Shan and U. Nackenhorst, “Applying Cauchy‐Born rule for converting atomistic model to continuum model,” PAMM. 2010. link Times cited: 4 Abstract: The Cauchy‐Born rule has been applied in the Quasicontinuum … read moreAbstract: The Cauchy‐Born rule has been applied in the Quasicontinuum method to derive continuum material properties based on underlying atomistic model in a physically consistent way. In this short work, the procedure is demonstrated, where the resulted materials constants are compared with experimental data found in literature. Moreover, the condition for applying the Cauchy‐Born rule is discussed, with an intuitive explanation for why it can be only applied to crystalline materials with perfect structure. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim) read less NOT USED (low confidence) Y. Song, O. Akin-Ojo, and F. Wang, “Correcting for dispersion interaction and beyond in density functional theory through force matching.,” The Journal of chemical physics. 2010. link Times cited: 22 Abstract: The force matching method is used to improve density functio… read moreAbstract: The force matching method is used to improve density functional theory (DFT) by designing a supplemental potential to capture the difference in atomic forces between a DFT functional and a high-quality post Hartree-Fock method. The supplemental potential has two-body terms designed to correct for dispersion and hydrogen bond interactions. The potential also has one-body terms to improve the description of the intramolecular potential energy surface. Our procedure is tested by providing corrections to the Becke-Lee-Yang-Parr exchange-correlation functional for water and is found to perform significantly better than the standard DFT-D approach, giving QCISD quality predictions for relative cluster energies, atomic forces, and molecular structures. It is found that a simple Lennard-Jones term does a good job at correcting for van der Waals interactions and possibly also providing corrections to exchange repulsion. The one-body corrections, while contributing only slightly to improving relative cluster energies, significantly reduce the errors in binding energies and atomic forces for the systems studied. read less NOT USED (low confidence) P. Tiwary, A. Walle, B. Jeon, and N. Grønbech-Jensen, “Interatomic potentials for mixed oxide and advanced nuclear fuels,” Physical Review B. 2010. link Times cited: 19 Abstract: We extend our recently developed interatomic potentials for … read moreAbstract: We extend our recently developed interatomic potentials for UO_2 to the fuel system (U,Pu,Np)O_2. We do so by fitting against an extensive database of ab initio results as well as to experimental measurements. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We therefore expect these to be reliable potentials for carrying out damage simulations (and molecular dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies. 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) J. Fish, A. Li, and F. Yavari, “Adaptive generalized mathematical homogenization framework for nanostructured materials,” International Journal for Numerical Methods in Engineering. 2010. link Times cited: 8 Abstract: We present an adaptive generalized mathematical homogenizati… read moreAbstract: We present an adaptive generalized mathematical homogenization (AGMH) framework for modeling nanostructured materials with evolving defects at a finite temperature. By this approach molecular dynamics model is employed in the vicinity of defects whereas constitutive equation‐free continuum model is used away from the defects. The proposed framework consists of the following salient features: (i) a constitutive law‐free cohesive element whose behavior is modeled by the atomistic representative volume element (ARVE) and (ii) a dislocation detection band embedded in the ARVE aimed at detecting dislocations passing from or into the interior of the nanograins. These features of the model are critical to studying deformation of nanocrystals where only a small portion of the problem domain requires molecular resolution. Copyright © 2010 John Wiley & Sons, Ltd. read less NOT USED (low confidence) M. Fellinger, H. Park, and J. Wilkins, “Force-matched embedded-atom method potential for niobium,” Physical Review B. 2010. link Times cited: 115 Abstract: Large-scale simulations of plastic deformation and phase tra… read moreAbstract: Large-scale simulations of plastic deformation and phase transformations in alloys require reliable classical interatomic potentials. We construct an embedded-atom method potential for niobium as the first step in alloy potential development. Optimization of the potential parameters to a well-converged set of density-functional theory (DFT) forces, energies, and stresses produces a reliable and transferable potential for molecular dynamics simulations. The potential accurately describes properties related to the fitting data, and also produces excellent results for quantities outside the fitting range. Structural and elastic properties, defect energetics, and thermal behavior compare well with DFT results and experimental data, e.g., DFT surface energies are reproduced with less than 4% error, generalized stacking-fault energies differ from DFT values by less than 15%, and the melting temperature is within 2% of the experimental value. read less NOT USED (low confidence) M. C. Villet and G. Fredrickson, “Numerical coarse-graining of fluid field theories.,” The Journal of chemical physics. 2010. link Times cited: 31 Abstract: We present a formalism for the systematic numerical coarse-g… read moreAbstract: We present a formalism for the systematic numerical coarse-graining of field-theoretic models of fluids that draws upon techniques from both the Monte Carlo renormalization group and particle-based coarse-graining literature. A force-matching technique initially developed for coarse-graining particle-based interaction potentials is adapted to calculate renormalized field-theoretic coupling coefficients in a complex-valued field theory, and a related method is introduced for coarse-graining field-theoretic operators. The viability of this methodology is demonstrated by coarse-graining a field-theoretic model of a Gaussian-core fluid and thereby reducing lattice discretization errors. read less NOT USED (low confidence) F. Tavazza, L. Levine, and A. Chaka, “A HYBRID, QUANTUM-CLASSICAL APPROACH FOR THE COMPUTATION OF DISLOCATION PROPERTIES IN REAL MATERIALS: METHOD, LIMITATIONS AND APPLICATIONS,” International Journal of Modern Physics C. 2009. link Times cited: 0 Abstract: In this work we introduce a hybrid ab initio-classical simul… read moreAbstract: In this work we introduce a hybrid ab initio-classical simulation methodology designed to incorporate the chemistry into the description of phenomena that, intrinsically, require very large systems to be properly described. This hybrid approach allows us to conduct large-scale atomistic simulations with a simple classical potential (embedded atom method (EAM), for instance) while simultaneously using a more accurate ab initio approach for critical embedded regions. The coupling is made through shared atomic shells where the two atomistic modeling approaches are relaxed in an iterative, self-consistent manner. The magnitude of the incompatibility forces arising in the shared shell is analyzed, and possible terminations for the embedded region are discussed, as a way to reduce such forces. As a test case, the formation energy of a single vacancy in aluminum at different distances from an edge dislocation is studied. Results obtained using the hybrid approach are compared to those obtained using classical methods alone, and the range of validity for the classical approach is evaluated. read less NOT USED (low confidence) M. Betancourt and S. J. Omovie, “Pairwise energies for polypeptide coarse-grained models derived from atomic force fields.,” The Journal of chemical physics. 2009. link Times cited: 27 Abstract: The energy parametrization of geometrically simplified versi… read moreAbstract: The energy parametrization of geometrically simplified versions of polypeptides, better known as polypeptide or protein coarse-grained models, is obtained from molecular dynamics and statistical methods. Residue pairwise interactions are derived by performing atomic-level simulations in explicit water for all 210 pairs of amino acids, where the amino acids are modified to closer match their structure and charges in polypeptides. Radial density functions are computed from equilibrium simulations for each pair of residues, from which statistical energies are extracted using the Boltzmann inversion method. The resulting models are compared to similar potentials obtained by knowledge based methods and to hydrophobic scales, resulting in significant similarities in spite of the model simplicity. However, it was found that glutamine, asparagine, lysine, and arginine are more attractive to other residues than anticipated, in part, due to their amphiphilic nature. In addition, equally charged residues appear more repulsive than expected. Difficulties in the calculation of knowledge based potentials and hydrophobicity scale for these cases, as well as sensitivity of the force field to polarization effects are suspected to cause this discrepancy. It is also shown that the coarse-grained model can identify native structures in decoy databases nearly as well as more elaborate knowledge based methods, in spite of its resolution limitations. In a test conducted with several proteins and corresponding decoys, the coarse-grained potential was able to identify the native state structure but not the original atomic force field. read less NOT USED (low confidence) T. Murtola, A. Bunker, I. Vattulainen, M. Deserno, and M. Karttunen, “Multiscale modeling of emergent materials: biological and soft matter.,” Physical chemistry chemical physics : PCCP. 2009. link Times cited: 254 Abstract: In this review, we focus on four current related issues in m… read moreAbstract: In this review, we focus on four current related issues in multiscale modeling of soft and biological matter. First, we discuss how to use structural information from detailed models (or experiments) to construct coarse-grained ones in a hierarchical and systematic way. This is discussed in the context of the so-called Henderson theorem and the inverse Monte Carlo method of Lyubartsev and Laaksonen. In the second part, we take a different look at coarse graining by analyzing conformations of molecules. This is done by the application of self-organizing maps, i.e., a neural network type approach. Such an approach can be used to guide the selection of the relevant degrees of freedom. Then, we discuss technical issues related to the popular dissipative particle dynamics (DPD) method. Importantly, the potentials derived using the inverse Monte Carlo method can be used together with the DPD thermostat. In the final part we focus on solvent-free modeling which offers a different route to coarse graining by integrating out the degrees of freedom associated with solvent. read less NOT USED (low confidence) M. Shell, “The relative entropy is fundamental to multiscale and inverse thermodynamic problems.,” The Journal of chemical physics. 2008. link Times cited: 488 Abstract: We show that the relative entropy, S(rel) identical with Sig… read moreAbstract: We show that the relative entropy, S(rel) identical with Sigma(p(T)) ln(p(T)/p(M)), provides a fundamental and unifying framework for multiscale analysis and for inverse molecular-thermodynamic problems involving optimization of a model system (M) to reproduce the properties of a target one (T). We demonstrate that the relative entropy serves as a generating function for principles in variational mean-field theory and uniqueness and gives intuitive results for simple case scenarios in model development. Moreover, we suggest that the relative entropy provides a rigorous framework for multiscale simulations and offers new numerical techniques for linking models at different scales. Finally, we show that S(rel) carries physical significance by using it to quantify the deviations of a three-site model of water from simple liquids, finding that the relative entropy, a thermodynamic concept, even predicts water's kinetic anomalies. read less NOT USED (low confidence) O. Akin-Ojo, Y. Song, and F. Wang, “Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method.,” The Journal of chemical physics. 2008. link Times cited: 102 Abstract: A new method called adaptive force matching (AFM) has been d… read moreAbstract: A new method called adaptive force matching (AFM) has been developed that is capable of producing high quality force fields for condensed phase simulations. This procedure involves the parametrization of force fields to reproduce ab initio forces obtained from condensed phase quantum-mechanics/molecular-mechanics (QM/MM) calculations. During the procedure, the MM part of the QM/MM is iteratively improved so as to approach ab initio quality. In this work, the AFM method has been tested to parametrize force fields for liquid water so that the resulting force fields reproduce forces calculated using the ab initio MP2 and the Kohn-Sham density functional theory with the Becke-Lee-Yang-Parr (BLYP) and Becke three-parameter LYP (B3LYP) exchange correlation functionals. The AFM force fields generated in this work are very simple to evaluate and are supported by most molecular dynamics (MD) codes. At the same time, the quality of the forces predicted by the AFM force fields rivals that of very expensive ab initio calculations and are found to successfully reproduce many experimental properties. The site-site radial distribution functions (RDFs) obtained from MD simulations using the force field generated from the BLYP functional through AFM compare favorably with the previously published RDFs from Car-Parrinello MD simulations with the same functional. Technical aspects of AFM such as the optimal QM cluster size, optimal basis set, and optimal QM method to be used with the AFM procedure are discussed in this paper. read less NOT USED (low confidence) M. Masia, “Ab initio based polarizable force field parametrization.,” The Journal of chemical physics. 2008. link Times cited: 32 Abstract: Experimental and simulation studies of anion-water systems h… read moreAbstract: Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by approximately 30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car-Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations. read less NOT USED (low confidence) S. Olivier, R. Conte, and A. Fortunelli, “Derivation of an empirical potential for gold with angular corrections,” Physical Review B. 2008. link Times cited: 13 Abstract: From a detailed analysis of density-functional calculations … read moreAbstract: From a detailed analysis of density-functional calculations on gold model clusters and surfaces, an empirical potential for gold, which includes angular corrections, is derived. This potential introduces higher-order nonlinear terms (specifically, the product dipole-quadrupole) that do not seem to have been previously used, but that are necessary to describe directionality effects in the gold-gold interaction. Preliminary tests show that the proposed empirical potential possesses novel features with respect to the existing ones, such as a strong tendency of small Au clusters toward cage configurations, and represents a good starting point for future investigations. read less NOT USED (low confidence) J. R. Morris, U. Dahlborg, and M. Calvo-Dahlborg, “Recent developments and outstanding challenges in theory and modeling of liquid metals,” Journal of Non-crystalline Solids. 2007. link Times cited: 23 NOT USED (low confidence) different deformations, O. Politano, J. Salazar, and T. Montesin, “An empirical method to determine the free surface energy of solids at,” Surface Science. 2005. link Times cited: 14 NOT USED (low confidence) X. Li and E. Weinan, “Multiscale modeling of the dynamics of solids at finite temperature,” Journal of The Mechanics and Physics of Solids. 2005. link Times cited: 125 NOT USED (low confidence) G. Grochola, “Further application of the constrained fluid λ-integration method,” Journal of Chemical Physics. 2005. link Times cited: 16 Abstract: Previously we proposed a three stage, and recently a single … read moreAbstract: Previously we proposed a three stage, and recently a single stage nonphysical lambda-integration path for thermodynamically coupling bulk solid and liquid states directly. In this work we further apply these paths, specifically the newer single stage path, to the calculation of the complete truncated and shifted Lennard-Jones (R(cutoff)=2.5sigma) and aluminum glue potential melting lines, and the zero pressure melting point for a commonly used gold glue potential. The results showed accurate agreement with presently available literature. We found the single stage constrained fluid lambda-integration methodology to be robust in terms of reversibility over this extended range of temperatures, pressures, and intermolecular potentials. read less NOT USED (low confidence) A. Legris, “Recent Advances in Point Defect Studies Driven by Density Functional Theory,” Defect and Diffusion Forum. 2004. link Times cited: 3 Abstract: We highlight some of the most salient recent advances in poi… read moreAbstract: We highlight some of the most salient recent advances in point defects studies obtained from atomic-scale simulations performed in the framework of the density functional theory. The refinement of the theory, combined with its efficient numerical implementations and the (until now) everlasting growth of computer power allowed the transition from qualitative (in the beginning of the 90’) to quantitative results. Some of the longstanding controversies in the field have been tackled, and as far as aluminum is concerned, it has been shown that the curvature in the Arrheniusplot is due to anharmonic effects rather than to a two-defect diffusion mechanism. The anomalous diffusion in the b (bcc) phase of the group-IV elements has been related to the strong structural relaxation around vacancies, which significantly reduces their formation energy. Self-interstitials have been studied in materials of technological interest, their structure and mobility have been analyzed allowing a better interpretation of experimental results and an improved understanding of processes occurring under irradiation. Dilute interstitial solid solutions have been investigated. The strong binding between C and vacancies in bcc Fe may partially explain the observed influence of low amounts of C on Fe self-diffusion; the attraction of H to stacking faults in a Zr should favor planar dislocations glide. Intermetallics involving Fe (Fe-Al, Fe-Co) behave like highly correlated systems requiring methodological improvements of the DFT for a quantitative description. However, valuable trends concerning the structural point defects (those that allow nonstoichiometric compositions at low temperature) as well as the temperature dependence of point defects concentrations have been obtained. read less NOT USED (low confidence) L. Baffico, S. Bernard, Y. Maday, G. Turinici, and G. Zérah, “Parallel-in-time molecular-dynamics simulations.,” Physical review. E, Statistical, nonlinear, and soft matter physics. 2002. link Times cited: 124 Abstract: While there have been many progress in the field of multisca… read moreAbstract: While there have been many progress in the field of multiscale simulations in the space domain, in particular, due to efficient parallelization techniques, much less is known in the way to perform similar approaches in the time domain. In this paper we show on two examples that, provided we can describe in a rough but still accurate way the system under consideration, it is indeed possible to parallelize molecular dynamics simulations in time by using the recently introduced pararealalgorithm. The technique is most useful for ab initio simulations. read less NOT USED (low confidence) P. Tangney and S. Scandolo, “An ab initio parametrized interatomic force field for silica,” Journal of Chemical Physics. 2002. link Times cited: 193 Abstract: We present a classical interatomic force field for liquid Si… read moreAbstract: We present a classical interatomic force field for liquid SiO2 which has been parametrized using the forces, stresses and energies extracted from ab initio calculations. We show how inclusion of more electronic effects in a phenomenological way and parametrization at the relevant conditions of pressure and temperature allow the creation of more accurate force fields. We compare the results of simulations with this force field both to experiment and to the results of ab initio molecular dynamics simulations and show how our procedure leads to comparisons which are greatly improved with respect to the most widely used force fields for silica. read less NOT USED (low confidence) R. C. Picu, “On the functional form of non-local elasticity kernels,” Journal of The Mechanics and Physics of Solids. 2002. link Times cited: 59 NOT USED (low confidence) C.-L. Liu, “Modeling and Simulation for Microelectronic Materials Research,” Physica Status Solidi B-basic Solid State Physics. 2001. link Times cited: 3 Abstract: Recent development in modeling and simulation for microelect… read moreAbstract: Recent development in modeling and simulation for microelectronic materials research in the areas of Cu alloy interconnect is presented. A model for defect generation and diffusion through a Frenkel pair formation process at grain boundaries under electromigration conditions was developed. The model has consistently predicted the activation energies well for all the interconnect materials, namely Al, Al-Cu, Cu, and Cu alloys. A virtual simulation procedure was developed to screen a beneficial dopant to Cu based on the assumption that grain boundary (GB) diffusion dominantly controls the electromigration performance. The procedure covers dopant segregation to GB, dopant bulk diffusion, dopant and Cu diffusion along GB, and the effect of presence of a dopant on Cu diffusion at GB by dragging and blocking (stuffing) mechanisms. The success of the procedure has convincingly shown that modeling and simulation is the first choice to design advanced materials systems for next generation of interconnect. read less NOT USED (low confidence) M. Ortiz, A. Cuitiño, J. Knap, and M. Koslowski, “Mixed Atomistic-Continuum Models of Material Behavior: The Art of Transcending Atomistics and Informing Continua,” MRS Bulletin. 2001. link Times cited: 63 Abstract: The recent development of microscopes that allow for the exa… read moreAbstract: The recent development of microscopes that allow for the examination of defects at the atomic scale has made possible a more direct connection between the defects and the macroscopic response they engender (see, e.g., the December 1999 issue of MRS Bulletin ). read less 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) P. Lopes and M. Durfee, “Preface,” The Annals of the American Academy of Political and Social Science. 1999. link Times cited: 0 NOT USED (low confidence) A. Lyubartsev and A. Laaksonen, “Inverse Problems and Hierarchical Multiscale Modelling of Biological Matter.” 2021. link Times cited: 2 NOT USED (low confidence) C. Taft, J. G. S. Canchaya, J. D. dos Santos, and J. C. F. Silva, “Review: Simulation Models for Materials and Biomolecules.” 2021. link Times cited: 0 NOT USED (low confidence) T. Nematiaram et al., “Predictive Model of Charge Mobilities in Organic Semiconductor Small Molecules with Force-Matched Potentials.” 2020. link Times cited: 2 Abstract: Information ABSTRACT: Charge mobility of crystalline organic… read moreAbstract: Information ABSTRACT: Charge mobility of crystalline organic semiconductors (OSC) is limited by local dynamic disorder. Recently, the charge mobility for several high mobility OSCs, including TIPS-pentacene, were accurately predicted from a density functional theory (DFT) simulation constrained by the crystal structure and the inelastic neutron scattering spectrum, which provide direct measures of the structure and the dynamic disorder in the length scale and energy range of interest. However, the computational expense required for calculating all of the atomic and molecular forces is prohibitive. Here we demonstrate the use of density functional tight binding (DFTB), a semiempirical quantum mechanical method that is 2 to 3 orders of magnitude more e ffi cient than DFT. We show that force matching a many-body interaction potential to DFT derived forces yields highly accurate DFTB models capable of reproducing the low-frequency intricacies of experimental inelastic neutron scattering (INS) spectra and accurately predicting charge mobility. We subsequently predicted charge mobilities from our DFTB model of a number of previously unstudied structural analogues to TIPS-pentacene using dynamic disorder from DFTB and transient localization theory. The approach we establish here could provide a truly rapid simulation pathway for accurate materials properties prediction, in our vision applied to new OSCs with tailored read less NOT USED (low confidence) L. Kahle, “Modeling, understanding, and screening fast lithium-ion conductors for solid-state electrolytes.” 2019. link Times cited: 0 Abstract: The Li-ion batteries within the consumer electronics used in… read moreAbstract: The Li-ion batteries within the consumer electronics used in our everyday life suffer from well-known deficiencies due to the prevalent use of organic liquid electrolytes: the narrow electrochemical stability windows of the organic solvents used in these electrolytes prevent the use of high-voltage cathodes, and the flammability and volatility of the solvent molecules constitute a safety hazard. Replacing the organic liquid electrolytes with inorganic solid-state electrolytes could lead to significantly safer batteries with a higher energy density. However, most known solid-state Li-ion conductors are not yet suitable for application as electrolytes, since no material satisfies the stringent requirements for safety in a high-performance battery: a wide electrochemical stability window, high mechanical stability, very low electronic mobility, and fast Li-ion conduction. Searching for materials that satisfy those requirements by via experiment is too human-labor intensive to be done on a large scale due to the time-consuming materials synthesis and experimental characterization. Computational approaches can be easily parallelized, enabling the screening of thousands of materials to find new solid-state electrolytes for Li-ion batteries. Such a computational high-throughput screening requires an automated framework and methods that are accurate enough to predict the quantities of interest but also of sufficient computational efficiency to be applied on many materials. However, known methods to predict the Li-ion conductivity in a material are either computationally too expensive to be applied on a large scale, as is the case for first-principles molecular dynamics, or are not general enough to be performed across a wide range of materials. We present a model to calculate the Li-ion diffusion coefficient and conductivity efficiently by applying physically motivated approximations to the Hamiltonian of density-functional theory. The results obtained using this “pinball model” compare well to those from accurate first-principles molecular dynamics. This agreement provides interesting insights into the dependence of the valence electronic charge density of an ionic system on the motion of Li ions and suggests that the model can be used for screening applications. After its derivation and validation, we use the pinball model in a computational high-throughput screening to find structures with promising Li-ion diffusion. These candidate solid-state electrolytes are characterized with first-principles molecular dynamics to obtain more accurate predictions of the diffusion coefficients and pathways in these materials. The pinball model, combined with the efforts to automate molecular dynamics simulations, results in a large quantity of data stored in the form of molecular dynamics trajectories, motivating a read less 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) R. Lindsey, M. Kroonblawd, L. Fried, and N. Goldman, “Force Matching Approaches to Extend Density Functional Theory to Large Time and Length Scales,” Computational Approaches for Chemistry Under Extreme Conditions. 2019. link Times cited: 6 NOT USED (low confidence) С. Волегов, Р. М. Герасимов, and Р. П. Давлятшин, “MODELS OF MOLECULAR DYNAMICS: A REVIEW OF EAM-POTENTIALS. PART 2. POTENTIALS FOR MULTI-COMPONENT SYSTEMS.” 2018. link Times cited: 1 Abstract: Получена: 18 мая 2018 г. Принята: 25 июня 2018 г. Опубликова… read moreAbstract: Получена: 18 мая 2018 г. Принята: 25 июня 2018 г. Опубликована: 29 июня 2018 г. В статье представлена вторая часть обзора современных подходов и работ, посвященных построению потенциалов межатомного взаимодействия с использованием методологии погруженного атома (EAM-потенциалы). Эта часть обзора посвящена одной из наиболее остро стоящих проблем в молекулярной динамике – вопросам построения потенциалов, которые были бы пригодны для описания структуры и физико-механических свойств многокомпонентных (в первую очередь – бинарных и тернарных) материалов. Отмечены первые работы, в которых предлагались подходы к построению функций перекрестного взаимодействия для сплавов никеля и меди – как с использованием методологии EAM, так и несколько отличающийся по процедуре построения потенциал типа Финисса-Синклера. Рассматриваются работы, в которых производится сопоставление различных подходов к построению потенциалов, а также к процедуре идентификации их параметров на примере одних и тех же многокомпонентных систем (типа Al-Ni или Cu-Au). Кроме того, особый интерес представляют некоторые тернарные системы, например Fe–Ni–Cr, W–H– He или U–Mo–Xe, которые являются ключевыми для материалов атомной энергетики и которые в последние годы активно изучаются как возможные материалы для использования в термоядерных ректорах. Приведены примеры работ, в которых предлагаются и исследуются потенциалы для описания многокомпонентных систем, пригодных для использования в аэрокосмической промышленности и изготовленных прежде всего на основе никеля. Рассмотрены результаты исследований различных интерметаллических соединений, отмечены работы, в которых при помощи построенного EAM потенциала удалось количественно точно описать фазовые диаграммы соединений и вычислить характеристики фазовых переходов. read less NOT USED (low confidence) S. Thomas, “New Methods for Understanding and Controlling the Self-Assembly of Reacting Systems Using Coarse-Grained Molecular Dynamics.” 2018. link Times cited: 4 Abstract: This research aims at developing new computational methods t… read moreAbstract: This research aims at developing new computational methods to understand the molecular self-assembly of reacting systems whose complex structures depend on the thermodynamics of mixing, reaction kinetics, and diffusion kinetics. The specific reacting system examined in this study is epoxy, cured with linear chain thermoplastic tougheners whose complex microstructure is known from experiments to affect mechanical properties and to be sensitive to processing conditions. Mesoscale simulation techniques have helped to bridge the length and time scales needed to predict the microstructures of cured epoxies, but the prohibitive computational cost of simulating experimentally relevant system sizes has limited their impact. In this work we develop an open-source plugin for the molecular dynamics code HOOMD-Blue that permits epoxy crosslinking simulations of millions of particles to be routinely performed on a single modern graphics card. Using these capabilities, we are able to use ensembles of epoxy processing pathways to obtain realistic bond kinetics and relaxation times that sensitively depend on stochastic bonding rates and a diffusive drag parameter respectively. This work also demonstrates the first implementation of fully customizable temperature-time curing profiles and the largest cross-linked structures obtained using molecular dynamics simulation. We evaluate coarse-grained models based on Dissipative Particle Dynamics (DPD) and compare with Lennard-Jones(LJ) models for their suitability to study glassy dynamics which is important for modeling epoxies or any other glassy material. We find that “hard” particle potentials such as the LJ potential are necessary to model glassy materials and characterize multiple read less NOT USED (low confidence) M. Hodapp, “On flexible Green function methods for atomistic/continuum coupling.” 2018. link Times cited: 2 Abstract: Atomistic/continuum (A/C) coupling schemes have been develop… read moreAbstract: Atomistic/continuum (A/C) coupling schemes have been developed during the past twenty years to overcome the vast computational cost of fully atomistic models, but have not yet reached full maturity to address many problems of practical interest. This work is therefore devoted to the development and analysis of flexible Green function methods for A/C coupling. Thereby, the Green function of the harmonic crystal is computed a priori and subsequently employed during the simulation of a fully nonlinear atomistic problem to update its boundary conditions on-the-fly, based on the motion of the atoms and without the need of an explicit numerical discretization of the bulk material. The first part is devoted to the construction of a discrete boundary element method (DBEM) which bears several advantages over its continuous analog, i.a. nonsingular Green kernels and direct application to nonlocal elasticity. As is well-known from integral problems, the DBEM leads to dense system matrices which become quickly unfeasible due to their quadratic complexity. To overcome this computational burden, an implicit approximate representation using hierarchical matrices is proposed which have proven their efficiency in the context of boundary integral equations while preserving overall accuracy. In order to solve the coupled atomistic/DBEM problem, several staggered and monolithic solution procedures are assessed. An improvement of the overall accuracy by several orders of magnitude is found in comparison with naive clamped boundary conditions. To further account for plasticity in the continuum domain the coupled atomistic/discrete dislocations (CADD) method is examined, including the treatment of hybrid dislocation lines that span between the two domains. In particular, a detailed derivation of a quasistatic problem formulation is covered and a general algorithm to simulate the motion of the hybrid dislocations along A/C interfaces is presented. In addition, to avoid solving the complementary elasticity problem, a simplified solution procedure, which updates the boundary conditions based on the Green function of the entire dislocation network for obtaining accurate stress and displacement fields, is introduced and validated. The test problem consists of the bowout of a single dislocation in a semi-periodic box under an applied shear stress, and excellent results are obtained in comparison to fully-atomistic solutions of the same problem. read less NOT USED (low confidence) G. Anand and P. Chattopadhyay, “Computational Design of Microstructure: An Overview.” 2016. link Times cited: 0 Abstract: During the last couple of decades, treatment of microstructu… read moreAbstract: During the last couple of decades, treatment of microstructure in materials science has been shifted from the diagnostic to design paradigm. Design of microstructure is inherently complex problems due to non linear spatial and temporal interaction of composition and parameters leading to the target properties. In most of the cases, different properties are reciprocally correlated i.e., improvement of one lead to the degradation of other. Also, the design of microstructure is a multiscale problem, as the knowledge of phenomena at range of scales from electronic to mesoscale is required for precise compositionmicrostructure-property determination. In the view of above, present chapter provides the introduction to computationally driven microstructure engineering in the framework of constitutive length scale in microstructure design. The important issues pertaining to design such as phase stability and interfaces has been explained. Additionally, the bird-eye view of various computational techniques in order of length scale has been introduced, with an aim to present the picture of combination of various techniques for solving microstructural design problems under various scenarios. read less NOT USED (low confidence) S. Badu, R. Melnik, and S. Prabhakar, “RNA Nanostructures in Physiological Solutions: Multiscale Modeling and Applications.” 2015. link Times cited: 5 NOT USED (low confidence) Z. Chen, R. Chen, and B. Shan, “Nanomaterial Design and Computational Modeling.” 2014. link Times cited: 0 NOT USED (low confidence) E. Spiga, M. Degiacomi, and M. dal Peraro, “New strategies for integrative dynamic modeling of macromolecular assembly.,” Advances in protein chemistry and structural biology. 2014. link Times cited: 10 NOT USED (low confidence) G. Ackland, “1.10 – Interatomic Potential Development.” 2012. link Times cited: 10 NOT USED (low confidence) J. Leszczynski and M. Shukla, “Practical Aspects of Computational Chemistry V,” Practical Aspects of Computational Chemistry V. 2012. link Times cited: 57 NOT USED (low confidence) U. Nackenhorst, D. Kardas, T. Helmich, C. Lenz, and W. Shan, “Computational Techniques for Multiscale Analysis of Materials and Interfaces.” 2011. link Times cited: 5 NOT USED (low confidence) C. Hijón, P. Español, E. Vanden-Eijnden, and R. Delgado-Buscalioni, “Mori-Zwanzig formalism as a practical computational tool.,” Faraday discussions. 2010. link Times cited: 263 Abstract: An operational procedure is presented to compute explicitly … read moreAbstract: An operational procedure is presented to compute explicitly the different terms in the generalized Langevin equation (GLE) for a few relevant variables obtained within Mori-Zwanzig formalism. The procedure amounts to introducing an artificial controlled parameter which can be tuned in such a way that the so-called projected dynamics becomes explicit and the GLE reduces to a Markovian equation. The projected dynamics can be realised in practice by introducing constraints, and it is shown that the Green-Kubo formulae computed with these dynamics do not suffer from the plateau problem. The methodology is illustrated in the example of star polymer molecules in a melt using their center of mass as relevant variables. Through this example, we show that not only the effective potentials, but also the friction forces and the noise play a very important role in the dynamics. read less NOT USED (low confidence) B. Ensing and S. Nielsen, “Multiscale molecular dynamics and the reverse mapping problem.” 2010. link Times cited: 10 NOT USED (low confidence) M. Horstemeyer, “Multiscale Modeling: A Review.” 2009. link Times cited: 185 NOT USED (low confidence) F. Gao, “Box 4: Interatomic Potential.” 2009. link Times cited: 0 NOT USED (low confidence) V. Shenoy, V. Shenoy, and R. Phillips, “Finite Temperature Quasicontinuum Methods,” MRS Proceedings. 1998. link Times cited: 66 Abstract: In this paper the authors extend the quasi-continuum method … read moreAbstract: In this paper the authors extend the quasi-continuum method to study equilibrium properties of defects at finite temperatures. They present a derivation of an effective energy function to perform Monte Carlo simulations in a mixed atomistic and continuum setting. It is shown that the free energy minimization technique can be easily incorporated into the quasi-continuum frame work, permitting a reduction of the full set of atomistic degrees of freedom even in the finite temperature setting. The validity of the proposed methods is demonstrated by computing the thermal expansion and the temperature dependence of the elastic moduli for Cu. The authors employ the quasi-continuum free energy minimization method to study the finite temperature structure of a dislocation core in Al. read less NOT USED (low confidence) A. Vita and R. Car, “A Novel Scheme for Accurate Md Simulations of Large Systems,” MRS Proceedings. 1997. link Times cited: 26 Abstract: We present a simple and informationally efficient approach t… read moreAbstract: We present a simple and informationally efficient approach to electronic-structure-based simulations of large material science systems. The algorithm is based on a flexible embedding scheme, in which the parameters of a model potential are fitted at run time to some precise information relevant to localised portions of the system. Such information is computed separately on small subsystems by electronic-structure “black box” subprograms, e.g. based on tight-binding and/or ab initio models. The scheme allows to enforce electronic structure precision only when and where needed, and to minimise the computed information within a desired accuracy, which can be systematically controlled. Moreover, it is inherently linear scaling, and highly suitable for modern parallel platforms, including those based on non-uniform processing. The method is demonstrated by performing computations of tight-binding accuracy on solid state systems in the ten thousand atoms size scale. read less NOT USED (high confidence) R. K. Mudaliar and T. Schaerf, “An examination of force maps targeted at orientation interactions in moving groups,” PLOS ONE. 2023. link Times cited: 0 Abstract: Force mapping is an established method for inferring the und… read moreAbstract: Force mapping is an established method for inferring the underlying interaction rules thought to govern collective motion from trajectory data. Here we examine the ability of force maps to reconstruct interactions that govern individual’s tendency to orient, or align, their heading within a moving group, one of the primary factors thought to drive collective motion, using data from three established general collective motion models. Specifically, our force maps extract how individuals adjust their direction of motion on average as a function of the distance to neighbours and relative alignment in heading with these neighbours, or in more detail as a function of the relative coordinates and relative headings of neighbours. We also examine the association between plots of local alignment and underlying alignment rules. We find that the simpler force maps that examined changes in heading as a function of neighbour distances and differences in heading can qualitatively reconstruct the form of orientation interactions, but also overestimate the spatial range over which these interactions apply. More complex force maps that examine heading changes as a function of the relative coordinates of neighbours (in two spatial dimensions), can also reveal underlying orientation interactions in some cases, but are relatively harder to interpret. Responses to neighbours in both the simpler and more complex force maps are affected by group-level patterns of motion. We also find a correlation between the sizes of regions of high alignment in local alignment plots and the size of the region over which alignment rules apply when only an alignment interaction rule is in action. However, when data derived from more complex models is analysed, the shapes of regions of high alignment are clearly influenced by emergent patterns of motion, and these regions of high alignment can appear even when there is no explicit direct mechanism that governs alignment. read less NOT USED (high confidence) S. Stephan, S. Schmitt, H. Hasse, and H. Urbassek, “Molecular dynamics simulation of the Stribeck curve: Boundary lubrication, mixed lubrication, and hydrodynamic lubrication on the atomistic level,” Friction. 2023. link Times cited: 3 NOT USED (high confidence) I. A. Balyakin, R. Ryltsev, and N. Chtchelkatchev, “Liquid–Crystal Structure Inheritance in Machine Learning Potentials for Network-Forming Systems,” JETP Letters. 2023. link Times cited: 2 NOT USED (high confidence) B. Waters, D. S. Karls, I. Nikiforov, R. Elliott, E. Tadmor, and B. Runnels, “Automated determination of grain boundary energy and potential-dependence using the OpenKIM framework,” Computational Materials Science. 2022. link Times cited: 5 NOT USED (high confidence) M. Dharma-wardana, L. Stanek, and M. Murillo, “Yukawa-Friedel-tail pair potentials for warm dense matter applications.,” Physical review. E. 2022. link Times cited: 3 Abstract: Accurate equations of state (EOS) and plasma transport prope… read moreAbstract: Accurate equations of state (EOS) and plasma transport properties are essential for numerical simulations of warm dense matter encountered in many high-energy-density situations. Molecular dynamics (MD) is a simulation method that generates EOS and transport data using an externally provided potential to dynamically evolve the particles without further reference to the electrons. To minimize computational cost, pair potentials needed in MD may be obtained from the neutral-pseudoatom (NPA) approach, a form of single-ion density functional theory (DFT), where many-ion effects are included via ion-ion correlation functionals. Standard N-ion DFT-MD provides pair potentials via the force matching technique but at much greater computational cost. Here we propose a simple analytic model for pair potentials with physically meaningful parameters based on a Yukawa form with a thermally damped Friedel tail (YFT) applicable to systems containing free electrons. The YFT model accurately fits NPA pair potentials or the nonparametric force-matched potentials from N-ion DFT-MD, showing excellent agreement for a wide range of conditions. The YFT form provides accurate extrapolations of the NPA or force-matched potentials for small and large particle separations within a physical model. Our method can be adopted to treat plasma mixtures, allowing for large-scale simulations of multispecies warm dense matter. read less NOT USED (high confidence) K. S. Csizi and M. Reiher, “Universal QM/MM approaches for general nanoscale applications,” Wiley Interdisciplinary Reviews: Computational Molecular Science. 2022. link Times cited: 6 Abstract: Quantum mechanics/molecular mechanics (QM/MM) hybrid models … read moreAbstract: Quantum mechanics/molecular mechanics (QM/MM) hybrid models allow one to address chemical phenomena in complex molecular environments. Whereas this modeling approach can cope with a large system size at moderate computational costs, the models are often tedious to construct and require manual preprocessing and expertise. As a result, transferability to new application areas can be limited and the many parameters are not easy to adjust to reference data that are typically scarce. Therefore, it is desirable to devise automated procedures of controllable accuracy, which enables such modeling in a standardized and black‐box‐type manner. Although diverse best‐practice protocols have been set up for the construction of individual components of a QM/MM model (e.g., the MM potential, the type of embedding, the choice of the QM region), automated procedures that reconcile all steps of the QM/MM model construction are still rare. Here, we review the state of the art of QM/MM modeling with a focus on automation. We elaborate on MM model parametrization, on atom‐economical physically‐motivated QM region selection, and on embedding schemes that incorporate mutual polarization as critical components of the QM/MM model. In view of the broad scope of the field, we mostly restrict the discussion to methodologies that build de novo models based on first‐principles data, on uncertainty quantification, and on error mitigation with a high potential for automation. Ultimately, it is desirable to be able to set up reliable QM/MM models in a fast and efficient automated way without being constrained by specific chemical or technical limitations. read less NOT USED (high confidence) A. Mokshin and R. A. Khabibullin, “Is there a one-to-one correspondence between interparticle interactions and physical properties of liquid?,” Physica A: Statistical Mechanics and its Applications. 2022. link Times cited: 3 NOT USED (high confidence) M. Amezcua, J. Setiadi, Y. Ge, and D. Mobley, “An overview of the SAMPL8 host–guest binding challenge,” Journal of Computer-Aided Molecular Design. 2022. link Times cited: 13 NOT USED (high confidence) M. Stieffenhofer, C. Scherer, F. May, T. Bereau, and D. Andrienko, “Benchmarking coarse-grained models of organic semiconductors via deep backmapping,” Frontiers in Chemistry. 2022. link Times cited: 3 Abstract: The potential of mean force is an effective coarse-grained p… read moreAbstract: The potential of mean force is an effective coarse-grained potential, which is often approximated by pairwise potentials. While the approximated potential reproduces certain distributions of the reference all-atom model with remarkable accuracy, important cross-correlations are typically not captured. In general, the quality of coarse-grained models is evaluated at the coarse-grained resolution, hindering the detection of important discrepancies between the all-atom and coarse-grained ensembles. In this work, the quality of different coarse-grained models is assessed at the atomistic resolution deploying reverse-mapping strategies. In particular, coarse-grained structures for Tris-Meta-Biphenyl-Triazine are reverse-mapped from two different sources: 1) All-atom configurations projected onto the coarse-grained resolution and 2) snapshots obtained by molecular dynamics simulations based on the coarse-grained force fields. To assess the quality of the coarse-grained models, reverse-mapped structures of both sources are compared revealing significant discrepancies between the all-atom and the coarse-grained ensembles. Specifically, the reintroduced details enable force computations based on the all-atom force field that yield a clear ranking for the quality of the different coarse-grained models. read less NOT USED (high confidence) E. Ricci, G. Giannakopoulos, V. Karkaletsis, D. Theodorou, and N. Vergadou, “Developing Machine-Learned Potentials for Coarse-Grained Molecular Simulations: Challenges and Pitfalls,” Proceedings of the 12th Hellenic Conference on Artificial Intelligence. 2022. link Times cited: 7 Abstract: Coarse graining (CG) enables the investigation of molecular … read moreAbstract: Coarse graining (CG) enables the investigation of molecular properties for larger systems and at longer timescales than the ones attainable at the atomistic resolution. Machine learning techniques have been recently proposed to learn CG particle interactions, i.e. develop CG force fields. Graph representations of molecules and supervised training of a graph convolutional neural network architecture are used to learn the potential of mean force through a force matching scheme. In this work, the force acting on each CG particle is correlated to a learned representation of its local environment that goes under the name of SchNet, constructed via continuous filter convolutions. We explore the application of SchNet models to obtain a CG potential for liquid benzene, investigating the effect of model architecture and hyperparameters on the thermodynamic, dynamical, and structural properties of the simulated CG systems, reporting and discussing challenges encountered and future directions envisioned. read less 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) 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) F. Frommer and M. Hanke, “A variational framework for the inverse Henderson problem of statistical mechanics,” Letters in Mathematical Physics. 2022. link Times cited: 2 NOT USED (high confidence) E. Homer, G. Hart, C. B. Owens, D. M. Hensley, J. Spendlove, and L. H. Serafin, “Examination of computed aluminum grain boundary structures and energies that span the 5D space of crystallographic character,” Acta Materialia. 2022. link Times cited: 16 NOT USED (high 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 (high confidence) A. Włodarczyk, M. Uchroński, A. Podsiadły-Paszkowska, J. Irek, and B. Szyja, “Mixing ReaxFF parameters for transition metal oxides using force-matching method,” Journal of Molecular Modeling. 2021. link Times cited: 1 NOT USED (high confidence) W. Ko, J. S. Lee, and D.-H. Kim, “Atomistic simulations of Ag–Cu–Sn alloys based on a new modified embedded-atom method interatomic potential,” Journal of Materials Research. 2021. link Times cited: 3 Abstract: An interatomic potential for the ternary Ag–Cu–Sn system, an… read moreAbstract: An interatomic potential for the ternary Ag–Cu–Sn system, an important material system related to the applications of lead-free solders, is developed on the basis of the second nearest-neighbor modified embedded-atom-method formalism. Potential parameters for the ternary and related binary systems are determined based on the recently improved unary description of pure Sn and the present improvements to the unary descriptions of pure Ag and Cu. To ensure the sufficient performance of atomistic simulations in various applications, the optimization of potential parameters is conducted based on the force-matching method that utilizes density functional theory predictions of energies and forces on various atomic configurations. We validate that the developed interatomic potential exhibits sufficient accuracy and transferability to various physical properties of pure metals, intermetallic compounds, solid solutions, and liquid solutions. The proposed interatomic potential can be straightforwardly used in future studies to investigate atomic-scale phenomena in soldering applications. read less NOT USED (high confidence) J. Morado et al., “Generation of Quantum Configurational Ensembles Using Approximate Potentials.,” Journal of chemical theory and computation. 2021. link Times cited: 2 Abstract: Conformational analysis is of paramount importance in drug d… read moreAbstract: Conformational analysis is of paramount importance in drug design: it is crucial to determine pharmacological properties, understand molecular recognition processes, and characterize the conformations of ligands when unbound. Molecular Mechanics (MM) simulation methods, such as Monte Carlo (MC) and molecular dynamics (MD), are usually employed to generate ensembles of structures due to their ability to extensively sample the conformational space of molecules. The accuracy of these MM-based schemes strongly depends on the functional form of the force field (FF) and its parametrization, components that often hinder their performance. High-level methods, such as ab initio MD, provide reliable structural information but are still too computationally expensive to allow for extensive sampling. Therefore, to overcome these limitations, we present a multilevel MC method that is capable of generating quantum configurational ensembles while keeping the computational cost at a minimum. We show that FF reparametrization is an efficient route to generate FFs that reproduce QM results more closely, which, in turn, can be used as low-cost models to achieve the gold standard QM accuracy. We demonstrate that the MC acceptance rate is strongly correlated with various phase space overlap measurements and that it constitutes a robust metric to evaluate the similarity between the MM and QM levels of theory. As a more advanced application, we present a self-parametrizing version of the algorithm, which combines sampling and FF parametrization in one scheme, and apply the methodology to generate the QM/MM distribution of a ligand in aqueous solution. read less NOT USED (high confidence) L. Kahle and F. Zipoli, “Quality of uncertainty estimates from neural network potential ensembles.,” Physical review. E. 2021. link Times cited: 11 Abstract: Neural network potentials (NNPs) combine the computational e… read moreAbstract: Neural network potentials (NNPs) combine the computational efficiency of classical interatomic potentials with the high accuracy and flexibility of the ab initio methods used to create the training set, but can also result in unphysical predictions when employed outside their training set distribution. Estimating the epistemic uncertainty of a NNP is required in active learning or on-the-fly generation of potentials. Inspired from their use in other machine-learning applications, NNP ensembles have been used for uncertainty prediction in several studies, with the caveat that ensembles do not provide a rigorous Bayesian estimate of the uncertainty. To test whether NNP ensembles provide accurate uncertainty estimates, we train such ensembles in four different case studies and compare the predicted uncertainty with the errors on out-of-distribution validation sets. Our results indicate that NNP ensembles are often overconfident, underestimating the uncertainty of the model, and require to be calibrated for each system and architecture. We also provide evidence that Bayesian NNPs, obtained by sampling the posterior distribution of the model parameters using Monte Carlo techniques, can provide better uncertainty estimates. 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) L. Pártay, G. Csányi, and N. Bernstein, “Nested sampling for materials,” The European Physical Journal B. 2021. link Times cited: 6 NOT USED (high confidence) D. M. Zhang, D. Sun, and X. Gong, “Discovery of a paired Gaussian and long-tailed distribution of potential energies in nanoglasses,” Physical Review B. 2021. link Times cited: 2 Abstract: It is generally believed that the intrinsic properties of gl… read moreAbstract: It is generally believed that the intrinsic properties of glasses are intimately related to potential energy landscapes (PELs). However, little is known about the PELs of glasses below the glass transition temperature (Tg). Taking advantage of lower potential energy barriers in nano systems, we have systematically investigated the dynamics behavior of two nano glasses, Al43 and Al46. Structure transformation is identified in our pure molecular-dynamics simulation far below Tg, which manifests the existence of metabasins in PELs. Surprisingly, we find that the distribution of potential energies shows a paired-Gaussian and long-tailed distribution at temperatures below and approaching Tg, correspondingly the distribution of the α-relaxation time exhibits an exponential decay. In contrast to the Gaussian distribution of energy in typical liquids and solids, the paired-Gaussian and long-tailed distribution of potential energies, as well as the exponential distribution of the α-relaxation time, may be considered as the intrinsic feature of a glass or supercooled liquid. The current results are important not only for checking the reliability of various PEL-based models, but also for exploring the microscopic nature of glasses. read less NOT USED (high confidence) T. Schilling, “Coarse-grained modelling out of equilibrium,” Physics Reports. 2021. link Times cited: 23 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) P. Friederich, F. Häse, J. Proppe, and A. Aspuru-Guzik, “Machine-learned potentials for next-generation matter simulations,” Nature Materials. 2021. link Times cited: 166 NOT USED (high confidence) G. Cárdenas, P. Marquetand, S. Mai, and L. González, “A Force Field for a Manganese-Vanadium Water Oxidation Catalyst: Redox Potentials in Solution as Showcase,” Catalysts. 2021. link Times cited: 7 Abstract: We present a molecular mechanics force field in AMBER format… read moreAbstract: We present a molecular mechanics force field in AMBER format for the mixed-valence manganese vanadium oxide cluster [Mn4V4O17(OAc)3]3−—a synthetic analogue of the oxygen-evolving complex that catalyzes the water oxidation reaction in photosystem II—with parameter sets for two different oxidation states. Most force field parameters involving metal atoms have been newly parametrized and the harmonic terms refined using hybrid quantum mechanics/molecular mechanics reference simulations, although some parameters were adapted from pre-existing force fields of vanadate cages and manganese oxo dimers. The characteristic Jahn–Teller distortions of d4 MnIII ions in octahedral environments are recovered by the force field. As an application, the developed parameters have been used to calculate the redox potential of the [MnIIIMn3IV] ⇌ [Mn4IV]+e− half-reaction in acetonitrile by means of Marcus theory. read less NOT USED (high confidence) A. Kubo and Y. Umeno, “Machine-Learning-Based Atomistic Model Analysis on High-Temperature Compressive Creep Properties of Amorphous Silicon Carbide,” Materials. 2021. link Times cited: 5 Abstract: Ceramic matrix composites (CMCs) based on silicon carbide (S… read moreAbstract: Ceramic matrix composites (CMCs) based on silicon carbide (SiC) are used for high-temperature applications such as the hot section in turbines. For such applications, the mechanical properties at a high temperature are essential for lifetime prediction and reliability design of SiC-based CMC components. We developed an interatomic potential function based on the artificial neural network (ANN) model for silicon-carbon systems aiming at investigation of high-temperature mechanical properties of SiC materials. We confirmed that the developed ANN potential function reproduces typical material properties of the single crystals of SiC, Si, and C consistent with first-principles calculations. We also validated applicability of the developed ANN potential to a simulation of an amorphous SiC through the analysis of the radial distribution function. The developed ANN potential was applied to a series of creep test for an amorphous SiC model, focusing on the amorphous phase, which is expected to be formed in the SiC-based composites. As a result, we observed two types of creep behavior due to different atomistic mechanisms depending on the strain rate. The evaluated activation energies are lower than the experimental values in literature. This result indicates that an amorphous region can play an important role in the creep process in SiC composites. read less NOT USED (high confidence) J. Tiihonen, R. Clay, and J. Krogel, “Toward quantum Monte Carlo forces on heavier ions: Scaling properties.,” The Journal of chemical physics. 2021. link Times cited: 8 Abstract: Quantum Monte Carlo (QMC) forces have been studied extensive… read moreAbstract: Quantum Monte Carlo (QMC) forces have been studied extensively in recent decades because of their importance with spectroscopic observables and geometry optimization. Here, we benchmark the accuracy and computational cost of QMC forces. The zero-variance zero-bias (ZVZB) force estimator is used in standard variational and diffusion Monte Carlo simulations with mean-field based trial wavefunctions and atomic pseudopotentials. Statistical force uncertainties are obtained with a recently developed regression technique for heavy tailed QMC data [P. Lopez Rios and G. J. Conduit, Phys. Rev. E 99, 063312 (2019)]. By considering selected atoms and dimers with elements ranging from H to Zn (1 ≤ Zeff ≤ 20), we assess the accuracy and the computational cost of ZVZB forces as the effective pseudopotential valence charge, Zeff, increases. We find that the costs of QMC energies and forces approximately follow simple power laws in Zeff. The force uncertainty grows more rapidly, leading to a best case cost scaling relationship of approximately Zeff 6.5(3) for diffusion Monte Carlo. We find that the accessible system size at fixed computational cost scales as Zeff -2, insensitive to model assumptions or the use of the "space warp" variance-reduction technique. Our results predict the practical cost of obtaining forces for a range of materials, such as transition metal oxides where QMC forces have yet to be applied, and underscore the importance of further developing force variance-reduction techniques, particularly for atoms with high Zeff. read less NOT USED (high confidence) T. Sun, V. Minhas, N. Korolev, A. Mirzoev, A. Lyubartsev, and L. Nordenskiöld, “Bottom-Up Coarse-Grained Modeling of DNA,” Frontiers in Molecular Biosciences. 2021. link Times cited: 16 Abstract: Recent advances in methodology enable effective coarse-grain… read moreAbstract: Recent advances in methodology enable effective coarse-grained modeling of deoxyribonucleic acid (DNA) based on underlying atomistic force field simulations. The so-called bottom-up coarse-graining practice separates fast and slow dynamic processes in molecular systems by averaging out fast degrees of freedom represented by the underlying fine-grained model. The resulting effective potential of interaction includes the contribution from fast degrees of freedom effectively in the form of potential of mean force. The pair-wise additive potential is usually adopted to construct the coarse-grained Hamiltonian for its efficiency in a computer simulation. In this review, we present a few well-developed bottom-up coarse-graining methods, discussing their application in modeling DNA properties such as DNA flexibility (persistence length), conformation, “melting,” and DNA condensation. read less NOT USED (high confidence) M. Dharma-wardana, “Simple pair-potentials and pseudo-potentials for warm-dense matter applications.” 2021. link Times cited: 3 Abstract: We present methods for generating computationally simple par… read moreAbstract: We present methods for generating computationally simple parameter-free pair potentials useful for solids, liquids and plasma at arbitrary temperatures. They successfully treat warm-dense matter (WDM) systems like carbon or silicon with complex tetrahedral or other structural bonding features. Density functional theory asserts that only one-body electron densities, and one-body ion densities are needed for a complete description of electron-ion systems. DFT is used here to reduce both the electron many-body problem and the ion many-body problem to an exact one-body problem, namely that of the neutral pseudoatom (NPA). We compare the Stillinger-Weber (SW) class of multi-center potentials, and the embedded-atom approaches, with the NPA approach to show that many-ion effects are systematically included in this one-center method via one-body exchangecorrelation functionals. This computationally highly efficient “single-center” DFT-NPA approach is contrasted with the usual N-center DFT calculations that are coupled with molecular dynamics (MD) simulations to equilibriate the ion distribution. Comparisons are given with the pair-potential parts of the SW, ‘glue’ models, and the corresponding NPA pair-potentials to elucidate how the NPA potentials capture many-center effects using single-center one-body densities. read less NOT USED (high confidence) H. Chabba and D. Dafir, “Atomistic Simulation Study of Mechanical Deformation of Al-Mg-Si Alloys,” International Journal of Engineering Research in Africa. 2021. link Times cited: 0 Abstract: Aluminum alloys have been attracting significant attention. … read moreAbstract: Aluminum alloys have been attracting significant attention. Especially Al-Mg-Si alloys can exhibit an excellent balance between strength and ductility. Deformation mechanisms and microstructural evolution are still challenging issues. Accordingly, to describe how the type of phase influence mechanical behaviour of Al/Mg/Si alloys, in this paper atomic simulations are performed to investigate the uniaxial compressive behaviour of Al-Mg-Si ternary phases. The compression is at the same strain rate (3.1010 s−1); using Modified Embedded Atom Method (MEAM) potential to model the deformation behaviour. From these simulations, we get the total radial distribution function; the stress-strain responses to describe the elastic and plastic behaviors of GP-AlMg4Si6, U2-Al4Mg4Si4 and β-Al3Mg2Si6 phases. For a Detailed description of which phase influence hardness and ductility of these alloys; the mechanical properties are determined and presented. These stress-strain curves obtained show a rapid increase in stress up to a maximum followed by a gradual drop when the specimen fails by ductile fracture. From the results, it was found that GP-AlMg4Si6 & U2-Al4Mg4Si4 phases are brittle under uniaxial compressive loading while β-Al3Mg2Si6 phase is very ductile under the same compressive loading. The engineering stress-strain relationship suggests that β-Al3Mg2Si6 phase have high elasticity limit, ability to resist deformation and have the advantage of being highly malleable. Molecular dynamics software LAMMPS was used to simulate and build the Al-Mg-Si ternary system. read less NOT USED (high confidence) S. Bag and R. Mandal, “Interaction from structure using machine learning: in and out of equilibrium.,” Soft matter. 2020. link Times cited: 3 Abstract: Prediction of pair potential given a typical configuration o… read moreAbstract: Prediction of pair potential given a typical configuration of an interacting classical system is a difficult inverse problem. There exists no exact result that can predict the potential given the structural information. We demonstrate that using machine learning (ML) one can get a quick but accurate answer to the question: "which pair potential lead to the given structure (represented by pair correlation function)?" We use artificial neural network (NN) to address this question and show that this ML technique is capable of providing very accurate prediction of pair potential irrespective of whether the system is in a crystalline, liquid or gas phase. We show that the trained network works well for sample system configurations taken from both equilibrium and out of equilibrium simulations (active matter systems) when the later is mapped to an effective equilibrium system with a modified potential. We show that the ML prediction about the effective interaction for the active system is not only useful to make prediction about the MIPS (motility induced phase separation) phase but also identifies the transition towards this state. read less NOT USED (high confidence) F. Goujon et al., “Backbone oriented anisotropic coarse grains for efficient simulations of polymers.,” The Journal of chemical physics. 2020. link Times cited: 6 Abstract: Despite the fact that anisotropic particles have been introd… read moreAbstract: Despite the fact that anisotropic particles have been introduced to describe molecular interactions for decades, they have been poorly used for polymers because of their computing time overhead and the absence of a relevant proof of their impact in this field. We first report a method using anisotropic beads for polymers, which solves the computing time issue by considering that beads keep their principal orientation alongside the mean local backbone vector of the polymer chain, avoiding the computation of torques during the dynamics. Applying this method to a polymer bulk, we study the effect of anisotropic interactions vs isotropic ones for various properties such as density, pressure, topology of the chain network, local structure, and orientational order. We show that for different classes of potentials traditionally used in molecular simulations, those backbone oriented anisotropic beads can solve numerous issues usually encountered with isotropic interactions. We conclude that the use of backbone oriented anisotropic beads is a promising approach for the development of realistic coarse-grained potentials for polymers. read less NOT USED (high confidence) I. Tanis, B. Rousseau, L. Soulard, and C. Lemarchand, “Assessment of an anisotropic coarse-grained model for cis-1,4-polybutadiene: a bottom-up approach.,” Soft matter. 2020. link Times cited: 5 Abstract: The spherical representation usually utilized for the coarse… read moreAbstract: The spherical representation usually utilized for the coarse-grained particles of soft matter systems is an assumption and pertinent studies have shown that both structural and dynamical properties can depend on anisotropic effects. On these grounds, we develop coarse-grained equations of motion which take into account explicitly the anisotropy of the beads. As a first step, this model incorporates only conservative terms. Inclusion of the dissipative and random terms is in principle possible but is beyond the scope of this study. The translational dynamics of the beads is tracked using the position and momentum of their center of mass, while their rotational dynamics is modeled by representing their orientation through the use of quaternions, similarly to the case of rigid bodies. The associated force and torque controlling the motion are derived from atomistic molecular dynamics (MD) simulations via a bottom-up approach and define a coarse-grained potential. The assumptions of the model are clearly stated and checked for a reference system of a cis-1,4-polybutadiene melt. In particular, the choice of the angular velocity as a slow variable is justified by comparing its dynamics to atomic vibrations. The accuracy of this approach to reproduce static structural features of the polymer melt is assessed. read less NOT USED (high confidence) B. Lin, J. Wang, J. Li, and Z. Wang, “A neural-network based framework of developing cross interaction in alloy embedded-atom method potentials: application to Zr–Nb alloy,” Journal of Physics: Condensed Matter. 2020. link Times cited: 2 Abstract: Interaction potentials are critical to molecular dynamics si… read moreAbstract: Interaction potentials are critical to molecular dynamics simulations on fundamental mechanisms at atomic scales. Combination of well-developed single-element empirical potentials via cross interaction (CI) is an important and effective way to develop alloy embedded-atom method (EAM) potentials. In this work, based on neural-network (NN) models, firstly we proposed a framework to construct CI potential functions via utilizing single-element potentials. The framework contained four steps: (1) extracting characteristic points from single-element potential functions, (2) constructing CI functions by cubic spline interpolation, (3) evaluating the accuracy of CI functions by referring to first-principle (FP) data, and (4) searching for reasonable CI functions via NN models. Then with this framework, we developed a Zr–Nb alloy CI potential utilizing the MA-III (pure Zr potential developed by Mendelev and Ackland in 2007) and the Fellinger, Park and Wilkins (FPW) (pure Nb potential developed by FPW in 2010) potentials as single-element parts. The calculated results with this Zr–Nb alloy potential showed that: (1) the newly developed CI potential functions could simultaneously present the potential-function features of Zr and Nb; (2) the normalized energy–volume curves of L12 Zr3Nb, B2 ZrNb and L12 ZrNb3 calculated by this CI potential reasonably agreed with FP results; (3) the referred MA-III Zr and FPW Nb potentials can satisfactorily reproduce the priority of prismatic slip in Zr and the tension–compression asymmetry of 〈111〉{112} slip in Nb, while other ab initio developed Zr–Nb alloy potentials cannot. Our study indicates that, this NN based framework can take full advantage of single-element potentials, and is very convenient to develop EAM potentials of alloys; moreover, the new-developed Zr–Nb alloy EAM potential can reasonably describe the complicated deformation behaviors in Zr–Nb systems. read less NOT USED (high confidence) S. Y. Joshi and S. A. Deshmukh, “A review of advancements in coarse-grained molecular dynamics simulations,” Molecular Simulation. 2020. link Times cited: 89 Abstract: ABSTRACT Over the last few years, coarse-grained molecular d… read moreAbstract: ABSTRACT Over the last few years, coarse-grained molecular dynamics has emerged as a way to model large and complex systems in an efficient and inexpensive manner due to its lowered resolution, faster dynamics, and larger time steps. However, developing coarse-grained models and subsequently, the accurate interaction potentials (force-field parameters) is a challenging task. Traditional parameterisation techniques, although tedious, have been used extensively to develop CG models for a variety of solvent, soft-matter and biological systems. With the advent of sophisticated optimisation methods, machine learning, and hybrid approaches for force-field parameterisation, models with a higher degree of transferability and accuracy can be developed in a shorter period of time. We review here, some of these traditional and advanced parameterisation techniques while also shedding light on several transferable CG models developed in our group over the years using such an advanced method developed by us. These models, including solvents, polymers and biomolecules have helped us study important solute-solvent interactions and complex polymer architectures, thus paving a way to make experimentally verifiable observations. read less NOT USED (high confidence) Z. Zhang, C. Wang, X. Hu, and Y. Ni, “Shape Effect of Surface Defects on Nanohardness by Quasicontinuum Method,” Micromachines. 2020. link Times cited: 0 Abstract: Nanoindentation on a platinum thin film with surface defects… read moreAbstract: Nanoindentation on a platinum thin film with surface defects in a rectangular shape and triangular shape was simulated using the quasicontinuum method to study the shape effect of surface defects on nanohardness. The results show that the nanohardness of thin film with triangular defects is basically larger than those with rectangular defects, which is closely related to the height of the surface defects at the boundary near to the indenter. Moreover, the triangular defect might have an enhancement effect on nanohardness by a certain size of the defects and the boundary orientation of the defect, where such an enhancement effect increases as the defect grows. Furthermore, the nanohardness decreases when the defect is folded from wide to narrow in the same atom cavity, and particularly expresses a more obvious drop when the height of the defects increases. In addition, larger sizes of the rectangular defect induce more reduction in nanohardness, while the nanohardness of the triangular surface defect is sensitive to the periodic arrangement of atoms changed by the boundary orientation of the defect, which is well explained and demonstrated by the calculation formula theory of necessary load for dislocation emission. read less NOT USED (high confidence) R. Pandey, “A Monte Carlo simulation of a protein (CoVE) in a matrix of random barriers,” Physica A-statistical Mechanics and Its Applications. 2020. link Times cited: 0 NOT USED (high confidence) T. Heinemann and Y. J. Jung, “Coarse-graining strategy for modeling effective, highly diffusive fluids with reduced polydispersity: A dynamical study.,” The Journal of chemical physics. 2020. link Times cited: 1 Abstract: We present a coarse-graining strategy for reducing the numbe… read moreAbstract: We present a coarse-graining strategy for reducing the number of particle species in mixtures to achieve a simpler system with higher diffusion while preserving the total particle number and characteristic dynamic features. As a system of application, we chose the bidisperse Lennard-Jones-like mixture, discovered by Kob and Andersen [Phys. Rev. Lett. 73, 1376 (1994)], possessing a slow dynamics due to the fluid's multi-component character with its apparently unconventional choice for the pair potential of the type-A-type-B arrangement. We further established in a so-formed coarse-grained and temperature-independent monodisperse system an equilibrium structure with a radial distribution function resembling its mixture counterpart. This one-component system further possesses similar dynamic features such as glass transition temperature and critical exponents while subjected to Newtonian mechanics. This strategy may finally lead to the manufacturing of new nanoparticle/colloidal fluids by experimentally modeling only the outcoming effective pair potential(s) and no other macroscopic quantity. read less NOT USED (high 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 (high confidence) S. Badu, R. Melnik, and S. Singh, “Mathematical and computational models of RNA nanoclusters and their applications in data-driven environments,” Molecular Simulation. 2020. link Times cited: 7 Abstract: ABSTRACT Ribonucleic acid (RNA) is a fundamental molecule ha… read moreAbstract: ABSTRACT Ribonucleic acid (RNA) is a fundamental molecule having several favourable structural properties that can be used for various potential applications in the field of nanotechnology including biomedicine and bioengineering. Here in this review, we describe the computational and mathematical modellings of the RNA nanoclusters, such as the molecular dynamics simulation, coarse-grained modelling and continuum modelling. The RNA nanocubes, nanotubes and nanorings are some of the typical nanosized structures derived from RNA strands, and the details about such nanostructures have also been presented in this review. The RNA nanoprisms made out of the RNA building blocks via self-assembly of the RNA nanotriangles and their potential applications have been described. Furthermore, special attention is given to the earlier developed RNA nanoscaffolds from the RNA building blocks. We also present some recent results to describe the physical behaviour of the RNA nanotubes in different kinds of physiological solutions using molecular dynamics simulations. Finally, the recent applications of these computational models in several areas of medical sciences such as radiotherapy and drug delivery for cancer treatment and construction of RNA nanodevices have been highlighted. Several potential applications of artificial intelligence in this fast-growing field of RNA engineering have also been presented. read less NOT USED (high confidence) R. Lindsey, N. Goldman, L. Fried, and S. Bastea, “Many-body reactive force field development for carbon condensation in C/O systems under extreme conditions.,” The Journal of chemical physics. 2020. link Times cited: 16 Abstract: We describe the development of a reactive force field for C/… read moreAbstract: We describe the development of a reactive force field for C/O systems under extreme temperatures and pressures, based on the many-body Chebyshev Interaction Model for Efficient Simulation (ChIMES). The resulting model, which targets carbon condensation under thermodynamic conditions of 6500 K and 2.5 g cm-3, affords a balance between model accuracy, complexity, and training set generation expense. We show that the model recovers much of the accuracy of density functional theory for the prediction of structure, dynamics, and chemistry when applied to dissociative condensed phase systems at 1:1 and 1:2 C:O ratios, as well as molten carbon. Our C/O modeling approach exhibits a 104 increase in efficiency for the same system size (i.e., 128 atoms) and a linear system size scalability over standard quantum molecular dynamics methods, allowing the simulation of significantly larger systems than previously possible. We find that the model captures the condensed-phase reaction-coupled formation of carbon clusters implied by recent experiments, and that this process is susceptible to strong finite size effects. Overall, we find the present ChIMES model to be well suited for studying chemical processes and cluster formation at pressures and temperatures typical of shock waves. We expect that the present C/O modeling paradigm can serve as a template for the development of a broader high pressure-high temperature force-field for condensed phase chemistry in organic materials. read less NOT USED (high confidence) B. Husic et al., “Coarse graining molecular dynamics with graph neural networks.,” The Journal of chemical physics. 2020. link Times cited: 102 Abstract: Coarse graining enables the investigation of molecular dynam… read moreAbstract: Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at an atomic resolution. However, a coarse graining model must be formulated such that the conclusions we draw from it are consistent with the conclusions we would draw from a model at a finer level of detail. It has been proved that a force matching scheme defines a thermodynamically consistent coarse-grained model for an atomistic system in the variational limit. Wang et al. [ACS Cent. Sci. 5, 755 (2019)] demonstrated that the existence of such a variational limit enables the use of a supervised machine learning framework to generate a coarse-grained force field, which can then be used for simulation in the coarse-grained space. Their framework, however, requires the manual input of molecular features to machine learn the force field. In the present contribution, we build upon the advance of Wang et al. and introduce a hybrid architecture for the machine learning of coarse-grained force fields that learn their own features via a subnetwork that leverages continuous filter convolutions on a graph neural network architecture. We demonstrate that this framework succeeds at reproducing the thermodynamics for small biomolecular systems. Since the learned molecular representations are inherently transferable, the architecture presented here sets the stage for the development of machine-learned, coarse-grained force fields that are transferable across molecular systems. read less NOT USED (high confidence) P. Lory et al., “Impact of structural complexity and disorder on lattice dynamics and thermal conductivity in the o-
Al13Co4
phase,” Physical Review B. 2020. link Times cited: 5 Abstract: Combining inelastic neutron and x-ray scattering with atomic… read moreAbstract: Combining inelastic neutron and x-ray scattering with atomic scale simulation we report on a comprehensive study of the lattice dynamics and its relationship with the low thermal conductivity of the o-Al 13 Co 4 phase, a periodic approximant (about 100 atoms per cell) to a decagonal quasicrystal. The obtained experimental data, phonon lifetimes and temperature independent lattice thermal conductivity, can only be fully described by molecular dynamics simulations, using oscillating pair potential, when the disorder of 12 Al sites is properly taken into account. Our results pave the way for a detailed understanding of materials where structural complexity and local disorder are at play. read less NOT USED (high confidence) J. Byggmastar, K. Nordlund, and F. Djurabekova, “Gaussian approximation potentials for body-centered-cubic transition metals,” Physical Review Materials. 2020. link Times cited: 22 Abstract: We develop a set of machine-learning interatomic potentials … read moreAbstract: We develop a set of machine-learning interatomic potentials for elemental V, Nb, Mo, Ta, and W using the Gaussian approximation potential framework. The potentials show good accuracy and transferability for elastic, thermal, liquid, defect, and surface properties. All potentials are augmented with accurate repulsive potentials, making them applicable to radiation damage simulations involving high-energy collisions. We study melting and liquid properties in detail and use the potentials to provide melting curves up to 400 GPa for all five elements. read less NOT USED (high confidence) M. Deng et al., “Fine regulation of crystallisation tendency to optimize the BHJ nanostructure and performance of polymer solar cells.,” Nanoscale. 2020. link Times cited: 5 Abstract: Optimizing the nanostructure of the active layer of polymer … read moreAbstract: Optimizing the nanostructure of the active layer of polymer solar cells (PSCs) is one of the main challenges to achieve high device performances. The phase separation of the donor polymer and molecular acceptor within the bulk heterojunction (BHJ) layer is often driven by the crystallisation of the acceptor molecules. Hence, a suitable crystallisation tendency of the chosen acceptor is ultimately important. In this work, we identified melting temperature as an indicator for the crystallisation tendency and introduced extended fused-aromatic rings to the end groups of the nonfullerene acceptor molecule to enhance the intermolecular binding energy as well as its crystallisation tendency. The crystallinity, crystal regularity and average crystal size were significantly increased for those molecules with larger fused end groups. The devices containing molecule IDTTC with two fused thiophene rings, which displayed intermediate crystallisation tendency, were found to possess an optimized phase separation scale, balanced hole/electron mobility and highest device performances with the fill factor as high as 73.2% and a power conversion efficiency of 13.49%. With the above observations, we established a new route and paradigm to adjust the crystallisation tendency and BHJ nanostructure of nonfullerene acceptor molecules, thus enhancing the device performances through molecular engineering. read less NOT USED (high confidence) S. O. Kart, H. H. Kart, and T. Çagin, “Atomic-scale insights into structural and thermodynamic stability of spherical Al@Ni and Ni@Al core–shell nanoparticles,” Journal of Nanoparticle Research. 2020. link Times cited: 6 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) A. Liwo and C. Czaplewski, “Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins.,” The Journal of chemical physics. 2020. link Times cited: 8 Abstract: The force-matching approach to coarse graining, in which the… read moreAbstract: The force-matching approach to coarse graining, in which the forces that act on site centers are fitted to the respective average forces computed from all-atom molecular dynamics simulations, provides a link between coarse-grained and all-atom molecular dynamics. In the existing implementations, radial site-site interaction potentials are assumed, thus precluding extensive coarse-graining that usually requires anisotropic potentials. In this work, we extended the force-matching approach to coarse-grained models with axially symmetric sites and implemented it to the UNRES model of polypeptide chains developed in our laboratory, in which the only interaction sites are united peptide groups and united side chains, the α-carbon atoms serving as anchor points. The optimizable parameters were those of the UNRES energy function and not whole potential profiles, which provide better transferability. We tested the implementation with the 20-residue tryptophan-cage miniprotein, selected as the training protein, starting from the NEWCT-9P variant of UNRES. The reference forces were obtained from implicit- and explicit-solvent simulations. Using a target function composed of a force-matching term and a maximum-likelihood term that drives the force field at reproducing the NMR-determined conformational ensembles at three selected temperatures, force fields were obtained which did not produce site-site clashes for the structures simulated with all-atom molecular dynamics with AMBER, and modeled the structures of α-helical proteins with resolution comparable to that of the NEWCT-9P force field. The new force fields also produced the free-energy landscapes of tryptophan cage similar to those obtained from the all-atom molecular dynamics runs. read less NOT USED (high confidence) C. Pan, C. Liu, J.-hui Peng, P. Y. Ren, and X. Huang, “Three‐site and five‐site fixed‐charge water models compatible with AMOEBA force field,” Journal of Computational Chemistry. 2020. link Times cited: 2 Abstract: In a typical biomolecular simulation using Atomic Multipole … read moreAbstract: In a typical biomolecular simulation using Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field, the vast majority molecules in the simulation box consist of water, and these water molecules consume the most CPU power due to the explicit mutual induction effect. To improve the computational efficiency, we here develop two new nonpolarizable water models (with flexible bonds and fixed charges) that are compatible with AMOEBA solute: the 3‐site AW3C and 5‐site AW5C. To derive the force‐field parameters for AW3C and AW5C, we fit to six experimental liquid thermodynamic properties: liquid density, enthalpy of vaporization, dielectric constant, isobaric heat capacity, isothermal compressibility and thermal expansion coefficient, at a broad range of temperatures from 261.15 to 353.15 K under 1.0 atm pressure. We further validate our AW3C and AW5C water models by showing that they can well reproduce the radial distribution function g(r), self‐diffusion constant D, and hydration free energy from the AMOEBA03 water model and the experimental observations. Furthermore, we show that our AW3C and AW5C water models can greatly accelerate (>5 times) the bulk water as well as biomolecular simulations when compared to AMOEBA water. Specifically, we demonstrate that the applications of AW3C and AW5C water models to simulate a DNA duplex lead to a threefold acceleration, and in the meanwhile well maintain the structural properties as the fully polarizable AMOEBA water. We expect that our AW3C and AW5C water models hold great promise to be widely applied to simulate complex bio‐molecules using the AMOEBA force field. read less NOT USED (high confidence) M. Mendelev et al., “Development of a semi-empirical potential suitable for molecular dynamics simulation of vitrification in Cu-Zr alloys.,” The Journal of chemical physics. 2019. link Times cited: 50 Abstract: The fast increase in available computation power allowed us … read moreAbstract: The fast increase in available computation power allowed us to decrease the cooling rate in molecular dynamics (MD) simulation of vitrification by several orders of magnitude. While the reliability of the MD simulation should obviously benefit from this increase in the computational power, in some cases, it led to unexpected results. In particular, Ryltsev et al. [J. Chem. Phys. 149, 164502 (2018)] found that the most popular potentials for the Cu-Zr and Cu-Zr-Al alloys from Mendelev et al. [Philos. Mag. 89, 967 (2009)] and Cheng et al. [Phys. Rev. Lett. 102, 245501 (2009)] do not actually describe good glass forming systems but in contradiction with experiment predict rather fast crystallization of the Cu64.5Zr35.5 alloy which is the well-known example of bulk metallic glasses. In this paper, we present a new Cu-Zr semiempirical potential suitable to simulate vitrification. No crystal nucleation was observed in MD simulation using this potential in the concentration range from 75% to 5% of Zr. Since the new potential leads to about the same liquid structure and viscosity as the Cu-Zr potential from Mendelev et al. [Philos. Mag. 89, 967 (2009)] which failed to describe the good glass formability, our study clearly shows that no reliable conclusions about the glass formability can be deduced based solely on the analysis of the liquid properties and a nucleation/crystal growth study should be performed to address this question. read less NOT USED (high confidence) Y. Hu, B. Szajewski, D. Rodney, and W. Curtin, “Atomistic dislocation core energies and calibration of non-singular discrete dislocation dynamics,” Modelling and Simulation in Materials Science and Engineering. 2019. link Times cited: 15 Abstract: The total energy of an atomistic dislocation includes contri… read moreAbstract: The total energy of an atomistic dislocation includes contributions from the inelastic/large-distortion ‘core’ region. Capturing this inelastic ‘core’ energy is important, especially for dislocations with a curvature in the 10–100 nm scale. Current implementations of discrete dislocation dynamics (DDD) mesoscale simulations either approximate or neglect the core energy and so do not provide consistency with fully-atomistic studies. Using established interatomic potentials for FCC metals, the total dislocation energy is computed directly in atomistic simulations of straight dislocations and a core energy at any desired cut-off core radius is obtained as a function of dislocation character. A proper introduction of the atomistic core energy into the ParaDiS DDD code that uses a non-singular theory (Cai et al 2006 J. Mech. Phys. Solids 54 561–87) is then presented. The resulting atomistically-informed ParaDiS DDD is used to simulate the periodic bow-out of edge and screw dislocations in near-elastically-isotropic aluminum at various length and stress, with comparisons to fully-atomistic simulations. Generally good agreement is obtained between DDD and atomistics, with the best agreement achieved using a non-singular regularization parameter in the range of a = 5 – 10b. The analysis is then extended to compute the core energy of the Shockley partial dislocations that arise in the dissociation of perfect dislocations in fcc metals. read less NOT USED (high confidence) K. M. Lebold and W. Noid, “Dual-potential approach for coarse-grained implicit solvent models with accurate, internally consistent energetics and predictive transferability.,” The Journal of chemical physics. 2019. link Times cited: 18 Abstract: The dual-potential approach promises coarse-grained (CG) mod… read moreAbstract: The dual-potential approach promises coarse-grained (CG) models that accurately reproduce both structural and energetic properties, while simultaneously providing predictive estimates for the temperature-dependence of the effective CG potentials. In this work, we examine the dual-potential approach for implicit solvent CG models that reflect large entropic effects from the eliminated solvent. Specifically, we construct implicit solvent models at various resolutions, R, by retaining a fraction 0.10 ≤ R ≤ 0.95 of the molecules from a simple fluid of Lennard-Jones spheres. We consider the dual-potential approach in both the constant volume and constant pressure ensembles across a relatively wide range of temperatures. We approximate the many-body potential of mean force for the remaining solutes with pair and volume potentials, which we determine via multiscale coarse-graining and self-consistent pressure-matching, respectively. Interestingly, with increasing temperature, the pair potentials appear increasingly attractive, while the volume potentials become increasingly repulsive. The dual-potential approach not only reproduces the atomic energetics but also quite accurately predicts this temperature-dependence. We also derive an exact relationship between the thermodynamic specific heat of an atomic model and the energetic fluctuations that are observable at the CG resolution. With this generalized fluctuation relationship, the approximate CG models quite accurately reproduce the thermodynamic specific heat of the underlying atomic model. 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) E. Laurini, D. Marson, M. Fermeglia, and S. Pricl, “In silico design of self-assembly nanostructured polymer systems by multiscale molecular modeling,” Science, Technology and Innovation. 2019. link Times cited: 1 Abstract: The fast development of digitalization and computational sci… read moreAbstract: The fast development of digitalization and computational science is opening new possibilities for a rapid design of new materials. Computational tools coupled with focused experiments can be successfully used for the design of new nanostructured materials in different sectors, particularly in the area of biomedical applications. This paper starts with a general introduction on the future of computational tools for the design of new materials and introduces the paradigm of multiscale molecular modeling. It then continues with the description of the multiscale (i.e., atomistic, mesoscale and finite element calculations) computational recipe for the prediction of novel materials and structures for biomedical applications. Finally, the comparison of in silico and experimental results on selected systems of interest in the area of life sciences is reported and discussed. The quality of the agreement obtained between virtual and real data for such complex systems indeed confirms the validity of computational tools for the design of nanostructured polymer systems for biomedical applications.
read less NOT USED (high confidence) P. Reinholdt, S. Wind, D. Wüstner, and J. Kongsted, “Computational Characterization of a Cholesterol Based Molecular Rotor in Lipid Membranes.,” The journal of physical chemistry. B. 2019. link Times cited: 2 Abstract: Biophysical properties of cellular membranes critically depe… read moreAbstract: Biophysical properties of cellular membranes critically depend on their content of cholesterol and its interaction with various other lipid species. Cholesterol-dependent friction at the nanoscale can be studied with molecular rotors, whose quantum yield depends on rotational dynamics of functional groups during their excited state lifetime. Here, we present a detailed computational analysis of a phenyl-BODIPY linked cholesterol based molecular rotor in direct comparison with the well-known TopFluor-cholesterol. We describe a new parameterization strategy of force field parameters for the BODIPY moiety and carry out extensive molecular dynamics simulations of the probe in membranes in the absence or presence of cholesterol. Our study quantifies the extent of membrane perturbation by these probes, analyzes their tilting resistance in the bilayer and derives dynamic properties directly related to the rotor propensity. We show that phenyl-BODIPY-cholesterol bears the potential as a cholesterol-dependent molecular rotor to report about microviscosity of sterol-containing model and cell membranes. read less NOT USED (high confidence) J. G. S. Canchaya et al., “Development of a coarse-grain model for the description of the metal oxide-polymer interface from a bottom-up approach,” The Journal of Chemical Physics. 2019. link Times cited: 8 Abstract: We present a coarse-grained model for using dissipative part… read moreAbstract: We present a coarse-grained model for using dissipative particle dynamics simulations to study the interaction between cis-1,4 polybutadiene polymer chains and a metal oxide (Cu2O) surface at the mesoscopic scale. We employ a bottom-up approach in order to link the structural properties with their underlying molecular properties over a wide range of time and length scales. The parameterization of the model was realized using a recently developed Bayesian scheme that is based on trajectory matching of an atomistic description of the system. The model is used to investigate the local structure of polymers in a confined slab geometry by means of density profiles, radius of gyration, orientation with respect to the surface, and their adsorption.We present a coarse-grained model for using dissipative particle dynamics simulations to study the interaction between cis-1,4 polybutadiene polymer chains and a metal oxide (Cu2O) surface at the mesoscopic scale. We employ a bottom-up approach in order to link the structural properties with their underlying molecular properties over a wide range of time and length scales. The parameterization of the model was realized using a recently developed Bayesian scheme that is based on trajectory matching of an atomistic description of the system. The model is used to investigate the local structure of polymers in a confined slab geometry by means of density profiles, radius of gyration, orientation with respect to the surface, and their adsorption. read less 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) N. Vergadou and D. Theodorou, “Molecular Modeling Investigations of Sorption and Diffusion of Small Molecules in Glassy Polymers,” Membranes. 2019. link Times cited: 54 Abstract: With a wide range of applications, from energy and environme… read moreAbstract: With a wide range of applications, from energy and environmental engineering, such as in gas separations and water purification, to biomedical engineering and packaging, glassy polymeric materials remain in the core of novel membrane and state-of the art barrier technologies. This review focuses on molecular simulation methodologies implemented for the study of sorption and diffusion of small molecules in dense glassy polymeric systems. Basic concepts are introduced and systematic methods for the generation of realistic polymer configurations are briefly presented. Challenges related to the long length and time scale phenomena that govern the permeation process in the glassy polymer matrix are described and molecular simulation approaches developed to address the multiscale problem at hand are discussed. read less NOT USED (high confidence) K. Kanekal and T. Bereau, “Resolution limit of data-driven coarse-grained models spanning chemical space.,” The Journal of chemical physics. 2019. link Times cited: 15 Abstract: Increasing the efficiency of materials design remains a sign… read moreAbstract: Increasing the efficiency of materials design remains a significant challenge given the large size of chemical compound space (CCS). The use of a chemically transferable coarse-grained model enables different molecular fragments to map to the same bead type, significantly increasing screening efficiency. Here, we propose new criteria for the design of coarse-grained models allowing for the optimization of their chemical transferability and evaluate the Martini model within this framework. We further investigate the scope of this transferability by parameterizing three Martini-like models in which the number of bead types ranges from 5 to 16. These force fields are fully compatible with existing Martini environments because they are parameterized by interpolating the Martini interaction matrix. We then implement a Bayesian approach to determining which chemical groups are likely to be present on fragments corresponding to specific bead types for each model. We demonstrate that a level of accuracy comparable to Martini is obtained with a force field with fewer bead types, using the water/octanol partitioning free energy (ΔGW→Ol) as our metric for comparison. However, the advantage of including more bead types is a reduction of uncertainty when back-mapping these bead types to specific chemistries. Just as reducing the size of the coarse-grained particles leads to a finer mapping of conformational space, increasing the number of bead types yields a finer mapping of CCS. Finally, we note that, due to the large size of fragments mapping to a single Martini bead, a resolution limit arises when using ΔGW→Ol as the only descriptor when coarse-graining CCS. read less NOT USED (high confidence) C. A. Latorre, J. Ewen, C. Gattinoni, and D. Dini, “Simulating Surfactant-Iron Oxide Interfaces: From Density Functional Theory to Molecular Dynamics.,” The journal of physical chemistry. B. 2019. link Times cited: 23 Abstract: Understanding the behaviour of surfactant molecules on iron … read moreAbstract: Understanding the behaviour of surfactant molecules on iron oxide surfaces is important for many industrial applications. Molecular dynamics (MD) simulations of such systems have been limited by the absence of a force-field (FF) which accurately describes the molecule-surface interactions. In this study, interaction energies from density functional theory (DFT) + U calculations with a van der Waals functional are used to parameterize a classical FF for MD simulations of amide surfactants on iron oxide surfaces. The Original FF, which was derived using mixing rules and surface Lennard-Jones (LJ) parameters developed for nonpolar molecules, were shown to significantly underestimate the adsorption energy and overestimate the equilibrium adsorption distance compared to DFT. Conversely, the Optimized FF showed excellent agreement with the interaction energies obtained from DFT calculations for a wide range of surface coverages and molecular conformations near to and adsorbed on α-Fe2O3(0001). This was facilitated through the use of a Morse potential for strong chemisorption interactions, modified LJ parameters for weaker physisorption interactions, and adjusted partial charges for the electrostatic interactions. The Original FF and Optimized FF were compared in classical nonequilibrium molecular dynamics (NEMD) simulations of amide molecules confined between iron oxide surfaces. When the Optimized FF was employed, the amide molecules were pulled closer to the surface and the orientation of the headgroups was more similar to that observed in the DFT calculations compared to the Original FF. The Optimized FF proposed here facilitates classical MD simulations of anhydrous amide-iron oxide interfaces in which the interactions are representative of accurate DFT calculations. read less NOT USED (high confidence) S. Scandolo, “Machine learning provides realistic model of complex phase transition,” Proceedings of the National Academy of Sciences. 2019. link Times cited: 4 Abstract: Nature has provided us with many more types of phases than t… read moreAbstract: Nature has provided us with many more types of phases than the elementary ones—solid, liquid, and gas—that we learn in school textbooks. Some of them can be rather exotic, such as the one considered in the PNAS article by Robinson et al. (1), which deals with a remarkable but not so uncommon state of matter found in several elemental solids when they are compressed to gigapascal pressures (1 GPa = 10,000 bar). The solid in this specific case, elemental rubidium, crystallizes in a tetragonal structure composed of two interpenetrating lattices with incommensurate periodicity (Fig. 1). When heated, the “host” chain sublattice loses its long-range periodic order while the “guest” sublattice remains crystalline.
Fig. 1.
Crystal structure of the incommensurate host–guest structure observed in sodium, potassium, and rubidium at high pressure. The guest chains (dark green atoms) fill the channels of the host sublattice (light green atoms). At low temperature, the periodicity of the two sublattices is incommensurate along the chain direction. At high temperature, the chain sublattice loses long-range order. Adapted with permission from ref. 7, which is licensed under CC BY 4.0.
Microscopically complex state changes such as the ones observed in host–guest structures raise fundamental questions regarding how the system disorders as temperature is raised. Is chain disordering a phase transition? Why do the two interpenetrating lattices melt at different temperatures? Do different types of order, or rather disorder, appear?
Determining the nature of phase transitions, and especially temperature-induced phase transitions, …
[↵][1]1Email: scandolo{at}ictp.it.
[1]: #xref-corresp-1-1 read less NOT USED (high confidence) R. Barrett, M. Chakraborty, D. Amirkulova, H. A. Gandhi, and A. White, “A GPU-Accelerated Machine Learning Framework for Molecular Simulation: HOOMD-blue with TensorFlow.” 2019. link Times cited: 4 Abstract:
As interest grows in applying machine learning force-f… read moreAbstract:
As interest grows in applying machine learning force-fields and methods to molecular simulation, there is a need for
state-of-the-art inference methods to use trained models within efficient molecular simulation engines. We have designed and implemented software that enables integration of a scalable GPU-accelerated molecular mechanics engine,
HOOMD-blue, with the machine learning (ML) TensorFlow package. TensorFlow is a GPU-accelerated, scalable,
graph-based tensor computation model building package that has been the implementation of many recent innovations
in deep learning and other ML tasks. TensorFlow models are constructed in Python and can be visualized or debugged
using the rich set of tools implemented in the TensorFlow package. In this article, we present four major examples of
tasks this software can accomplish which would normally require multiple different tools: (1) we train a neural network
to reproduce a force field of a Lennard-Jones simulation; (2) we perform online force matching of methanol; (3) we
compute the maximum entropy bias of a Lennard-Jones collective variable; (4) we calculate the scattering profile of
an ongoing TIP4P water molecular dynamics simulation. This work should accelerate both the design of new neural network based models in computational chemistry research and reproducible model specification by leveraging a
widely-used ML package. read less 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. Metsanurk and M. Klintenberg, “Sampling-dependent systematic errors in effective harmonic models,” Physical Review B. 2019. link Times cited: 6 Abstract: Effective harmonic methods allow for calculating temperature… read moreAbstract: Effective harmonic methods allow for calculating temperature dependent phonon frequencies by incorporating the anharmonic contributions into an effective harmonic Hamiltonian. The systematic errors arising from such an approximation are explained theoretically and quantified by density functional theory based numerical simulations. Two techniques with different approaches for sampling the finite temperature phase space in order to generate the force-displacement data are compared. It is shown that the error in free energy obtained by using either can exceed that obtained from 0 K harmonic lattice dynamics analysis which neglects the anharmonic effects. read less NOT USED (high confidence) R. D. Kamachali, “Surface-Induced Phase Transition During Coalescence of Au Nanoparticles: A Molecular Dynamics Simulation Study,” arXiv: Materials Science. 2019. link Times cited: 1 Abstract: In this study, the melting and coalescence of Au nanoparticl… read moreAbstract: In this study, the melting and coalescence of Au nanoparticles were investigated using molecular dynamics simulation. The melting points of nanoparticles were calculated by studying the potential energy and Lindemann indices as a function of temperature. The simulations show that coalescence of two Au nanoparticles of the same size occurs at far lower temperatures than their corresponding melting temperature. For smaller nanoparticles, the difference between melting and coalescence temperature increases. Detailed analyses of the Lindemann indices and potential energy distribution across the nanoparticles show that the surface melting in nanoparticles begins at several hundred degrees below the melting point. This suggests that the coalescence is governed by the liquid-phase surface diffusion. Furthermore, the surface reduction during the coalescence accelerates its kinetics. It is found that for small enough particles and/or at elevated temperatures, the heat released due to the surface reduction result in a melting transition of the two attached nanoparticles. read less NOT USED (high confidence) F. L. Kearns, L. Warrensford, S. Boresch, and H. Woodcock, “The Good, the Bad, and the Ugly: ‘HiPen’, a New Dataset for Validating (S)QM/MM Free Energy Simulations,” Molecules. 2019. link Times cited: 8 Abstract: Indirect (S)QM/MM free energy simulations (FES) are vital to… read moreAbstract: Indirect (S)QM/MM free energy simulations (FES) are vital to efficiently incorporating sufficient sampling and accurate (QM) energetic evaluations when estimating free energies of practical/experimental interest. Connecting between levels of theory, i.e., calculating ΔAlow→high, remains to be the most challenging step within an indirect FES protocol. To improve calculations of ΔAlow→high, we must: (1) compare the performance of all FES methods currently available; and (2) compile and maintain datasets of ΔAlow→high calculated for a wide-variety of molecules so that future practitioners may replicate or improve upon the current state-of-the-art. Towards these two aims, we introduce a new dataset, “HiPen”, which tabulates ΔAgasMM→3ob (the free energy associated with switching from an MM to an SCC−DFTB molecular description using the 3ob parameter set in gas phase), calculated for 22 drug-like small molecules. We compare the calculation of this value using free energy perturbation, Bennett’s acceptance ratio, Jarzynski’s equation, and Crooks’ equation. We also predict the reliability of each calculated ΔAgasMM→3ob by evaluating several convergence criteria including sample size hysteresis, overlap statistics, and bias metric (Π). Within the total dataset, three distinct categories of molecules emerge: the “good” molecules, for which we can obtain converged ΔAgasMM→3ob using Jarzynski’s equation; “bad” molecules which require Crooks’ equation to obtain a converged ΔAgasMM→3ob; and “ugly” molecules for which we cannot obtain reliably converged ΔAgasMM→3ob with either Jarzynski’s or Crooks’ equations. We discuss, in depth, results from several example molecules in each of these categories and describe how dihedral discrepancies between levels of theory cause convergence failures even for these gas phase free energy simulations. read less 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) L. Zhang, Y. Shibuta, X. Huang, C. Lu, and M. Liu, “Grain boundary induced deformation mechanisms in nanocrystalline Al by molecular dynamics simulation: From interatomic potential perspective,” Computational Materials Science. 2019. link Times cited: 39 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) S. Longbottom and P. Brommer, “Uncertainty quantification for classical effective potentials: an extension to potfit,” Modelling and Simulation in Materials Science and Engineering. 2018. link Times cited: 12 Abstract: Effective potentials are an essential ingredient of classica… read moreAbstract: Effective potentials are an essential ingredient of classical molecular dynamics (MD) simulations. Little is understood of the consequences of representing the complex energy landscape of an atomic configuration by an effective potential or force field containing considerably fewer parameters. The probabilistic potential ensemble method has been implemented in the potfit force matching code. This introduces uncertainty quantification into the interatomic potential generation process. Uncertainties in the effective potential are propagated through MD to obtain uncertainties in quantities of interest (QoI), which are a measure of the confidence in the model predictions. We demonstrate the technique using three potentials for nickel: two simple pair potentials, Lennard-Jones and Morse, and a local density dependent embedded atom method potential. A potential ensemble fit to density functional theory (DFT) reference data is constructed for each potential to calculate the uncertainties in lattice constants, elastic constants and thermal expansion. We quantitatively illustrate the cases of poor model selection and fit, highlighted by the uncertainties in the quantities calculated. This shows that our method can capture the effects of the error incurred in QoI resulting from the potential generation process without resorting to comparison with experiment or DFT, which is an essential part to assess the predictive power of MD simulations. read less NOT USED (high confidence) P. Dauber-Osguthorpe and A. Hagler, “Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?,” Journal of Computer-Aided Molecular Design. 2018. link Times cited: 58 NOT USED (high confidence) W. Ko, D.-H. Kim, Y. Kwon, and M. Lee, “Atomistic Simulations of Pure Tin Based on a New Modified Embedded-Atom Method Interatomic Potential,” Metals. 2018. link Times cited: 22 Abstract: A new interatomic potential for the pure tin (Sn) system is … read moreAbstract: A new interatomic potential for the pure tin (Sn) system is developed on the basis of the second-nearest-neighbor modified embedded-atom-method formalism. The potential parameters were optimized based on the force-matching method utilizing the density functional theory (DFT) database of energies and forces of atomic configurations under various conditions. The developed potential significantly improves the reproducibility of many fundamental physical properties compared to previously reported modified embedded-atom method (MEAM) potentials, especially properties of the β phase that is stable at the ambient condition. Subsequent free energy calculations based on the quasiharmonic approximation and molecular-dynamics simulations verify that the developed potential can be successfully applied to study the allotropic phase transformation between α and β phases and diffusion phenomena of pure tin. read less NOT USED (high confidence) T. Mane, P. Bhat, V. Yang, and D. Sundaram, “Energy accommodation under non-equilibrium conditions for aluminum-inert gas systems,” Surface Science. 2018. link Times cited: 17 NOT USED (high confidence) M. Tripathy, U. Agarwal, and P. B. S. Kumar, “Toward Transferable Coarse-Grained Potentials for Poly-Aromatic Hydrocarbons: A Force Matching Approach,” Macromolecular Theory and Simulations. 2018. link Times cited: 6 NOT USED (high confidence) G. Megariotis, G. G. Vogiatzis, A. Sgouros, and D. Theodorou, “Slip Spring-Based Mesoscopic Simulations of Polymer Networks: Methodology and the Corresponding Computational Code,” Polymers. 2018. link Times cited: 22 Abstract: In previous work by the authors, a new methodology was devel… read moreAbstract: In previous work by the authors, a new methodology was developed for Brownian dynamics/kinetic Monte Carlo (BD/kMC) simulations of polymer melts. In this study, this methodology is extended for dynamical simulations of crosslinked polymer networks in a coarse-grained representation, wherein chains are modeled as sequences of beads, each bead encompassing a few Kuhn segments. In addition, the C++ code embodying these simulations, entitled Engine for Mesoscopic Simulations for Polymer Networks (EMSIPON) is described in detail. A crosslinked network of cis-1,4-polyisoprene is chosen as a test system. From the thermodynamic point of view, the system is fully described by a Helmholtz energy consisting of three explicit contributions: entropic springs, slip springs and non-bonded interactions. Entanglements between subchains in the network are represented by slip springs. The ends of the slip springs undergo thermally activated hops between adjacent beads along the chain backbones, which are tracked by kinetic Monte Carlo simulation. In addition, creation/destruction processes are included for the slip springs at dangling subchain ends. The Helmholtz energy of non-bonded interactions is derived from the Sanchez–Lacombe equation of state. The isothermal compressibility of the polymer network is predicted from equilibrium density fluctuations in very good agreement with the underlying equation of state and with experiment. Moreover, the methodology and the corresponding C++ code are applied to simulate elongational deformations of polymer rubbers. The shear stress relaxation modulus is predicted from equilibrium simulations of several microseconds of physical time in the undeformed state, as well as from stress-strain curves of the crosslinked polymer networks under deformation. read less NOT USED (high confidence) A. A. Saltos, N. Peters, and K. Hammond, “Thermal neutron scattering cross sections of 238U and 235U in the γ phase,” Journal of Physics: Condensed Matter. 2018. link Times cited: 4 Abstract: The development of metallic, low-enrichment uranium fuels re… read moreAbstract: The development of metallic, low-enrichment uranium fuels requires accurate prediction of their neutron transport properties and reactivity parameters, which in turn require thermal neutron scattering data. Accurate prediction of thermal neutron scattering data, including thermal cross sections, requires knowledge of the phonon scattering properties of the medium, but such matrix binding effects in next-generation fuels such as U–Mo, U–Zr, and U–Si are typically neglected because these effects are often difficult to measure or calculate. Using molecular dynamics simulations with previously published interatomic potentials, we calculate the phonon dispersion relations and phonon densities of states for 235U and 238U in the α and γ phases. The performance of these potentials was evaluated using published ab initio simulation data and inelastic neutron scattering data. The phonon densities of states obtained by each potential were then utilized to calculate the thermal neutron scattering cross sections of 235U and 238U at 1113 K using the NJOY program. The resulting thermal neutron scattering cross sections are assessed by comparison to data obtained from available experimental densities of states. The cross sections generated show how the addition of binding effects decreases the cross section by up to a factor of six over the free-atom model. A definite effect on reactivity is also demonstrated by the use of these thermal libraries on a simple core model. As a consequence, the cross sections generated in this work provide a better description of the true cross section than the free-atom data currently available. We also discuss the sensitivity of the thermal scattering cross sections to the phonon density of states. read less NOT USED (high confidence) J. J. Moller et al., “110
planar faults in strained bcc metals: Origins and implications of a commonly observed artifact of classical potentials,” Physical Review Materials. 2018. link Times cited: 18 Abstract: Large-scale atomistic simulations with classical potentials … read moreAbstract: Large-scale atomistic simulations with classical potentials can provide valuable insights into microscopic deformation mechanisms and defect-defect interactions in materials. Unfortunately, these assets often come with the uncertainty of whether the observed mechanisms are based on realistic physical phenomena or whether they are artifacts of the employed material models. One such example is the often reported occurrence of stable planar faults (PFs) in body-centered cubic (bcc) metals subjected to high strains, e.g., at crack tips or in strained nano-objects. In this paper, we study the strain dependence of the generalized stacking fault energy (GSFE) of {110} planes in various bcc metals with material models of increasing sophistication, i.e., (modified) embedded atom method, angular-dependent, Tersoff, and bond-order potentials as well as density functional theory. We show that under applied tensile strains the GSFE curves of many classical potentials exhibit a local minimum which gives rise to the formation of stable PFs. These PFs do not appear when more sophisticated material models are used and have thus to be regarded as artifacts of the potentials. We demonstrate that the local GSFE minimum is not formed for reasons of symmetry and we recommend including the determination of the strain-dependent (110) GSFE as a benchmark for newly developed potentials. read less 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) F. Baras, V. Turlo, O. Politano, S. Vadchenko, A. Rogachev, and A. Mukasyan, “SHS in Ni/Al Nanofoils: A Review of Experiments and Molecular Dynamics Simulations,” Advanced Engineering Materials. 2018. link Times cited: 38 Abstract: Non‐isothermal processes in nanometric metallic multilayers … read moreAbstract: Non‐isothermal processes in nanometric metallic multilayers are reviewed, both experimentally and theoretically. The Ni/Al nanofoil is considered as a model system. On the one hand, the experimental methods of elaboration and analysis are presented and, on the other hand, the modeling approach at the macroscopic and atomic scale. The basic experimental features are reported together with recent achievements. Molecular dynamics investigation of the reactivity of Ni/Al systems is reported for bulk systems and nanosystems including nanoparticles, nanowires, nanofilms, and multilayers. The focus is on atomic‐scale modeling versus experiments. Molecular dynamics approaches allow us to elucidate the mechanisms of non‐isothermal processes occurring in nanoscale systems, such as phase transformations and self‐propagation reactions. read less NOT USED (high confidence) A. Rizzi et al., “Overview of the SAMPL6 host–guest binding affinity prediction challenge,” Journal of Computer-Aided Molecular Design. 2018. link Times cited: 103 NOT USED (high confidence) S. Hocker, H. Lipp, E. Eisfeld, S. Schmauder, and J. Roth, “Precipitation strengthening in Cu-Ni-Si alloys modeled with ab initio based interatomic potentials.,” The Journal of chemical physics. 2018. link Times cited: 3 Abstract: Effective interaction potentials suitable for Cu/δ-Ni2Si and… read moreAbstract: Effective interaction potentials suitable for Cu/δ-Ni2Si and Cu/β-Ni3Si are developed. We optimise the potential parameters of an embedded atom method potential to reproduce forces, energies, and stresses obtained from ab initio calculations. Details of the potential generation are given, and its validation is demonstrated. The potentials are used in molecular dynamics simulations of shear tests to study the interactions of edge dislocations with coherent δ-Ni2Si and β-Ni3Si precipitates embedded in a copper matrix. In spite of significantly different crystallographic structures of copper and δ-Ni2Si which usually result in circumvention of dislocations, we also observed cutting processes in our simulations. Dislocations cut for a specific orientation of the δ-Ni2Si precipitate and in some cases where dislocation loops originating from previous circumvention processes are present in the glide plane. It is found that β-Ni3Si precipitates have a similar effect on precipitation strengthening as δ-Ni2Si. Dislocations usually cut β-Ni3Si but increased coherency strain can lead to circumvention processes. read less NOT USED (high confidence) L. Wu et al., “Calculation of solid–liquid interfacial free energy and its anisotropy in undercooled system,” Rare Metals. 2018. link Times cited: 6 NOT USED (high confidence) L. Kahle, A. Marcolongo, and N. Marzari, “Modeling lithium-ion solid-state electrolytes with a pinball model,” Physical Review Materials. 2018. link Times cited: 30 Abstract: We introduce a simple and efficient model to describe the po… read moreAbstract: We introduce a simple and efficient model to describe the potential energy surface of lithium diffusing in a solid-state ionic conductor. First, we assume that the Li atoms are fully ionized and we neglect the weak dependence of the electronic valence charge density on the instantaneous position of the Li ions. Second, we freeze the atoms of the host lattice in their equilibrium positions; consequently, also the valence charge density is frozen. We thus obtain a computational setup (the "pinball model") for which extremely inexpensive molecular dynamics simulation can be performed. To assess the accuracy of the model, we contrast it with full first-principles molecular dynamics simulations performed either with a free or frozen host lattice; in this latter case, the charge density still readjusts itself self-consistently to the actual positions of the diffusing Li ions. We show that the pinball model is able to reproduce accurately the static and dynamic properties of the diffusing Li ions - including forces, power spectra, and diffusion coefficients - when compared to the self-consistent frozen-host lattice simulations. The frozen-lattice approximation itself is often accurate enough, and certainly a good proxy in most materials. These observations unlock efficient ways to simulating the diffusion of lithium in the solid state, and provide additional physical insight into the respective roles of charge-density rearrangements or lattice vibrations in affecting lithium diffusion. read less NOT USED (high confidence) W. Setyawan, N. Gao, and R. Kurtz, “A tungsten-rhenium interatomic potential for point defect studies,” Journal of Applied Physics. 2018. link Times cited: 22 Abstract: A tungsten-rhenium (W-Re) classical interatomic potential is… read moreAbstract: A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures in the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancies and self-interstitial defects sufficiently accurately and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures in the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancies and self-interstitial defects sufficiently accurately and gives the correct ground state self-interstitial configuration. Furthermore, by including liqu... read less NOT USED (high confidence) N. Medvedev, V. Tkachenko, V. Lipp, Z. Li, and B. Ziaja, “Various damage mechanisms in carbon and silicon materials under femtosecond X-ray irradiation.” 2018. link Times cited: 59 Abstract: We review the results of our research on damage mechanisms i… read moreAbstract: We review the results of our research on damage mechanisms in materials irradiated with femtosecond free-electron-laser (FEL) pulses. They were obtained using our hybrid approach, X-ray-induced thermal and non-thermal transitions (XTANT). Various damage mechanisms are discussed with respect to the pulse fluence and material properties on examples of diamond, amorphous carbon, C60 crystal, and silicon. We indicate the following conditions: those producing thermal melting of targets as a result of electron-ion energy exchange; non-thermal phase transitions due to modification of the interatomic potential; Coulomb explosion due to accumulated net charge in finite-size systems; spallation or ablation at higher fluences due to detachment of sample fragments; and warm dense matter formation. Transient optical coefficients are compared with experimental data whenever available, proving the validity of our modeling approach. Predicted diffraction patterns can be compared with the results of ongoing or future FEL experiments. Limitations of our model and possible future directions of development are outlined. read less NOT USED (high confidence) V. Sokhan and I. Todorov, “Dissipative particle dynamics: dissipative forces from atomistic simulation,” Molecular Simulation. 2018. link Times cited: 2 Abstract: ABSTRACT We present a novel approach of mapping dissipative … read moreAbstract: ABSTRACT We present a novel approach of mapping dissipative particle dynamics (DPD) into classical molecular dynamics. By introducing the invariant volume element representing the swarm of atoms, we show that the interactions between the emerging Brownian quasiparticles arise naturally from its geometric definition and include both conservative repulsion and dissipative drag forces. The quasiparticles, which are composed of atomistic host solvent rather than being simply immersed in it, provide a link between the atomistic and DPD levels and a practical route to extract the DPD parameters as direct statistical averages over the atomistic host system. The method thus provides the molecular foundations for the mesoscopic DPD. It is illustrated on the example of simple monatomic supercritical fluid demonstrating good agreement in thermodynamic and transport properties calculated for the atomistic system and DPD using the obtained parameters. read less NOT USED (high confidence) Y. Yuan, J. Li, X.-Z. Li, and F. Wang, “The strengths and limitations of effective centroid force models explored by studying isotopic effects in liquid water.,” The Journal of chemical physics. 2018. link Times cited: 3 Abstract: The development of effective centroid potentials (ECPs) is e… read moreAbstract: The development of effective centroid potentials (ECPs) is explored with both the constrained-centroid and quasi-adiabatic force matching using liquid water as a test system. A trajectory integrated with the ECP is free of statistical noises that would be introduced when the centroid potential is approximated on the fly with a finite number of beads. With the reduced cost of ECP, challenging experimental properties can be studied in the spirit of centroid molecular dynamics. The experimental number density of H2O is 0.38% higher than that of D2O. With the ECP, the H2O number density is predicted to be 0.42% higher, when the dispersion term is not refit. After correction of finite size effects, the diffusion constant of H2O is found to be 21% higher than that of D2O, which is in good agreement with the 29.9% higher diffusivity for H2O observed experimentally. Although the ECP is also able to capture the redshifts of both the OH and OD stretching modes in liquid water, there are a number of properties that a classical simulation with the ECP will not be able to recover. For example, the heat capacities of H2O and D2O are predicted to be almost identical and higher than the experimental values. Such a failure is simply a result of not properly treating quantized vibrational energy levels when the trajectory is propagated with classical mechanics. Several limitations of the ECP based approach without bead population reconstruction are discussed. read less NOT USED (high confidence) A. Gola and L. Pastewka, “Embedded atom method potential for studying mechanical properties of binary Cu–Au alloys,” Modelling and Simulation in Materials Science and Engineering. 2018. link Times cited: 13 Abstract: We present an embedded atom method (EAM) potential for the b… read moreAbstract: We present an embedded atom method (EAM) potential for the binary Cu–Au system. The unary phases are described by two well-tested unary EAM potentials for Cu and Au. We fitted the interaction between Cu and Au to experimental properties of the binary intermetallic phases Cu3Au, CuAu and CuAu3. Particular attention has been paid to reproducing stacking fault energies in order to obtain a potential suitable for studying deformation in this binary system. The resulting energies, lattice constant, elastic properties and melting points are in good agreement with available experimental data. We use nested sampling to show that our potential reproduces the phase boundaries between intermetallic phases and the disordered face-centered cubic solid solution. We benchmark our potential against four popular Cu–Au EAM parameterizations and density-functional theory calculations. read less NOT USED (high confidence) E. Lale, R. Rezakhani, M. Alnaggar, and G. Cusatis, “Homogenization coarse graining (HCG) of the lattice discrete particle model (LDPM) for the analysis of reinforced concrete structures,” Engineering Fracture Mechanics. 2018. link Times cited: 25 NOT USED (high confidence) J. Yeo et al., “Materials-by-design: computation, synthesis, and characterization from atoms to structures,” Physica Scripta. 2018. link Times cited: 36 Abstract: In the 50 years that succeeded Richard Feynman’s exposition … read moreAbstract: In the 50 years that succeeded Richard Feynman’s exposition of the idea that there is ‘plenty of room at the bottom’ for manipulating individual atoms for the synthesis and manufacturing processing of materials, the materials-by-design paradigm is being developed gradually through synergistic integration of experimental material synthesis and characterization with predictive computational modeling and optimization. This paper reviews how this paradigm creates the possibility to develop materials according to specific, rational designs from the molecular to the macroscopic scale. We discuss promising techniques in experimental small-scale material synthesis and large-scale fabrication methods to manipulate atomistic or macroscale structures, which can be designed by computational modeling. These include recombinant protein technology to produce peptides and proteins with tailored sequences encoded by recombinant DNA, self-assembly processes induced by conformational transition of proteins, additive manufacturing for designing complex structures, and qualitative and quantitative characterization of materials at different length scales. We describe important material characterization techniques using numerous methods of spectroscopy and microscopy. We detail numerous multi-scale computational modeling techniques that complements these experimental techniques: DFT at the atomistic scale; fully atomistic and coarse-grain molecular dynamics at the molecular to mesoscale; continuum modeling at the macroscale. Additionally, we present case studies that utilize experimental and computational approaches in an integrated manner to broaden our understanding of the properties of two-dimensional materials and materials based on silk and silk-elastin-like proteins. read less NOT USED (high confidence) M. R. Bonilla, A. Lozano, B. Escribano, J. Carrasco, and E. Akhmatskaya, “Revealing the Mechanism of Sodium Diffusion in NaxFePO4 Using an Improved Force Field,” Journal of Physical Chemistry C. 2018. link Times cited: 13 Abstract: Olivine NaFePO4 is a promising cathode material for Na-ion b… read moreAbstract: Olivine NaFePO4 is a promising cathode material for Na-ion batteries. Intermediate phases such as Na0.66FePO4 govern phase stability during intercalation-deintercalation processes, yet little is known about Na+ diffusion in NaxFePO4 (0 < x < 1). Here we use an advanced simulation technique, Randomized Shell Mass Generalized Shadow Hybrid Monte Carlo Method (RSM-GSHMC) in combination with a specifically developed force field for describing NaxFePO4 over the whole range of sodium compositions, to thoroughly examine Na+ diffusion in this material. We reveal a novel mechanism through which Na+/Fe2+ antisite defect formation halts transport of Na+ in the main diffusion direction [010], while simultaneously activating diffusion in the [001] channels. A similar mechanism was reported for Li+ in LiFePO4, suggesting that a transition from one- to two-dimensional diffusion prompted by antisite defect formation is common to olivine structures, in general. read less NOT USED (high confidence) C. Burnham, Z. Futera, and N. J. English, “Study of hydrogen-molecule guests in type II clathrate hydrates using a force-matched potential model parameterised from ab initio molecular dynamics.,” The Journal of chemical physics. 2018. link Times cited: 18 Abstract: The force-matching method has been applied to parameterise a… read moreAbstract: The force-matching method has been applied to parameterise an empirical potential model for water-water and water-hydrogen intermolecular interactions for use in clathrate-hydrate simulations containing hydrogen guest molecules. The underlying reference simulations constituted ab initio molecular dynamics (AIMD) of clathrate hydrates with various occupations of hydrogen-molecule guests. It is shown that the resultant model is able to reproduce AIMD-derived free-energy curves for the movement of a tagged hydrogen molecule between the water cages that make up the clathrate, thus giving us confidence in the model. Furthermore, with the aid of an umbrella-sampling algorithm, we calculate barrier heights for the force-matched model, yielding the free-energy barrier for a tagged molecule to move between cages. The barrier heights are reasonably large, being on the order of 30 kJ/mol, and are consistent with our previous studies with empirical models [C. J. Burnham and N. J. English, J. Phys. Chem. C 120, 16561 (2016) and C. J. Burnham et al., Phys. Chem. Chem. Phys. 19, 717 (2017)]. Our results are in opposition to the literature, which claims that this system may have very low barrier heights. We also compare results to that using the more ad hoc empirical model of Alavi et al. [J. Chem. Phys. 123, 024507 (2005)] and find that this model does very well when judged against the force-matched and ab initio simulation data. read less NOT USED (high confidence) D. Rosenberger and N. V. D. van der Vegt, “Addressing the temperature transferability of structure based coarse graining models.,” Physical chemistry chemical physics : PCCP. 2018. link Times cited: 26 Abstract: Systematically derived coarse grained (CG) models for molecu… read moreAbstract: Systematically derived coarse grained (CG) models for molecular liquids do not inherently guarantee transferability to a state point different from its reference, especially when derived on the basis of structure based CG methods like Inverse Monte Carlo (IMC). Several efforts made in the past years to improve the transferability of these models focused on including thermodynamic constraints or on the application of multistate parametrization. Das and Andersen (DA) [Das et al., J. Chem. Phys., 2010, 132, 164106.] proposed a different Ansatz. They derived a correction term added to the system's Hamiltonian to reproduce the virial pressure and the volume fluctuations of the reference system in the CG resolution which does not require further adjustment of the effective pair potential. Herein, we discuss the possibility to achieve temperature transferability with IMC models for selected alkanes following the optimization of the DA approach as proposed by Dunn and Noid (DN) [Dunn et al., J. Chem. Phys., 2015, 143, 243148.]. The work focuses on a novel approach to determine the DN correction term for different state points by linear interpolation. read less NOT USED (high confidence) C. O’Brien, C. M. Barr, P. M. Price, K. Hattar, and S. Foiles, “Grain boundary phase transformations in PtAu and relevance to thermal stabilization of bulk nanocrystalline metals,” Journal of Materials Science. 2018. link Times cited: 61 NOT USED (high confidence) X. Bian, Z. Li, and N. A. Adams, “A note on hydrodynamics from dissipative particle dynamics,” Applied Mathematics and Mechanics. 2017. link Times cited: 0 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) Y. Mo, Y. He, X. Feng, and S. Jiang, “Alternative long-ranged charge optimized many-body potential for aluminium,” Journal of Physics: Condensed Matter. 2017. link Times cited: 0 Abstract: A new COMB3 potential was developed for aluminium, which foc… read moreAbstract: A new COMB3 potential was developed for aluminium, which focuses on long-range interaction and phase transition. The potential was developed by fitting the equilibrium lattice properties of different phases and defects to ensure its transferability to general systems. The quality of the potential was tested in several problems and compared with the EAM potential as well as the published COMB3 potential, the effect of the cutoff method was studied in detail to demonstrate the necessity to extend the cutoff region. Systems of strong deformations along the Bain path, under a trigonal strain and with planar stacking faults were calculated and the present potential performed as well as the EAM potential. At last, a surface process that involves adsorption and diffusion was studied using the present potential. read less NOT USED (high confidence) S. N. Divi, G. Agrahari, S. Kadulkar, S. Kumar, and A. Chatterjee, “Improved prediction of heat of mixing and segregation in metallic alloys using tunable mixing rule for embedded atom method,” Modelling and Simulation in Materials Science and Engineering. 2017. link Times cited: 17 Abstract: Capturing segregation behavior in metal alloy nanoparticles … read moreAbstract: Capturing segregation behavior in metal alloy nanoparticles accurately using computer simulations is contingent upon the availability of high-fidelity interatomic potentials. The embedded atom method (EAM) potential is a widely trusted interatomic potential form used with pure metals and their alloys. When limited experimental data is available, the A-B EAM cross-interaction potential for metal alloys AxB1−x are often constructed from pure metal A and B potentials by employing a pre-defined ‘mixing rule’ without any adjustable parameters. While this approach is convenient, we show that for AuPt, NiPt, AgAu, AgPd, AuNi, NiPd, PtPd and AuPd such mixing rules may not even yield the correct alloy properties, e.g., heats of mixing, that are closely related to the segregation behavior. A general theoretical formulation based on scaling invariance arguments is introduced that addresses this issue by tuning the mixing rule to better describe alloy properties. Starting with an existing pure metal EAM potential that is used extensively in literature, we find that the mixing rule fitted to heats of mixing for metal solutions usually provides good estimates of segregation energies, lattice parameters and cohesive energy, as well as equilibrium distribution of metals within a nanoparticle using Monte Carlo simulations. While the tunable mixing rule generally performs better than non-adjustable mixing rules, the use of the tunable mixing rule may still require some caution. For e.g., in Pt–Ni system we find that the segregation behavior can deviate from the experimentally observed one at Ni-rich compositions. Despite this the overall results suggest that the same approach may be useful for developing improved cross-potentials with other existing pure metal EAM potentials as well. As a further test of our approach, mixing rule estimated from binary data is used to calculate heat of mixing in AuPdPt, AuNiPd, AuPtNi, AgAuPd and NiPtPd. Excellent agreement with experiments is observed for AuPdPt. read less NOT USED (high confidence) R. Lindsey, L. Fried, and N. Goldman, “ChIMES: A Force Matched Potential with Explicit Three-Body Interactions for Molten Carbon.,” Journal of chemical theory and computation. 2017. link Times cited: 50 Abstract: We present a new force field and development scheme for atom… read moreAbstract: We present a new force field and development scheme for atomistic simulations of materials under extreme conditions. These models, which explicitly include two- and three-body interactions, are generated by fitting linear combinations of Chebyshev polynomials through force matching to trajectories from Kohn-Sham density functional theory (DFT). We apply our method to liquid carbon near the diamond/graphite/liquid triple point and at higher densities and temperatures, where metallization and many-body effects may be substantial. We show that explicit inclusion of three-body interaction terms allows our model to yield improved descriptions of both dynamic and structural properties over previous empirical potential efforts, while exhibiting transferability to nearby state points. The simplicity of our functional form and subsequent efficiency of parameter determination allow for extension of DFT to experimental time and length scales while retaining most of its accuracy. read less NOT USED (high confidence) F. Fracchia, G. D. Frate, G. Mancini, W. Rocchia, and V. Barone, “Force Field Parametrization of Metal Ions from Statistical Learning Techniques,” Journal of Chemical Theory and Computation. 2017. link Times cited: 33 Abstract: A novel statistical procedure has been developed to optimize… read moreAbstract: A novel statistical procedure has been developed to optimize the parameters of nonbonded force fields of metal ions in soft matter. The criterion for the optimization is the minimization of the deviations from ab initio forces and energies calculated for model systems. The method exploits the combination of the linear ridge regression and the cross-validation techniques with the differential evolution algorithm. Wide freedom in the choice of the functional form of the force fields is allowed since both linear and nonlinear parameters can be optimized. In order to maximize the information content of the data employed in the fitting procedure, the composition of the training set is entrusted to a combinatorial optimization algorithm which maximizes the dissimilarity of the included instances. The methodology has been validated using the force field parametrization of five metal ions (Zn2+, Ni2+, Mg2+, Ca2+, and Na+) in water as test cases. read less NOT USED (high confidence) H. Sun, D. Kang, Y. Hou, and J. Dai, “Transport properties of warm and hot dense iron from orbital free and corrected Yukawa potential molecular dynamics,” Matter and Radiation at Extremes. 2017. link Times cited: 17 NOT USED (high confidence) J. Wu, L. Shen, and W. Yang, “Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.,” The Journal of chemical physics. 2017. link Times cited: 28 Abstract: Ab initio quantum mechanics/molecular mechanics (QM/MM) mole… read moreAbstract: Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes. read less NOT USED (high confidence) L. Vlček, R. Vasudevan, S. Jesse, and S. V. Kalinin, “Consistent Integration of Experimental and Ab Initio Data into Effective Physical Models.,” Journal of chemical theory and computation. 2017. link Times cited: 17 Abstract: We describe and test theoretical principles for consistent i… read moreAbstract: We describe and test theoretical principles for consistent integration of experimental and ab initio data from diverse sources into a single statistical mechanical model. The approach is based on the recently introduced concept of statistical distance between partition functions, uses a simple vector algebra formalism to describe measurement outcomes and coarse-graining operations, and takes advantage of thermodynamic perturbation expressions for fast exploration of the model parameter space. The methodology is demonstrated on a combination of thermodynamic, structural, spectroscopic, and imaging pseudoexperimental data along with ab initio-type trajectories, which are incorporated into models describing the behavior of a near-critical fluid, liquid water, thin-film mixed oxides, and binary alloys. We evaluate how different target data constrain the model parameters and how the uncertainty associated with incomplete target information and limited sampling of the system's phase space might influence the choice of optimal parameters. read less NOT USED (high confidence) M. R. DeLyser and W. Noid, “Extending pressure-matching to inhomogeneous systems via local-density potentials.,” The Journal of chemical physics. 2017. link Times cited: 44 Abstract: Bottom-up coarse-grained models describe the intermolecular … read moreAbstract: Bottom-up coarse-grained models describe the intermolecular structure of all-atom (AA) models with desirable accuracy and efficiency. Unfortunately, structure-based models for liquids tend to dramatically overestimate the thermodynamic pressure and, consequently, tend to vaporize under ambient conditions. By employing a volume potential to introduce additional cohesion, self-consistent pressure-matching provides a simple and robust method for accurately reproducing the pressure equation of state (EoS) for homogeneous fluids, while still preserving an accurate description of intermolecular structure. Because they depend upon the global density, though, volume potentials cannot be directly employed for inhomogeneous systems, such as liquid-vapor interfaces. In the present work, we demonstrate that volume potentials can be readily adapted as potentials of the local density. The resulting local-density potentials provide an accurate description of the structure, pressure EoS, and local density fluctuations of an AA model for liquid methanol. Moreover, we demonstrate that very slight modifications to these local-density potentials allow for a quantitative description of either local or global density fluctuations. Most importantly, we demonstrate that the resulting potentials, which were parameterized to describe a homogeneous liquid, also generate stable liquid-vapor coexistence. However, further work is necessary to more accurately reproduce the interfacial density profile. read less NOT USED (high confidence) B. Bauerhenne, E. S. Zijlstra, and M. E. Garcia, “Molecular dynamics simulations of a femtosecond-laser-induced solid-to-solid transition in antimony,” Applied Physics A. 2017. link Times cited: 7 NOT USED (high confidence) V. Turlo, F. Baras, and O. Politano, “Comparative study of embedded-atom methods applied to the reactivity in the Ni–Al system,” Modelling and Simulation in Materials Science and Engineering. 2017. link Times cited: 23 Abstract: Structural, thermodynamic, atomic and thermal transport prop… read moreAbstract: Structural, thermodynamic, atomic and thermal transport properties of solid and liquid phases of the Ni–Al system were studied by means of MD simulations using three embedded-atom method (EAM) potentials developed by Mishin and colleagues (Mishin et al 2002 Phys. Rev. B 65 224114; Mishin 2004 Acta Mater. 52 145167; Purja Pun and Mishin 2009 Phil. Mag. 89 32453267). The extracted properties (lattice parameter, enthalpy, heat capacity, mass diffusivity and thermal conductivity) were compared with experimental data. The limitations of EAM potentials for studying different aspects of reactivity were assessed for each potential separately. read less NOT USED (high confidence) L. Vlček, W. Sun, and P. Kent, “Combining configurational energies and forces for molecular force field optimization.,” The Journal of chemical physics. 2017. link Times cited: 11 Abstract: While quantum chemical simulations have been increasingly us… read moreAbstract: While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. Here we propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information is used to optimize a molecular force field by minimizing the statistical distance similarity metric. We illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method. read less 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) H. Nagashima, S. Tsuda, N. Tsuboi, A. Hayashi, and T. Tokumasu, “A molecular dynamics study of nuclear quantum effect on diffusivity of hydrogen molecule.,” The Journal of chemical physics. 2017. link Times cited: 8 Abstract: In this paper, the nuclear quantum effect of the hydrogen mo… read moreAbstract: In this paper, the nuclear quantum effect of the hydrogen molecule on its diffusivity was analyzed using the molecular dynamics (MD) method. The centroid MD (CMD) method was applied to reproduce the time evolution of the molecules. The diffusion coefficient of hydrogen was calculated using the Green-Kubo method over a wide temperature region, and the temperature dependence of the quantum effect of the hydrogen molecule on its diffusivity was addressed. The calculated results were compared with classical MD results based on the principle of corresponding state (PCS). It was confirmed that the difference in the diffusion coefficient calculated in the CMD and classical MD methods was small, and the PCS appears to be satisfied on the temperature dependence of the diffusion coefficient, even though the quantum effect of the hydrogen molecules was taken into account. It was clarified that this result did not suggest that the quantum effect on the diffusivity of the hydrogen molecule was small but that the two changes in the intermolecular interaction of hydrogen due to the quantum effect offset each other. Moreover, it was found that this tendency was related to the temperature dependence of the ratio of the kinetic energy of the quantum fluctuational motion to the classical kinetic energy. read less NOT USED (high confidence) J. Schofield, “Optimization and Automation of the Construction of Smooth Free Energy Profiles.,” The journal of physical chemistry. B. 2017. link Times cited: 4 Abstract: An adaptive procedure is introduced to construct smooth anal… read moreAbstract: An adaptive procedure is introduced to construct smooth analytical profiles of the free energy along a reaction coordinate using sampled data from multiple biased simulations. The procedure is based upon identifying problematic regions encountered in maximum likelihood estimators of the profile where there are statistically relevant discrepancies between the empirical and parametrized cumulative distribution functions and preferentially improving the construction of the parametric profile in these regions. The method is designed to produce continuous and smooth analytical fits that satisfy statistical goodness-of-fit tests with a minimum number of parameters. The accuracy of the profile obtained from the adaptive construction is compared by numerical computation to that of smooth interpolations based on an optimally chosen weighted histogram method for a solvated ion pair system and for an activated process for which the analytical form of the potential of mean force is available. In the model where the exact profile is known, the adaptive procedure is shown to reduce the integrated error relative to the optimal histogram construction by a factor of 3 or more in the typical case where the sampling is not extensive. It is demonstrated that the adaptive procedure can be used to produce statistically accurate smooth analytical representations of the free energy profile that can be evaluated with little computational effort and require little user input. read less NOT USED (high confidence) W. Verestek, A.-P. Prskalo, M. Hummel, P. Binkele, and S. Schmauder, “Molecular dynamics investigations of the strengthening of Al-Cu alloys during thermal ageing,” Physical Mesomechanics. 2017. link Times cited: 16 NOT USED (high confidence) H. Huang, F. Cao, L. Wu, and H. Sun, “All-atom and coarse-grained force fields for polydimethylsiloxane,” Molecular Simulation. 2017. link Times cited: 6 Abstract: By combining the bottom-up and top-down approaches, we have … read moreAbstract: By combining the bottom-up and top-down approaches, we have developed a new all-atom (AA) force field from quantum mechanics and experimental data and a new coarse grained (CG) force field from AA simulation and experimental data, for polydimethylsiloxane (PDMS). The AA force field is developed based on the TEAM force field database. The CG force field uses a mapping rule that splits the connecting oxygen into neighbouring CG beads to maintain the charge neutrality of the beads, analytical functional forms including anharmonic terms in the valence terms, and the temperature-dependent free-energy functional form to describe the inter-bead interactions. Broad range of thermodynamic properties of PDMS including density, surface tension, solubility parameter, radius of gyration and glass transition temperature are calculated to validate the force fields, and good agreements with the experimental data are obtained. read less NOT USED (high confidence) G. Po, M. Lazar, N. Admal, and N. Ghoniem, “A non-singular theory of dislocations in anisotropic crystals,” arXiv: Materials Science. 2017. link Times cited: 56 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) R. Pandey and B. L. Farmer, “Structure and dynamics of a free aquaporin (AQP1) by a coarse-grained Monte Carlo simulation,” Structural Chemistry. 2017. link Times cited: 2 NOT USED (high confidence) N. Seriani, C. Pinilla, and S. Scandolo, “Titania–silica mixed oxides investigated with density functional theory and molecular dynamics simulations,” physica status solidi (b). 2017. link Times cited: 6 Abstract: Mixed phases of titania and silica have raised interest for … read moreAbstract: Mixed phases of titania and silica have raised interest for their high activity as photocatalysts and for their optical properties, such as a high refractive index. To rationalize their properties, it is necessary to understand their atomic structure in crystalline and amorphous phases. We have investigated Ti–Si mixed oxide phases by density functional theory and molecular dynamics. A polarizable potential has been developed for TiSiO4 and has been employed to sample the configuration space. Mixed phases are metastable with respect to separate TiO2 and SiO2 , but they are only slightly higher in energy, and therefore might form under technologically relevant conditions. All Ti–Si mixed oxides considered, regardless of cation coordination, display peaks in IR and Raman spectra in the region of frequencies 880–950 cm−1 , while Ti‐only phases do not, even if titanium is in a tetrahedral coordination. Our calculations thus confirm that these peaks are a signature of Ti–O–Si links, but they do not deliver information on the actual atomic structure of the material. Phases with titanium in a tetrahedral coordination display a higher electronic band gap than phases with titanium in octahedral coordination. This should have important consequences for the photocatalytic activity of mixed oxides of titania and silica. read less NOT USED (high confidence) H. Sha and F. Zhu, “Parameter Optimization for Interaction between C-Terminal Domains of HIV-1 Capsid Protein,” Journal of chemical information and modeling. 2017. link Times cited: 1 Abstract: HIV-1 capsid proteins (CAs) assemble into a capsid that encl… read moreAbstract: HIV-1 capsid proteins (CAs) assemble into a capsid that encloses the viral RNA. The binding between a pair of C-terminal domains (CTDs) constitutes a major interface in both the CA dimers and the large CA assemblies. Here, we attempt to use a general residue-level coarse-grained model to describe the interaction between two isolated CTDs in Monte Carlo simulations. With the standard parameters that depend only on the residue types, the model predicts a much weaker binding in comparison to the experiments. Detailed analysis reveals that some Lennard-Jones parameters are not compatible with the experimental CTD dimer structure, thus resulting in an unfavorable interaction energy. To improve the model for the CTD binding, we introduce ad hoc modifications to a small number of Lennard-Jones parameters for some specific pairs of residues at the binding interface. Through a series of extensive Monte Carlo simulations, we identify the optimal parameters for the CTD-CTD interactions. With the refined model parameters, both the binding affinity (with a dissociation constant of 13 ± 2 μM) and the binding mode are in good agreement with the experimental data. This study demonstrates that the general interaction model based on the Lennard-Jones potential, with some modest adjustment of the parameters for key residues, could correctly reproduce the reversible protein binding, thus potentially applicable for simulating the thermodynamics of the CA assemblies. read less NOT USED (high confidence) J. Hu, Z. Liu, Y. Cui, F. Liu, and Z. Zhuang, “A New View of Incipient Plastic Instability during Nanoindentation,” Chinese Physics Letters. 2017. link Times cited: 1 NOT USED (high confidence) A. Rokhmanenkov, A. Kuksin, and A. Yanilkin, “Simulation of hydrogen diffusion in TiHx structures,” Physics of Metals and Metallography. 2017. link Times cited: 9 NOT USED (high confidence) V. Zhakhovsky, K. Migdal, N. Inogamov, and S. Anisimov, “MD simulation of steady shock-wave fronts with phase transition in single-crystal iron.” 2017. link Times cited: 18 Abstract: Overdriven shock waves propagating in main crystallographic … read moreAbstract: Overdriven shock waves propagating in main crystallographic directions of single-crystal bcc iron were studied with moving-window molecular dynamics (MD) technique. To simulate correctly the shock-induced bcc-to-hcp phase transition in iron a new EAM potential fitted to the cold pressure curves and pressure transition at 13 GPa was developed with the stress matching method. We demonstrate that structure of shock fronts depends on orientation of crystal. A peculiar structure of steady shock-wave front in [100] direction is observed. While the ultra-fast α → e transition initiated in uniaxially compressed crystal along [100] in elastic zone transforms bcc completely to hcp phase, transformation in other directions is performed only partially with production of metastable composition of nanometer-sized bcc-hcp-fcc grains. read less NOT USED (high confidence) L. Koziol, L. Fried, and N. Goldman, “Using Force Matching To Determine Reactive Force Fields for Water under Extreme Thermodynamic Conditions.,” Journal of chemical theory and computation. 2017. link Times cited: 24 Abstract: We present a method for the creation of classical force fiel… read moreAbstract: We present a method for the creation of classical force fields for water under dissociative thermodynamic conditions by force matching to molecular dynamics trajectories from Kohn-Sham density functional theory (DFT). We apply our method to liquid water under dissociative conditions, where molecular lifetimes are less than 1 ps, and superionic water, where hydrogen ions diffuse at liquid-like rates through an oxygen lattice. We find that, in general, our new models are capable of accurately reproducing the structural and dynamic properties computed from DFT, as well as the molecular concentrations and lifetimes. Overall, our force-matching approach presents a relatively simple way to create classical reactive force fields for a single thermodynamic state point that largely retains the accuracy of DFT while having the potential to access experimental time and length scales. read less NOT USED (high confidence) S. Vandenbrande, M. Waroquier, V. Speybroeck, and T. Verstraelen, “The Monomer Electron Density Force Field (MEDFF): A Physically Inspired Model for Noncovalent Interactions.,” Journal of chemical theory and computation. 2017. link Times cited: 48 Abstract: We propose a methodology to derive pairwise-additive noncova… read moreAbstract: We propose a methodology to derive pairwise-additive noncovalent force fields from monomer electron densities without any empirical input. Energy expressions are based on the symmetry-adapted perturbation theory (SAPT) decomposition of interaction energies. This ensures a physically motivated force field featuring an electrostatic, exchange-repulsion, dispersion, and induction contribution, which contains two types of parameters. First, each contribution depends on several fixed atomic parameters, resulting from a partitioning of the monomer electron density. Second, each of the last three contributions (exchange-repulsion, dispersion, and induction) contains exactly one linear fitting parameter. These three so-called interaction parameters in the model are initially estimated separately using SAPT reference calculations for the S66x8 database of noncovalent dimers. In a second step, the three interaction parameters are further refined simultaneously to reproduce CCSD(T)/CBS interaction energies for the same database. The limited number of parameters that are fitted to dimer interaction energies (only three) avoids ill-conditioned fits that plague conventional parameter optimizations. For the exchange-repulsion and dispersion component, good results are obtained for all dimers in the S66x8 database using one single value for the associated interaction parameters. The values of those parameters can be considered universal and can also be used for dimers not present in the original database used for fitting. For the induction component such an approach is only viable for the dispersion-dominated dimers in the S66x8 database. For other dimers (such as hydrogen-bonded complexes), we show that our methodology remains applicable. However, the interaction parameter needs to be determined on a case-specific basis. As an external validation, the force field predicts interaction energies in good agreement with CCSD(T)/CBS values for dispersion-dominated dimers extracted from an HIV-II protease crystal structure with a bound ligand (indinavir). Furthermore, experimental second virial coefficients of small alkanes and alkenes are well reproduced. read less NOT USED (high confidence) Z. Li, H. S. Lee, E. F. Darve, and G. Karniadakis, “Computing the non-Markovian coarse-grained interactions derived from the Mori-Zwanzig formalism in molecular systems: Application to polymer melts.,” The Journal of chemical physics. 2017. link Times cited: 82 Abstract: Memory effects are often introduced during coarse-graining o… read moreAbstract: Memory effects are often introduced during coarse-graining of a complex dynamical system. In particular, a generalized Langevin equation (GLE) for the coarse-grained (CG) system arises in the context of Mori-Zwanzig formalism. Upon a pairwise decomposition, GLE can be reformulated into its pairwise version, i.e., non-Markovian dissipative particle dynamics (DPD). GLE models the dynamics of a single coarse particle, while DPD considers the dynamics of many interacting CG particles, with both CG systems governed by non-Markovian interactions. We compare two different methods for the practical implementation of the non-Markovian interactions in GLE and DPD systems. More specifically, a direct evaluation of the non-Markovian (NM) terms is performed in LE-NM and DPD-NM models, which requires the storage of historical information that significantly increases computational complexity. Alternatively, we use a few auxiliary variables in LE-AUX and DPD-AUX models to replace the non-Markovian dynamics with a Markovian dynamics in a higher dimensional space, leading to a much reduced memory footprint and computational cost. In our numerical benchmarks, the GLE and non-Markovian DPD models are constructed from molecular dynamics (MD) simulations of star-polymer melts. Results show that a Markovian dynamics with auxiliary variables successfully generates equivalent non-Markovian dynamics consistent with the reference MD system, while maintaining a tractable computational cost. Also, transient subdiffusion of the star-polymers observed in the MD system can be reproduced by the coarse-grained models. The non-interacting particle models, LE-NM/AUX, are computationally much cheaper than the interacting particle models, DPD-NM/AUX. However, the pairwise models with momentum conservation are more appropriate for correctly reproducing the long-time hydrodynamics characterised by an algebraic decay in the velocity autocorrelation function. 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) P. Netz, R. Potestio, and K. Kremer, “Adaptive resolution simulation of oligonucleotides.,” The Journal of chemical physics. 2016. link Times cited: 15 Abstract: Nucleic acids are characterized by a complex hierarchical st… read moreAbstract: Nucleic acids are characterized by a complex hierarchical structure and a variety of interaction mechanisms with other molecules. These features suggest the need of multiscale simulation methods in order to grasp the relevant physical properties of deoxyribonucleic acid (DNA) and RNA using in silico experiments. Here we report an implementation of a dual-resolution modeling of a DNA oligonucleotide in physiological conditions; in the presented setup only the nucleotide molecule and the solvent and ions in its proximity are described at the atomistic level; in contrast, the water molecules and ions far from the DNA are represented as computationally less expensive coarse-grained particles. Through the analysis of several structural and dynamical parameters, we show that this setup reliably reproduces the physical properties of the DNA molecule as observed in reference atomistic simulations. These results represent a first step towards a realistic multiscale modeling of nucleic acids and provide a quantitatively solid ground for their simulation using dual-resolution methods. read less 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) M. Wen, J. Li, P. Brommer, R. Elliott, J. Sethna, and E. Tadmor, “A KIM-compliant potfit for fitting sloppy interatomic potentials: application to the EDIP model for silicon,” Modelling and Simulation in Materials Science and Engineering. 2016. link Times cited: 16 Abstract: Fitted interatomic potentials are widely used in atomistic s… read moreAbstract: Fitted interatomic potentials are widely used in atomistic simulations thanks to their ability to compute the energy and forces on atoms quickly. However, the simulation results crucially depend on the quality of the potential being used. Force matching is a method aimed at constructing reliable and transferable interatomic potentials by matching the forces computed by the potential as closely as possible, with those obtained from first principles calculations. The potfit program is an implementation of the force-matching method that optimizes the potential parameters using a global minimization algorithm followed by a local minimization polish. We extended potfit in two ways. First, we adapted the code to be compliant with the KIM Application Programming Interface (API) standard (part of the Knowledgebase of Interatomic Models project). This makes it possible to use potfit to fit many KIM potential models, not just those prebuilt into the potfit code. Second, we incorporated the geodesic Levenberg–Marquardt (LM) minimization algorithm into potfit as a new local minimization algorithm. The extended potfit was tested by generating a training set using the KIM environment-dependent interatomic potential (EDIP) model for silicon and using potfit to recover the potential parameters from different initial guesses. The results show that EDIP is a ‘sloppy model’ in the sense that its predictions are insensitive to some of its parameters, which makes fitting more difficult. We find that the geodesic LM algorithm is particularly efficient for this case. The extended potfit code is the first step in developing a KIM-based fitting framework for interatomic potentials for bulk and two-dimensional materials. The code is available for download via https://www.potfit.net. read less NOT USED (high confidence) P. Zhang and D. Trinkle, “A modified embedded atom method potential for interstitial oxygen in titanium,” Computational Materials Science. 2016. link Times cited: 13 NOT USED (high confidence) Q. J. Li, J. Li, Z. Shan, and E. Ma, “Strongly correlated breeding of high-speed dislocations,” Acta Materialia. 2016. link Times cited: 22 NOT USED (high confidence) D. Rosenberger, M. Hanke, and N. V. D. van der Vegt, “Comparison of iterative inverse coarse-graining methods,” The European Physical Journal Special Topics. 2016. link Times cited: 26 NOT USED (high confidence) M. Widom, “Frequency Estimate for Multicomponent Crystalline Compounds,” Journal of Statistical Physics. 2016. link Times cited: 7 NOT 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 NOT USED (high confidence) T. Heinemann and S. Klapp, “Coarse-graining strategy for molecular pair interactions: A reaction coordinate study for two- and three-dimensional systems.,” The Journal of chemical physics. 2016. link Times cited: 1 Abstract: We investigate and provide optimal sets of reaction coordina… read moreAbstract: We investigate and provide optimal sets of reaction coordinates for mixed pairs of molecules displaying polar, uniaxial, or spherical symmetry in two and three dimensions. These coordinates are non-redundant, i.e., they implicitly involve the molecules' symmetries. By tabulating pair interactions in these coordinates, resulting tables are thus minimal in length and require a minimal memory space. The intended fields of application are computer simulations of large ensembles of molecules or colloids with rather complex interactions in a fluid or liquid crystalline phase at low densities. Using effective interactions directly in the form of tables can help bridging the time and length scales without introducing errors stemming from any modeling procedure. Finally, we outline an exemplary computational methodology for gaining an effective pair potential in these coordinates, based on the Boltzmann inversion principle, by providing a step-by-step recipe. read less NOT USED (high confidence) N. Admal, J. Marian, and G. Po, “The atomistic representation of first strain-gradient elastic tensors,” Journal of The Mechanics and Physics of Solids. 2016. link Times cited: 36 NOT USED (high confidence) J. Li and F. Wang, “The effects of replacing the water model while decoupling water-water and water-solute interactions on computed properties of simple salts.,” The Journal of chemical physics. 2016. link Times cited: 4 Abstract: The effects of decoupling the water-water and water-solute i… read moreAbstract: The effects of decoupling the water-water and water-solute interactions are studied with selected mono-valent ions as the solute. Using the ion-water cross terms developed for the BLYPSP-4F water model, we replaced the water potential with WAIL, TIP4P, and TIP3P without changing the ion-water parameters. When the adaptive force matching (AFM) derived BLYPSP-4F model is replaced by the other AFM derived WAIL model, the difference in ion properties, such as hydration free energies, radial distribution functions, relative diffusion constants, is negligible, demonstrating the feasibility for combining AFM parameters from different sources. Interestingly, when the AFM-derived ion-water cross-terms are used with a non-AFM based water model, only small changes in the ion properties are observed. The final combined models with TIP3P or TIP4P water reproduce the salt hydration free energies within 6% of experiments. The feasibility of combining AFM models with other non-AFM models is of significance since such combinations allow more complex systems to be studied without specific parameterization. In addition, the study suggests an interesting prospect of reusing the cross-terms when a part of a general force field is replaced with a different model. The prevailing practice, which is to re-derive all cross-terms with combining rules, may not have been optimal. read less NOT USED (high confidence) K. Kreis and R. Potestio, “The relative entropy is fundamental to adaptive resolution simulations.,” The Journal of chemical physics. 2016. link Times cited: 10 Abstract: Adaptive resolution techniques are powerful methods for the … read moreAbstract: Adaptive resolution techniques are powerful methods for the efficient simulation of soft matter systems in which they simultaneously employ atomistic and coarse-grained (CG) force fields. In such simulations, two regions with different resolutions are coupled with each other via a hybrid transition region, and particles change their description on the fly when crossing this boundary. Here we show that the relative entropy, which provides a fundamental basis for many approaches in systematic coarse-graining, is also an effective instrument for the understanding of adaptive resolution simulation methodologies. We demonstrate that the use of coarse-grained potentials which minimize the relative entropy with respect to the atomistic system can help achieve a smoother transition between the different regions within the adaptive setup. Furthermore, we derive a quantitative relation between the width of the hybrid region and the seamlessness of the coupling. Our results do not only shed light on the what and how of adaptive resolution techniques but will also help setting up such simulations in an optimal manner. read less NOT USED (high 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 (high confidence) R. Everaers, “Thermodynamic translational invariance in concurrent multiscale simulations of liquids,” The European Physical Journal Special Topics. 2016. link Times cited: 11 NOT USED (high confidence) A. Köster et al., “Assessing the accuracy of improved force‐matched water models derived from Ab initio molecular dynamics simulations,” Journal of Computational Chemistry. 2016. link Times cited: 13 Abstract: The accuracy of water models derived from ab initio molecula… read moreAbstract: The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force‐matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force‐matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc. read less NOT USED (high confidence) A. Cardellini, M. Fasano, E. Chiavazzo, and P. Asinari, “Towards a Multiscale Simulation Approach of Nanofluids for Volumetric Solar Receivers: Assessing Inter-particle Potential Energy,” Energy Procedia. 2016. link Times cited: 7 NOT USED (high confidence) J. Novak, “Molecular dynamics simulation of aluminium melting,” Materials and Geoenvironment. 2016. link Times cited: 0 Abstract: Solid–liquid phase transition has been simulated by the mole… read moreAbstract: Solid–liquid phase transition has been simulated by the molecular dynamics method, using isobaric–isoenthalpic ensemble. For interatomic potential, glue potential has been selected. The original algorithm for bookkeeping of the information on neighbouring relationships of the atoms has been developed and used in this research. Time consumption for calculation of interatomic forces has been reduced from o(N2) to o(N) by the use of this algorithm. Calculations show that phase transition from solid to liquid occurs between 1,000 K and 1,300 K. The simulated temperature of phase transition is higher than the experimental value due to the absence of crystal defects. If constant heat flux is supplied, temperature decreases during melting because the superheated state becomes unstable. During the cooling process, no significant changes of the observed variables were detected due to the high cooling rate, which prevents crystallisation. read less NOT USED (high confidence) N. J. H. Dunn and W. Noid, “Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures.,” The Journal of chemical physics. 2016. link Times cited: 44 Abstract: This work investigates the promise of a "bottom-up"… read moreAbstract: This work investigates the promise of a "bottom-up" extended ensemble framework for developing coarse-grained (CG) models that provide predictive accuracy and transferability for describing both structural and thermodynamic properties. We employ a force-matching variational principle to determine system-independent, i.e., transferable, interaction potentials that optimally model the interactions in five distinct heptane-toluene mixtures. Similarly, we employ a self-consistent pressure-matching approach to determine a system-specific pressure correction for each mixture. The resulting CG potentials accurately reproduce the site-site rdfs, the volume fluctuations, and the pressure equations of state that are determined by all-atom (AA) models for the five mixtures. Furthermore, we demonstrate that these CG potentials provide similar accuracy for additional heptane-toluene mixtures that were not included their parameterization. Surprisingly, the extended ensemble approach improves not only the transferability but also the accuracy of the calculated potentials. Additionally, we observe that the required pressure corrections strongly correlate with the intermolecular cohesion of the system-specific CG potentials. Moreover, this cohesion correlates with the relative "structure" within the corresponding mapped AA ensemble. Finally, the appendix demonstrates that the self-consistent pressure-matching approach corresponds to minimizing an appropriate relative entropy. 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) 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 (high confidence) N. Orekhov and V. Stegailov, “Simulation of the adhesion properties of the polyethylene/carbon nanotube interface,” Polymer Science Series A. 2016. link Times cited: 7 NOT USED (high confidence) N. Nasruddin, E. Kosasih, S. Supriyadi, and I. Zulkarnain, “Isotropic Potential Model of Hydrogen Physisorption on Exohedral of Single Walled Carbon Nanotubes with Various Diameter.” 2016. link Times cited: 0 Abstract: Abstract. This work presents step-by-step procedure of model… read moreAbstract: Abstract. This work presents step-by-step procedure of modeling accurate interaction potential energy between hydrogen and outer surface of zigzag Single Walled Carbon Nanotube (CNT) as a function of its diameter. First principles calculations at MP2 method level and def2-SVP basis-set were performed to predict the interaction potential energy of hydrogen gas molecule on outer surface of CNT cluster model. The result shows that the physisorption energy is ranging between 1.05 kcal/mol to 1.14 kcal/mol. Using force-matching method, Lennard-Jones potential parameters were approximated for interaction between united-atom model of hydrogen molecules and the CNT. Assuming constant σ = 3.2 A, the result shows that the e parameter can be defined as a function of CNT diameter. Keywords. Hydrogen, Carbon Nanotube, First principles, Ab initio, Binding Energy, Force-matching Method, Lennard-Jones Potential read less NOT USED (high confidence) W. Nöhring and W. Curtin, “Thermodynamic properties of average-atom interatomic potentials for alloys,” Modelling and Simulation in Materials Science and Engineering. 2016. link Times cited: 17 Abstract: The atomistic mechanisms of deformation in multicomponent ra… read moreAbstract: The atomistic mechanisms of deformation in multicomponent random alloys are challenging to model because of their extensive structural and compositional disorder. For embedded-atom-method interatomic potentials, a formal averaging procedure can generate an average-atom EAM potential and this average-atom potential has recently been shown to accurately predict many zero-temperature properties of the true random alloy. Here, the finite-temperature thermodynamic properties of the average-atom potential are investigated to determine if the average-atom potential can represent the true random alloy Helmholtz free energy as well as important finite-temperature properties. Using a thermodynamic integration approach, the average-atom system is found to have an entropy difference of at most 0.05 kB/atom relative to the true random alloy over a wide temperature range, as demonstrated on FeNiCr and Ni85Al15 model alloys. Lattice constants, and thus thermal expansion, and elastic constants are also well-predicted (within a few percent) by the average-atom potential over a wide temperature range. The largest differences between the average atom and true random alloy are found in the zero temperature properties, which reflect the role of local structural disorder in the true random alloy. Thus, the average-atom potential is a valuable strategy for modeling alloys at finite temperatures. read less NOT USED (high confidence) A. S. Christensen, T. Kubař, Q. Cui, and M. Elstner, “Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications,” Chemical Reviews. 2016. link Times cited: 263 Abstract: Semiempirical (SE) methods can be derived from either Hartre… read moreAbstract: Semiempirical (SE) methods can be derived from either Hartree–Fock or density functional theory by applying systematic approximations, leading to efficient computational schemes that are several orders of magnitude faster than ab initio calculations. Such numerical efficiency, in combination with modern computational facilities and linear scaling algorithms, allows application of SE methods to very large molecular systems with extensive conformational sampling. To reliably model the structure, dynamics, and reactivity of biological and other soft matter systems, however, good accuracy for the description of noncovalent interactions is required. In this review, we analyze popular SE approaches in terms of their ability to model noncovalent interactions, especially in the context of describing biomolecules, water solution, and organic materials. We discuss the most significant errors and proposed correction schemes, and we review their performance using standard test sets of molecular systems for quantum chemical methods and several recent applications. The general goal is to highlight both the value and limitations of SE methods and stimulate further developments that allow them to effectively complement ab initio methods in the analysis of complex molecular systems. read less NOT USED (high confidence) J. Roth, H. Trebin, A. Kiselev, and D. Rapp, “Laser ablation of Al–Ni alloys and multilayers,” Applied Physics A. 2016. link Times cited: 10 NOT USED (high confidence) K. Wang, W. Zhu, S. Xiao, J. Chen, and W. Hu, “A new embedded-atom method approach based on the pth moment approximation,” Journal of Physics: Condensed Matter. 2016. link Times cited: 5 Abstract: Large scale atomistic simulations with suitable interatomic … read moreAbstract: Large scale atomistic simulations with suitable interatomic potentials are widely employed by scientists or engineers of different areas. The quick generation of high-quality interatomic potentials is urgently needed. This largely relies on the developments of potential construction methods and algorithms in this area. Quantities of interatomic potential models have been proposed and parameterized with various methods, such as the analytic method, the force-matching approach and multi-object optimization method, in order to make the potentials more transferable. Without apparently lowering the precision for describing the target system, potentials of fewer fitting parameters (FPs) are somewhat more physically reasonable. Thus, studying methods to reduce the FP number is helpful in understanding the underlying physics of simulated systems and improving the precision of potential models. In this work, we propose an embedded-atom method (EAM) potential model consisting of a new manybody term based on the pth moment approximation to the tight binding theory and the general transformation invariance of EAM potentials, and an energy modification term represented by pairwise interactions. The pairwise interactions are evaluated by an analytic-numerical scheme without the need to know their functional forms a priori. By constructing three potentials of aluminum and comparing them with a commonly used EAM potential model, several wonderful results are obtained. First, without losing the precision of potentials, our potential of aluminum has fewer potential parameters and a smaller cutoff distance when compared with some constantly-used potentials of aluminum. This is because several physical quantities, usually serving as target quantities to match in other potentials, seem to be uniquely dependent on quantities contained in our basic reference database within the new potential model. Second, a key empirical parameter in the embedding term of the commonly used EAM model is found to be related to the effective order of moments of local density of states. This may provide a way to improve the precision of EAM potentials further through more precise approximations to tight binding theory. In addition, some critical details about construction procedures are discussed. read less NOT USED (high confidence) H. Wang, H. Nakamura, and I. Fukuda, “A critical appraisal of the zero-multipole method: Structural, thermodynamic, dielectric, and dynamical properties of a water system.,” The Journal of chemical physics. 2016. link Times cited: 22 Abstract: We performed extensive and strict tests for the reliability … read moreAbstract: We performed extensive and strict tests for the reliability of the zero-multipole (summation) method (ZMM), which is a method for estimating the electrostatic interactions among charged particles in a classical physical system, by investigating a set of various physical quantities. This set covers a broad range of water properties, including the thermodynamic properties (pressure, excess chemical potential, constant volume/pressure heat capacity, isothermal compressibility, and thermal expansion coefficient), dielectric properties (dielectric constant and Kirkwood-G factor), dynamical properties (diffusion constant and viscosity), and the structural property (radial distribution function). We selected a bulk water system, the most important solvent, and applied the widely used TIP3P model to this test. In result, the ZMM works well for almost all cases, compared with the smooth particle mesh Ewald (SPME) method that was carefully optimized. In particular, at cut-off radius of 1.2 nm, the recommended choices of ZMM parameters for the TIP3P system are α ≤ 1 nm(-1) for the splitting parameter and l = 2 or l = 3 for the order of the multipole moment. We discussed the origin of the deviations of the ZMM and found that they are intimately related to the deviations of the equilibrated densities between the ZMM and SPME, while the magnitude of the density deviations is very small. read less NOT USED (high confidence) J. Yu, Y. Zhang, and J. Hales, “Milestone report on MD potential development for uranium silicide.” 2016. link Times cited: 0 Abstract: This report summarizes the progress on the interatomic poten… read moreAbstract: This report summarizes the progress on the interatomic potential development of triuranium-disilicide (U3Si2) for molecular dynamics (MD) simulations. The development is based on the Tersoff type potentials for single element U and Si. The Si potential is taken from the literature and a Tersoff type U potential is developed in this project. With the primary focus on the U3Si2 phase, some other U-Si systems such as U3Si are also included as a test of the transferability of the potentials for binary U-Si phases. Based on the potentials for unary U and Si, two sets of parameters for the binary U-Si system are developed using the Tersoff mixing rules and the cross-term fitting, respectively. The cross-term potential is found to give better results on the enthalpy of formation, lattice constants and elastic constants than those produced by the Tersoff mixing potential, with the reference data taken from either experiments or density functional theory (DFT) calculations. In particular, the results on the formation enthalpy and lattice constants for the U3Si2 phase and lattice constants for the high temperature U3Si (h-U3Si) phase generated by the cross-term potential agree well with experimental data. Reasonable agreements are also reached on the elastic constants of U3Si2,more » on the formation enthalpy for the low temperature U3Si (m-U3Si) and h-U3Si phases, and on the lattice constants of m-U3Si phase. All these phases are predicted to be mechanically stable. The unary U potential is tested for three metallic U phases (α, β, γ). The potential is found capable to predict the cohesive energies well against experimental data for all three phases. It matches reasonably with previous experiments on the lattice constants and elastic constants of αU.« less read less NOT USED (high confidence) S. Xu, L. Xiong, Y. Chen, and D. McDowell, “Sequential slip transfer of mixed-character dislocations across Σ3 coherent twin boundary in FCC metals: a concurrent atomistic-continuum study.” 2016. link Times cited: 92 NOT USED (high confidence) H.-L. Chen, C. Su, S. Ju, S.-H. Liu, and H. T. Chen, “Local structural evolution of Fe54C18Cr16Mo12 bulk metallic glass during tensile deformation and a temperature elevation process: a molecular dynamics study,” RSC Advances. 2015. link Times cited: 3 Abstract: The mechanical and thermal properties of Fe54C18Cr16Mo12 bul… read moreAbstract: The mechanical and thermal properties of Fe54C18Cr16Mo12 bulk metallic glasses (BMGs) were investigated by a molecular dynamics simulation with the 2NN modified embedded-atom method (MEAM) potential. The fitting process of the cross-element parameters of 2NN MEAM (Fe–C, Fe–Cr, Fe–Mo, C–Cr, C–Mo, and Cr–Mo) was carried out first by the force matching method (FMM) on the basis of the reference data from density functional theory (DFT) calculations. With these fitted parameters, the structure of Fe54C18Cr16Mo12 BMG was constructed by the simulated-annealing basin-hopping (SABH) method, and the angle distribution range of the X-ray diffraction profile of the predicted Fe54C18Cr16Mo12 BMG closely matches that of the experiment profile, indicating the fitted 2NN MEAM parameters can accurately reflect the interatomic interactions of Fe54C18Cr16Mo12 BMG. The Honeycutt–Andersen (HA) index analysis results show a significant percentage of icosahedral-like structures within Fe54C18Cr16Mo12 BMG, which suggests an amorphous state. According to the tensile test results, the estimated Young's modulus of Fe54Cr16Mo12C18 bulk metallic glass is about 139 GPa and the large plastic region of the stress–strain curve shows that the Fe54C18Cr16Mo12 BMG possesses good ductility. Local strain distribution was used to analyze the deformation mechanism, and the results show that a shear band develops homogeneously with the tensile fracture angle (θT) at about 50 degrees, in agreement with experimental results 45° < θT < 90°. For the temperature elevation results, the discontinuity of the enthalpy–temperature profile indicates the melting point of Fe54Cr16Mo12C18 BMG is about 1310 K. The diffusion coefficients near the melting point were derived by the Einstein equation from the mean-square-displacement (MSD) profiles between 800–1400 K. On the basis of diffusion coefficients at different temperatures, the diffusion barriers of Fe54Cr16Mo12C18 can be determined by the Arrhenius equation. The diffusion barriers of total for Fe, Cr, Mo, C are 31.88, 24.68, 35.26, 22.50 and 31.79 kJ mol−1, respectively. The diffusion barriers of Fe and Cr atoms are relatively lower, indicating Fe and Cr atoms more easily diffuse with the increasing temperature. read less NOT USED (high confidence) E. Tsuchida, Y. Choe, and T. Ohkubo, “An adaptive finite-element method for large-scale ab initio molecular dynamics simulations.,” Physical chemistry chemical physics : PCCP. 2015. link Times cited: 18 Abstract: We present the current status of the finite-element method f… read moreAbstract: We present the current status of the finite-element method for large-scale atomistic simulations based on the density-functional theory. After a brief overview of our formulation, we describe recent developments, including the optimal choice of adaptive coordinates, an efficient implementation of the ground-state calculations, and a remedy for the eggbox effect. As a new application of our formulation, we present ab initio molecular dynamics simulations on sulfonated poly(4-phenoxybenzoyl-1,4-phenylene) (SPPBP), which is a typical example of polymer electrolyte membranes for fuel cells. read less NOT USED (high confidence) A. Hagler, “Quantum Derivative Fitting and Biomolecular Force Fields: Functional Form, Coupling Terms, Charge Flux, Nonbond Anharmonicity, and Individual Dihedral Potentials.,” Journal of chemical theory and computation. 2015. link Times cited: 27 Abstract: Computer simulations are increasingly prevalent, complementi… read moreAbstract: Computer simulations are increasingly prevalent, complementing experimental studies in all fields of biophysics, chemistry, and materials. Their utility, however, is critically dependent on the validity of the underlying force fields employed. In this Perspective we review the ability of quantum mechanics, and in particular analytical ab initio derivatives, to inform on the nature of intra- and intermolecular interactions. The power inherent in the exploitation of forces and second derivatives (Hessians) to derive force fields for a variety of compound types, including inorganic, organic, and biomolecules, is explored. We discuss the use of these quantities along with QM energies and geometries to determine force constants, including nonbond and electrostatic parameters, and to assess the functional form of the energy surface. The latter includes the optimal form of out-of-plane interactions and the necessity for anharmonicity, and terms to account for coupling between internals, to adequately represent the energy of intramolecular deformations. In addition, individual second derivatives of the energy with respect to selected interaction coordinates, such as interatomic distances or individual dihedral angles, have been shown to select out for the corresponding interactions, annihilating other interactions in the potential expression. Exploitation of these quantities allows one to probe the individual interaction and explore phenomena such as, for example, anisotropy of atom-atom nonbonded interactions, charge flux, or the functional form of isolated dihedral angles, e.g., a single dihedral X-C-C-Y about a tetrahedral C-C bond. read less NOT USED (high confidence) Z. Li, X. Bian, X. Li, and G. Karniadakis, “Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism.,” The Journal of chemical physics. 2015. link Times cited: 116 Abstract: The Mori-Zwanzig formalism for coarse-graining a complex dyn… read moreAbstract: The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model. read less NOT USED (high confidence) A. A. Mansour, Y. Sereda, J. Yang, and P. Ortoleva, “Prospective on multiscale simulation of virus-like particles: Application to computer-aided vaccine design.,” Vaccine. 2015. link Times cited: 11 NOT USED (high confidence) A. Duff, “MEAMfit: A reference-free modified embedded atom method (RF-MEAM) energy and force-fitting code,” Comput. Phys. Commun. 2015. link Times cited: 33 NOT USED (high confidence) A. Lyubartsev, A. Naômé, D. P. Vercauteren, and A. Laaksonen, “Systematic hierarchical coarse-graining with the inverse Monte Carlo method.,” The Journal of chemical physics. 2015. link Times cited: 32 Abstract: We outline our coarse-graining strategy for linking micro- a… read moreAbstract: We outline our coarse-graining strategy for linking micro- and mesoscales of soft matter and biological systems. The method is based on effective pairwise interaction potentials obtained in detailed ab initio or classical atomistic Molecular Dynamics (MD) simulations, which can be used in simulations at less accurate level after scaling up the size. The effective potentials are obtained by applying the inverse Monte Carlo (IMC) method [A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E 52(4), 3730-3737 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. An in-house software package MagiC is developed to obtain the effective potentials for arbitrary molecular systems. In this work we compute effective potentials to model DNA-protein interactions (bacterial LiaR regulator bound to a 26 base pairs DNA fragment) at physiological salt concentration at a coarse-grained (CG) level. Normally the IMC CG pair-potentials are used directly as look-up tables but here we have fitted them to five Gaussians and a repulsive wall. Results show stable association between DNA and the model protein as well as similar position fluctuation profile. read less NOT USED (high confidence) L. Vlček and A. Chialvo, “Rigorous force field optimization principles based on statistical distance minimization.,” The Journal of chemical physics. 2015. link Times cited: 19 Abstract: We use the concept of statistical distance to define a measu… read moreAbstract: We use the concept of statistical distance to define a measure of distinguishability between a pair of statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the model's static measurable properties to those of the target. We exploit this feature to define a rigorous basis for the development of accurate and robust effective molecular force fields that are inherently compatible with coarse-grained experimental data. The new model optimization principles and their efficient implementation are illustrated through selected examples, whose outcome demonstrates the higher robustness and predictive accuracy of the approach compared to other currently used methods, such as force matching and relative entropy minimization. We also discuss relations between the newly developed principles and established thermodynamic concepts, which include the Gibbs-Bogoliubov inequality and the thermodynamic length. read less NOT USED (high confidence) H. Do and A. Troisi, “Developing accurate molecular mechanics force fields for conjugated molecular systems.,” Physical chemistry chemical physics : PCCP. 2015. link Times cited: 14 Abstract: A rapid method to parameterize the intramolecular component … read moreAbstract: A rapid method to parameterize the intramolecular component of classical force fields for complex conjugated molecules is proposed. The method is based on a procedure of force matching with a reference electronic structure calculation. It is particularly suitable for those applications where molecular dynamics simulations are used to generate structures that are therefore analysed by electronic structure methods, because it is possible to build force fields that are consistent with electronic structure calculations that follow classical simulations. Such applications are commonly encountered in organic electronics, spectroscopy of complex systems and photobiology (e.g. photosynthetic systems). We illustrate the method by parameterizing the force fields of a molecule used in molecular semiconductors (2,2-dicyanovinyl-capped S,N-heteropentacene or DCV-SN5), a polymeric semiconductor (thieno[3,2-b]thiophene-diketopyrrolopyrrole TT-DPP) and a chromophore embedded in a protein environment (15,16-dihydrobiliverdin or DBV) where several hundreds of parameters need to be optimized in parallel. read less NOT USED (high confidence) H. Chen and C. Ortner, “QM/MM Methods for Crystalline Defects. Part 2: Consistent Energy and Force-Mixing,” Multiscale Model. Simul. 2015. link Times cited: 31 Abstract: QM/MM hybrid methods employ accurate quantum (QM) models onl… read moreAbstract: QM/MM hybrid methods employ accurate quantum (QM) models only in regions of interest (defects) and switch to computationally cheaper interatomic potential (MM) models to describe the crystalline bulk.
We develop two QM/MM hybrid methods for crystalline defect simulations, an energy-based and a force-based formulation, employing a tight binding QM model. Both methods build on two principles: (i) locality of the QM model; and (ii) constructing the MM model as an explicit and controllable approximation of the QM model. This approach enables us to establish explicit convergence rates in terms of the size of QM region. read less NOT USED (high confidence) M. Guenza, “Advancements in multi scale modeling: Adaptive resolution simulations and related issues,” The European Physical Journal Special Topics. 2015. link Times cited: 7 NOT USED (high confidence) M. Wen, S. Whalen, R. Elliott, and E. Tadmor, “Interpolation effects in tabulated interatomic potentials,” Modelling and Simulation in Materials Science and Engineering. 2015. link Times cited: 23 Abstract: Empirical interatomic potentials are widely used in atomisti… read moreAbstract: Empirical interatomic potentials are widely used in atomistic simulations due to their ability to compute the total energy and interatomic forces quickly relative to more accurate quantum calculations. The functional forms in these potentials are sometimes stored in a tabulated format, as a collection of data points (argument–value pairs), and a suitable interpolation (often spline-based) is used to obtain the function value at an arbitrary point. We explore the effect of these interpolations on the potential predictions by calculating the quasi-harmonic thermal expansion and finite-temperature elastic constant of a one-dimensional chain compared with molecular dynamics simulations. Our results show that some predictions are affected by the choice of interpolation regardless of the number of tabulated data points. Our results clearly indicate that the interpolation must be considered part of the potential definition, especially for lattice dynamics properties that depend on higher-order derivatives of the potential. This is facilitated by the Knowledgebase of Interatomic Models (KIM) project, in which both the tabulated data (‘parameterized model’) and the code that interpolates them to compute energy and forces (‘model driver’) are stored and given unique citeable identifiers. We have developed cubic and quintic spline model drivers for pair functional type models (EAM, FS, EMT) and uploaded them to the OpenKIM repository (https://openkim.org). 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) M. Rupp, “Machine learning for quantum mechanics in a nutshell,” International Journal of Quantum Chemistry. 2015. link Times cited: 301 Abstract: Models that combine quantum mechanics (QM) with machine lear… read moreAbstract: Models that combine quantum mechanics (QM) with machine learning (ML) promise to deliver the accuracy of QM at the speed of ML. This hands-on tutorial introduces the reader to QM/ML models based on kernel learning, an elegant, systematically nonlinear form of ML. Pseudocode and a reference implementation are provided, enabling the reader to reproduce results from recent publications where atomization energies of small organic molecules are predicted using kernel ridge regression. © 2015 Wiley Periodicals, Inc. read less NOT USED (high confidence) P. Mirau, B. Farmer, and R. Pandey, “Structural variation of alpha-synuclein with temperature by a coarse-grained approach with knowledge-based interactions,” AIP Advances. 2015. link Times cited: 10 Abstract: Despite enormous efforts, our understanding the structure an… read moreAbstract: Despite enormous efforts, our understanding the structure and dynamics of α-synuclein (ASN), a disordered protein (that plays a key role in neurodegenerative disease) is far from complete. In order to better understand sequence-structure-property relationships in α-SYNUCLEIN we have developed a coarse-grained model using knowledge-based residue-residue interactions and used it to study the structure of free ASN as a function of temperature (T) with a large-scale Monte Carlo simulation. Snapshots of the simulation and contour contact maps show changes in structure formation due to self-assembly as a function of temperature. Variations in the residue mobility profiles reveal clear distinction among three segments along the protein sequence. The N-terminal (1-60) and C-terminal (96-140) regions contain the least mobile residues, which are separated by the higher mobility non-amyloid component (NAC) (61-95). Our analysis of the intra-protein contact profile shows a higher frequency of residue aggregation (clumping) in the N-terminal region relative to that in the C-terminal region, with little or no aggregation in the NAC region. The radius of gyration (Rg) of ASN decays monotonically with decreasing the temperature, consistent with the finding of Allison et al. (JACS, 2009). Our analysis of the structure function provides an insight into the mass (N) distribution of ASN, and the dimensionality (D) of the structure as a function of temperature. We find that the globular structure with D ≈ 3 at low T, a random coil, D ≈ 2 at high T and in between (2 ≤ D ≤ 3) at the intermediate temperatures. The magnitudes of D are in agreement with experimental estimates (J. Biological Chem 2002). read less NOT USED (high confidence) H.-L. Chen, S. Ju, T.-Y. Wu, S.-H. Liu, and H.-T. Chen, “Investigation of the mechanical properties and local structural evolution of Ti60Zr10Ta15Si15 bulk metallic glass during tensile deformation: a molecular dynamics study,” RSC Advances. 2015. link Times cited: 15 Abstract: Ti60Zr10Ta15Si15 bulk metallic glass (BMG) has been proven t… read moreAbstract: Ti60Zr10Ta15Si15 bulk metallic glass (BMG) has been proven to have potential for use in orthopedic bone fixation devices, and further studies on its structural properties and deformation mechanism under uniaxial tension have been conducted using molecular dynamics (MD) simulations. The Honeycutt–Andersen (HA) index analysis, Voronoi tessellation method and Warren–Cowley short-range order parameter are employed to investigate its structural properties. The results show a high content of icosahedral-like structures, which suggests an amorphous state and a trend for silicon to pair with a metal atom. In its tensile test, the Ti60Zr10Ta15Si15 bulk metallic glass showed good ductility and an estimated Young's modulus of about 93 GPa, which is close to the experimental value. Local strain distribution was used to analyze the deformation mechanism, and the results show that shear bands develop homogeneously, which enhances the plasticity. The Voronoi tessellation analysis and HA index were used to further investigate the plastic/elastic deformation mechanism. The results of the HA analysis show that icosahedral local structures (1551, 1541, 1431) transfer to less dense structures (1422 and 1311), which shows an increase of open volume which can be attributed to the formation of the shear bands. In addition, the Voronoi tessellation analysis also shows a notable change from perfect icosahedra to distorted icosahedra. Further investigation shows the variations of the Voronoi index are mostly the Ti and Si-centered clusters. This suggests that the structures around Ti and Si atoms undergo a severe evolution during the tension process. read less NOT USED (high confidence) J. F. Rudzinski and W. Noid, “A generalized-Yvon-Born-Green method for coarse-grained modeling,” The European Physical Journal Special Topics. 2015. link Times cited: 36 NOT USED (high confidence) L. Wu, B. Xu, Q. Li, W. Liu, and M. Li, “Anisotropic crystal–melt interfacial energy and stiffness of aluminum,” Journal of Materials Research. 2015. link Times cited: 21 Abstract: The crystal–melt interfacial free energy is an important qua… read moreAbstract: The crystal–melt interfacial free energy is an important quantity governing many kinetic phenomena including solidification and crystal growth. Although general calculation methods are available, it is still difficult to obtain the interfacial energies that differ only slightly due to anisotropy. Here, we report such a calculation of Al crystal–melt interfacial energy based on the general framework of the capillary fluctuation method (CFM). The subtle dependence of both the melting temperature and interfacial free energy at melting temperature on the crystal interface orientation was examined. For Al, the average melting temperature is obtained at 934.79 ± 5 K and the orientationally averaged mean interfacial free energy is 98.35 mJ/m^2. In addition, the anisotropy of the interfacial free energy is found weak, nevertheless with the values ranked as γ_100 > γ_110 > γ_111. read less NOT USED (high confidence) D. Smirnova et al., “Atomistic modeling of the self-diffusion in γ-U and γ-U-Mo,” The Physics of Metals and Metallography. 2015. link Times cited: 31 NOT USED (high confidence) É. Maras, N. Salles, R. Tétot, T. Ala‐Nissila, and H. Jónsson, “Improved tight-binding charge transfer model and calculations of energetics of a step on the rutile TiO2(110) surface,” Journal of Physical Chemistry C. 2015. link Times cited: 11 Abstract: A second-moment, tight-binding charge equilibration (SMTB-Q)… read moreAbstract: A second-moment, tight-binding charge equilibration (SMTB-Q) model for the atomic interactions in TiO2 is refined by comparison with results of density functional theory (DFT) calculations within t... read less NOT USED (high confidence) F. Leonarski and J. Trylska, “RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models.,” Biophysical journal. 2015. link Times cited: 7 NOT USED (high confidence) X. Li and J. Lu, “Traction boundary conditions for molecular static simulations,” Computer Methods in Applied Mechanics and Engineering. 2015. link Times cited: 5 NOT USED (high confidence) M. Welborn, J. Chen, L. P. Wang, and T. Voorhis, “Why many semiempirical molecular orbital theories fail for liquid water and how to fix them,” Journal of Computational Chemistry. 2015. link Times cited: 15 Abstract: Water is an extremely important liquid for chemistry and the… read moreAbstract: Water is an extremely important liquid for chemistry and the search for more accurate force fields for liquid water continues unabated. Neglect of diatomic differential overlap (NDDO) molecular orbital methods provide and intriguing generalization of classical force fields in this regard because they can account both for bond breaking and electronic polarization of molecules. However, we show that most standard NDDO methods fail for water because they give an incorrect description of hydrogen bonding, water's key structural feature. Using force matching, we design a reparameterized NDDO model and find that it qualitatively reproduces the experimental radial distribution function of water, as well as various monomer, dimer, and bulk properties that PM6 does not. This suggests that the apparent limitations of NDDO models are primarily due to poor parameterization and not to the NDDO approximations themselves. Finally, we identify the physical parameters that most influence the condensed phase properties. These results help to elucidate the chemistry that a semiempirical molecular orbital picture of water must capture. We conclude that properly parameterized NDDO models could be useful for simulations that require electronically detailed explicit solvent, including the calculation of redox potentials and simulation of charge transfer and photochemistry. © 2015 Wiley Periodicals, Inc. read less NOT USED (high confidence) H.-L. Chen, S. Ju, T.-Y. Wu, J. Hsieh, and S.-H. Liu, “Investigation of Zr and Si diffusion behaviors during reactive diffusion – a molecular dynamics study,” RSC Advances. 2015. link Times cited: 8 Abstract: Molecular dynamics simulation was used to investigate the di… read moreAbstract: Molecular dynamics simulation was used to investigate the diffusion behaviors of Zr and Si atoms during a reactive diffusion which produces Zr silicide. The simulation results were compared with those in Roy's experimental results. The profiles of mean square displacements (MSDs) of Zr and Si atoms at different temperatures were first used to evaluate the melting point above which the significant inter-diffusions of Zr and Si atom occur. The diffusion coefficients near the melting point were derived by the Einstein equation from MSD profiles. On the basis of diffusion coefficients at different temperatures, the diffusion barriers of Zr and Si atoms can be calculated by the Arrhenius equation. Compared to the corresponding experimental values, the predicted diffusion barriers at the Zr–Si interface were 23 times lower than the measured values in Roy's study. The main reason for this is that the Zr and Si atoms within the inter-diffusion region form different local ZrSi crystal alloys in the experiment, resulting in the lower diffusion coefficients and higher diffusion barriers found in the experimental observation. read less NOT USED (high confidence) S. Ju, T.-Y. Wu, and S.-H. Liu, “Mechanical and dynamical behaviors of ZrSi and ZrSi2 bulk metallic glasses: A molecular dynamics study,” Journal of Applied Physics. 2015. link Times cited: 8 Abstract: The mechanical and dynamical properties of ZrSi and ZrSi2 bu… read moreAbstract: The mechanical and dynamical properties of ZrSi and ZrSi2 bulk metallic glasses (BMGs) have been investigated by molecular dynamics simulation. The Honeycutt-Anderson (HA) index analysis indicates that the major indexes in ZrSi and ZrSi2 bulk metallic glasses are 1551, 1541, and 1431, which refers to the liquid structure. For uniaxial tension, the results show that the ZrSi and ZrSi2 BMGs are more ductile than their crystal counterparts. The evolution of the distribution of atomic local shear strain clearly shows the initialization of shear transformation zones (STZs), the extension of STZs, and the formation of shear bands along a direction 45° from the tensile direction when the tensile strain gradually increases. The self-diffusion coefficients of ZrSi and ZrSi2 BMGs at temperatures near their melting points were calculated by the Einstein equation according to the slopes of the MSD profiles at the long-time limit. Because the HA fraction summation of icosahedral-like structures of ZrSi BMG is higher t... 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) H. Geng, “Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface,” J. Comput. Phys. 2014. link Times cited: 13 NOT USED (high confidence) K. Choudhary et al., “Charge optimized many-body potential for aluminum,” Journal of Physics: Condensed Matter. 2014. link Times cited: 19 Abstract: An interatomic potential for Al is developed within the thir… read moreAbstract: An interatomic potential for Al is developed within the third generation of the charge optimized many-body (COMB3) formalism. The database used for the parameterization of the potential consists of experimental data and the results of first-principles and quantum chemical calculations. The potential exhibits reasonable agreement with cohesive energy, lattice parameters, elastic constants, bulk and shear modulus, surface energies, stacking fault energies, point defect formation energies, and the phase order of metallic Al from experiments and density functional theory. In addition, the predicted phonon dispersion is in good agreement with the experimental data and first-principles calculations. Importantly for the prediction of the mechanical behavior, the unstable stacking fault energetics along the direction on the (1 1 1) plane are similar to those obtained from first-principles calculations. The polycrsytal when strained shows responses that are physical and the overall behavior is consistent with experimental observations. read less NOT USED (high confidence) D. Andrienko, “Simulations of Morphology and Charge Transport in Supramolecular Organic Materials.” 2014. link Times cited: 8 Abstract: In this chapter, we describe the current state of the art of… read moreAbstract: In this chapter, we describe the current state of the art of microscopic charge transport simulations in partially ordered and disordered organic semiconductors, including simulations of atomistic morphologies, evaluation of electronic couplings, driving forces, charge transfer rates, and charge carrier mobilities. Special attention is paid to finite-size effects, long-range interactions, and charge localization. read less NOT USED (high confidence) J. Rest, Z. Insepov, B. Ye, and D. Yun, “A multiscale method for the analysis of defect behavior in Mo during electron irradiation,” Computational Materials Science. 2014. link Times cited: 7 NOT USED (high confidence) R. Asahi, C. Freeman, P. Saxe, and E. Wimmer, “Thermal expansion, diffusion and melting of Li2O using a compact forcefield derived from ab initio molecular dynamics,” Modelling and Simulation in Materials Science and Engineering. 2014. link Times cited: 9 Abstract: This work shows a straightforward procedure to derive forcef… read moreAbstract: This work shows a straightforward procedure to derive forcefields (FFs) which are able to describe the structural, thermal and transport properties of condensed phases. The approach is based on ab initio molecular dynamics trajectories and an empirical calibration such as the melting point. This is demonstrated for lithium oxide using a Buckingham-type potential and optimized effective atomic charges. The present FF reproduces the density and thermal expansion of Li2O very well, including an anomaly related to the known superionic behaviour, i.e. a pre-melting of the Li sublattice at a critical temperature of Tc = 1200 K. Calculations of the diffusion coefficient as a function of temperature show a strong dependence on vacancy concentration for temperatures below Tc, consistent with previous simulations. Extensions to other ionic systems and compositions are made straightforward by the compact form of the FF and the present methodology employed in the parameter fitting. read less NOT USED (high confidence) A. Kubo, J. Wang, and Y. Umeno, “Development of interatomic potential for Nd–Fe–B permanent magnet and evaluation of magnetic anisotropy near the interface and grain boundary,” Modelling and Simulation in Materials Science and Engineering. 2014. link Times cited: 9 Abstract: An interatomic potential based on the angular-dependent pote… read moreAbstract: An interatomic potential based on the angular-dependent potential model was developed for the neodymium magnet (Nd2Fe14B) and Nd crystal system. The developed potential very accurately reproduces the complex crystal structure of Nd2Fe14B together with other important crystal properties, including lattice parameters and elastic coefficients. Molecular dynamics simulations using the potential were performed for the Nd/Nd2Fe14B interfaces and a Nd2Fe14B grain boundary to determine their structures at the atomic level. The magnetoelastic anisotropy in the vicinity of the interfaces and the grain boundary was also evaluated. We find that the disorderliness of atomic structures and the magnetoelastic anisotropy strongly depend on the interface and grain boundary orientations. read less NOT USED (high confidence) S. Wilson and M. Mendelev, “Dependence of solid–liquid interface free energy on liquid structure,” Modelling and Simulation in Materials Science and Engineering. 2014. link Times cited: 17 Abstract: The Turnbull relation is widely believed to enable predictio… read moreAbstract: The Turnbull relation is widely believed to enable prediction of solid–liquid interface (SLI) free energies from measurements of the latent heat and the solid density. Ewing proposed an additional contribution to the SLI free energy to account for variations in liquid structure near the interface. In the present study, molecular dynamics (MD) simulations were performed to investigate whether SLI free energy depends on liquid structure. Analysis of the MD simulation data for 11 fcc metals demonstrated that the Turnbull relation is only a rough approximation for highly ordered liquids, whereas much better agreement is observed with Ewing's theory. A modification to Ewing's relation is proposed in this study that was found to provide excellent agreement with MD simulation data. read less NOT USED (high confidence) M. Masia, E. Guàrdia, and P. Nicolini, “The force matching approach to multiscale simulations: Merits, shortcomings, and future perspectives,” International Journal of Quantum Chemistry. 2014. link Times cited: 7 Abstract: Among the various approaches to multiscale simulations, in r… read moreAbstract: Among the various approaches to multiscale simulations, in recent years, force matching has been known for a quick growth. The method is based on a least-square fit of reference properties obtained from simulations at a certain scale, to parameterize the force field for coarser-grained scale simulations. Its advantage with respect to conventional schemes used for parameterizing force fields, lies in that only physically accessible configurations are sampled, and that the number of reference data per configuration is large. In this perspective article, we discuss some recent findings on the tailoring of the objective function, on the choice of the empirical potential, and on the way to improve the quality of the reference calculations. We present pros and cons of the algorithm, and we propose a road map to future developments. (C) 2014 Wiley Periodicals, Inc. read less NOT USED (high confidence) R. Potestio, C. Peter, and K. Kremer, “Computer Simulations of Soft Matter: Linking the Scales,” Entropy. 2014. link Times cited: 89 Abstract: In the last few decades, computer simulations have become a … read moreAbstract: In the last few decades, computer simulations have become a fundamental tool in the field of soft matter science, allowing researchers to investigate the properties of a large variety of systems. Nonetheless, even the most powerful computational resources presently available are, in general, sufficient to simulate complex biomolecules only for a few nanoseconds. This limitation is often circumvented by using coarse-grained models, in which only a subset of the system’s degrees of freedom is retained; for an effective and insightful use of these simplified models; however, an appropriate parametrization of the interactions is of fundamental importance. Additionally, in many cases the removal of fine-grained details in a specific, small region of the system would destroy relevant features; such cases can be treated using dual-resolution simulation methods, where a subregion of the system is described with high resolution, and a coarse-grained representation is employed in the rest of the simulation domain. In this review we discuss the basic notions of coarse-graining theory, presenting the most common methodologies employed to build low-resolution descriptions of a system and putting particular emphasis on their similarities and differences. The AdResS and H-AdResS adaptive resolution simulation schemes are reported as examples of dual-resolution approaches, especially focusing in particular on their theoretical background. read less NOT USED (high confidence) K. Farrell and J. T. Oden, “Calibration and validation of coarse-grained models of atomic systems: application to semiconductor manufacturing,” Computational Mechanics. 2014. link Times cited: 15 NOT USED (high confidence) G. Bonny, D. Terentyev, A. Bakaev, P. Grigorev, and D. V. Neck, “Many-body central force potentials for tungsten,” Modelling and Simulation in Materials Science and Engineering. 2014. link Times cited: 79 Abstract: Tungsten and tungsten-based alloys are the primary candidate… read moreAbstract: Tungsten and tungsten-based alloys are the primary candidate materials for plasma facing components in fusion reactors. The exposure to high-energy radiation, however, severely degrades the performance and lifetime limits of the in-vessel components. In an effort to better understand the mechanisms driving the materials' degradation at the atomic level, large-scale atomistic simulations are performed to complement experimental investigations. At the core of such simulations lies the interatomic potential, on which all subsequent results hinge. In this work we review 19 central force many-body potentials and benchmark their performance against experiments and density functional theory (DFT) calculations. As basic features we consider the relative lattice stability, elastic constants and point-defect properties. In addition, we also investigate extended lattice defects, namely: free surfaces, symmetric tilt grain boundaries, the 1/2〈1 1 1〉{1 1 0} and 1/2〈1 1 1〉 {1 1 2} stacking fault energy profiles and the 1/2〈1 1 1〉 screw dislocation core. We also provide the Peierls stress for the 1/2〈1 1 1〉 edge and screw dislocations as well as the glide path of the latter at zero Kelvin. The presented results serve as an initial guide and reference list for both the modelling of atomically-driven phenomena in bcc tungsten, and the further development of its potentials. read less NOT USED (high confidence) A. Thuresson, M. Ullner, and M. Turesson, “Interaction and aggregation of charged platelets in electrolyte solutions: a coarse-graining approach.,” The journal of physical chemistry. B. 2014. link Times cited: 7 Abstract: A coarse-graining approach has been developed to replace the… read moreAbstract: A coarse-graining approach has been developed to replace the effect of explicit ions with an effective pair potential between charged sites in anisotropic colloidal particles by optimizing a potential of mean force against the results of simulations of two such colloidal particles with all ions in a cell model. More specifically, effective pair potentials were obtained for charged platelets in electrolyte solutions by simulating two rotating parallel platelets with ions at the primitive model level, enclosed in a cylindrical cell. One-component bulk simulations of many platelets interacting via the effective pair potentials are in excellent agreement with the corresponding bulk simulations with all mobile charges present. The bulk simulations were mainly used to study the effects of platelet size, flexibility, and surface charge density on platelet aggregation in an aqueous 2:1 electrolyte, but systems in a 1:1 electrolyte were also investigated. read less NOT USED (high confidence) W. Yu and Z. Wang, “Interactions between edge lattice dislocations and Σ11 symmetrical tilt grain boundary: comparisons among several FCC metals and interatomic potentials,” Philosophical Magazine. 2014. link Times cited: 15 Abstract: Interactions between edge dislocations and a symmetrical til… read moreAbstract: Interactions between edge dislocations and a symmetrical tilt grain boundary (GB) in face-centred cubic metals of Ni and Al are studied via a quasicontinuum method (QCM). A variety of embedding atom method potentials are used, and the results are compared to previous studies of Cu [W.S. Yu, Z.Q. Wang, Acta Mater., 60 (2012) 5010]. Different potentials do not significantly affect the edge dislocation–GB interactions in these metals. Edge dislocations can easily transmit across grain boundaries in Ni and Cu, even for a single incoming dislocation. However, slip-transmission in Al occurs only after the GB absorbs many incoming dislocations. Stable nucleation of grain boundary dislocations (GBD) in Cu and Ni plays an important role in the slip-transmissions. The slip transmission in Al is found to be difficult due to the metastable nucleation of GBD. The incoming leading and trailing partials in Al are absorbed together by the GB because of the larger values of (, and are the shear modulus, magnitude of Burgers vector of a partial dislocation and the stable stacking fault (SF) energy, respectively). The parameter ( as the unstable SF energy) [Z.H. Jin et al., Acta. Mater. 56 (2008) 1126] incorporates and , and can be used to measure the slip transmission ability of an edge dislocation in these metals. It is also shown that certain loading conditions can help enhance the nucleation of GBDs and GBD dipoles in Al, such that the incoming, leading and trailing partial dislocations can be absorbed separately. read less NOT USED (high confidence) T. C. Moore, C. Iacovella, and C. McCabe, “Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion.,” The Journal of chemical physics. 2014. link Times cited: 158 Abstract: In this work, an extension is proposed to the standard itera… read moreAbstract: In this work, an extension is proposed to the standard iterative Boltzmann inversion (IBI) method used to derive coarse-grained potentials. It is shown that the inclusion of target data from multiple states yields a less state-dependent potential, and is thus better suited to simulate systems over a range of thermodynamic states than the standard IBI method. The inclusion of target data from multiple states forces the algorithm to sample regions of potential phase space that match the radial distribution function at multiple state points, thus producing a derived potential that is more representative of the underlying interactions. It is shown that the algorithm is able to converge to the true potential for a system where the underlying potential is known. It is also shown that potentials derived via the proposed method better predict the behavior of n-alkane chains than those derived via the standard IBI method. Additionally, through the examination of alkane monolayers, it is shown that the relative weight given to each state in the fitting procedure can impact bulk system properties, allowing the potentials to be further tuned in order to match the properties of reference atomistic and/or experimental systems. read less NOT USED (high confidence) E. Metsanurk, A. Caro, A. Tamm, A. Aabloo, and M. Klintenberg, “First-principles study of point defects at a semicoherent interface,” Scientific Reports. 2014. link Times cited: 11 NOT USED (high confidence) I. Fukuda, N. Kamiya, and H. Nakamura, “The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: analysis of the accuracy and application to liquid systems.,” The Journal of chemical physics. 2014. link Times cited: 16 Abstract: In the preceding paper [I. Fukuda, J. Chem. Phys. 139, 17410… read moreAbstract: In the preceding paper [I. Fukuda, J. Chem. Phys. 139, 174107 (2013)], the zero-multipole (ZM) summation method was proposed for efficiently evaluating the electrostatic Coulombic interactions of a classical point charge system. The summation takes a simple pairwise form, but prevents the electrically non-neutral multipole states that may artificially be generated by a simple cutoff truncation, which often causes large energetic noises and significant artifacts. The purpose of this paper is to judge the ability of the ZM method by investigating the accuracy, parameter dependencies, and stability in applications to liquid systems. To conduct this, first, the energy-functional error was divided into three terms and each term was analyzed by a theoretical error-bound estimation. This estimation gave us a clear basis of the discussions on the numerical investigations. It also gave a new viewpoint between the excess energy error and the damping effect by the damping parameter. Second, with the aid of these analyses, the ZM method was evaluated based on molecular dynamics (MD) simulations of two fundamental liquid systems, a molten sodium-chlorine ion system and a pure water molecule system. In the ion system, the energy accuracy, compared with the Ewald summation, was better for a larger value of multipole moment l currently induced until l ≲ 3 on average. This accuracy improvement with increasing l is due to the enhancement of the excess-energy accuracy. However, this improvement is wholly effective in the total accuracy if the theoretical moment l is smaller than or equal to a system intrinsic moment L. The simulation results thus indicate L ∼ 3 in this system, and we observed less accuracy in l = 4. We demonstrated the origins of parameter dependencies appearing in the crossing behavior and the oscillations of the energy error curves. With raising the moment l we observed, smaller values of the damping parameter provided more accurate results and smoother behaviors with respect to cutoff length were obtained. These features can be explained, on the basis of the theoretical error analyses, such that the excess energy accuracy is improved with increasing l and that the total accuracy improvement within l ⩽ L is facilitated by a small damping parameter. Although the accuracy was fundamentally similar to the ion system, the bulk water system exhibited distinguishable quantitative behaviors. A smaller damping parameter was effective in all the practical cutoff distance, and this fact can be interpreted by the reduction of the excess subset. A lower moment was advantageous in the energy accuracy, where l = 1 was slightly superior to l = 2 in this system. However, the method with l = 2 (viz., the zero-quadrupole sum) gave accurate results for the radial distribution function. We confirmed the stability in the numerical integration for MD simulations employing the ZM scheme. This result is supported by the sufficient smoothness of the energy function. Along with the smoothness, the pairwise feature and the allowance of the atom-based cutoff mode on the energy formula lead to the exact zero total-force, ensuring the total-momentum conservations for typical MD equations of motion. read less NOT USED (high confidence) H. Hsu, J. Chien, J. Huang, L. Chu, and S. Fu, “Nanoscale bondability between Cu-Al intermetallic compound for Cu wirebonding,” 2014 International Conference on Electronics Packaging (ICEP). 2014. link Times cited: 0 Abstract: In this paper, the interfacial nanoscale bondability between… read moreAbstract: In this paper, the interfacial nanoscale bondability between copper (Cu) and Aluminum (Al) intermetallic compound (IMC) for Cu wirebonding has been carefully investigated. Preliminary results demonstrated that IMC cracks from the edge of bonding interface and spreads into the center area. This is the cause of open fail. The IMC between Cu and Al was initially generated in the form of CuAl2, and gradually increased the content of Cu and turned into CuAl when the working temperature was increased. The final stage of IMC growth is Cu9Al4 and the aluminum pad will be vanished as the result of Cu diffusivity. Nanoscale atomic modulus and rupture strength are predicted by using molecular dynamics (MD) simulations. Atomic-level tensile stress and tensile strain are predicted to examine the IMC bonding strength along the bonding interface. Temperature and tensile speed are two major factors on determining the bonding strength. Material in high temperature has greater kinetic energy and has better formability. Higher pulling speed in tensile test would results in material easier fracture. Interfacial fracture is different in different tensile speed as well as the working temperature. Nano-indentation tests demonstrate an excellent agreement with the MD simulation. A series of comprehensive s studies are conducted in the present research. read less NOT USED (high confidence) J. F. Rudzinski and W. Noid, “Investigation of coarse-grained mappings via an iterative generalized Yvon-Born-Green method.,” The journal of physical chemistry. B. 2014. link Times cited: 52 Abstract: Low resolution coarse-grained (CG) models enable highly effi… read moreAbstract: Low resolution coarse-grained (CG) models enable highly efficient simulations of complex systems. The interactions in CG models are often iteratively refined over multiple simulations until they reproduce the one-dimensional (1-D) distribution functions, e.g., radial distribution functions (rdfs), of an all-atom (AA) model. In contrast, the multiscale coarse-graining (MS-CG) method employs a generalized Yvon-Born-Green (g-YBG) relation to determine CG potentials directly (i.e., without iteration) from the correlations observed for the AA model. However, MS-CG models do not necessarily reproduce the 1-D distribution functions of the AA model. Consequently, recent studies have incorporated the g-YBG equation into iterative methods for more accurately reproducing AA rdfs. In this work, we consider a theoretical framework for an iterative g-YBG method. We numerically demonstrate that the method robustly determines accurate models for both hexane and also a more complex molecule, 3-hexylthiophene. By examining the MS-CG and iterative g-YBG models for several distinct CG representations of both molecules, we investigate the approximations of the MS-CG method and their sensitivity to the CG mapping. More generally, we explicitly demonstrate that CG models often reproduce 1-D distribution functions of AA models at the expense of distorting the cross-correlations between the corresponding degrees of freedom. In particular, CG models that accurately reproduce intramolecular 1-D distribution functions may still provide a poor description of the molecular conformations sampled by the AA model. We demonstrate a simple and predictive analysis for determining CG mappings that promote an accurate description of these molecular conformations. read less NOT USED (high confidence) H. Nagashima, S. Tsuda, N. Tsuboi, M. Koshi, K. Hayashi, and T. Tokumasu, “An analysis of quantum effects on the thermodynamic properties of cryogenic hydrogen using the path integral method.,” The Journal of chemical physics. 2014. link Times cited: 7 Abstract: In this paper, we describe the analysis of the thermodynamic… read moreAbstract: In this paper, we describe the analysis of the thermodynamic properties of cryogenic hydrogen using classical molecular dynamics (MD) and path integral MD (PIMD) method to understand the effects of the quantum nature of hydrogen molecules. We performed constant NVE MD simulations across a wide density-temperature region to establish an equation of state (EOS). Moreover, the quantum effect on the difference of molecular mechanism of pressure-volume-temperature relationship was addressed. The EOS was derived based on the classical mechanism idea only using the MD simulation results. Simulation results were compared with each MD method and experimental data. As a result, it was confirmed that although the EOS on the basis of classical MD cannot reproduce the experimental data of saturation property of hydrogen in the high-density region, the EOS on the basis of PIMD well reproduces those thermodynamic properties of hydrogen. Moreover, it was clarified that taking quantum effects into account makes the repulsion force larger and the potential well shallower. Because of this mechanism, the intermolecular interaction of hydrogen molecules diminishes and the virial pressure increases. read less NOT USED (high confidence) A. Thompson, B. Meredig, and C. Wolverton, “An improved interatomic potential for xenon in UO2: a combined density functional theory/genetic algorithm approach,” Journal of Physics: Condensed Matter. 2014. link Times cited: 11 Abstract: We have created an improved xenon interatomic potential for … read moreAbstract: We have created an improved xenon interatomic potential for use with existing UO2 potentials. This potential was fit to density functional theory calculations with the Hubbard U correction (DFT + U) using a genetic algorithm approach called iterative potential refinement (IPR). We examine the defect energetics of the IPR-fitted xenon interatomic potential as well as other, previously published xenon potentials. We compare these potentials to DFT + U derived energetics for a series of xenon defects in a variety of incorporation sites (large, intermediate, and small vacant sites). We find the existing xenon potentials overestimate the energy needed to add a xenon atom to a wide set of defect sites representing a range of incorporation sites, including failing to correctly rank the energetics of the small incorporation site defects (xenon in an interstitial and xenon in a uranium site neighboring uranium in an interstitial). These failures are due to problematic descriptions of Xe–O and/or Xe–U interactions of the previous xenon potentials. These failures are corrected by our newly created xenon potential: our IPR-generated potential gives good agreement with DFT + U calculations to which it was not fitted, such as xenon in an interstitial (small incorporation site) and xenon in a double Schottky defect cluster (large incorporation site). Finally, we note that IPR is very flexible and can be applied to a wide variety of potential forms and materials systems, including metals and EAM potentials. read less NOT USED (high confidence) S. Starikov et al., “Soft picosecond X-ray laser nanomodification of gold and aluminum surfaces,” Applied Physics B. 2014. link Times cited: 25 NOT USED (high confidence) T. Spura, C. John, S. Habershon, and T. Kühne, “Nuclear quantum effects in liquid water from path-integral simulations using an ab initio force-matching approach,” Molecular Physics. 2014. link Times cited: 35 Abstract: We have applied path integral simulations, in combination wi… read moreAbstract: We have applied path integral simulations, in combination with new ab initio based water potentials, to investigate nuclear quantum effects in liquid water. Because direct ab initio path integral simulations are computationally expensive, a flexible water model is parameterised by force-matching to density functional theory-based molecular dynamics simulations. Static and dynamic properties of liquid water at ambient conditions are presented and the role of nuclear quantum effects, exchange-correlation functionals and dispersion corrections are discussed in regards to reproducing the experimental properties of liquid water. read less NOT USED (high confidence) A. Giri, N. K. Das, and P. Barat, “Oscillatory Shannon entropy in the process of equilibration of nonequilibrium crystalline systems,” Chinese Physics B. 2014. link Times cited: 2 Abstract: We present a study of the equilibration process of some none… read moreAbstract: We present a study of the equilibration process of some nonequilibrium crystalline systems by means of molecular dynamics simulation technique. The nonequilibrium conditions are achieved in the systems by randomly defining velocity components of the constituent atoms. The calculated Shannon entropy from the probability distribution of the kinetic energy among the atoms at different instants during the process of equilibration shows oscillation as the system relaxes towards equilibrium. Fourier transformations of these oscillating Shannon entropies reveal the existence of Debye frequency of the concerned system. read less NOT USED (high confidence) D. González and S. Davis, “Fitting of interatomic potentials without forces: A parallel particle swarm optimization algorithm,” Comput. Phys. Commun. 2014. link Times cited: 8 NOT USED (high confidence) B. Onat and S. Durukanoğlu, “An optimized interatomic potential for Cu–Ni alloys with the embedded-atom method,” Journal of Physics: Condensed Matter. 2014. link Times cited: 86 Abstract: We have developed a semi-empirical and many-body type model … read moreAbstract: We have developed a semi-empirical and many-body type model potential using a modified charge density profile for Cu–Ni alloys based on the embedded-atom method (EAM) formalism with an improved optimization technique. The potential is determined by fitting to experimental and first-principles data for Cu, Ni and Cu–Ni binary compounds, such as lattice constants, cohesive energies, bulk modulus, elastic constants, diatomic bond lengths and bond energies. The generated potentials were tested by computing a variety of properties of pure elements and the alloy of Cu, Ni: the melting points, alloy mixing enthalpy, lattice specific heat, equilibrium lattice structures, vacancy formation and interstitial formation energies, and various diffusion barriers on the (100) and (111) surfaces of Cu and Ni. read less 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) J. Sarsam, M. Finnis, and P. Tangney, “Atomistic force field for alumina fit to density functional theory.,” The Journal of chemical physics. 2013. link Times cited: 13 Abstract: We present a force field for bulk alumina (Al2O3), which has… read moreAbstract: We present a force field for bulk alumina (Al2O3), which has been parametrized by fitting the energies, forces, and stresses of a large database of reference configurations to those calculated with density functional theory (DFT). We use a functional form that is simpler and computationally more efficient than some existing models of alumina parametrized by a similar technique. Nevertheless, we demonstrate an accuracy of our potential that is comparable to those existing models and to DFT. We present calculations of crystal structures and energies, elastic constants, phonon spectra, thermal expansion, and point defect formation energies. read less NOT USED (high confidence) M. Mechelke and M. Habeck, “Estimation of Interaction Potentials through the Configurational Temperature Formalism.,” Journal of chemical theory and computation. 2013. link Times cited: 11 Abstract: Molecular interaction potentials are difficult to measure ex… read moreAbstract: Molecular interaction potentials are difficult to measure experimentally and hard to compute from first principles, especially for large systems such as proteins. It is therefore desirable to estimate the potential energy that underlies a thermodynamic ensemble from simulated or experimentally determined configurations. This inverse problem of statistical mechanics is challenging because the various potential energy terms can exhibit subtle indirect and correlated effects on the resulting ensemble. A direct approach would try to adapt the force field parameters such that the given configurations are highly probable in the resulting ensemble. But this would require a full simulation of the system whenever a parameter changes. We introduce an extension of the configurational temperature formalism that allows us to circumvent these difficulties and efficiently estimate interaction potentials from molecular configurations. We illustrate the approach for various systems including fluids and a coarse-grained protein model. read less NOT USED (high confidence) M. Marinica et al., “Interatomic potentials for modelling radiation defects and dislocations in tungsten,” Journal of Physics: Condensed Matter. 2013. link Times cited: 258 Abstract: We have developed empirical interatomic potentials for study… read moreAbstract: We have developed empirical interatomic potentials for studying radiation defects and dislocations in tungsten. The potentials use the embedded atom method formalism and are fitted to a mixed database, containing various experimentally measured properties of tungsten and ab initio formation energies of defects, as well as ab initio interatomic forces computed for random liquid configurations. The availability of data on atomic force fields proves critical for the development of the new potentials. Several point and extended defect configurations were used to test the transferability of the potentials. The trends predicted for the Peierls barrier of the 1 2 ⟨ 111 ⟩ ?> screw dislocation are in qualitative agreement with ab initio calculations, enabling quantitative comparison of the predicted kink-pair formation energies with experimental data. read less NOT USED (high confidence) H. Hsu et al., “An investigation on nanoscale bondability between Cu-Al intermetallic compound,” 2013 8th International Microsystems, Packaging, Assembly and Circuits Technology Conference (IMPACT). 2013. link Times cited: 2 Abstract: The aim of present research is to investigate the interfacia… read moreAbstract: The aim of present research is to investigate the interfacial nanoscale bondability between copper and Aluminum intermetallic compound (IMC) for copper wire and aluminum pad. In addition, the growth mechanism of IMC layer is carefully examined. Preliminary results demonstrated that IMC cracks from the edge of bonding interface and spreads into the center area. This is the cause of open fail. The IMC between Cu and Al was initially generated in the form of CuAl2, and gradually increased the content of Cu and turned into CuAl when the working temperature was increased. The final stage of IMC growth is Cu9Al4 and the aluminum pad will be vanished as the result of Cu diffusivity. Bondability on nanoscale IMC of CuAl2, CuAl and Cu9Al4 are also cautiously investigated by using a special self-designed pull test fixture. Nanoscale atomic modulus and rupture strength are validated by using molecular dynamics (MD) simulations. Atomic-level tensile stress and tensile strain are predicted to examine the bonding strength of two IMCs along the bonding interface. Temperature and tensile speed are two major factors on determining the bonding strength. Material in high temperature has greater kinetic energy and has better formability. Higher pulling speed in tensile test would results in material easier fracture. Interfacial fracture is different in different tensile speed as well as the working temperature. A series of experimental works and MD simulations are conducted in this research. read less NOT USED (high confidence) A. V. Fedorov and A. V. Shul’gin, “Complex modeling of melting of an aluminum nanoparticle,” Combustion, Explosion, and Shock Waves. 2013. link Times cited: 14 NOT USED (high confidence) R. Pandey, Z. Kuang, and B. Farmer, “A Hierarchical Coarse-Grained (All-Atom-to-All-Residue) Computer Simulation Approach: Self-Assembly of Peptides,” PLoS ONE. 2013. link Times cited: 10 Abstract: A hierarchical computational approach (all-atom residue to a… read moreAbstract: A hierarchical computational approach (all-atom residue to all-residue peptide) is introduced to study self-organizing structures of peptides as a function of temperature. A simulated residue-residue interaction involving all-atom description, analogous to knowledge-based analysis (with different input), is used as an input to a phenomenological coarse-grained interaction for large scales computer simulations. A set of short peptides P1 (1H 2S 3S 4Y 5W 6Y 7A 8F 9N 10N 11K 12T) is considered as an example to illustrate the utility. We find that peptides assemble rather fast into globular aggregates at low temperatures and disperse as random-coil at high temperatures. The specificity of the mass distribution of the self-assembly depends on the temperature and spatial lengths which are identified from the scaling of the structure factor. Analysis of energy and mobility profiles, gyration radius of peptide, and radial distribution function of the assembly provide insight into the multi-scale (intra- and inter-chain) characteristics. Thermal response of the global assembly with the simulated residue-residue interaction is consistent with that of the knowledge-based analysis despite expected quantitative differences. read less NOT USED (high confidence) P. Zhang and D. Trinkle, “Database optimization for empirical interatomic potential models,” Modelling and Simulation in Materials Science and Engineering. 2013. link Times cited: 8 Abstract: Weighted least squares fitting to a database of quantum mech… read moreAbstract: Weighted least squares fitting to a database of quantum mechanical calculations can determine the optimal parameters of empirical potential models. While algorithms exist to provide optimal potential parameters for a given fitting database of structures with corresponding energy-related predictions and to estimate prediction errors using Bayesian sampling, defining an optimal fitting database based on potential predictions remains elusive. A testing set of structures and energy-related predictions provides an empirical measure of potential transferability. Here, we propose an objective function for fitting databases based on testing set errors. The objective function allows the optimization of the weights in a fitting database, the assessment of the adding or removing of structures in the fitting database, or the comparison of two different fitting databases. To showcase this technique, we consider an example Lennard-Jones potential for Ti, where modeling multiple complicated crystal structures is difficult for a radial pair potential. The algorithm finds different optimal fitting databases, depending on the objective function of potential prediction error for a testing set. read less NOT USED (high confidence) S. Patnaik and E. K. Iskrenova, “Transport Properties of Water and Sodium Dodecyl Sulfate (Postprint).” 2013. link Times cited: 3 Abstract: : In this work, results from atomistic molecular dynamics st… read moreAbstract: : In this work, results from atomistic molecular dynamics studies investigating the effect of surfactant concentration on the transport properties of bulk surfactant aqueous solutions, focusing on the anionic surfactant sodium dodecyl sulfate (SDS), are reported. The surfactant self-diffusion and the thermal conductivity of bulk aqueous SDS solutions were computed at a range of concentrations at room and boiling temperatures. Additionally, MP2f, one of the new generation water potentials is assessed for its suitability in reproducing the transport and thermal properties of bulk water. The thermal conductivity of MP2f water model was found to be: 0.64 W/(m_K) at 298K and 0.66 W/(m_K) at 373 K, in much better agreement with the experimental values compared to both the rigid and the flexible TIP3P water model. read less NOT USED (high confidence) L. R. Hill, V. Randlè, and O. Engler, “Five parameter distribution of planes in AA 5182 aluminium alloys with relevance to intergranular corrosion resistance,” Materials Science and Technology. 2013. link Times cited: 2 Abstract: Alloys of AA 5182 are commonly used in the automotive indust… read moreAbstract: Alloys of AA 5182 are commonly used in the automotive industry to provide weight reductions in vehicle chassis. The strength of such alloys is based on the Mg content, with Mg causing the precipitation of a β-Al8Mg5 phase along the length of the grain boundaries in the microstructure. These precipitates are vulnerable to intergranular corrosion (IGC) in acidic environments. For this reason, the proportions of Mg in the microstructure must be limited, with >3 wt-%Mg causing intergranular attack. The alloys used in this study had an Mg content of 4·43%, so were vulnerable to IGC. Standard nitric acid mass loss tests were applied to determine the level of corrosion resistance in two samples subjected to various treatments. Using ‘five parameter’ analysis, the importance of the grain boundary plane and thermomechanical history to IGC resistance was determined. ‘Special’ planes were identified in the microstructure and their impact on IGC resistance was assessed. From such analysis, it was found that a high deformation level of 50% together with a simulated batch annealing heat treatment yielded the highest proportions of ‘special’ boundaries within the microstructure. ‘Special’ boundaries in this study were identified to be low angle boundaries, <111> twist boundaries and <110> tilt boundaries, which are associated with a reduced energy compared to random high angle boundaries. As precipitation generally occurs along high energy boundaries, ‘special’ boundaries reduce precipitate formation, thus reducing IGC intensity. Future implications include the introduction of a higher proportion of ‘special’ boundaries into the microstructure, allowing for an increase in Mg content in these alloys. read less NOT USED (high confidence) Yuan-Yuan 圆圆 Ju 巨, Q. Zhang 张, Zi-Zheng 自正 Gong 龚, and Guang-Fu 广富 Ji 姬, “Molecular dynamics simulation of self-diffusion coefficients for liquid metals,” Chinese Physics B. 2013. link Times cited: 25 Abstract: The temperature-dependent coefficients of self-diffusion for… read moreAbstract: The temperature-dependent coefficients of self-diffusion for liquid metals are simulated by molecular dynamics methods based on the embedded-atom-method (EAM) potential function. The simulated results show that a good inverse linear relation exists between the natural logarithm of self-diffusion coefficients and temperature, though the results in the literature vary somewhat, due to the employment of different potential functions. The estimated activation energy of liquid metals obtained by fitting the Arrhenius formula is close to the experimental data. The temperature-dependent shear-viscosities obtained from the Stokes—Einstein relation in conjunction with the results of molecular dynamics simulation are generally consistent with other values in the literature. read less NOT USED (high confidence) M. Fukuda, H. Zhang, T. Ishiguro, K. Fukuzawa, and S. Itoh, “Structure-based coarse-graining for inhomogeneous liquid polymer systems.,” The Journal of chemical physics. 2013. link Times cited: 14 Abstract: The iterative Boltzmann inversion (IBI) method is used to de… read moreAbstract: The iterative Boltzmann inversion (IBI) method is used to derive interaction potentials for coarse-grained (CG) systems by matching structural properties of a reference atomistic system. However, because it depends on such thermodynamic conditions as density and pressure of the reference system, the derived CG nonbonded potential is probably not applicable to inhomogeneous systems containing different density regimes. In this paper, we propose a structure-based coarse-graining scheme to devise CG nonbonded potentials that are applicable to different density bulk systems and inhomogeneous systems with interfaces. Similar to the IBI, the radial distribution function (RDF) of a reference atomistic bulk system is used for iteratively refining the CG nonbonded potential. In contrast to the IBI, however, our scheme employs an appropriately estimated initial guess and a small amount of refinement to suppress transfer of the many-body interaction effects included in the reference RDF into the CG nonbonded potential. To demonstrate the application of our approach to inhomogeneous systems, we perform coarse-graining for a liquid perfluoropolyether (PFPE) film coated on a carbon surface. The constructed CG PFPE model favorably reproduces structural and density distribution functions, not only for bulk systems, but also at the liquid-vacuum and liquid-solid interfaces, demonstrating that our CG scheme offers an easy and practical way to accurately determine nonbonded potentials for inhomogeneous systems. read less NOT USED (high confidence) E. Brini, E. Algaer, P. Ganguly, C. Li, F. Rodríguez-Ropero, and N. V. D. Vegt, “Systematic coarse-graining methods for soft matter simulations - a review,” Soft Matter. 2013. link Times cited: 270 Abstract: Multiscale modelling of soft matter is an emerging field tha… read moreAbstract: Multiscale modelling of soft matter is an emerging field that has made rapid progress in the past decade. Several methods for systematic coarse-graining of molecular liquids and soft matter systems have been proposed in recent years. Herein, we review these methods and discuss a selected number of applications as well as limitations of the models and remaining challenges in developing representative and transferable pair potentials. read less NOT USED (high confidence) E. Spiga, D. Alemani, M. Degiacomi, M. Cascella, and M. D. Peraro, “Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins.,” Journal of chemical theory and computation. 2013. link Times cited: 29 Abstract: We present a new generation of coarse-grained (CG) potential… read moreAbstract: We present a new generation of coarse-grained (CG) potentials that account for a simplified electrostatic description of soluble proteins. The treatment of permanent electrostatic dipoles of the backbone and polar side-chains allows to simulate proteins, preserving an excellent structural and dynamic agreement with respective reference structures and all-atom molecular dynamics simulations. Moreover, multiprotein complexes can be well described maintaining their molecular interfaces thanks to the ability of this scheme to better describe the actual electrostatics at a CG level of resolution. An efficient and robust heuristic algorithm based on particle swarm optimization is used for the derivation of CG parameters via a force-matching procedure. The ability of this protocol to deal with high dimensional search spaces suggests that the extension of this optimization procedure to larger data sets may lead to the generation of a fully transferable CG force field. At the present stage, these electrostatic-consistent CG potentials are easily and efficiently parametrized, show a good degree of transferability, and can be used to simulate soluble proteins or, more interestingly, large macromolecular assemblies for which long all-atom simulations may not be easily affordable. read less NOT USED (high confidence) M. Morales, R. Clay, C. Pierleoni, and D. Ceperley, “First Principles Methods: A Perspective from Quantum Monte Carlo,” Entropy. 2013. link Times cited: 26 Abstract: Quantum Monte Carlo methods are among the most accurate algo… read moreAbstract: Quantum Monte Carlo methods are among the most accurate algorithms for predicting properties of general quantum systems. We briefly introduce ground state, path integral at finite temperature and coupled electron-ion Monte Carlo methods, their merits and limitations. We then discuss recent calculations using these methods for dense liquid hydrogen as it undergoes a molecular/atomic (metal/insulator) transition. We then discuss a procedure that can be used to assess electronic density functionals, which in turn can be used on a larger scale for first principles calculations and apply this technique to dense hydrogen and liquid water. read less NOT USED (high confidence) N. Tsakiris and L. J. Lewis, “Phase diagram of aluminum from EAM potentials,” The European Physical Journal B. 2013. link Times cited: 2 NOT USED (high confidence) R. Bradley and R. Radhakrishnan, “Coarse-Grained Models for Protein-Cell Membrane Interactions,” Polymers. 2013. link Times cited: 55 Abstract: The physiological properties of biological soft matter are t… read moreAbstract: The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across time and length scales in a multiscale model explains how atomistic information propagates to larger scales. This paper reviews continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes. read less NOT USED (high confidence) A. V. Fedorov and A. Shulgin, “Complex modeling of melting of an aluminum nanoparticle,” Combustion, Explosion, and Shock Waves. 2013. link Times cited: 1 NOT USED (high confidence) Y. Li, B. C. Abberton, M. Kröger, and W. K. Liu, “Challenges in Multiscale Modeling of Polymer Dynamics,” Polymers. 2013. link Times cited: 170 Abstract: The mechanical and physical properties of polymeric material… read moreAbstract: The mechanical and physical properties of polymeric materials originate from the interplay of phenomena at different spatial and temporal scales. As such, it is necessary to adopt multiscale techniques when modeling polymeric materials in order to account for all important mechanisms. Over the past two decades, a number of different multiscale computational techniques have been developed that can be divided into three categories: (i) coarse-graining methods for generic polymers; (ii) systematic coarse-graining methods and (iii) multiple-scale-bridging methods. In this work, we discuss and compare eleven different multiscale computational techniques falling under these categories and assess them critically according to their ability to provide a rigorous link between polymer chemistry and rheological material properties. For each technique, the fundamental ideas and equations are introduced, and the most important results or predictions are shown and discussed. On the one hand, this review provides a comprehensive tutorial on multiscale computational techniques, which will be of interest to readers newly entering this field; on the other, it presents a critical discussion of the future opportunities and key challenges in the multiscale modeling of polymeric materials and how these methods can help us to optimize and design new polymeric materials. read less NOT USED (high confidence) S. Markutsya, A. Devarajan, J. Y. Baluyut, T. Windus, M. Gordon, and M. H. Lamm, “Evaluation of coarse-grained mapping schemes for polysaccharide chains in cellulose.,” The Journal of chemical physics. 2013. link Times cited: 26 Abstract: A fundamental understanding of the intermolecular forces tha… read moreAbstract: A fundamental understanding of the intermolecular forces that bind polysaccharide chains together in cellulose is crucial for designing efficient methods to overcome the recalcitrance of lignocellulosic biomass to hydrolysis. Because the characteristic time and length scales for the degradation of cellulose by enzymatic hydrolysis or chemical pretreatment span orders of magnitude, it is important to closely integrate the molecular models used at each scale so that, ultimately, one may switch seamlessly between quantum, atomistic, and coarse-grained descriptions of the system. As a step towards that goal, four multiscale coarse-grained models for polysaccharide chains in a cellulose-Iα microfiber are considered. Using the force matching method, effective coarse-grained forces are derived from all-atom trajectories. Performance of the coarse-grained models is evaluated by comparing the intrachain radial distribution functions with those obtained using the all-atom reference data. The all-atom simulation reveals a double peak in the radial distribution function for sites within each glucose residue that arises from the distinct conformations sampled by the primary alcohol group in the glucose residues. The three-site and four-site coarse-grained models have sufficient degrees of freedom to predict this double peak while the one-site and two-site models do not. This is the first time that coarse-grained models have been shown to reproduce such subtle, yet important, molecular features in a polysaccharide chain. The relative orientations between glucose residues along the polysaccharide chain are evaluated and it is found that the four-site coarse-grained model is best at reproducing the glucose-glucose conformations observed in the all-atom simulation. The success of the four-site coarse-grained model underscores the importance of decoupling the pyranose ring from the oxygen atom in the glycosidic bond when developing all-atom to coarse-grained mapping schemes for polysaccharides. read less NOT USED (high confidence) M. Bhattacharya, A. Dutta, and P. Barat, “Quasistatic stick-slip of a dislocation core and the Frenkel-Kontorova chain,” Physical Review B. 2013. link Times cited: 1 Abstract: Department of Metallurgical and Materials Engineering,Jadavp… read moreAbstract: Department of Metallurgical and Materials Engineering,Jadavpur University, Kolkata 700032, India(Dated: April 23, 2013)By means of atomistic simulations, we demonstrate that a dislocation core exhibits intermittentquasistatic restructuring during incremental shear within the same Peierls valley. This can be re-garded as a stick-slip transition, which is also reproduced for a one-dimensional Frenkel-Kontorovachain under rigid boundary conditions. This occurs due to a discontinuous jump in an order pa-rameter of the system, which signi es the extent of region forbidden for the presence of particles inthe chain. The stick-slip phenomenon observed in the dislocation core is also shown to be reectedafter dimensionality reduction of the multidimensional atomic coordinates, which provides a basisfor comparison with the simple one-dimensional chain. read less NOT USED (high confidence) Z. Pei et al., “Ab initio and atomistic study of generalized stacking fault energies in Mg and Mg–Y alloys,” New Journal of Physics. 2013. link Times cited: 107 Abstract: Magnesium–yttrium alloys show significantly improved room te… read moreAbstract: Magnesium–yttrium alloys show significantly improved room temperature ductility when compared with pure Mg. We study this interesting phenomenon theoretically at the atomic scale employing quantum-mechanical (so-called ab initio) and atomistic modeling methods. Specifically, we have calculated generalized stacking fault energies for five slip systems in both elemental magnesium (Mg) and Mg–Y alloys using (i) density functional theory and (ii) a set of embedded-atom-method (EAM) potentials. These calculations predict that the addition of yttrium results in a reduction in the unstable stacking fault energy of basal slip systems. Specifically in the case of an I2 stacking fault, the predicted reduction of the stacking fault energy due to Y atoms was verified by experimental measurements. We find a similar reduction for the stable stacking fault energy of the non-basal slip system. On the other hand, other energies along this particular γ-surface profile increase with the addition of Y. In parallel to our quantum-mechanical calculations, we have also developed a new EAM Mg–Y potential and thoroughly tested its performance. The comparison of quantum-mechanical and atomistic results indicates that the new potential is suitable for future large-scale atomistic simulations. read less NOT USED (high confidence) D. Smirnova et al., “A ternary EAM interatomic potential for U–Mo alloys with xenon,” Modelling and Simulation in Materials Science and Engineering. 2013. link Times cited: 71 Abstract: A new interatomic potential for a uranium–molybdenum system … read moreAbstract: A new interatomic potential for a uranium–molybdenum system with xenon is developed in the framework of an embedded atom model using a force-matching technique and a dataset of ab initio atomic forces. The verification of the potential proves that it is suitable for the investigation of various compounds existing in the system as well as for simulation of pure elements: U, Mo and Xe. Computed lattice constants, thermal expansion coefficients, elastic properties and melting temperatures of U, Mo and Xe are consistent with the experimentally measured values. The energies of the point defect formation in pure U and Mo are proved to be comparable to the density-functional theory calculations. We compare this new U–Mo–Xe potential with the previously developed U and Mo–Xe potentials. A comparative study between the different potential functions is provided. The key purpose of the new model is to study the atomistic processes of defect evolution taking place in the U–Mo nuclear fuel. Here we use the potential to simulate bcc alloys containing 10 wt% of intermetallic Mo and U2Mo. read less NOT USED (high confidence) M. Todorović, D. Bowler, M. Gillan, and T. Miyazaki, “Density-functional theory study of gramicidin A ion channel geometry and electronic properties,” Journal of The Royal Society Interface. 2013. link Times cited: 9 Abstract: Understanding the mechanisms underlying ion channel function… read moreAbstract: Understanding the mechanisms underlying ion channel function from the atomic-scale requires accurate ab initio modelling as well as careful experiments. Here, we present a density functional theory (DFT) study of the ion channel gramicidin A (gA), whose inner pore conducts only monovalent cations and whose conductance has been shown to depend on the side chains of the amino acids in the channel. We investigate the ground state geometry and electronic properties of the channel in vacuum, focusing on their dependence on the side chains of the amino acids. We find that the side chains affect the ground state geometry, while the electrostatic potential of the pore is independent of the side chains. This study is also in preparation for a full, linear scaling DFT study of gA in a lipid bilayer with surrounding water. We demonstrate that linear scaling DFT methods can accurately model the system with reasonable computational cost. Linear scaling DFT allows ab initio calculations with 10 000–100 000 atoms and beyond, and will be an important new tool for biomolecular simulations. read less NOT USED (high confidence) J. Zhong, R. Shakiba, and J. B. Adams, “Molecular dynamics simulation of severe adhesive wear on a rough aluminum substrate,” Journal of Physics D: Applied Physics. 2013. link Times cited: 41 Abstract: Severe adhesive wear on a rough aluminum (Al) substrate is s… read moreAbstract: Severe adhesive wear on a rough aluminum (Al) substrate is simulated by a hard Lennard-Jones asperity impacting an Al-asperity at high speeds using molecular dynamics (MD). Multiple simulations investigate the effects of variations in the inter-asperity bonding, the geometric overlap between two asperities, the relative impact velocity and the starting temperature. The effect of these experimental variables on degree of adhesive wear and the temperature profiles are discussed, and a design of experiments method is used to help interpret the results. The results indicate that increasing the inter-asperity bonding, the geometric overlap and the starting temperature of two asperities will substantially increase the wear rate, while raising the impact velocity slightly decreases the wear rate. It is observed that the deformation mechanism involves local melting and the formation of a liquid like layer in the contact area between two asperities, and the amorphous deformation of the Al-asperity. read less NOT USED (high confidence) G. Norman, S. Starikov, V. Stegailov, I. Saitov, and P. Zhilyaev, “Atomistic Modeling of Warm Dense Matter in the Two‐Temperature State,” Contributions to Plasma Physics. 2013. link Times cited: 45 Abstract: Warm dense matter is the state between the heated condensed … read moreAbstract: Warm dense matter is the state between the heated condensed matter and plasma. The importance of the development of warm dense matter theoretical description is determined by the fact that such conditions may arise in the variety of different scientific and industrial applications. For instance, warm dense matter is formed: in the matter impacted by femto‐ and picoseconds laser pulses; in nuclear materials at the formation of radiation track, etc. In these phenomena, the initial state of the system is a two‐temperature state and the electron temperature may be several orders higher than the ion one. In this work, the attempt of development of the united atomistic model of a warm dense matter is carried out. The special consideration is given to the twotemperature effects and the influence of the electron pressure on the behavior of ions. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) read less NOT USED (high confidence) M. A. Bhatia, K. Solanki, A. Moitra, and M. Tschopp, “Investigating Damage Evolution at the Nanoscale: Molecular Dynamics Simulations of Nanovoid Growth in Single-Crystal Aluminum,” Metallurgical and Materials Transactions A. 2013. link Times cited: 36 NOT USED (high confidence) A. Ghavami, E. van der Giessen, and P. Onck, “Coarse-Grained Potentials for Local Interactions in Unfolded Proteins.,” Journal of chemical theory and computation. 2013. link Times cited: 64 Abstract: Recent studies have revealed the key role of natively unfold… read moreAbstract: Recent studies have revealed the key role of natively unfolded proteins in many important biological processes. In order to study the conformational changes of these proteins, a one-bead-per-amino-acid coarse grained (CG) model is developed, and a method is proposed to extract the potential functions for the local interactions between CG beads. Experimentally obtained Ramachandran data for the coil regions of proteins are converted into distributions of pseudo-bond and pseudo-dihedral angles between neighboring alpha-carbons in the polypeptide chain. These are then used to derive bending and torsion potentials, which are residue and sequence specific. The validity of the developed model is testified by studying the radius of gyration as well as the hydrodynamic properties of chemically denatured proteins. read less NOT USED (high confidence) V. Pisarev, “Determination of free energy of the crystal-melt interface,” High Temperature. 2012. link Times cited: 4 NOT USED (high confidence) H. Hsu, J. Chien, C.-yi Wang, C.-che Liu, S. Fu, and M. Bair, “An investigation on secondary EFO copper wire - from a nanoscale perspective view,” 2012 14th International Conference on Electronic Materials and Packaging (EMAP). 2012. link Times cited: 0 Abstract: The aim of present research is to investigate the characteri… read moreAbstract: The aim of present research is to investigate the characteristic of secondary EFO (electronic flame-off) Pd-coated copper wire. The term of “secondary” is twice EFO performed by a bonding apparatus, K&S 1488 wire bonder. As a result, secondary EFO Cu wire demonstrates a longer heat affected zone (HAZ) and a softer free air ball (FAB) which results in a decrease in the squeeze of aluminum bond pad. It is also observed that the surface roughness is a major factor to reduce the aluminum pad squeezing. The interfacial coefficient of frictional force at a nanoscale surface level was measured by Atomic Force Microscopy (AFM). The coefficient of frictional force needs to measure both the normal force (corresponds to loading force-distance curve) and a lateral force (corresponds to friction force) on a sliding contact. In addition, mechanical property of FAB surface on Pd-coated copper wire was determined by nanoindenter. A well-defined contact area is measured to study the frictional force and friction stress. Thermal aging effect has been conducted to reduce the strength of Cu wire and increase the reliability. The study of roughness parameters corresponds to evaluate the friction and the interfacial strengths. Local variation in nano tribology is also measured. Nanotribology is crucial in describing manipulations of molecules behavior. The measured surface topography (3D profiles) are then applied to determinate the potential energy in molecular dynamic (MD) method to study the atomic scale frictional interactions. A series of experimental works and MD predictions are conducted to investigate the interfacial behavior along the Cu FAB and Al Pad. read less NOT USED (high confidence) C.-C. Fu, P. M. Kulkarni, M. Shell, and L. Leal, “A test of systematic coarse-graining of molecular dynamics simulations: thermodynamic properties.,” The Journal of chemical physics. 2012. link Times cited: 53 Abstract: Coarse-graining (CG) techniques have recently attracted grea… read moreAbstract: Coarse-graining (CG) techniques have recently attracted great interest for providing descriptions at a mesoscopic level of resolution that preserve fluid thermodynamic and transport behaviors with a reduced number of degrees of freedom and hence less computational effort. One fundamental question arises: how well and to what extent can a "bottom-up" developed mesoscale model recover the physical properties of a molecular scale system? To answer this question, we explore systematically the properties of a CG model that is developed to represent an intermediate mesoscale model between the atomistic and continuum scales. This CG model aims to reduce the computational cost relative to a full atomistic simulation, and we assess to what extent it is possible to preserve both the thermodynamic and transport properties of an underlying reference all-atom Lennard-Jones (LJ) system. In this paper, only the thermodynamic properties are considered in detail. The transport properties will be examined in subsequent work. To coarse-grain, we first use the iterative Boltzmann inversion (IBI) to determine a CG potential for a (1-φ)N mesoscale particle system, where φ is the degree of coarse-graining, so as to reproduce the radial distribution function (RDF) of an N atomic particle system. Even though the uniqueness theorem guarantees a one to one relationship between the RDF and an effective pairwise potential, we find that RDFs are insensitive to the long-range part of the IBI-determined potentials, which provides some significant flexibility in further matching other properties. We then propose a reformulation of IBI as a robust minimization procedure that enables simultaneous matching of the RDF and the fluid pressure. We find that this new method mainly changes the attractive tail region of the CG potentials, and it improves the isothermal compressibility relative to pure IBI. We also find that there are optimal interaction cutoff lengths for the CG system, as a function of φ, that are required to attain an adequate potential while maintaining computational speedup. To demonstrate the universality of the method, we test a range of state points for the LJ liquid as well as several LJ chain fluids. read less NOT USED (high confidence) E. Brini and N. V. D. Vegt, “Chemically transferable coarse-grained potentials from conditional reversible work calculations.,” The Journal of chemical physics. 2012. link Times cited: 61 Abstract: The representability and transferability of effective pair p… read moreAbstract: The representability and transferability of effective pair potentials used in multiscale simulations of soft matter systems is ill understood. In this paper, we study liquid state systems composed of n-alkanes, the coarse-grained (CG) potential of which may be assumed pairwise additive and has been obtained using the conditional reversible work (CRW) method. The CRW method is a free-energy-based coarse-graining procedure, which, by means of performing the coarse graining at pair level, rigorously provides a pair potential that describes the interaction free energy between two mapped atom groups (beads) embedded in their respective chemical environments. The pairwise nature of the interactions combined with their dependence on the chemically bonded environment makes CRW potentials ideally suited in studies of chemical transferability. We report CRW potentials for hexane using a mapping scheme that merges two heavy atoms in one CG bead. It is shown that the model is chemically and thermodynamically transferable to alkanes of different chain lengths in the liquid phase at temperatures between the melting and the boiling point under atmospheric (1 atm) pressure conditions. It is further shown that CRW-CG potentials may be readily obtained from a single simulation of the liquid state using the free energy perturbation method, thereby providing a fast and versatile molecular coarse graining method for aliphatic molecules. read less NOT USED (high confidence) C. Zhang, “Temperature measurement from perturbations,” Physical Review E. 2012. link Times cited: 1 Abstract: The notion of configuration temperature is extended to disco… read moreAbstract: The notion of configuration temperature is extended to discontinuous systems by identifying the temperature as the nontrivial root of several integral equations regarding the distribution of the energy change upon configuration perturbations. The relations are generalized to pressure and a distribution mean force. read less NOT USED (high confidence) S. Izvekov and B. Rice, “Free-energy based pair-additive potentials for bulk Ni-Al systems: application to study Ni-Al reactive alloying.,” The Journal of chemical physics. 2012. link Times cited: 11 Abstract: We present new numerical pair-additive Al, Ni, and Al-Ni pot… read moreAbstract: We present new numerical pair-additive Al, Ni, and Al-Ni potentials by force-matching (FM) ionic force and virial data from single (bulk liquid) phase ab initio molecular dynamics (MD) simulations using the Born-Oppenheimer method. The potentials are represented by piece-wise functions (splines) and, therefore, are not constrained to a particular choice of analytical functional form. The FM method with virial constraint naturally yields a potential which maps out the ionic free-energy surface of the reference ensemble. To further improve the free energetics of the FM ensemble, the FM procedure is modified to bias the potentials to reproduce the experimental melting temperatures of the reference (FCC-Al, FCC-Ni, B2-NiAl) phases, the only macroscopic data included in the fitting set. The performance of the resultant potentials in simulating bulk metallic phases is then evaluated. The new model is applied to perform MD simulations of self-propagating exothermic reaction in Ni-Al bilayers at P = 0-5 GPa initiated at T = 1300 K. Consistent with experimental observations, the new model describes realistically a sequence of peritectic phase transformations throughout the reaction and at a realistic rate. The reaction proceeds through interlayer diffusion of Al and Ni atoms at the interface with formation of B2-NiAl in the Al melt. Such material responses have, in the past, been proven to be difficult to observe with then-existing potentials. read less NOT USED (high confidence) I. Fukuda and H. Nakamura, “Non-Ewald methods: theory and applications to molecular systems,” Biophysical Reviews. 2012. link Times cited: 51 NOT USED (high confidence) K. L. Baker and D. H. Warner, “Extended timescale atomistic modeling of crack tip behavior in aluminum,” Modelling and Simulation in Materials Science and Engineering. 2012. link Times cited: 17 Abstract: Traditional molecular dynamics (MD) simulations are limited … read moreAbstract: Traditional molecular dynamics (MD) simulations are limited not only by their spatial domain, but also by the time domain that they can examine. Considering that many of the events associated with plasticity are thermally activated, and thus rare at atomic timescales, the limited time domain of traditional MD simulations can present a significant challenge when trying to realistically model the mechanical behavior of materials. A wide variety of approaches have been developed to address the timescale challenge, each having their own strengths and weaknesses dependent upon the specific application. Here, we have simultaneously applied three distinct approaches to model crack tip behavior in aluminum at timescales well beyond those accessible to traditional MD simulation. Specifically, we combine concurrent multiscale modeling (to reduce the degrees of freedom in the system), parallel replica dynamics (to parallelize the simulations in time) and hyperdynamics (to accelerate the exploration of phase space). Overall, the simulations (1) provide new insight into atomic-scale crack tip behavior at more typical timescales and (2) illuminate the potential of common extended timescale techniques to enable atomic-scale modeling of fracture processes at typical experimental timescales. read less NOT USED (high confidence) R. Pandey, Z. Kuang, B. Farmer, S. S. Kim, and R. Naik, “Stability of peptide (P1 and P2) binding to a graphene sheet via an all-atom to all-residue coarse-grained approach,” Soft Matter. 2012. link Times cited: 50 Abstract: Peptide binding to a graphene sheet is studied by a coarse-g… read moreAbstract: Peptide binding to a graphene sheet is studied by a coarse-grained approach. All-atom molecular dynamics (MD) is used to assess the adsorption energy (e.g. binding) of each amino acid with graphene. The relative adsorption energy of each residue is normalized to describe its coarse-grained interactions with graphene which is used as an input to a phenomenological interaction in an all-residue coarse-grained (ARCG) representation of the peptide chain. Large scale Monte Carlo (MC) simulations are performed to study the stability of peptides (P1: 1H–2S–3S–4Y–5W–6Y–7A–8F–9N–10N–11K–12T and P2: 1E–2P–3L–4Q–5L–6K–7M) binding to a graphene sheet as a function of temperature. A number of local and global physical quantities are analyzed including mobility and substrate-in-contact profiles of each residue, density profiles, root mean square displacement of the center of mass of each peptide and its radius of gyration. We find that P1 has a higher probability of binding to a graphene sheet than P2 supported by both local and global physical quantities. All residues of P1 can bind to the graphene sheet at low temperatures; however, three residues 4Y–5W–6Y seem to anchor it most strongly at higher temperatures, which is consistent with an all-atom MD simulation. read less NOT USED (high confidence) M. Jochum, D. Andrienko, K. Kremer, and C. Peter, “Structure-based coarse-graining in liquid slabs.,” The Journal of chemical physics. 2012. link Times cited: 38 Abstract: Structure-based coarse-graining relies on matching the pair … read moreAbstract: Structure-based coarse-graining relies on matching the pair correlation functions of a reference (atomistic) and a coarse-grained system. As such, it is designed for systems with uniform density distributions. Here, we demonstrate how it can be generalized for inhomogeneous systems by coarse-graining slabs of liquid water and methanol in vacuum, as well as a single benzene molecule at the water-vacuum interface. Our conclusion is that coarse-graining performed in inhomogeneous systems improves thermodynamic properties and the structure of interfaces without significant alterations to the local structure of the bulk liquid. read less NOT USED (high confidence) I. Fukuda, N. Kamiya, Y. Yonezawa, and H. Nakamura, “Simple and accurate scheme to compute electrostatic interaction: zero-dipole summation technique for molecular system and application to bulk water.,” The Journal of chemical physics. 2012. link Times cited: 37 Abstract: The zero-dipole summation method was extended to general mol… read moreAbstract: The zero-dipole summation method was extended to general molecular systems, and then applied to molecular dynamics simulations of an isotropic water system. In our previous paper [I. Fukuda, Y. Yonezawa, and H. Nakamura, J. Chem. Phys. 134, 164107 (2011)], for evaluating the electrostatic energy of a classical particle system, we proposed the zero-dipole summation method, which conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple cutoff truncation. Here, we consider the application of this scheme to molecular systems, as well as some fundamental aspects of general cutoff truncation protocols. Introducing an idea to harmonize the bonding interactions and the electrostatic interactions in the scheme, we develop a specific algorithm. As in the previous study, the resulting energy formula is represented by a simple pairwise function sum, enabling facile applications to high-performance computation. The accuracy of the electrostatic energies calculated by the zero-dipole summation method with the atom-based cutoff was numerically investigated, by comparison with those generated by the Ewald method. We obtained an electrostatic energy error of less than 0.01% at a cutoff length longer than 13 Å for a TIP3P isotropic water system, and the errors were quite small, as compared to those obtained by conventional truncation methods. The static property and the stability in an MD simulation were also satisfactory. In addition, the dielectric constants and the distance-dependent Kirkwood factors were measured, and their coincidences with those calculated by the particle mesh Ewald method were confirmed, although such coincidences are not easily attained by truncation methods. We found that the zero damping-factor gave the best results in a practical cutoff distance region. In fact, in contrast to the zero-charge scheme, the damping effect was insensitive in the zero-charge and zero-dipole scheme, in the molecular system we treated. We discussed the origin of this difference between the two schemes and the dependence of this fact on the physical system. The use of the zero damping-factor will enhance the efficiency of practical computations, since the complementary error function is not employed. In addition, utilizing the zero damping-factor provides freedom from the parameter choice, which is not trivial in the zero-charge scheme, and eliminates the error function term, which corresponds to the time-consuming Fourier part under the periodic boundary conditions. read less NOT USED (high confidence) E. Brini, C. Herbers, G. Deichmann, and N. V. D. van der Vegt, “Thermodynamic transferability of coarse-grained potentials for polymer-additive systems.,” Physical chemistry chemical physics : PCCP. 2012. link Times cited: 28 Abstract: In this work we study the transferability of systematically … read moreAbstract: In this work we study the transferability of systematically coarse-grained (CG) potentials for polymer-additive systems. The CG nonbonded potentials between the polymer (atactic polystyrene) and three different additives (ethylbenzene, methane and neopentane) are derived using the Conditional Reversible Work (CRW) method, recently proposed by us [Brini et al., Phys. Chem. Chem. Phys., 2011, 13, 10468-10474]. A CRW-based effective pair potential corresponds to the interaction free energy between the two atom groups of an atomistic parent model that represent the coarse-grained interaction sites. Since the CRW coarse-graining procedure does not involve any form of parameterisation, thermodynamic and structural properties of the condensed phase are predictions of the model. We show in this work that CRW-based CG models of polymer-additive systems are capable of predicting the correct structural correlations in the mixture. Furthermore, the excess chemical potentials of the additives obtained with the CRW-based CG models and the united-atom parent models are in satisfactory agreement and the CRW-based CG models show a good temperature transferability. The temperature transferability of the model is discussed by analysing the entropic and enthalpic contributions to the excess chemical potentials. We find that CRW-based CG models provide good predictions of the excess entropies, while discrepancies are observed in the excess enthalpies. Overall, we show that the CRW CG potentials are suitable to model structural and thermodynamic properties of polymer-penetrant systems. read less NOT USED (high confidence) H. Sheng, E. Ma, and M. Kramer, “Relating Dynamic Properties to Atomic Structure in Metallic Glasses,” JOM. 2012. link Times cited: 100 NOT USED (high confidence) E. Pinnick, S. Erramilli, and F. Wang, “Predicting the melting temperature of ice-Ih with only electronic structure information as input.,” The Journal of chemical physics. 2012. link Times cited: 25 Abstract: The melting temperature of ice-Ih was calculated with only e… read moreAbstract: The melting temperature of ice-Ih was calculated with only electronic structure information as input by creating a problem-specific force field. The force field, Water model by AFM for Ice and Liquid (WAIL), was developed with the adaptive force matching (AFM) method by fitting to post-Hartree-Fock quality forces obtained in quantum mechanics∕molecular mechanics calculations. WAIL predicts the ice-Ih melting temperature to be 270 K. The model also predicts the densities of ice and water, the temperature of maximum density of water, the heat of vaporizations, and the radial distribution functions for both ice and water in good agreement with experimental measurements. The non-dissociative WAIL model is very similar to a flexible version of the popular TIP4P potential and has comparable computational cost. By customizing to problem-specific configurations with the AFM approach, the resulting model is remarkably more accurate than any variants of TIP4P for simulating ice-Ih and water in the temperature range from 253 K and 293 K under ambient pressure. read less NOT USED (high confidence) G. Norman, S. Starikov, and V. Stegailov, “Atomistic simulation of laser ablation of gold: Effect of pressure relaxation,” Journal of Experimental and Theoretical Physics. 2012. link Times cited: 56 NOT USED (high confidence) Z. Insepov et al., “Derivation of kinetic coefficients by atomistic methods for studying defect behavior in Mo,” Journal of Nuclear Materials. 2012. link Times cited: 15 NOT USED (high confidence) P. Beck, P. Brommer, J. Roth, and H. Trebin, “Influence of polarizability on metal oxide properties studied by molecular dynamics simulations,” Journal of Physics: Condensed Matter. 2012. link Times cited: 10 Abstract: We have studied the dependence of metal oxide properties in … read moreAbstract: We have studied the dependence of metal oxide properties in molecular dynamics (MD) simulations on the polarizability of oxygen ions. We present studies of both liquid and crystalline structures of silica (SiO2), magnesia (MgO) and alumina (Al2O3). For each of the three oxides, two separately optimized sets of force fields were used: (i) long-range Coulomb interactions between oxide and metal ions combined with a short-range pair potential; (ii) extension of force field (i) by adding polarizability to the oxygen ions. We show that while an effective potential of type (i) without polarizable oxygen ions can describe radial distributions and lattice constants reasonably well, potentials of type (ii) are required to obtain correct values for bond angles and the equation of state. The importance of polarizability for metal oxide properties decreases with increasing temperature. 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) S. Markutsya, Y. Kholod, A. Devarajan, T. Windus, M. Gordon, and M. H. Lamm, “A coarse-grained model for β-d-glucose based on force matching,” Theoretical Chemistry Accounts. 2012. link Times cited: 11 NOT USED (high confidence) C. Knight and G. Voth, “Coarse-graining away electronic structure: a rigorous route to accurate condensed phase interaction potentials,” Molecular Physics. 2012. link Times cited: 12 Abstract: The molecular simulation of condensed phase systems with ele… read moreAbstract: The molecular simulation of condensed phase systems with electronic structure methods can be prohibitively expensive if the length and time scales necessary to observe the desired chemical phenomena are too large. One solution is to map the results of a representative electronic structure simulation onto a computationally more efficient model that reproduces the original calculation, while allowing for statistical sampling relevant to the required length and time scales. The statistical mechanical multiscale coarse-graining procedure is one methodology in which a model can be developed by integrating over the subset of fast degrees of freedom to construct a reduced representation of the original system that reproduces thermodynamic, and in some instances dynamic, properties. The coarse-graining away of electronic structure is one application of this general method, wherein the electronic degrees of freedom are integrated out and the full dimensionality of the system is mapped to that of only the nuclei. The forces on the nuclei in this reduced representation are obtained from a variational force-matching procedure applied to the Hellman–Feynman forces of the original full electron + nuclear system. This work discusses the coarse-graining procedure and its application to ab initio molecular dynamics simulations of the aqueous hydroxide ion. read less NOT USED (high confidence) D. Smirnova, S. Starikov, and V. Stegailov, “New interatomic potential for computation of mechanical and thermodynamic properties of uranium in a wide range of pressures and temperatures,” The Physics of Metals and Metallography. 2012. link Times cited: 12 NOT USED (high confidence) J. Sala, E. Guàrdia, J. Martí, D. Spångberg, and M. Masia, “Fitting properties from density functional theory based molecular dynamics simulations to parameterize a rigid water force field.,” The Journal of chemical physics. 2012. link Times cited: 11 Abstract: In the quest towards coarse-grained potentials and new water… read moreAbstract: In the quest towards coarse-grained potentials and new water models, we present an extension of the force matching technique to parameterize an all-atom force field for rigid water. The methodology presented here allows to improve the matching procedure by first optimizing the weighting exponents present in the objective function. A new gauge for unambiguously evaluating the quality of the fit has been introduced; it is based on the root mean square difference of the distributions of target properties between reference data and fitted potentials. Four rigid water models have been parameterized; the matching procedure has been used to assess the role of the ghost atom in TIP4P-like models and of electrostatic damping. In the former case, burying the negative charge inside the molecule allows to fit better the torques. In the latter, since short-range interactions are damped, a better fit of the forces is obtained. Overall, the best performing model is the one with a ghost atom and with electrostatic damping. The approach shown in this paper is of general validity and could be applied to any matching algorithm and to any level of coarse graining, also for non-rigid molecules. read less NOT USED (high confidence) N. Marzari, A. Mostofi, J. Yates, I. Souza, and D. Vanderbilt, “Maximally-localized Wannier Functions: Theory and Applications,” Reviews of Modern Physics. 2011. link Times cited: 1626 Abstract: The electronic ground state of a periodic system is usually … read moreAbstract: The electronic ground state of a periodic system is usually described in terms of extended Bloch orbitals, but an alternative representation in terms of localized "Wannier functions" was introduced by Gregory Wannier in 1937. The connection between the Bloch and Wannier representations is realized by families of transformations in a continuous space of unitary matrices, carrying a large degree of arbitrariness. Since 1997, methods have been developed that allow one to iteratively transform the extended Bloch orbitals of a first-principles calculation into a unique set of maximally localized Wannier functions, accomplishing the solid-state equivalent of constructing localized molecular orbitals, or "Boys orbitals" as previously known from the chemistry literature. These developments are reviewed here, and a survey of the applications of these methods is presented. This latter includes a description of their use in analyzing the nature of chemical bonding, or as a local probe of phenomena related to electric polarization and orbital magnetization. Wannier interpolation schemes are also reviewed, by which quantities computed on a coarse reciprocal-space mesh can be used to interpolate onto much finer meshes at low cost, and applications in which Wannier functions are used as efficient basis functions are discussed. Finally the construction and use of Wannier functions outside the context of electronic-structure theory is presented, for cases that include phonon excitations, photonic crystals, and cold-atom optical lattices. read less NOT USED (high confidence) J. F. Rudzinski and W. Noid, “Coarse-graining entropy, forces, and structures.,” The Journal of chemical physics. 2011. link Times cited: 128 Abstract: Coarse-grained (CG) models enable highly efficient simulatio… read moreAbstract: Coarse-grained (CG) models enable highly efficient simulations of complex processes that cannot be effectively studied with more detailed models. CG models are often parameterized using either force- or structure-motivated approaches. The present work investigates parallels between these seemingly divergent approaches by examining the relative entropy and multiscale coarse-graining (MS-CG) methods. We demonstrate that both approaches can be expressed in terms of an information function that discriminates between the ensembles generated by atomistic and CG models. While it is well known that the relative entropy approach minimizes the average of this information function, the present work demonstrates that the MS-CG method minimizes the average of its gradient squared. We generalize previous results by establishing conditions for the uniqueness of structure-based potentials and identify similarities with corresponding conditions for the uniqueness of MS-CG potentials. We analyze the mapping entropy and extend the MS-CG and generalized-Yvon-Born-Green formalisms for more complex potentials. Finally, we present numerical calculations that highlight similarities and differences between structure- and force-based approaches. We demonstrate that both methods obtain identical results, not only for a complete basis set, but also for an incomplete harmonic basis set in Cartesian coordinates. However, the two methods differ when the incomplete basis set includes higher order polynomials of Cartesian coordinates or is expressed as functions of curvilinear coordinates. read less NOT USED (high confidence) J. M. McMahon, M. Morales, C. Pierleoni, and D. Ceperley, “The Properties of Hydrogen and Helium Under Extreme Conditions.” 2011. link Times cited: 330 Abstract: Hydrogen and helium are the most abundant elements in the Un… read moreAbstract: Hydrogen and helium are the most abundant elements in the Universe. They are also, in principle, the most simple. Nonetheless, they display remarkable properties under extreme conditions of pressure and temperature that have fascinated theoreticians and experimentalists for over a century. Advances in computational methods have made it possible to elucidate ever more of their properties. Some of these methods that have been applied in recent years, in particular, those that perform simulations directly from the physical picture of electrons and ions, such as density functional theory and quantum Monte Carlo are reviewed. The predictions from such methods as applied to the phase diagram of hydrogen, with particular focus on the solid phases and the liquid-liquid transition are discussed. The predictions of ordered quantum states, including the possibilities of a lowor zero-temperature quantum fluid and high-temperature superconductivity are also considered. Finally, pure helium and hydrogen-helium mixtures, the latter which has particular relevance to planetary physics, are discussed. read less NOT USED (high confidence) J. Chu and C. Steeves, “Thermal expansion and recrystallization of amorphous Al and Ti: A molecular dynamics study,” Journal of Non-crystalline Solids. 2011. link Times cited: 23 NOT USED (high confidence) D. Schopf, P. Brommer, B. Frigan, and H. Trebin, “Embedded atom method potentials for Al-Pd-Mn phases,” Physical Review B. 2011. link Times cited: 23 Abstract: A novel embedded atom method (EAM) potential for the Ξ phase… read moreAbstract: A novel embedded atom method (EAM) potential for the Ξ phases of Al-Pd-Mn has been determined with the force-matching method. Different combinations of analytic functions were tested for the pair and transfer part. The best results are obtained if one allows for oscillations on two different length scales. These potentials stabilize structure models of the Ξ phases and describe their energy with high accuracy. Simulations at temperatures up to 1200 K show very good agreement with ab initio results with respect to stability and dynamics of the system. read less NOT USED (high confidence) D. Belashchenko, A. V. Vorotyagin, and B. R. Gelchinsky, “Computer simulation of aluminum in the high-pressure range,” High Temperature. 2011. link Times cited: 9 NOT USED (high confidence) M. Müller, “Studying Amphiphilic Self-assembly with Soft Coarse-Grained Models,” Journal of Statistical Physics. 2011. link Times cited: 101 NOT USED (high confidence) R. Devanathan, F. Gao, and X. Sun, “Challenges in Modeling the Degradation of Ceramic Waste Forms.” 2011. link Times cited: 4 Abstract: We identify the state of the art, gaps in current understand… read moreAbstract: We identify the state of the art, gaps in current understanding, and key research needs in the area of modeling the long-term degradation of ceramic waste forms for nuclear waste disposition. The directed purpose of this report is to define a roadmap for Waste IPSC needs to extend capabilities of waste degradation to ceramic waste forms, which overlaps with the needs of the subconsinuum scale of FMM interests. The key knowledge gaps are in the areas of (i) methodology for developing reliable interatomic potentials to model the complex atomic-level interactions in waste forms; (ii) characterization of water interactions at ceramic surfaces and interfaces; and (iii) extension of atomic-level insights to the long time and distance scales relevant to the problem of actinide and fission product immobilization. read less NOT USED (high confidence) D. Bowler, D. Bowler, and T. Miyazaki, “methods in electronic structure calculations,” Reports on Progress in Physics. 2011. link Times cited: 365 Abstract: Linear-scaling methods, or methods, have computational and m… read moreAbstract: Linear-scaling methods, or methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high-performance computers. The linear-scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas are then discussed. The applications of linear-scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear-scaling methods are discussed. read less NOT USED (high confidence) P. Beck, P. Brommer, J. Roth, and H. Trebin, “Ab initio based polarizable force field generation and application to liquid silica and magnesia.,” The Journal of chemical physics. 2011. link Times cited: 20 Abstract: We extend the program potfit, which generates effective atom… read moreAbstract: We extend the program potfit, which generates effective atomic interaction potentials from ab initio data, to electrostatic interactions and induced dipoles. The potential parametrization algorithm uses the Wolf direct, pairwise summation method with spherical truncation. The polarizability of oxygen atoms is modeled with the Tangney-Scandolo interatomic force field approach. Due to the Wolf summation, the computational effort in simulation scales linearly in the number of particles, despite the presence of electrostatic interactions. Thus, this model allows to perform large-scale molecular dynamics simulations of metal oxides with realistic potentials. Details of the implementation are given, and the generation of potentials for SiO(2) and MgO is demonstrated. The approach is validated by simulations of microstructural, thermodynamic, and vibrational properties of liquid silica and magnesia. read less NOT USED (high confidence) C. R. Ellis, J. F. Rudzinski, and W. Noid, “Generalized-Yvon-Born-Green model of toluene,” Macromolecular Theory and Simulations. 2011. link Times cited: 21 NOT USED (high confidence) V. Rühle and C. Junghans, “Hybrid Approaches to Coarse-Graining using the VOTCA Package: Liquid Hexane,” Macromolecular Theory and Simulations. 2011. link Times cited: 46 Abstract: Several systematic coarse-graining techniques have been deve… read moreAbstract: Several systematic coarse-graining techniques have been developed in recent years. The method of choice depends on the system of interest and the properties to be reproduced. We present three hybrid schemes to combine force-matching and Boltzmann inversion. The methods are tested on liquid hexane and the results are compared to iterative Boltzmann inversion. All approaches can easily be extended to mixtures of molecules and provide insight for parametrizing building blocks of bigger molecules. An implementation is provided in the VOTCA package which is available under an open source software license. read less NOT USED (high confidence) E. Holm, G. Rohrer, S. Foiles, A. Rollett, H. Miller, and D. Olmsted, “Validating computed grain boundary energies in fcc metals using the grain boundary character distribution,” Acta Materialia. 2011. link Times cited: 67 NOT USED (high confidence) A.-P. Hynninen, J. Matthews, G. Beckham, M. Crowley, and M. Nimlos, “Coarse-Grain Model for Glucose, Cellobiose, and Cellotetraose in Water.,” Journal of chemical theory and computation. 2011. link Times cited: 28 Abstract: We present a coarse-grain (CG) simulation model for aqueous … read moreAbstract: We present a coarse-grain (CG) simulation model for aqueous solutions of β-d-glucose, cellobiose, and cellotetraose, based on atomistic simulation data for each system. In the model, three spherical beads are used to represent glucose, and a single bead is used to represent water. For glucose, the force field is calculated using force matching by minimizing the sum of the square differences between forces calculated from atomistic and CG simulations. For cellobiose and cellotetraose, we use a hybrid method where the nonbonded interactions are obtained using force matching and the bonded interactions are obtained using Boltzmann inversion. We demonstrate excellent agreement in the structural properties between the atomistic simulations and the CG simulations. This model represents the first step in developing a CG force field for cellulose, as it is of significant interest to study cellulose behavior at much longer time and length scales relative to atomistic simulations. read less NOT USED (high confidence) F. Wang, O. Akin-Ojo, E. Pinnick, and Y. Song, “Approaching post-Hartree–Fock quality potential energy surfaces with simple pair-wise expressions: parameterising point-charge-based force fields for liquid water using the adaptive force matching method,” Molecular Simulation. 2011. link Times cited: 38 Abstract: This article summarises the adaptive force matching (AFM) me… read moreAbstract: This article summarises the adaptive force matching (AFM) method recently developed by the Wang group. The AFM method is capable of parameterising force fields in the condensed phase by fitting electronic structure forces obtained through quantum mechanics/molecular mechanics (QM/MM) calculations. The AFM method utilises an iterative procedure to ensure good sampling and high-quality MM models for QM/MM calculations. By fitting forces directly in the condensed phase, simple pair-wise additive potentials parameterised following AFM can account for many-body effects implicitly. The AFM method provides a mechanism for judging the effectiveness of force field terms and the quality and transferability of the final force field. Realising the limitation of simple potentials, AFM emphasises fitting problem-specific force fields instead of a universal force field. This article provides a demonstration using the recently developed density functional theory/supplemental potential method to provide reference forces to parameterise a four-site point-charge model, BLYPSP-4F, for liquid water in the temperature range from 0 to 40°C. No experimental information was used for the development of BLYPSP-4F the model is found to satisfactorily reproduce experimental properties. read less NOT USED (high confidence) P. Español and I. Zúñiga, “Obtaining fully dynamic coarse-grained models from MD.,” Physical chemistry chemical physics : PCCP. 2011. link Times cited: 67 Abstract: We present a general method to obtain parametrised models fo… read moreAbstract: We present a general method to obtain parametrised models for the drift and diffusion terms of the Fokker-Planck equation of a coarse-grained description of molecular systems. The method is based on the minimisation of the relative entropy defined in terms of the two-time joint probability and thus captures the full dynamics of the coarse-grained description. In addition, we show an alternative Bayesian argument that starts from the path probability of a diffusion process which allows one to obtain the best parametrised model that fits an actual observed path of the coarse-grained variables. Both approaches lead to exactly the same optimisation function giving strong support to the methodology. We provide an heuristic argument that explains how both approaches are connected. read less NOT USED (high confidence) S. Izvekov and J. Swanson, “Using force-matching to reveal essential differences between density functionals in ab initio molecular dynamics simulations.,” The Journal of chemical physics. 2011. link Times cited: 15 Abstract: The exchange-correlation (XC) functional and value of the el… read moreAbstract: The exchange-correlation (XC) functional and value of the electronic fictitious mass μ can be two major sources of systematic errors in ab initio Car-Parrinello Molecular Dynamics (CPMD) simulations, and have a significant impact on the structural and dynamic properties of condensed-phase systems. In this work, an attempt is made to identify the origin of differences in liquid water properties generated from CPMD simulations run with the BLYP and HCTH∕120 XC functionals and two different values of μ (representative of "small" and "large" limits) by analyzing the effective pairwise atom-atom interactions. The force-matching (FM) algorithm is used to map CPMD interactions into non-polarizable, empirical potentials defined by bonded interactions, pairwise short-ranged interactions in numerical form, and Coulombic interactions via atomic partial charges. The effective interaction models are derived for the BLYP XC functional with μ=340 a.u. and μ=1100 a.u. (BLYP-340 and BLYP-1100 simulations) and the HCTH∕120 XC functional with μ=340 a.u. (HCTH-340 simulation). The BLYP-340 simulation results in overstructured water with slow dynamics. In contrast, the BLYP-1100 and HCTH-340 simulations both produce radial distribution functions (indicative of structure) that are in reasonably good agreement with experiment. It is shown that the main difference between the BLYP-340 and HCTH-340 effective potentials arises in the short-ranged nonbonded interactions (in hydrogen bonding regions), while the difference between the BLYP-340 and BLYP-1100 interactions is mainly in the long-ranged electrostatic components. Collectively, these results demonstrate how the FM method can be used to further characterize various simulation ensembles (e.g., density-functional theory via CPMD). An analytical representation of each effective interaction water model, which is easy to implement, is presented. read less NOT USED (high confidence) L. Hung and E. Carter, “Ductile processes at aluminium crack tips: comparison of orbital-free density functional theory with classical potential predictions,” Modelling and Simulation in Materials Science and Engineering. 2011. link Times cited: 23 Abstract: We compare behaviour of quasi-two-dimensional aluminium crac… read moreAbstract: We compare behaviour of quasi-two-dimensional aluminium crack tips undergoing mode I loading using orbital-free density functional theory (OFDFT) and the classical embedded atom method (EAM). Low-index crack orientations are compared in the context of the Griffith, Rice and Tadmor–Hai continuum criteria, using values from Kohn–Sham DFT (KSDFT). All orientations are predicted to be ductile, and twinning is expected to occur only in certain orientations of low-dimensional or low-temperature Al. OFDFT and the EAM predict similar values to KSDFT for the relevant properties. In simulations of two crack orientations, the critical stress intensity factor in EAM simulations is close to continuum predictions while crack tips modelled by OFDFT do not exhibit plasticity until loaded at least 13% over the continuum prediction. The EAM and OFDFT give qualitatively similar results for a crack orientation that emits edge dislocations. For a twinning orientation, OFDFT simulations emit partial dislocations in the same order, even with different pseudopotentials. However, EAM simulations predict that a partial is emitted along a different slip plane from OFDFT. Differences between EAM and OFDFT simulations suggest that methods that give accurate stacking fault energies, elastic constants and surface energies may not necessarily reproduce all important physical processes at crack tips. read less NOT USED (high confidence) H. Sheng, M. Kramer, A. Cadien, T. Fujita, and M. Chen, “Highly optimized embedded-atom-method potentials for fourteen fcc metals,” Physical Review B. 2011. link Times cited: 387 Abstract: Highly optimized embedded-atom-method (EAM) potentials have … read moreAbstract: Highly optimized embedded-atom-method (EAM) potentials have been developed for 14 face-centered-cubic (fcc) elements across the periodic table. The potentials were developed by fitting the potential-energy surface (PES) of each element derived from high-precision first-principles calculations. The as-derived potential-energy surfaces were shifted and scaled to match experimental reference data. In constructing the PES, a variety of properties of the elements were considered, including lattice dynamics, mechanical properties, thermal behavior, energetics of competing crystal structures, defects, deformation paths, liquid structures, and so forth. For each element, the constructed EAM potentials were tested against the experiment data pertaining to thermal expansion, melting, and liquid dynamics via molecular dynamics computer simulation. The as-developed potentials demonstrate high fidelity and robustness. Owing to their improved accuracy and wide applicability, the potentials are suitable for high-quality atomistic computer simulation of practical applications. read less NOT USED (high confidence) E. Edlund, O. Lindgren, and M. N. Jacobi, “Novel self-assembled morphologies from isotropic interactions.,” Physical review letters. 2011. link Times cited: 13 Abstract: We present results from particle simulations with isotropic … read moreAbstract: We present results from particle simulations with isotropic medium range interactions in two dimensions. At low temperature novel types of aggregated structures appear. We show that these structures can be explained by spontaneous symmetry breaking in analytic solutions to an adaptation of the spherical spin model. We predict the critical particle number where the symmetry breaking occurs and show that the resulting phase diagram agrees well with results from particle simulations. read less NOT USED (high confidence) M. Böckmann, D. Marx, C. Peter, L. Site, K. Kremer, and N. Doltsinis, “Multiscale modelling of mesoscopic phenomena triggered by quantum events: light-driven azo-materials and beyond.,” Physical chemistry chemical physics : PCCP. 2011. link Times cited: 47 Abstract: The macroscopic functionality of soft (bio-)materials is oft… read moreAbstract: The macroscopic functionality of soft (bio-)materials is often triggered by quantum-mechanical events which are highly local in space and time. In order to arrive at the resulting macroscopically observable phenomena, many orders of magnitude need to be bridged on both the time and the length scale. In the present paper, we first introduce a range of simulation methods at different scales as well as theoretical approaches to form bridges between them. We then outline a strategy to develop an adaptive multiscale simulation approach which connects the quantum to the mesoscopic level by bringing together ab initio molecular dynamics (QM), classical (force field) molecular dynamics (MM), and coarse grained (CG) simulation techniques. With a multitude of photoactive materials in mind, we apply our methodology to a prototypical test case-light-induced phase transitions in a liquid crystal containing the azobenzene photoswitch. read less NOT USED (high confidence) A. Kashinath and M. Demkowicz, “A predictive interatomic potential for He in Cu and Nb,” Modelling and Simulation in Materials Science and Engineering. 2011. link Times cited: 53 Abstract: First principles calculations show that two-body forces are … read moreAbstract: First principles calculations show that two-body forces are sufficient to describe interactions of He with fcc Cu and bcc Nb. This property is explained directly from calculated charge density distributions and used to construct a Cu–Nb–He interatomic potential that predicts accurate He impurity energies despite not being fitted to them. read less NOT USED (high confidence) A. Chaimovich and M. Shell, “Coarse-graining errors and numerical optimization using a relative entropy framework.,” The Journal of chemical physics. 2011. link Times cited: 206 Abstract: The ability to generate accurate coarse-grained models from … read moreAbstract: The ability to generate accurate coarse-grained models from reference fully atomic (or otherwise "first-principles") ones has become an important component in modeling the behavior of complex molecular systems with large length and time scales. We recently proposed a novel coarse-graining approach based upon variational minimization of a configuration-space functional called the relative entropy, S(rel), that measures the information lost upon coarse-graining. Here, we develop a broad theoretical framework for this methodology and numerical strategies for its use in practical coarse-graining settings. In particular, we show that the relative entropy offers tight control over the errors due to coarse-graining in arbitrary microscopic properties, and suggests a systematic approach to reducing them. We also describe fundamental connections between this optimization methodology and other coarse-graining strategies like inverse Monte Carlo, force matching, energy matching, and variational mean-field theory. We suggest several new numerical approaches to its minimization that provide new coarse-graining strategies. Finally, we demonstrate the application of these theoretical considerations and algorithms to a simple, instructive system and characterize convergence and errors within the relative entropy framework. read less NOT USED (high confidence) A. Chamaani et al., “Thermodynamics and molecular dynamics investigation of a possible new critical size for surface and inner cohesive energy of Al nanoparticles,” Journal of Nanoparticle Research. 2011. link Times cited: 18 NOT USED (high confidence) S. Patinet and L. Proville, “Dislocation pinning by substitutional impurities in an atomic-scale model for Al(Mg) solid solutions,” Philosophical Magazine. 2011. link Times cited: 24 Abstract: We report our atomic-scale computations for the static depin… read moreAbstract: We report our atomic-scale computations for the static depinning threshold of dislocations in Al(Mg) solid solutions. The interaction between the dislocations and the isolated obstacles is studied for different types of obstacle, i.e. single solute atoms situated at different positions, and solute dimers with different bond directions. Part of this work is used to apply different standard analytical theories for solid solution hardening, the predictions of which are finally compared with our direct atomic-scale simulations (AS) for dislocation depinning in random Al(Mg) solid solutions. According to our comparisons, the dislocation statistics in our AS is qualitatively well described by the Mott–Nabarro–Labusch theory. In agreement with earlier results about a different system, namely Ni(Al), the depinning thresholds are similar for the edge and for the screw dislocations. read less NOT USED (high confidence) M. Chassagne, M. Legros, and D. Rodney, “Atomic-scale simulation of screw dislocation/coherent twin boundary interaction in Al, Au, Cu and Ni,” Acta Materialia. 2011. link Times cited: 124 NOT USED (high confidence) L. P. Wang and T. V. Voorhis, “Communication: Hybrid ensembles for improved force matching.,” The Journal of chemical physics. 2010. link Times cited: 21 Abstract: Force matching is a method for parameterizing empirical pote… read moreAbstract: Force matching is a method for parameterizing empirical potentials in which the empirical parameters are fitted to a reference potential energy surface (PES). Typically, training data are sampled from a canonical ensemble generated with either the empirical potential or the reference PES. In this Communication, we show that sampling from either ensemble risks excluding critical regions of configuration space, leading to fitted potentials that deviate significantly from the reference PES. We present a hybrid ensemble which combines the Boltzmann probabilities of both potential surfaces into the fitting procedure, and we demonstrate that this technique improves the quality and stability of empirical potentials. read less NOT USED (high confidence) L. Khounlavong, V. Pryamitsyn, and V. Ganesan, “Many-body interactions and coarse-grained simulations of structure of nanoparticle-polymer melt mixtures.,” The Journal of chemical physics. 2010. link Times cited: 28 Abstract: We present a computational approach for coarse-grained simul… read moreAbstract: We present a computational approach for coarse-grained simulations of nanoparticle-polymer melt mixtures. We first examine the accuracy of an effective one-component approach based on a pair interaction approximation to polymer-mediated interactions, and demonstrate that even at low particle volume fractions, the polymer-mediated many-body interaction effects can prove significant in determining the structural characteristics of mixtures of nanoparticles and polymer melts. The origin of such effects is shown to arise from the extent of polymer perturbations resulting from the presence of the nanoparticles. To account for such effects, we propose a new simulation approach that employs a coarse-grained representation of the polymers to capture the many-body corrections to the polymer-mediated pair interaction potentials. The results of the coarse-grained simulations are shown to be in good quantitative agreement with the reference simulations. The method developed in this article is proposed as a tractable approach to coarse-grain and effect computer simulations of atomistic descriptions of polymer-nanoparticle systems. read less NOT USED (high confidence) C. Becker and M. J. Kramer, “Atomistic comparison of volume-dependent melt properties from four models of aluminum,” Modelling and Simulation in Materials Science and Engineering. 2010. link Times cited: 30 Abstract: With the increasing use of simulations in materials research… read moreAbstract: With the increasing use of simulations in materials research and design, it is important to quantify the differences between, and accuracy of, models used in these simulations. Here we present the results of such a comparison for four embedded-atom models of aluminum that were optimized to have good liquid properties, particularly the melting temperatures. The effects of temperature and volume are systematically examined in the melts for bulk thermodynamic quantities, pair correlation functions and structure factors and diffusion coefficients for each interatomic potential. Where possible, these are then compared with experimental values. We find quantitative differences in the properties determined from the various interatomic potentials despite the fact that they were fit with similar sets of data. read less NOT USED (high confidence) E. Tsuchida, “Ab initio mass tensor molecular dynamics.,” The Journal of chemical physics. 2010. link Times cited: 16 Abstract: Mass tensor molecular dynamics method was first introduced b… read moreAbstract: Mass tensor molecular dynamics method was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio molecular dynamics simulations with minimal computational overhead. Test calculations on liquid water show a threefold reduction in computational effort without making the fixed geometry approximation. We also present a simple recipe for estimating the optimal atomic masses using only the first derivatives of the potential energy. read less NOT USED (high confidence) B. Waldher, J. Kuta, S. Chen, N. Henson, and A. Clark, “ForceFit: A code to fit classical force fields to quantum mechanical potential energy surfaces,” Journal of Computational Chemistry. 2010. link Times cited: 45 Abstract: The ForceFit program package has been developed for fitting … read moreAbstract: The ForceFit program package has been developed for fitting classical force field parameters based upon a force matching algorithm to quantum mechanical gradients of configurations that span the potential energy surface of the system. The program, which runs under UNIX and is written in C++, is an easy‐to‐use, nonproprietary platform that enables gradient fitting of a wide variety of functional force field forms to quantum mechanical information obtained from an array of common electronic structure codes. All aspects of the fitting process are run from a graphical user interface, from the parsing of quantum mechanical data, assembling of a potential energy surface database, setting the force field, and variables to be optimized, choosing a molecular mechanics code for comparison to the reference data, and finally, the initiation of a least squares minimization algorithm. Furthermore, the code is based on a modular templated code design that enables the facile addition of new functionality to the program. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 read less NOT USED (high confidence) L. Proville and S. Patinet, “Atomic-scale models for hardening in fcc solid solutions,” Physical Review B. 2010. link Times cited: 31 Abstract: Atomic-scale simulations are associated with an elastic line… read moreAbstract: Atomic-scale simulations are associated with an elastic line model to analyze thoroughly the pinning strength experienced by an edge dislocation in some face-centered-cubic solid solutions, Al Mg and Ni Al with solute concentration comprise between 1 and 10 at. %. The one-dimensional elastic line model is developed to sketch out the details of the atomic scale. The account of such details is shown to yield a proper description of the dislocation statistics for the different systems. The quantitative departure between hardening in Al Mg and Ni Al is then demonstrated to hinge on the difference in the short-range interaction between the partial dislocations and the isolated impurities. It is also shown that an accurate description of the solidsolution hardening requires the account for the dislocation geometry and the dislocation interaction with clusters of solute atoms. The elastic line model allows us to perform some computations at the microscopic scales meanwhile accounting for the most important atomic details. A comparison with experimental data is attempted. read less NOT USED (high confidence) S. Izvekov, P. Chung, and B. Rice, “The multiscale coarse-graining method: assessing its accuracy and introducing density dependent coarse-grain potentials.,” The Journal of chemical physics. 2010. link Times cited: 91 Abstract: The ability of particle-based coarse-grain potentials, deriv… read moreAbstract: The ability of particle-based coarse-grain potentials, derived using the recently proposed multiscale coarse-graining (MS-CG) methodology [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] to reconstruct atomistic free-energy surfaces in coarse-grain coordinates is discussed. The MS-CG method is based on force-matching generalized forces associated with the coarse-grain coordinates. In this work, we show that the MS-CG method recovers only part of the atomistic free-energy landscape in the coarse-grain coordinates (termed the potential of mean force contribution). The portion of the atomistic free-energy landscape that is left out in the MS-CG procedure contributes to a pressure difference between atomistic and coarse-grain ensembles. Employing one- and two-site coarse-graining of nitromethane as worked examples, we discuss the virial and compressibility constraints to incorporate a pressure correction interaction into the MS-CG potentials and improve performance at different densities. The nature of the pressure correction interaction is elucidated and compared with those used in structure-based coarse-graining. As pairwise approximations to the atomistic free-energy, the MS-CG potentials naturally depend on the variables describing a thermodynamic state, such as temperature and density. Such dependencies limit state-point transferability. For nitromethane, the one- and two-site MS-CG potentials appear to be transferable across a broad range of temperatures. In particular, the two-site models, which are matched to low and ambient temperature liquid states, perform well in simulations of the ambient crystal structure. In contrast, the transferability of the MS-CG models of nitromethane across different densities is found to be problematic. To achieve better state-point transferability, density dependent MS-CG potentials are introduced and their performance is examined in simulations of nitromethane under various thermodynamic conditions, including shocked states. read less NOT USED (high confidence) V. Tozzini, “Minimalist models for proteins: a comparative analysis,” Quarterly Reviews of Biophysics. 2010. link Times cited: 97 Abstract: The last decade has witnessed a renewed interest in the coar… read moreAbstract: The last decade has witnessed a renewed interest in the coarse-grained (CG) models for biopolymers, also stimulated by the needs of modern molecular biology, dealing with nano- to micro-sized bio-molecular systems and larger than microsecond timescale. This combination of size and timescale is, in fact, hard to access by atomic-based simulations. Coarse graining the system is a route to be followed to overcome these limits, but the ways of practically implementing it are many and different, making the landscape of CG models very vast and complex. In this paper, the CG models are reviewed and their features, applications and performances compared. This analysis, restricted to proteins, focuses on the minimalist models, namely those reducing at minimum the number of degrees of freedom without losing the possibility of explicitly describing the secondary structures. This class includes models using a single or a few interacting centers (beads) for each amino acid. From this analysis several issues emerge. The difficulty in building these models resides in the need for combining transferability/predictive power with the capability of accurately reproducing the structures. It is shown that these aspects could be optimized by accurately choosing the force field (FF) terms and functional forms, and combining different parameterization procedures. In addition, in spite of the variety of the minimalist models, regularities can be found in the parameters values and in FF terms. These are outlined and schematically presented with the aid of a generic phase diagram of the polypeptide in the parameter space and, hopefully, could serve as guidelines for the development of minimalist models incorporating the maximum possible level of predictive power and structural accuracy. read less NOT USED (high confidence) V. Krishna and L. Larini, “A generalized mean field theory of coarse-graining.,” The Journal of chemical physics. 2010. link Times cited: 11 Abstract: A general mean field theory is presented for the constructio… read moreAbstract: A general mean field theory is presented for the construction of equilibrium coarse-grained models. Inverse methods that reconstruct microscopic models from low resolution experimental data can be derived as particular implementations of this theory. The theory also applies to the opposite problem of reduction, where relevant information is extracted from available equilibrium ensemble data. Additionally, a complementary approach is presented and problems of representability in coarse-grained modeling analyzed using information theoretic arguments. These problems are central to the construction of coarse-grained representations of complex systems, and commonly used coarse-graining methods and variational principles for coarse-graining are derived as particular cases of the general theory. read less NOT USED (high confidence) M. Mendelev et al., “Experimental and computer simulation determination of the structural changes occurring through the liquid–glass transition in Cu–Zr alloys,” Philosophical Magazine. 2010. link Times cited: 44 Abstract: Molecular dynamics (MD) simulations were performed of the st… read moreAbstract: Molecular dynamics (MD) simulations were performed of the structural changes occurring through the liquid–glass transition in Cu–Zr alloys. The total scattering functions (TSF), and their associated primary diffuse scattering peak positions (K p), heights (K h) and full-widths at half maximum (K FWHM) were used as metrics to compare the simulations to high-energy X-ray scattering data. The residuals of difference between the model and experimental TSFs are ∼0.03 for the liquids and about 0.07 for the glasses. Over the compositional range studied, Zr1− x Cu x (0.1 ≤ x ≤ 0.9), K p, K h and K FWHM show a strong dependence on composition and temperature. The simulation and experimental data correlate well between each other. MD simulation revealed that the Cu–Zr bonds undergo the largest changes during cooling of the liquid, whereas the Cu–Cu bonds change the least. Changes in the partial-pair correlations are more readily seen in the second and third shells. The Voronoi polyhedra (VP) in glasses are dominated by only a few select types that are compositionally dependent. The relative concentrations of the dominant VPs rapidly change in their relative proportion in the deeply undercooled liquid. The experimentally determined region of best glass formability, x Cu ∼ 65%, shows the largest temperature dependent changes for the deeply undercooled liquid in the MD simulation. This region also exhibits very strong temperature dependence for the diffusivity and the total energy of the system. These data point to a strong topological change in the best glass-forming alloys and a concurrent change in the VP chemistry in the deeply undercooled liquid. read less NOT USED (high confidence) P. Spijker, B. van Hoof, M. Debertrand, A. J. Markvoort, N. Vaidehi, and P. Hilbers, “Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems,” International Journal of Molecular Sciences. 2010. link Times cited: 22 Abstract: Many biological cellular processes occur at the micro- or mi… read moreAbstract: Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG) can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide. read less NOT USED (high confidence) V. Bortolani, A. Franchini, G. Santoro, and M. Brigazzi, “Theory of Friction with Applied Load,” Tribology Letters. 2010. link Times cited: 3 NOT USED (high confidence) L. Gallington and A. Bongiorno, “Thermodynamic stability limits of simple monoatomic materials.,” The Journal of chemical physics. 2010. link Times cited: 19 Abstract: This computational study addresses the thermodynamical stabi… read moreAbstract: This computational study addresses the thermodynamical stability of superheated crystals. Molecular dynamics simulations are employed to derive the caloric curves of the solid and liquid phases of a material. Caloric curves are used to derive thermodynamic state functions, the parameters of the equilibrium melting phase transition, and the regions of thermodynamical stability of the liquid and solid phases. Molecular dynamics trajectories are also analyzed to gain insight on the mechanisms leading to the instability of the homogeneous superheated solid phase. This study shows that in simple and homogeneous solids the configurational entropy is not zero and that its excitations can occur without disrupting the crystallinity of the lattice. The superheating and supercooling limits of the solid and liquid phases are found to correspond to states of equal entropy and enthalpy. 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) L. E. Kar’kina, I. N. Kar’kin, and Y. Gornostyrev, “Process of faceting in nanoparticles of FCC metals: Results of simulation by the molecular-dynamics method,” The Physics of Metals and Metallography. 2010. link Times cited: 4 NOT USED (high confidence) M. Paliy, R. Melnik, and B. Shapiro, “Coarse-graining RNA nanostructures for molecular dynamics simulations,” Physical Biology. 2010. link Times cited: 34 Abstract: A series of coarse-grained models have been developed for st… read moreAbstract: A series of coarse-grained models have been developed for study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Such a treatment allows us to reach, for systems of thousands of nucleotides, a time scale of microseconds (i.e. by three orders of magnitude longer than in full atomistic modeling) and thus to enable simulations of large RNA polymers in the context of bionanotechnology. We find that the three-beads-per-nucleotide models, described by a set of just a few universal parameters, are able to describe different RNA conformations and are comparable in structural precision to the models where detailed values of the backbone P-C4′ dihedrals taken from a reference structure are included. These findings are discussed in the context of RNA conformation classes. read less NOT USED (high confidence) M. Wander and A. Clark, “Gradient fit functions for two-body potential energy surfaces based upon a harmonic series,” Molecular Simulation. 2010. link Times cited: 0 Abstract: While force-field development has been discussed extensively… read moreAbstract: While force-field development has been discussed extensively in the literature, the question of what analytical expressions make the best function choices, particularly in the context of matching quantum mechanic potential energy surfaces (PES), is less explored. Traditional forms based upon harmonic oscillators and Lennard-Jones types have dominated the field owing to the focus on fitting properties. However, with the advent of gradient-fitting approaches, it is now possible with the correct force-field expressions to achieve consistent high-accuracy results with molecular dynamics calculations. Using the general principle that power series can fit surfaces of any shape well, we have utilised harmonic series functions to fit a two-body PES represented by a Morse function. The harmonic functions are fast because they have only integer exponents, and they fit accurately with a limited number of terms. read less NOT USED (high confidence) P. Brommer, P. Beck, A. Chatzopoulos, F. Gähler, J. Roth, and H. Trebin, “Direct Wolf summation of a polarizable force field for silica.,” The Journal of chemical physics. 2010. link Times cited: 31 Abstract: We extend the Wolf direct, pairwise r(-1) summation method w… read moreAbstract: We extend the Wolf direct, pairwise r(-1) summation method with spherical truncation to dipolar interactions in silica. The Tangney-Scandolo interatomic force field for silica takes regard of polarizable oxygen atoms whose dipole moments are determined by iteration to a self-consistent solution. With Wolf summation, the computational effort scales linearly in the system size and can easily be distributed among many processors, thus making large-scale simulations of dipoles possible. The details of the implementation are explained. The approach is validated by estimations of the error term and simulations of microstructural and thermodynamic properties of silica. 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) J. A. Elliott, Y. Shibuta, and D. J. Wales, “Global minima of transition metal clusters described by Finnis–Sinclair potentials: A comparison with semi-empirical molecular orbital theory,” Philosophical Magazine. 2009. link Times cited: 39 Abstract: We present putative global minimum energy structures for nan… read moreAbstract: We present putative global minimum energy structures for nanoscopic transition metal clusters, with sizes ranging from N = 3 to 100 atoms, described by the original embedded atom potential of Finnis and Sinclair (FS), using their parameter sets for molybdenum and iron, and compare selected results with predictions from semi-empirical molecular orbital (SE-MO) theory via further optimization using the AM1* and PM6 Hamiltonians. We find that, for Fe clusters, the global minima found for the FS potential consist mainly of polyicosahedral structures with magic numbers N = 13, 19, 23, 26, 29, 39, 60 and 78, whereas, for Mo clusters with sizes N > 30, they are more likely to be bcc terminated by {110} and {100}-type surface facets. We find that the global minimum energy structures obtained for the FS potential are, in general, very good starting points for further SE-MO optimization, although the relative ordering of the resulting structures by energy compared to those obtained from global minima of other potentials used to model metal clusters does not, in general, agree. read less NOT USED (high confidence) M. Mendelev, M. Asta, M. J. Rahman, and J. Hoyt, “Development of interatomic potentials appropriate for simulation of solid–liquid interface properties in Al–Mg alloys,” Philosophical Magazine. 2009. link Times cited: 126 Abstract: Different approaches are analyzed for construction of semi-e… read moreAbstract: Different approaches are analyzed for construction of semi-empirical potentials for binary alloys, focusing specifically on the capability of these potentials to describe solid–liquid phase equilibria, as a pre-requisite to studies of solidification phenomena. Fitting ab initio compound data does not ensure correct reproduction of the dilute solid-solution formation energy, and explicit inclusion of this quantity in the potential development procedure does not guarantee that the potential will predict the correct solid–liquid phase diagram. Therefore, we conclude that fitting only to solid phase properties, as is done in most potential development procedures, generally is not sufficient to develop a semi-empirical potential suitable for the simulation of solidification. A method is proposed for the incorporation of data for liquid solution energies in the potential development procedure, and a new semi-empirical potential developed suitable for simulations of dilute alloys of Mg in Al. The potential correctly reproduces both zero-temperature solid properties and solidus and liquid lines on the Al-rich part of the Al–Mg phase diagram. read less NOT USED (high confidence) G. P. P. Pun and Y. Mishin, “Development of an interatomic potential for the Ni-Al system,” Philosophical Magazine. 2009. link Times cited: 341 Abstract: We construct an interatomic potential for the Ni-Al system w… read moreAbstract: We construct an interatomic potential for the Ni-Al system within the embedded-atom method formalism. The potential is based on previously developed accurate potentials for pure Ni and Al. The cross-interactions are fitted to experimental cohesive energy, lattice parameter and elastic constants of B2-NiAl, as well as to ab initio formation energies of several real or imaginary intermetallic compounds with different crystal structures and chemical compositions. The potential accurately reproduces a variety of physical properties of the NiAl and Ni3Al phases, and shows reasonable agreement with experimental and ab initio data for phase stability across the Ni-Al phase diagram. Most of the properties reproduced by the new potential were not involved in the fitting process, which demonstrates its excellent transferability. Advantages and certain weaknesses of the new potential in comparison with other existing potentials are discussed in detail. The potential is expected to be especially suitable for simulations of heterophase interfaces and mechanical behavior of Ni-Al alloys. read less NOT USED (high confidence) D. Farkas and L. Patrick, “Tensile deformation of fcc Ni as described by an EAM potential,” Philosophical Magazine. 2009. link Times cited: 28 Abstract: We present the results of a large-scale atomistic study of t… read moreAbstract: We present the results of a large-scale atomistic study of tensile deformation in a virtual fcc polycrystalline sample with columnar grain structure and a [110] texture. The atomic interaction was described by a volume-dependent central interatomic potential based on first principle calculations and experimental data for fcc Ni. The sample contained nine grains of 40 nm average size, created using a Voronoi construction with a common [110] axis, so that the grain boundaries were all pure tilt with random misorientation angles and crystallographic orientation of the grain boundary plane. We report the stress–strain behavior of the sample and the particular details of dislocation emission and dislocation interaction. Different grain boundaries acted as emission sites at different stresses due to their different local structure and orientation with respect to the applied stress. It was found that boundaries close to a twin misorientation can emit dislocations easily and become closer to the twin misorientation as a result of the emission process. Low angle boundaries were observed to disappear as a result of the deformation process. The emission of leading and trailing Shockley partials was observed and as the deformation proceeds, dislocation debris accumulates in the sample. The results also show that, as the deformation proceeds, the strain can localize in certain grains and grain regions, driven solely by the particular local structure and orientation of the various grain boundaries. read less NOT USED (high confidence) Q. Peng, X. Zhang, and G. Lu, “Quantum mechanical simulations of nanoindentation of Al thin film,” Computational Materials Science. 2009. link Times cited: 12 NOT USED (high confidence) J. W. Mullinax and W. Noid, “Extended ensemble approach for deriving transferable coarse-grained potentials,” Journal of Chemical Physics. 2009. link Times cited: 102 Abstract: Coarse-grained (CG) models provide a computationally efficie… read moreAbstract: Coarse-grained (CG) models provide a computationally efficient means for investigating biological and soft-matter processes that evolve on long time scales and large length scales. The present work introduces an extended ensemble framework for calculating transferable CG potentials that accurately reproduce the structure of atomistic models for multiple systems. This framework identifies a generalized potential of mean force (PMF) as the appropriate CG potential for reproducing the structural correlations of an atomistic extended ensemble. A variational approach is developed for calculating transferable potentials that provide an optimal approximation to this PMF. Calculations for binary mixtures of alkanes and alcohols demonstrate that the extended ensemble potentials provide improved transferability relative to potentials calculated for a single system. read less NOT USED (high confidence) T. Murtola, M. Karttunen, and I. Vattulainen, “Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer.,” The Journal of chemical physics. 2009. link Times cited: 55 Abstract: We present a two-dimensional coarse-grained (CG) model for a… read moreAbstract: We present a two-dimensional coarse-grained (CG) model for a lipid membrane composed of phospholipids and cholesterol. The effective CG interactions are determined using radial distribution functions (RDFs) from atom-scale molecular dynamics simulations using the inverse Monte Carlo (IMC) technique, based on our earlier work [T. Murtola et al., J. Chem. Phys. 121, 9156 (2004); J. Chem. Phys. 126, 075101 (2007)]. Here, the original model is improved by including an internal discrete degree of freedom for the phospholipid tails to describe chain ordering. We also discuss the problem of RDF inversion in the presence of internal states, in general, and present a modified IMC method for their inclusion. The new model agrees with the original models on large-scale structural features such as density fluctuations in pure dipalmitoylphosphocholine and cholesterol domain formation at intermediate concentrations and also indicates that ordered and disordered domains form at all cholesterol concentrations, even if the global density remains uniform. The inclusion of ordering also improves transferability of the interactions between different concentrations, but does not eliminate transferability problems completely. We also present a general discussion of problems related to RDF inversion. read less NOT USED (high confidence) Q. Peng and G. Lu, “A comparative study of fracture in Al: Quantum mechanical vs. empirical atomistic description,” Journal of The Mechanics and Physics of Solids. 2009. link Times cited: 12 NOT USED (high confidence) P. Puri and V. Yang, “Effect of voids and pressure on melting of nano-particulate and bulk aluminum,” Journal of Nanoparticle Research. 2009. link Times cited: 23 NOT USED (high confidence) R. E. Miller and E. Tadmor, “A unified framework and performance benchmark of fourteen multiscale atomistic/continuum coupling methods,” Modelling and Simulation in Materials Science and Engineering. 2009. link Times cited: 385 Abstract: A partitioned-domain multiscale method is a computational fr… read moreAbstract: A partitioned-domain multiscale method is a computational framework in which certain key regions are modeled atomistically while most of the domain is treated with an approximate continuum model (such as finite elements). The goal of such methods is to be able to reproduce the results of a fully atomistic simulation at a reduced computational cost. In recent years, a large number of partitioned-domain methods have been proposed. Theoretically, these methods appear very different to each other making comparison difficult. Surprisingly, it turns out that at the implementation level these methods are in fact very similar. In this paper, we present a unified framework in which fourteen leading multiscale methods can be represented as special cases. We use this common framework as a platform to test the accuracy and efficiency of the fourteen methods on a test problem; the structure and motion of a Lomer dislocation dipole in face-centered cubic aluminum. This problem was carefully selected to be sufficiently simple to be quick to simulate and straightforward to analyze, but not so simple to unwittingly hide differences between methods. The analysis enables us to identify generic features in multiscale methods that correlate with either high or low accuracy and either fast or slow performance. All tests were performed using a single unified computer code in which all fourteen methods are implemented. This code is being made available to the public along with this paper. read less NOT USED (high confidence) J. Yasi, T. Nogaret, D. Trinkle, Y. Qi, L. G. Hector, and W. A. Curtin, “Basal and prism dislocation cores in magnesium: comparison of first-principles and embedded-atom-potential methods predictions,” Modelling and Simulation in Materials Science and Engineering. 2009. link Times cited: 120 Abstract: The core structures of screw and edge dislocations on the ba… read moreAbstract: The core structures of screw and edge dislocations on the basal and prism planes in Mg, and the associated gamma surfaces, were studied using an ab initio method and the embedded-atom-method interatomic potentials developed by Sun et al and Liu et al. The ab initio calculations predict that the basal plane dislocations dissociate into partials split by 16.7 Å (edge) and 6.3 Å (screw), as compared with 14.3 Å and 12.7 Å (Sun and Liu edge), and 6.3 Å and 1.4 Å (Sun and Liu screw), with the Liu screw dislocation being metastable. In the prism plane, the screw and edge cores are compact and the edge core structures are all similar, while ab initio does not predict a stable prismatic screw in stress-free conditions. These results are qualitatively understood through an examination of the gamma surfaces for interplanar sliding on the basal and prism planes. The Peierls stresses at T = 0 K for basal slip are a few megapascals for the Sun potential, in agreement with experiments, but are ten times larger for the Liu potential. The Peierls stresses for prism slip are 10–40 MPa for both potentials. Overall, the dislocation core structures from ab initio are well represented by the Sun potential in all cases while the Liu potential shows some notable differences. These results suggest that the Sun potential is preferable for studying other dislocations in Mg, particularly the ⟨c + a⟩ dislocations, for which the core structures are much larger and not accessible by ab initio methods. read less NOT USED (high confidence) A. Eriksson, M. N. Jacobi, J. Nystrom, and K. Tunstrøm, “Determining interaction rules in animal swarms,” Behavioral Ecology. 2009. link Times cited: 84 Abstract: In this paper, we introduce a method for determining local i… read moreAbstract: In this paper, we introduce a method for determining local interaction rules in animal swarms. The method is based on the assumption that the behavior of individuals in a swarm can be treated as a set of mechanistic rules.The principal idea behind the technique is to vary parameters that define a set of hypothetical interactions, as for example, a rule for aligning with neighbors. The parameter values are optimized so that the deviation between the observed movements in an animal swarm and the movements predicted by the assumed rule set is minimal. We demonstrate the method by reconstructing the interaction rules from the trajectories produced by a computer simulation. Copyright 2010, Oxford University Press. read less NOT USED (high confidence) 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 (high confidence) M. Mendelev, M. Kramer, R. Ott, D. Sordelet, D. Yagodin, and P. Popel,’ “Development of suitable interatomic potentials for simulation of liquid and amorphous Cu–Zr alloys,” Philosophical Magazine. 2009. link Times cited: 334 Abstract: We present a new semi-empirical potential suitable for molec… read moreAbstract: We present a new semi-empirical potential suitable for molecular dynamics simulations of liquid and amorphous Cu–Zr alloys. To provide input data for developing the potential, new experimental measurements of the structure factors for amorphous Cu64.5Zr35.5 alloy were performed. In this work, we propose a new method to include diffraction data in the potential development procedure, which also includes fitting to first-principles and liquid density and enthalpy of mixing data. To refine the new potential, we used first-principles and liquid enthalpy of mixing data published earlier combined with the densities of liquid Cu64.5Zr35.5 measured over a range of temperatures. We show that the potential predicts a liquid-to-glass transition temperature that agrees reasonably well with experimental data. Finally, we compare the new potential with two previously developed semi-empirical potentials for Cu–Zr alloys and examine their comparative and contrasting descriptions of structure and properties for Cu64.5Zr35.5 liquids and glasses. 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) J. J. Ojwang, R. A. Santen, G. Kramer, A. V. Duin, and W. Goddard, “Predictions of melting, crystallization, and local atomic arrangements of aluminum clusters using a reactive force field.,” The Journal of chemical physics. 2008. link Times cited: 50 Abstract: A parametrized reactive force field model for aluminum ReaxF… read moreAbstract: A parametrized reactive force field model for aluminum ReaxFF(Al) has been developed based on density functional theory (DFT) data. A comparison has been made between DFT and ReaxFF(Al) outputs to ascertain whether ReaxFF(Al) is properly parametrized and to check if the output of the latter has correlation with DFT results. Further checks include comparing the equations of state of condensed phases of Al as calculated from DFT and ReaxFF(Al). There is a good match between the two results, again showing that ReaxFF(Al) is correctly parametrized as per the DFT input. Simulated annealing has been performed on aluminum clusters Al(n) using ReaxFF(Al) to find the stable isomers of the clusters. A plot of stability function versus cluster size shows the existence of highly stable clusters (magic clusters). Quantum mechanically these magic clusters arise due to the complete filling of the orbital shells. However, since force fields do not care about electrons but work on the assumption of validity of Born-Oppenheimer approximation, the magic clusters are therefore correlated with high structural symmetry. There is a rapid decline in surface energy contribution due to the triangulated nature of the surface atoms leading to higher coordination number. The bulk binding energy is computed to be 76.8 kcal/mol. This gives confidence in the suitability of ReaxFF for studying and understanding the underlying dynamics in aluminum clusters. In the quantification of the growth of cluster it is seen that as the size of the clusters increase there is preference for the coexistence of fcc/hcp orders at the expense of simple icosahedral ordering, although there is some contribution from distorted icosahedral ordering. It is found that even for aluminum clusters with 512 atoms distorted icosahedral ordering exists. For clusters with N>/=256 atoms fcc ordering dominates, which implies that at this point we are already on the threshold of bulklike bonding. read less NOT USED (high confidence) H. Jarmakani et al., “Molecular dynamics simulations of shock compression of nickel: From monocrystals to nanocrystals,” Acta Materialia. 2008. link Times cited: 109 NOT USED (high confidence) S. Paramore, L. Cheng, and B. Berne, “A Systematic Comparison of Pairwise and Many-Body Silica Potentials.,” Journal of chemical theory and computation. 2008. link Times cited: 15 Abstract: The role of many-body effects in modeling silica was investi… read moreAbstract: The role of many-body effects in modeling silica was investigated using self-consistent force matching. Both pairwise and polarizable classical force fields were developed systematically from ab initio density functional theory force calculations, allowing for a direct comparison of the role of polarization in silica. It was observed that the pairwise potential performed remarkably well at reproducing the basic silica tetrahedral structure. However, the Si-O-Si angle that links the silica tetrahedra showed small but distinct differences with the polarizable potential, a result of the inability of the pairwise potential to properly account for variations in the polarization of the oxygens. Furthermore, the transferability of the polarizable potential was investigated and suggests that additional forces may be necessary to more completely describe silica annealing. read less NOT USED (high confidence) Y. Cheng, E. Ma, and H. Sheng, “Alloying strongly influences the structure, dynamics, and glass forming ability of metallic supercooled liquids,” Applied Physics Letters. 2008. link Times cited: 114 Abstract: The addition of a relatively small amount of alloying elemen… read moreAbstract: The addition of a relatively small amount of alloying element(s) can induce major changes in the viscosity, fragility, and glass forming ability of supercooled liquids. A microscopic understanding of this behavior from the structural perspective has been elusive. Through comparisons between Cu–Zr–Al and Cu–Zr supercooled liquids, here we demonstrate the strong effects of Al alloying on the atomic-scale structure, in particular, the evolution of icosahedral local motifs, as well as the resulting dramatic slowing down of relaxation dynamics. The composition-structure-dynamics relationship uncovered for realistic bulk metallic glass forming liquids is important for understanding the glass transition and glass forming ability. read less NOT USED (high confidence) Q. Peng, X. Zhang, L. Hung, E. Carter, and G. Lu, “Quantum simulation of materials at micron scales and beyond,” Physical Review B. 2008. link Times cited: 39 Abstract: We present a multiscale modeling approach that can simulate … read moreAbstract: We present a multiscale modeling approach that can simulate multimillion atoms effectively via densityfunctional theory. The method is based on the framework of the quasicontinuum QC approach with orbitalfree density-functional theory OFDFT as its sole energetics formulation. The local QC part is formulated by the Cauchy-Born hypothesis with OFDFT calculations for strain energy and stress. The nonlocal QC part is treated by an OFDFT-based embedding approach, which couples OFDFT nonlocal atoms to local region atoms. The method—QCDFT—is applied to a nanoindentation study of an Al thin film, and the results are compared to a conventional QC approach. The results suggest that QCDFT represents a new direction for the quantum simulation of materials at length scales that are relevant to experiments. read less NOT USED (high confidence) M. Malshe, R. Narulkar, L. Raff, M. Hagan, S. Bukkapatnam, and R. Komanduri, “Parametrization of analytic interatomic potential functions using neural networks.,” The Journal of chemical physics. 2008. link Times cited: 29 Abstract: A generalized method that permits the parameters of an arbit… read moreAbstract: A generalized method that permits the parameters of an arbitrary empirical potential to be efficiently and accurately fitted to a database is presented. The method permits the values of a subset of the potential parameters to be considered as general functions of the internal coordinates that define the instantaneous configuration of the system. The parameters in this subset are computed by a generalized neural network (NN) with one or more hidden layers and an input vector with at least 3n-6 elements, where n is the number of atoms in the system. The Levenberg-Marquardt algorithm is employed to efficiently affect the optimization of the weights and biases of the NN as well as all other potential parameters being treated as constants rather than as functions of the input coordinates. In order to effect this minimization, the usual Jacobian employed in NN operations is modified to include the Jacobian of the computed errors with respect to the parameters of the potential function. The total Jacobian employed in each epoch of minimization is the concatenation of two Jacobians, one containing derivatives of the errors with respect to the weights and biases of the network, and the other with respect to the constant parameters of the potential function. The method provides three principal advantages. First, it obviates the problem of selecting the form of the functional dependence of the parameters upon the system's coordinates by employing a NN. If this network contains a sufficient number of neurons, it will automatically find something close to the best functional form. This is the case since Hornik et al., [Neural Networks 2, 359 (1989)] have shown that two-layer NNs with sigmoid transfer functions in the first hidden layer and linear functions in the output layer are universal approximators for analytic functions. Second, the entire fitting procedure is automated so that excellent fits are obtained rapidly with little human effort. Third, the method provides a procedure to avoid local minima in the multidimensional parameter hyperspace. As an illustrative example, the general method has been applied to the specific case of fitting the ab initio energies of Si(5) clusters that are observed in a molecular dynamics (MD) simulation of the machining of a silicon workpiece. The energies of the Si(5) configurations obtained in the MD calculations are computed using the B3LYP procedure with a 6-31G(**) basis set. The final ab initio database, which comprises the density functional theory energies of 10 202 Si(5) clusters, is fitted to an empirical Tersoff potential containing nine adjustable parameters, two of which are allowed to be the functions of the Si(5) configuration. The fitting error averaged over all 10 202 points is 0.0148 eV (1.43 kJ mol(-1)). This result is comparable to the accuracy achieved by more general fitting methods that do not rely on an assumed functional form for the potential surface. read less NOT USED (high confidence) W. Noid et al., “The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models.,” The Journal of chemical physics. 2008. link Times cited: 305 Abstract: The multiscale coarse-graining (MS-CG) method [S. Izvekov an… read moreAbstract: The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM(+)NO(3) (-) ionic liquid are provided to illustrate the method. read less NOT USED (high confidence) R. L. C. Akkermans, “Mesoscale model parameters from molecular cluster calculations.,” The Journal of chemical physics. 2008. link Times cited: 26 Abstract: We present an efficient, systematic, and universal method to… read moreAbstract: We present an efficient, systematic, and universal method to estimate the interaction parameters used in mesoscale simulation methods such as dissipative particle dynamics and self-consistent field methods from molecular cluster calculations. The method is based on a generalized Flory-Huggins model in which molecules, or fragments thereof, are in contact with their van der Waals surface. We sample the density of states of molecular clusters in the space spanned by the coarse-grained degrees of freedom. From here, we calculate the sum over states and free energy of the cluster at a temperature of interest by histogram reweighting. The method allows to calculate the energy and entropy contributions to the cluster free energy explicitly. For two components, we then obtain the excess free energy of mixing and the Flory-Huggins chi-parameter, and their energetic and entropic contributions. We present two applications of the method: a simple liquid mixture of hexane and nitrobenzene, and a series of polymer blends. In the case of hexane/nitrobenzene, we compare to alternative simulation methods; here we find that the energy of mixing alone is too high to explain the critical point. By including the excess entropy of mixing, however, the predicted phase behavior is in reasonable agreement with experiment. The tendency of calculations based on average energy alone to overestimate the chi-parameter is also apparent in the polymer blend calculations. read less NOT USED (high confidence) N. Inogamov et al., “Theoretical and experimental study of hydrodynamics of metal target irradiated by ultrashort laser pulse,” High-Power Laser Ablation. 2008. link Times cited: 11 Abstract: Theoretical consideration of the ablation of laser heated me… read moreAbstract: Theoretical consideration of the ablation of laser heated metal target based on two-temperature hydrodynamic calculation is performed for aluminum and gold targets. Concurrent with the hydrodynamic calculation the molecular dynamics simulation of the ablation was carried out in the case of aluminum. The initial state of matter for the molecular dynamics is taken as a final state of hydrodynamic calculation. Molecular dynamics simulation is extended to cover late stages of the evolution of two-phase foam placed between the crater and spalled cupola. Theoretical results are in a good agreement with the experimental data obtained by the microinterferometer diagnostics of the femtosecond laser ablation both for aluminum and gold. read less NOT 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 NOT USED (high confidence) M. Mendelev, M. Kramer, C. Becker, and M. Asta, “Analysis of semi-empirical interatomic potentials appropriate for simulation of crystalline and liquid Al and Cu,” Philosophical Magazine. 2008. link Times cited: 365 Abstract: We investigate the application of embedded atom method (EAM)… read moreAbstract: We investigate the application of embedded atom method (EAM) interatomic potentials in the study of crystallization kinetics from deeply undercooled melts, focusing on the fcc metals Al and Cu. For this application, it is important that the EAM potential accurately reproduces melting properties and liquid structure, in addition to the crystalline properties most commonly fit in its development. To test the accuracy of previously published EAM potentials and to guide the development of new potential in this work, first-principles calculations have been performed and new experimental measurements of the Al and Cu liquid structure factors have been undertaken by X-ray diffraction. We demonstrate that the previously published EAM potentials predict a liquid structure that is too strongly ordered relative to measured diffraction data. We develop new EAM potentials for Al and Cu to improve the agreement with the first-principles and measured liquid diffraction data. Furthermore, we calculate liquid-phase diffusivities and find that this quantity correlates well with the liquid structure. Finally, we perform molecular dynamics simulations of crystal nucleation from the melt during quenching at constant cooling rate. We find that EAM potentials, which predict the same zero-temperature crystal properties but different liquid structures, can lead to quite different crystallization kinetics. More interestingly, we find that two potentials predicting very similar equilibrium solid and liquid properties can still produce very different crystallization kinetics under far-from-equilibrium conditions characteristic of the rapid quenching simulations employed here. read less NOT USED (high confidence) S. Xu and X. Deng, “Nanoscale void nucleation and growth and crack tip stress evolution ahead of a growing crack in a single crystal,” Nanotechnology. 2008. link Times cited: 55 Abstract: A constrained three-dimensional atomistic model of a cracked… read moreAbstract: A constrained three-dimensional atomistic model of a cracked aluminum single crystal has been employed to investigate the growth behavior of a nanoscale crack in a single crystal using molecular dynamics simulations with the EAM potential. This study is focused on the stress field around the crack tip and its evolution during fast crack growth. Simulation results of the observed nanoscale fracture behavior are presented in terms of atomistic stresses. Major findings from the simulation results are the following: (a) crack growth is in the form of void nucleation, growth and coalescence ahead of the crack tip, thus resembling that of ductile fracture at the continuum scale; (b) void nucleation occurs at a certain distance ahead of the current crack tip or the forward edge of the leading void ahead of the crack tip; (c) just before void nucleation the mean atomic stress (or equivalently its ratio to the von Mises effective stress, which is called the stress constraint or triaxiality) has a high concentration at the site of void nucleation; and (d) the stress field ahead of the current crack tip or the forward edge of the leading void is more or less self-similar (so that the forward edge of the leading void can be viewed as the effective crack tip). read less NOT USED (high confidence) P. Chantrenne, “Multiscale simulations: application to the heat transfer simulation of sliding solids,” International Journal of Material Forming. 2008. link Times cited: 8 NOT USED (high confidence) K. Spiegel et al., “Parameterization of azole‐bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure,” Journal of Computational Chemistry. 2008. link Times cited: 31 Abstract: Azole‐bridged diplatinum compounds are promising new antican… read moreAbstract: Azole‐bridged diplatinum compounds are promising new anticancer drugs designed to induce small distortions upon DNA alkylation, able to circumvent resistance problems of existing platinum drugs. Hybrid quantum classical (QM/MM) molecular dynamics (MD) simulations of different azole‐bridged platinum drugs have recently revealed the nature of the local deformations at the DNA binding site. However, the description of global slow converging rearrangements cannot be addressed by QM/MM MD due to the short time scale accessible. Extensive classical MD simulations are therefore mandatory to describe accurately the structural distortions in the DNA double helix. This issue is now addressed by developing a new set of accurate force field parameters of the platinated moiety via a recently proposed force matching procedure of the classical forces to ab initio forces obtained from QM/MM trajectories. The accuracy of our force field parameters is validated by comparison of structural properties from classical MD and hybrid QM/MM simulations. The structural characteristics of the Pt‐lesion are well reproduced during classical MD compared with QM/MM simulations and available experimental data. The global distortions in the DNA duplex upon binding of dinuclear Pt‐compounds are very small and rather opposite to those induced by cisplatin. Thus, the force match approach significantly extends the potentialities of molecular simulations in the study of anticancer drugs and of the interactions with their biological targets. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 read less NOT USED (high confidence) G. Tóth, “Effective potentials from complex simulations: a potential-matching algorithm and remarks on coarse-grained potentials,” Journal of Physics: Condensed Matter. 2007. link Times cited: 36 Abstract: The projection of complex interactions onto simple distance-… read moreAbstract: The projection of complex interactions onto simple distance-dependent or angle-dependent classical mechanical functions is a long-standing theoretical challenge in the field of computational sciences concerning biomolecules, colloids, aggregates and simple systems as well. The construction of an effective potential may be based on theoretical assumptions, on the application of fitting procedures on experimental data and on the simplification of complex molecular simulations. Recently, a force-matching method was elaborated to project the data of Car–Parrinello ab initio molecular dynamics simulations onto two-particle classical interactions (Izvekov et al 2004 J. Chem. Phys. 120 10896). We have developed a potential-matching algorithm as a practical analogue of this force-matching method. The algorithm requires a large number of configurations (particle positions) and a single value of the potential energy for each configuration. We show the details of the algorithm and the test calculations on simple systems. The test calculation on water showed an example in which a similar structure was obtained for qualitatively different pair interactions. The application of the algorithm on reverse Monte Carlo configurations was tried as well. We detected inconsistencies in a part of our calculations. We found that the coarse graining of potentials cannot be performed perfectly both for the structural and the thermodynamic data. For example, if one applies an inverse method with an input of the pair-correlation function, it provides energetics data for the configurations uniquely. These energetics data can be different from the desired ones obtained by all atom simulations, as occurred in the testing of our potential-matching method. read less NOT USED (high confidence) P. Puri and V. Yang, “Effect of Particle Size on Melting of Aluminum at Nano Scales,” Journal of Physical Chemistry C. 2007. link Times cited: 170 Abstract: Molecular-dynamics simulations are performed using isobaric−… read moreAbstract: Molecular-dynamics simulations are performed using isobaric−isoenthalpic (NPH) ensembles to predict the melting of nanosized aluminum particles in the range of 2−9 nm and to investigate the effect of surface charge development on the melting. Five different potential functions (the Lennard-Jones, glue, embedded-atom, Streitz−Mintmire, and Sutton−Chen potentials) are implemented, and the results are evaluated using the particle-size dependence of the melting phenomenon as a benchmark. A combination of structural and thermodynamic parameters, including the potential energy, Lindemann index, translational-order parameter, and radial-distribution functions, are used to characterize the melting process. Both bulk and particle melting are considered. The former features sharp changes in structural and thermodynamic properties across the melting point, as opposed to the smooth variations seen in particle melting in which surface premelting plays an important role. The melting temperature of a nanoparticle increa... read less NOT USED (high confidence) G. Tóth, “Interactions from diffraction data: historical and comprehensive overview of simulation assisted methods,” Journal of Physics: Condensed Matter. 2007. link Times cited: 22 Abstract: A large part of statistical mechanics is concerned with the … read moreAbstract: A large part of statistical mechanics is concerned with the determination of condensed matter structure on the basis of known microscopic interactions. An increasing emphasis has been put on the opposite situation in the last decades as well, where structural data, e.g. pair-distance statistics, are known from diffraction experiments, and one looks for the corresponding interaction functions. The solution of this inverse problem was searched for within the integral equation theories of condensed matter in the early investigations, but before long computer simulation assisted methods were suggested. The interest in this field showed an increasing trend after some attempts appeared in the late 1980s. Several methods were published in the 1990s, and one–two methods appear annually nowadays. In this paper a comprehensive and historical overview is given on the solution of the inverse problem with simulation assisted methods. Emphasis is put on the theoretical grounds of the methods, on the choice of possible input structural functions, on the numerically local or global schemes of the potential modifications, on some advantages and limits of the different methods and on the scientific impact of the methods. read less NOT USED (high confidence) J. Zhou, I. F. Thorpe, S. Izvekov, and G. Voth, “Coarse-grained peptide modeling using a systematic multiscale approach.,” Biophysical journal. 2007. link Times cited: 164 Abstract: A systematic new approach to derive multiscale coarse-graine… read moreAbstract: A systematic new approach to derive multiscale coarse-grained (MS-CG) models has been recently developed. The approach employs information from atomistically detailed simulations to derive CG forces and associated effective potentials. In this work, the MS-CG methodology is extended to study two peptides representing distinct structural motifs, alpha-helical polyalanine and the beta-hairpin V(5)PGV(5). These studies represent the first known application of this approach to peptide systems. Good agreement between the MS-CG and atomistic models is achieved for several structural properties including radial distribution functions, root mean-square deviation, and radius of gyration. The new MS-CG models are able to preserve the native states of these peptides within approximately 1 A backbone root mean-square deviation during CG simulations. The MS-CG approach, as with most coarse-grained models, has the potential to increase the length and timescales accessible to molecular simulations. However, it is also able to maintain a clear connection to the underlying atomistic-scale interactions. read less NOT USED (high confidence) J. Zhong and J. B. Adams, “Adsorption and Decomposition Pathways of Vinyl Phosphonic and Ethanoic Acids on the Al(111) Surface: a Density Functional Analysis,” Journal of Physical Chemistry C. 2007. link Times cited: 12 Abstract: Density functional theory is employed to investigate optimal… read moreAbstract: Density functional theory is employed to investigate optimal adsorption geometries and binding energies of vinyl phosphonic and ethanoic acids on the Al(111) surface. Tribridged, bi-bridged, and unidentate coordinations for adsorbates are examined to determine optimal binding sites on the surface. An analysis of charge density of states of oxygen involved in reacting with aluminum ions reveals changes in atomic bonding. For these acid molecules, the favorable decomposition pathways lead to fragments of vinyl and alkyl chains bonding to the Al(111) surface with phosphorus and carbon ions. The final optimal decomposition geometries and binding energies for various decomposition stages are also discussed. read less NOT USED (high confidence) S. Iuchi, S. Izvekov, and G. Voth, “Are many-body electronic polarization effects important in liquid water?,” The Journal of chemical physics. 2007. link Times cited: 38 Abstract: Many-body electronic polarization effects may be important f… read moreAbstract: Many-body electronic polarization effects may be important for an accurate description of aqueous environments. As a result, numerous polarizable water models have been developed to include explicit polarization effects in intermolecular potential functions. In this paper, it is shown for liquid water at ambient conditions that such many-body polarization interactions can be decomposed into effective pairwise contributions using the force-matching (FM) method [Izvekov et al., J. Chem. Phys. 120, 10896 (2004)]. It is found that an effective pairwise water model obtained by the FM method can accurately reproduce various bulk structural and thermodynamic properties obtained from an accurate fully polarizable water model. In addition, the effective pairwise water model also provides a reasonable description of the water liquid-vapor interface, thus exhibiting a degree of transferability to heterogeneous environments. These results suggest that the role and importance of many-body electronic polarization effects in aqueous systems might be fruitfully explored relative to the best possible pairwise decomposable bulk phase model as the reference state. read less NOT USED (high confidence) P. Brommer and F. Gähler, “Potfit: effective potentials from ab initio data,” Modelling and Simulation in Materials Science and Engineering. 2007. link Times cited: 180 Abstract: We present a program called potfit which generates an effect… read moreAbstract: We present a program called potfit which generates an effective atomic interaction potential by matching it to a set of reference data computed in first-principles calculations. It thus allows one to perform large-scale atomistic simulations of materials with physically justified potentials. We describe the fundamental principles behind the program, emphasizing its flexibility in adapting to different systems and potential models, while also discussing its limitations. The program has been used successfully in creating effective potentials for a number of complex intermetallic alloys, notably quasicrystals. read less NOT USED (high confidence) M. Kramer, “A strategy for rapid analysis of the variations in the reduced distribution function of liquid metals and metallic glasses,” Journal of Applied Crystallography. 2007. link Times cited: 9 Abstract: Pulsed neutron sources and third-generation synchrotron sour… read moreAbstract: Pulsed neutron sources and third-generation synchrotron sources provide sufficiently high flux to acquire high wave momentum diffraction patterns suitable for pair distribution function (PDF) analysis in a matter of minutes to seconds, and even less. This allows for sequential data acquisition of a sample subjected to thermal, mechanical and even magnetic forces. Understanding the dynamics of the material's response to external stimuli will require new ways of analyzing the massive amounts of data collected during these time-resolved studies. The change in the PDF can be quickly evaluated using only the change in the measured intensities from an arbitrary initial state. With appropriate scaling factor, these can provide a quantitative measure of how the pairwise correlations change with external stimuli. read less NOT USED (high confidence) P. Brommer, F. Gähler, and M. Mihalkovi[cbreve], “Ordering and correlation of cluster orientations in CaCd6,” Philosophical Magazine. 2007. link Times cited: 10 Abstract: In order to study the low-temperature phase transition in Ca… read moreAbstract: In order to study the low-temperature phase transition in CaCd6, which is attributed to a reordering of the innermost tetrahedral cluster shells, accurate Embedded-Atom-Method potentials are developed for this system. With these potentials, the ideal cluster structure and the couplings between neighbouring clusters are determined. From these data, an effective Hamiltonian for the cluster orientations is derived. The Hamiltonian is used in Monte Carlo simulations, which exhibit a sharp jump in the internal energy near the expected transition temperature. read less NOT USED (high confidence) V. Dubois, E. Bourasseau, and J. Maillet, “New potential model for molecular dynamic simulation of liquid HF. II – Parameter optimization for repulsion-dispersion potential,” Molecular Physics. 2007. link Times cited: 2 Abstract: In order to build a complete potential model to perform clas… read moreAbstract: In order to build a complete potential model to perform classical molecular dynamic simulations of liquid HF, a new optimization method is proposed to obtain transferable parameters for repulsion-dispersion potential on the basis of ab initio reference data. This process is decomposed into two steps. The first step, using the force-matching method, consists in exploring the parameter space and selecting a first potential used as a starting point for the second step. This last step consists in optimizing the parameters of the selected potential in order to reproduce reference thermodynamic and structural data. The potential obtained correctly reproduces radial distribution functions and the pressures of liquid HF over a large range of thermodynamic states. read less NOT USED (high confidence) A. Perron, O. Politano, and V. Vignal, “Formation of surface roughness on nanocrystalline aluminium samples under straining by molecular dynamics studies,” Philosophical Magazine. 2007. link Times cited: 6 Abstract: The surface roughening of nanocrystalline aluminium samples … read moreAbstract: The surface roughening of nanocrystalline aluminium samples was investigated by molecular dynamics simulations. Attention was focused on the fact that roughness increases with the grain size and the strain. The elastic–plastic transition was found at around 3.5% strain and a reverse Hall–Petch effect was observed under straining conditions. Then, different strain distributions in grains and grain boundaries at the sample surface were highlighted, yielding to the formation of local roughness. Finally, a linear relationship between the magnitude of roughness and the out-of-plane strain component was found. read less NOT USED (high confidence) A. Mokshin, R. Yulmetyev, R. Khusnutdinov, and P. Hänggi, “Collective dynamics in liquid aluminum near the melting temperature: Theory and computer simulation,” Journal of Experimental and Theoretical Physics. 2006. link Times cited: 24 NOT USED (high confidence) S. Prudhomme, P. Bauman, and P. J. Tinsley Oden, “Error Control for Molecular Statics Problems,” International Journal for Multiscale Computational Engineering. 2006. link Times cited: 78 Abstract: In this paper, we present an extension of goal-oriented erro… read moreAbstract: In this paper, we present an extension of goal-oriented error estimation and adaptation to the simulation of multiscale problems of molecular statics. Computable error estimates for the quasicontinuum method are developed with respect to specific quantities of interest, and an adaptive strategy based on these estimates is proposed for error control. The theoretical results are illustrated on a nanoindentation problem in which the quantity of interest is the force acting on the indenter. The promising capability of such error estimates and adaptive procedure for the solution of multiscale problems is demonstrated on numerical examples. read less NOT USED (high confidence) G. Cisneros, J. P. Piquemal, and T. Darden, “Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods.,” The Journal of chemical physics. 2006. link Times cited: 98 Abstract: The simulation of biological systems by means of current emp… read moreAbstract: The simulation of biological systems by means of current empirical force fields presents shortcomings due to their lack of accuracy, especially in the description of the nonbonded terms. We have previously introduced a force field based on density fitting termed the Gaussian electrostatic model-0 (GEM-0) J.-P. Piquemal et al. [J. Chem. Phys. 124, 104101 (2006)] that improves the description of the nonbonded interactions. GEM-0 relies on density fitting methodology to reproduce each contribution of the constrained space orbital variation (CSOV) energy decomposition scheme, by expanding the electronic density of the molecule in s-type Gaussian functions centered at specific sites. In the present contribution we extend the Coulomb and exchange components of the force field to auxiliary basis sets of arbitrary angular momentum. Since the basis functions with higher angular momentum have directionality, a reference molecular frame (local frame) formalism is employed for the rotation of the fitted expansion coefficients. In all cases the intermolecular interaction energies are calculated by means of Hermite Gaussian functions using the McMurchie-Davidson [J. Comput. Phys. 26, 218 (1978)] recursion to calculate all the required integrals. Furthermore, the use of Hermite Gaussian functions allows a point multipole decomposition determination at each expansion site. Additionally, the issue of computational speed is investigated by reciprocal space based formalisms which include the particle mesh Ewald (PME) and fast Fourier-Poisson (FFP) methods. Frozen-core (Coulomb and exchange-repulsion) intermolecular interaction results for ten stationary points on the water dimer potential-energy surface, as well as a one-dimensional surface scan for the canonical water dimer, formamide, stacked benzene, and benzene water dimers, are presented. All results show reasonable agreement with the corresponding CSOV calculated reference contributions, around 0.1 and 0.15 kcal/mol error for Coulomb and exchange, respectively. Timing results for single Coulomb energy-force calculations for (H(2)O)(n), n=64, 128, 256, 512, and 1024, in periodic boundary conditions with PME and FFP at two different rms force tolerances are also presented. For the small and intermediate auxiliaries, PME shows faster times than FFP at both accuracies and the advantage of PME widens at higher accuracy, while for the largest auxiliary, the opposite occurs. read less NOT USED (high confidence) M. Mendelev, J. Schmalian, C. Wang, J. R. Morris, and K. Ho, “Interface mobility and the liquid-glass transition in a one-component system described by an embedded atom method potential,” Physical Review B. 2006. link Times cited: 32 NOT USED (high confidence) L. Proville, D. Rodney, Y. Bréchet, and G. Martin, “Atomic-scale study of dislocation glide in a model solid solution,” Philosophical Magazine. 2006. link Times cited: 39 Abstract: Based on atomic-scale simulation techniques, we study the di… read moreAbstract: Based on atomic-scale simulation techniques, we study the dislocation pinning mechanism in a dilute Ni(Al) model solid solution. For a solute concentration between 1 and 10 at.% , we found that the pinning of the dislocation on obstacles made of Al pairs is an interaction that operates significantly. The statistics of the dislocation motion is then modified accordingly to the nature of the obstacles and follows modified Mott–Nabarro statistics. Finally, a method to address thermal activation is proposed and exemplified on a periodic row of solute pairs. read less NOT USED (high confidence) V. Bulatov, W. Cai, R. Baran, and K. Kang, “Geometric aspects of the ideal shear resistance in simple crystal lattices,” Philosophical Magazine. 2006. link Times cited: 14 Abstract: We present and analyze results of a large series of atomisti… read moreAbstract: We present and analyze results of a large series of atomistic calculations of crystal resistance to shearing along rational planes of different orientations. The data computed for bcc and fcc crystals suggests that the interplanar spacing, d, is not a pertinent scaling parameter for the ideal shear resistance and that instead, plane orientation angle, θ, is a more appropriate predictor of the resistance variations among crystal planes in the same crystallographic zone. By counting the interatomic bonds reaching across the shear plane, we obtain interpolation functions that accurately match the computed resistances in the whole range of plane orientations. Entirely defined by the lattice symmetries and geometry, the interpolation functions are universal for a given crystallographic class of materials. Within a given class, material specificity of the shear resistance is accounted for with just a few scaling parameters entering the interpolation functions. read less NOT USED (high confidence) J. Hoyt, M. Asta, and D. Sun, “Molecular dynamics simulations of the crystal–melt interfacial free energy and mobility in Mo and V,” Philosophical Magazine. 2006. link Times cited: 40 Abstract: Molecular dynamics simulations, based on embedded-atom metho… read moreAbstract: Molecular dynamics simulations, based on embedded-atom method potentials, have been used to compute thermodynamic and kinetic properties of crystal–melt interfaces in the bcc metals Mo and V. The interfacial free energy and its associated crystalline anisotropy have been obtained with the capillary fluctuation method and for both metals the anisotropy and the value of the Turnbull coefficient are found to be significantly lower than for the case of fcc materials. The interface mobility, or kinetic coefficient, which relates the isothermal crystallization rate to interface undercooling, was computed by non-equilibrium molecular dynamics simulations. Mobilities in the range 9-16 cm s−1K−1 are obtained. For Mo the mobility in the (110) crystallographic growth direction is larger than in the (100) and (111) directions, whereas for V the growth is found to be isotropic within numerical uncertainty. The kinetic-coefficient results are discussed within the framework of a density-functional-based theory of crystal growth. read less NOT USED (high confidence) M. Buehler, “Atomistic and continuum modeling of mechanical properties of collagen: Elasticity, fracture, and self-assembly,” Journal of Materials Research. 2006. link Times cited: 268 Abstract: We report studies of the mechanical properties of tropocolla… read moreAbstract: We report studies of the mechanical properties of tropocollagen molecules under different types of mechanical loading including tension, compression, shear, and bending. Our modeling yields predictions of the fracture strength of single tropocollagen molecules and polypeptides, and also allows for quantification of the interactions between tropocollagen molecules. Atomistic modeling predicts a persistence length of tropocollagen molecules ξ ≈ 23.4 nm, close to experimental measurements. Our studies suggest that to describe large-strain or hyperelastic properties, it is critical to include a correct description of the bond behavior and breaking processes at large bond stretch, information that stems from the quantum chemical details of bonding. We use full atomistic calculations to derive parameters for a mesoscopic bead-spring model of tropocollagen molecules. We demonstrate that the mesoscopic model enables one to study the finite temperature, long-time scale behavior of tropocollagen fibers, illustrating the dynamics of solvated tropocollagen molecules for different molecular lengths. 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) F. Rösch, H. Trebin, and P. Gumbsch, “Interatomic potentials and the simulation of fracture: C15
NbCr2,” International Journal of Fracture. 2006. link Times cited: 12 NOT USED (high confidence) B. Lee and K. Cho, “Extended embedded-atom method for platinum nanoparticles,” Surface Science. 2006. link Times cited: 19 NOT USED (high confidence) S. Peláez, P. García-Mochales, and P. Serena, “A comparison between EAM interatomic potentials for Al and Ni: from bulk systems to nanowires,” physica status solidi (a). 2006. link Times cited: 7 Abstract: Two different kinds of interatomic potentials within the Emb… read moreAbstract: Two different kinds of interatomic potentials within the Embedded Atom Method (EAM) have been used to study several properties of selected crystalline structures and nanowire configurations (ordered and helical) for Al and Ni based systems. Reliability of these potentials has been explored when describing cohesive energy and geometrical properties of the systems under consideration as the atomic coordination number decreases. Results provide a criteria for stablishing the limits of validity of EAM potentials when applied to such systems as metallic ultra‐narrow or single atom nanowires. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) read less NOT USED (high confidence) E. Noya, J. Doye, and F. Calvo, “Theoretical study of the melting of aluminum clusters,” Physical Review B. 2006. link Times cited: 40 Abstract: The melting of Al clusters in the size range 49 <= N <= 62 h… read moreAbstract: The melting of Al clusters in the size range 49 <= N <= 62 has been studied using two model interatomic potentials. The results for the two models are significantly different. The glue potential exhibits a smooth relatively featureless heat capacity curve for all sizes except for N = 54 and N = 55, sizes at which icosahedral structures are favoured over the polytetrahedral. Gupta heat capacity curves, instead, show a well-defined peak that is indicative of a first-order-like transition. The differences between the two models reflect the different ground-state structures, and neither potential is able to reproduce or explain the size dependence of the melting transition recently observed in experiments. read less NOT USED (high confidence) P. Brommer and F. Gähler, “Effective potentials for quasicrystals from ab-initio data,” Philosophical Magazine. 2006. link Times cited: 98 Abstract: Classical effective potentials are indispensable for any lar… read moreAbstract: Classical effective potentials are indispensable for any large-scale atomistic simulations, and the relevance of simulation results crucially depends on the quality of the potentials used. For complex alloys such as quasicrystals, however, realistic effective potentials are almost non-existent. We report here our efforts to develop effective potentials especially for quasicrystalline alloy systems. We use the so-called force-matching method, in which the potential parameters are adapted so as to reproduce the forces and energies optimally in a set of suitably chosen reference configurations. These reference data are calculated with ab-initio methods. As a first application, embedded-atom method potentials for decagonal Al–Ni–Co, icosahedral Ca–Cd, and both icosahedral and decagonal Mg–Zn quasicrystals have been constructed. The influence of the potential range and degree of specialization on the accuracy and other properties is discussed and compared. read less NOT USED (high confidence) F. Rösch, H. Trebin, and P. Gumbsch, “Fracture of complex metallic alloys: an atomistic study of model systems,” Philosophical Magazine. 2006. link Times cited: 10 Abstract: Molecular dynamics simulations of crack propagation are perf… read moreAbstract: Molecular dynamics simulations of crack propagation are performed for two extreme cases of complex metallic alloys. In a model quasicrystal the structure is determined by clusters of atoms, whereas the model C15 Laves phase is a simple periodic stacking of a unit cell. The simulations reveal that the basic building units of the structures also govern their fracture behaviour. Atoms in the Laves phase play a comparable role with the clusters in the quasicrystal. Although the latter are not rigid units, they have to be regarded as significant physical entities. read less NOT USED (high confidence) G. Grochola, S. Russo, and I. Snook, “On fitting a gold embedded atom method potential using the force matching method.,” The Journal of chemical physics. 2005. link Times cited: 232 Abstract: We fit a new gold embedded atom method (EAM) potential using… read moreAbstract: We fit a new gold embedded atom method (EAM) potential using an improved force matching methodology which included fitting to high-temperature solid lattice constants and liquid densities. The new potential shows a good overall improvement in agreement to the experimental lattice constants, elastic constants, stacking fault energy, radial distribution function, and fcc/hcp/bcc lattice energy differences over previous potentials by Foiles, Baskes, and Daw (FBD) [Phys. Rev. B 33, 7983 (1986)] Johnson [Phys. Rev. B 37, 3924 (1988)], and the glue model potential by Ercolessi et al. [Philos. Mag. A 50, 213 (1988)]. Surface energy was improved slightly as compared to potentials by FBD and Johnson but as a result vacancy formation energy is slightly inferior as compared to the same potentials. The results obtained here for gold suggest for other metal species that further overall improvements in potentials may still be possible within the EAM framework with an improved fitting methodology. On the other hand, we also explore the limitations of the EAM framework by attempting a brute force fit to all properties exactly which was found to be unsuccessful. The main conflict in such a brute force fit was between the surface energy and the liquid lattice constant where both could not be fitted identically. By intentionally using a very large number of spline sections for the pair potential, electron-density function, and embedding energy function, we eliminated a lack of functional freedom as a possible cause of this conflict and hence can conclude that it must result from a fundamental limitation in the EAM framework. read less NOT USED (high confidence) S. Izvekov and G. Voth, “Multiscale coarse graining of liquid-state systems.,” The Journal of chemical physics. 2005. link Times cited: 509 Abstract: A methodology is described to systematically derive coarse-g… read moreAbstract: A methodology is described to systematically derive coarse-grained (CG) force fields for molecular liquids from the underlying atomistic-scale forces. The coarse graining of an interparticle force field is accomplished by the application of a force-matching method to the trajectories and forces obtained from the atomistic trajectory and force data for the CG sites of the targeted system. The CG sites can be associated with the centers of mass of atomic groups because of the simplicity in the evaluation of forces acting on these sites from the atomistic data. The resulting system is called a multiscale coarse-grained (MS-CG) representation. The MS-CG method for liquids is applied here to water and methanol. For both liquids one-site and two-site CG representations without an explicit treatment of the long-ranged electrostatics have been derived. In addition, for water a two-site model having the explicit long-ranged electrostatics has been developed. To improve the thermodynamic properties (e.g., pressure and density) for the MS-CG models, the constraint for the instantaneous virial was included into the force-match procedure. The performance of the resulting models was evaluated against the underlying atomistic simulations and experiment. In contrast with existing approaches for coarse graining of liquid systems, the MS-CG approach is general, relies only on the interatomic interactions in the reference atomistic system. read less NOT USED (high confidence) Y. Mishin, M. Mehl, D. Papaconstantopoulos, and D. Papaconstantopoulos, “Phase stability in the Fe–Ni system: Investigation by first-principles calculations and atomistic simulations,” Acta Materialia. 2005. link Times cited: 261 NOT USED (high confidence) G. Tabacchi, J. Hutter, and C. Mundy, “A density-functional approach to polarizable models: a Kim-Gordon response density interaction potential for molecular simulations.,” The Journal of chemical physics. 2005. link Times cited: 15 Abstract: A combined linear-response-frozen electron-density model has… read moreAbstract: A combined linear-response-frozen electron-density model has been implemented in a molecular-dynamics scheme derived from an extended Lagrangian formalism. This approach is based on a partition of the electronic charge distribution into a frozen region described by Kim-Gordon theory [J. Chem. Phys. 56, 3122 (1972); J. Chem. Phys. 60, 1842 (1974)] and a response contribution determined by the instantaneous ionic configuration of the system. The method is free from empirical pair potentials and the parametrization protocol involves only calculations on properly chosen subsystems. We apply this method to a series of alkali halides in different physical phases and are able to reproduce experimental structural and thermodynamic properties with an accuracy comparable to Kohn-Sham density-functional calculations. read less NOT USED (high confidence) G. Lu, E. Tadmor, and E. Kaxiras, “From Electrons to Finite Elements: A Concurrent Multiscale Approach for Metals,” Physical Review B. 2005. link Times cited: 113 Abstract: Department of Physics and Division of Engineering and Applie… read moreAbstract: Department of Physics and Division of Engineering and Applied Sciences,Harvard University, Cambridge, Massachusetts 02138(Dated: February 2, 2008)We present a multiscale modeling approach that concurrently couples quantum mechanical, classi-cal atomistic and continuum mechanics simulations in a unified fashion for metals. This approach isparticular useful for systems where chemical interactions in a small region can affect the macroscopicproperties of a material. We discuss how the coupling across different scales can be accomplishedefficiently, and we apply the method to multiscale simulations of an edge dislocation in aluminumin the absence and presence of H impurities. read less NOT USED (high confidence) M. Soare and R. C. P. †, “Singular field decomposition based on path-independent integrals,” Philosophical Magazine. 2004. link Times cited: 5 Abstract: A method is developed by which the field generated by a sour… read moreAbstract: A method is developed by which the field generated by a source (measured or numerically evaluated) is decomposed in a series of singular self-equilibrating linear elastic field components. These elementary sources form an elastic equivalent of the real source, the set of their magnitudes representing a ‘spectral decomposition’ of the investigated field. The decomposition is performed using path–independent interaction integrals computed through the field of interest, far from the source. The method may be used to investigate internal field sources, such as dislocations, as well as sources of field perturbation, such as crack tips or wedges. The method is applied to the analysis of the core structure of an edge dislocation in aluminium. The dislocation is represented in an atomistic simulation and a model core is sought in the form of a series of multipoles or elementary linear elastic field sources. The field of the dislocation is composed from the Volterra solution and higher–order components induced by the nonlinear behaviour of the material in the core region. The magnitude of the component elementary sources is determined from the numerically evaluated field far from the core. This expansion characterizes the core structure. Its variation associated with the core deformation as the dislocation is loaded against the Peierls barrier is investigated. read less NOT USED (high confidence) R. Boyer, J. Li, S. Ogata, and S. Yip, “Analysis of shear deformations in Al and Cu: empirical potentials versus density functional theory,” Modelling and Simulation in Materials Science and Engineering. 2004. link Times cited: 40 Abstract: Multiplane shear deformation behaviour in face-centred cubic… read moreAbstract: Multiplane shear deformation behaviour in face-centred cubic metals, aluminium and copper, is studied and empirical many-body potential results are directly compared with ab initio electronic structure calculations. An analysis of stress–displacement, atomic relaxation, and gamma-surface for shear indicates that the potential for copper proposed by Mishin is able to capture the essential deformation behaviour. For aluminium the Mishin potential gives better results than the Ercolessi model in atomic relaxation and stress–displacement, although there remain details that neither are able to describe. Aluminium presents a greater challenge to empirical potential description because of the directional nature of its interatomic bonding. 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) K. Németh and M. Challacombe, “The quasi-independent curvilinear coordinate approximation for geometry optimization.,” The Journal of chemical physics. 2004. link Times cited: 20 Abstract: This paper presents an efficient alternative to well establi… read moreAbstract: This paper presents an efficient alternative to well established algorithms for molecular geometry optimization. This approach exploits the approximate decoupling of molecular energetics in a curvilinear internal coordinate system, allowing separation of the 3N-dimensional optimization problem into an O(N) set of quasi-independent one-dimensional problems. Each uncoupled optimization is developed by a weighted least squares fit of energy gradients in the internal coordinate system followed by extrapolation. In construction of the weights, only an implicit dependence on topologically connected internal coordinates is present. This new approach is competitive with the best internal coordinate geometry optimization algorithms in the literature and works well for large biological problems with complicated hydrogen bond networks and ligand binding motifs. read less NOT USED (high confidence) A. Verma, R. Rao, and B. Godwal, “Theoretical solid and liquid state shock Hugoniots of Al, Ta, Mo and W,” Journal of Physics: Condensed Matter. 2004. link Times cited: 29 Abstract: We present the Hugoniots of Al, Ta, Mo and W in their solid … read moreAbstract: We present the Hugoniots of Al, Ta, Mo and W in their solid as well as liquid phases. The liquid phase calculations are carried out on the basis of the corrected rigid spheres (CRIS) model. The 0 K isotherm of the solid phases, which are the necessary inputs for our computations, have been obtained by full potential first principles electronic structure calculations with generalized gradient approximation (GGA) for the exchange–correlation terms. The melting curve as a function of pressure was obtained according to the recently published model based on dislocation mediated melting, and also compared with that using Lindemann criterion. Though the adiabatic pressure–volume curve is affected little by melting, the pressure–temperature curve shows substantial change. read less NOT USED (high confidence) X. Liu, F. Ercolessi, and J. B. Adams, “Aluminium interatomic potential from density functional theory calculations with improved stacking fault energy,” Modelling and Simulation in Materials Science and Engineering. 2004. link Times cited: 147 Abstract: A new Al potential with improved stacking fault energy is co… read moreAbstract: A new Al potential with improved stacking fault energy is constructed using the force-matching method. The potential is fitted to an ab initio forces database and various experimental data. By using a slightly larger cut-off, we found that the new potential gives the relaxed stacking fault energy in the experimental range without changing the excellent thermal and surface properties of the original force-matching Al potential given by Ercolessi and Adams (1994 Europhys. Lett. 26 583). read less NOT USED (high confidence) S. Izvekov, M. Parrinello, C. Burnham, and G. Voth, “Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching.,” The Journal of chemical physics. 2004. link Times cited: 364 Abstract: A novel least-squares fitting approach is presented to obtai… read moreAbstract: A novel least-squares fitting approach is presented to obtain classical force fields from trajectory and force databases produced by ab initio (e.g., Car-Parrinello) molecular dynamics (MD) simulations. The method was applied to derive effective nonpolarizable three-site force fields for liquid water at ambient conditions from Car-Parrinello MD simulations in the Becke-Lee-Yang-Parr approximation to the electronic density functional theory. The force-matching procedure includes a fit of short-ranged nonbonded forces, bonded forces, and atomic partial charges. The various parameterizations of the water force field differ by an enforced smooth cut-off applied to the short-ranged interaction term. These were obtained by fitting to the trajectory and force data produced by Car-Parrinello MD simulations of systems of 32 and 64 H(2)O molecules. The new water force fields were developed assuming both flexible or rigid molecular geometry. The simulated structural and self-diffusion properties of liquid water using the fitted force fields are in close agreement with those observed in the underlying Car-Parrinello MD simulations. The resulting empirical models compare to experiment much better than many conventional simple point charge (SPC) models. The fitted potential is also shown to combine well with more sophisticated intramolecular potentials. Importantly, the computational cost of the new models is comparable to that for SPC-like potentials. read less NOT USED (high confidence) R. Pasianot and A. Moreno-Gobbi, “On the Peierls stress in Al and Cu: An atomistic simulation and comparison with experiment,” physica status solidi (b). 2004. link Times cited: 6 Abstract: An atomistic calculation of the Peierls stress in Al and Cu … read moreAbstract: An atomistic calculation of the Peierls stress in Al and Cu is undertaken in order to assess consistency with experiments. The measured yield stress extrapolated to 0 K results at least one order of magnitude smaller than the Peierls stress commonly derived from internal friction data. On the theoretical side, some calculations for Al are already available (using different approaches than presently) however none is for Cu. The simulations employ semi‐empirical many‐body interatomic potentials, fitted here to the generalized stacking fault energy surface (calculated elsewhere with ab initio electronic structure methods), as well as others from the literature. After a critical assessment, reasonable agreement is demonstrated between our results and the Peierls stress values derived from internal friction experiments within the framework of the kink pair formation model. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) read less NOT USED (high confidence) N. Choly, G. Lu, E. Weinan, and E. Kaxiras, “Multiscale simulations in simple metals: A density-functional-based methodology,” Physical Review B. 2004. link Times cited: 99 Abstract: We present a formalism for coupling a density-functional-the… read moreAbstract: We present a formalism for coupling a density-functional-theory-based quantum simulation to a classical simulation for the treatment of simple metallic systems. The formalism is applicable to multiscale simulations in which the part of the system requiring quantum-mechanical treatment is spatially confined to a small region. Such situations often arise in physical systems where chemical interactions in a small region can affect the macroscopic mechanical properties of a metal. We describe how this coupled treatment can be accomplished efficiently, and we present a coupled simulation for a bulk aluminum system. read less NOT USED (high confidence) T. Iwasaki, “Molecular-Dynamics Analysis of Interfacial Diffusion Between High-Permittivity Gate Dielectrics And Silicon Substrates,” Journal of Materials Research. 2004. link Times cited: 8 Abstract: Interfacial oxygen diffusion from high-permittivity gate die… read moreAbstract: Interfacial oxygen diffusion from high-permittivity gate dielectrics (ZrO_2 and HfO_2) into Si substrates in ultra-large-scale integrated circuits must be suppressed to prevent the formation of interfacial layers between the gate dielectrics and the Si substrates. Oxygen diffusion was analyzed by using a molecular dynamics technique that includes many-body interactions and charge transfer between different elements. The analysis results showed that the addition of Ti is effective in suppressing interfacial oxygen diffusion. The results also showed that the diffusion at the ZrO_2/Si(111) and HfO_2/Si(111) interfaces is much more suppressed than the diffusion at the ZrO_2/Si(001) and HfO_2/Si(001) interfaces. read less NOT USED (high confidence) W. Lai, Y. Osetsky, and D. Bacon, “Point-defect properties of and sputtering events in the 001 surfaces of Ni3Al I. Surface and point-defect properties,” Philosophical Magazine. 2004. link Times cited: 7 Abstract: Constant-area and fully relaxed molecular dynamics methods a… read moreAbstract: Constant-area and fully relaxed molecular dynamics methods are employed to study the properties of the surface and point defects at and near {001} surfaces of bulk and thin-film Ni, Al and Ni3Al respectively. The surface tension is larger than the surface energy for all {001} surfaces considered in the sequence: Al (1005 mJ m−2)< Ni3Al (mixed Ni–Al plane outermost, 1725 mJ m−2)< Ni3Al (all-Ni-atoms plane outermost, 1969 mJ m−2)< Ni (1993 mJ m−2). For a surface of bulk Ni3Al crystal with a Ni–Al mixed plane outermost, Al atoms stand out by 0.0679 Å compared with the surface Ni atoms and, for the all-Ni-atoms surface, Al atoms in the second layer stand out by 0.0205 Å compared with Ni atoms in the same layer. Vacancy formation energies are about half the bulk values in the first layer and reach a maximum in the second layer where the atomic energy is close to the bulk value but the change in embedding energy of neighbouring atoms before and after vacancy formation is greater than that in the bulk. Both the vacancy formation energy and the surface tension suggest that the fourth layer is in a bulk state for all the surfaces. The formation energy of adatoms, antisite defects and point-defect pairs at and near {001} surfaces of Ni3Al are also given. read less NOT USED (high confidence) M. Mendelev, S. Han, D. Srolovitz, G. Ackland, D. Sun, and M. Asta, “Development of new interatomic potentials appropriate for crystalline and liquid iron,” Philosophical Magazine. 2003. link Times cited: 1093 Abstract: Two procedures were developed to fit interatomic potentials … read moreAbstract: Two procedures were developed to fit interatomic potentials of the embedded-atom method (EAM) form and applied to determine a potential which describes crystalline and liquid iron. While both procedures use perfect crystal and crystal defect data, the first procedure also employs the first-principles forces in a model liquid and the second procedure uses experimental liquid structure factor data. These additional types of information were incorporated to ensure more reasonable descriptions of atomic interactions at small separations than is provided using standard approaches, such as fitting to the universal binding energy relation. The new potentials (provided herein) are, on average, in better agreement with the experimental or first-principles lattice parameter, elastic constants, point-defect energies, bcc–fcc transformation energy, liquid density, liquid structure factor, melting temperature and other properties than other existing EAM iron potentials. read less NOT USED (high confidence) J. Doye, “Identifying structural patterns in disordered metal clusters,” Physical Review B. 2003. link Times cited: 37 Abstract: University Chemical Laboratory, Lensfield Road, Cambridge CB2… read moreAbstract: University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom(Dated: February 2, 2008)Zinc and cadmium clusters interacting with a Gupta potential have previously been identified asprototypical metallic systems that exhibiting disordered cluster structures. Here, putative globalminima of the potential energy have been located for these clusters for all sizes up to N ≤ 125.Although none of the usual structural forms are lowest in energy and many of the clusters have nooverall order, strong structural preferences have been identified. Many of the clusters are based ondistorted oblate Marks decahedra, where the distortion involves the bringing together of atoms oneither side of a re-entrant groove of the Marks decahedron.I. INTRODUCTION read less NOT USED (high confidence) B. G. Janesko and D. Yaron, “Using molecular similarity to construct accurate semiempirical electronic structure theories.,” The Journal of chemical physics. 2003. link Times cited: 8 Abstract: Ab initio electronic structure methods give accurate results… read moreAbstract: Ab initio electronic structure methods give accurate results for small systems, but do not scale well to large systems. Chemical insight tells us that molecular functional groups will behave approximately the same way in all molecules, large or small. This molecular similarity is exploited in semiempirical methods, which couple simple electronic structure theories with parameters for the transferable characteristics of functional groups. We propose that high-level calculations on small molecules provide a rich source of parametrization data. In principle, we can select a functional group, generate a large amount of ab initio data on the group in various small-molecule environments, and "mine" this data to build a sophisticated model for the group's behavior in large environments. This work details such a model for electron correlation: a semiempirical, subsystem-based correlation functional that predicts a subsystem's two-electron density matrix as a functional of its one-electron density matrix. This model is demonstrated on two small systems: chains of linear, minimal-basis (H-H)(5), treated as a sum of four overlapping (H-H)(2) subsystems; and the aldehyde group of a set of HOC-R molecules. The results provide an initial demonstration of the feasibility of the approach. 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) J. Hoyt, M. Asta, and A. Karma, “Atomistic and continuum modeling of dendritic solidification,” Materials Science & Engineering R-reports. 2003. link Times cited: 332 NOT USED (high confidence) P. Tangney and S. Scandolo, “A many-body interatomic potential for ionic systems: Application to MgO,” Journal of Chemical Physics. 2003. link Times cited: 31 Abstract: An analytic representation of the short-range repulsion ener… read moreAbstract: An analytic representation of the short-range repulsion energy in ionic systems is described that allows for the fact that ions may change their size and shape depending on their environment. This function is extremely efficient to evaluate relative to previous methods of modeling the same physical effects. Using a well-defined parametrization procedure we have obtained parameter sets for this energy function that reproduce closely the density functional theory potential energy surface of bulk MgO. We show how excellent agreement can be obtained with experimental measurements of phonon frequencies and temperature and pressure dependences of the density by using this effective potential in conjunction with ab initio parametrization. read less 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) X. Duan and X. Gong, “Local bias potential in hyper molecular dynamics method,” Computational Materials Science. 2003. link Times cited: 5 NOT USED (high confidence) V.Sorkin, E. Polturak, and J. Adler, “Molecular dynamics study of melting of the bcc metal vanadium. I. Mechanical melting,” Physical Review B. 2003. link Times cited: 49 Abstract: We present molecular dynamics simulations of the homogeneous… read moreAbstract: We present molecular dynamics simulations of the homogeneous (mechanical) melting transition of a bcc metal, vanadium. We study both the nominally perfect crystal and one that includes point defects. According to the Borncriterion, a solid cannot be expanded above a critical volume, at which a "rigidity catastrophe" occurs. This catastrophe is caused by the vanishing of the elastic shear modulus. We found that this critical volume is independent of the route by which it is reached, whether by heating the crystal or by adding interstitials at a constant temperature which expand the lattice. Overall, these results are similar to what was found previously for an fcc metal, copper. The simulations establish a phase diagram of the mechanical melting temperature as a function of the concentration of interstitials. Our results show that the Born model of melting applies to bcc metals in both the nominally perfect state and the case where point defects are present. read less NOT USED (high confidence) Y. Li, D. J. Siegel, J. B. Adams, and X.-Y. Liu, “Embedded-atom-method tantalum potential developed by the force-matching method,” Physical Review B. 2003. link Times cited: 104 Abstract: An embedded-atom-method potential for tantalum (Ta) has been… read moreAbstract: An embedded-atom-method potential for tantalum (Ta) has been carefully constructed by fitting to a combination of experimental and density-functional theory (DFT) data. The fitted data include the elastic constants, lattice constant, cohesive energy, unrelaxed vacancy formation energy, and hundreds of force data calculated by DFT for a variety of structures such as liquids, surfaces, clusters, interstitials, vacancies, and stacking faults. We also fit to the cohesive energy vs volume data from the equation of state for the body-centered-cubic (bcc) Ta and to the calculated cohesive energy using DFT for the face-centered-cubic (fcc) Ta structure. We assess the accuracy of the new potential by comparing several calculated Ta properties with those obtained from other potentials previously reported in the literature. In many cases, the new potential yields superior accuracy at a comparable or lower computational cost. read less NOT USED (high confidence) J. Hoyt, J. W. Garvin, E. B. Webb, and M. Asta, “An embedded atom method interatomic potential for the Cu–Pb system,” Modelling and Simulation in Materials Science and Engineering. 2003. link Times cited: 57 Abstract: A simple procedure is used to formulate a Cu–Pb pair interac… read moreAbstract: A simple procedure is used to formulate a Cu–Pb pair interaction function within the embedded atom (EAM) method framework. Embedding, density and pair functions for pure Cu and pure Pb are taken from previously published EAM studies. Optimization of the Cu–Pb potential was achieved by comparing with experiment the computed heats of mixing for Cu–Pb liquid alloys and the equilibrium phase diagram, the latter being determined via a thermodynamic integration technique. The topology of the temperature-composition phase diagram computed with this EAM potential is consistent with experiment and features a liquid–liquid miscibility gap, low solubility of Pb in solid Cu and a monotectic reaction at approximately 1012 K. read less NOT USED (high confidence) J. Doye, “A model metal potential exhibiting polytetrahedral clusters,” Journal of Chemical Physics. 2003. link Times cited: 44 Abstract: Putative global minima have been located for clusters intera… read moreAbstract: Putative global minima have been located for clusters interacting with an aluminum glue potential for N⩽190. Virtually all the clusters have polytetrahedral structures, which for larger sizes involve an ordered array of disclinations that are similar to those in the Z, H, and σ Frank–Kasper phases. Comparisons of sequences of larger clusters suggest that the majority of the global minima will adopt the bulk face-centered-cubic structure beyond N≈500. read less NOT USED (high confidence) F. M. Márquez et al., “Semigrand-canonical ensemble simulations of the phase diagrams of alloys,” Modelling and Simulation in Materials Science and Engineering. 2003. link Times cited: 19 Abstract: We show how Monte Carlo simulations with the explicit interc… read moreAbstract: We show how Monte Carlo simulations with the explicit interchange of atoms and the use of the semigrand-canonical ensemble, can be used to calculate phase diagrams for alloys. We illustrate our approach with the system Pd/Rh using the embedded atom method with potential parameters derived from ab initio density functional calculations. Our techniques take full account of local structural distortion, clustering and thermal effects. read less NOT USED (high confidence) K. Merkle, L. J. Thompson, and F. Phillipp, “Thermally activated step motion observed by high-resolution electron microscopy at a (113) symmetric tilt grain-boundary in aluminium,” Philosophical Magazine Letters. 2002. link Times cited: 22 Abstract: Grain-boundary migration is demonstrated to proceed by later… read moreAbstract: Grain-boundary migration is demonstrated to proceed by lateral propagation of a small step in a (113), [110] symmetric Al tilt grain-boundary. In-situ high-resolution (transmission) electron microscopy (HREM) at 523K allowed the study of atomic-scale detail at video rates during the migration process. The grain-boundary translational states on both sides of the step are identical, which leads to a step dislocation. This defect can move laterally by a combination of climb and glide. Dynamic HREM images indicate considerable atomic agitation within the dislocation core. A detailed temporal analysis of the step movements shows small random displacements of the dislocation core. read less NOT USED (high confidence) G. Tabacchi, C. Mundy, J. Hutter, and M. Parrinello, “Classical polarizable force fields parametrized from ab initio calculations,” Journal of Chemical Physics. 2002. link Times cited: 56 Abstract: A computationally efficient molecular dynamics implementatio… read moreAbstract: A computationally efficient molecular dynamics implementation of a polarizable force field parametrized from ab initio data is presented. Our formulation, based on a second-order expansion of the energy density, models the density response using Gaussian basis functions derived from density functional linear response theory. Polarization effects are described by the time evolution of the basis function coefficients propagated via an extended Lagrangian formalism. We have devised a general protocol for the parametrization of the force field. We will show that a single parametrization of the model can describe the polarization effects of LiI in the condensed phase. read less NOT USED (high confidence) T. Rahman, J. Spangler, and A. Al-Rawi, “Theoretical studies of the surface phonon linewidth,” Journal of Physics: Condensed Matter. 2002. link Times cited: 9 Abstract: A brief review of two theoretical methods for calculating th… read moreAbstract: A brief review of two theoretical methods for calculating the linewidth of surface phonons is presented with specific application to the low-Miller-index surfaces of Ag, Cu, and Al. In the quasi-analytic method, linewidths are calculated by treating the cubic term of a reliable interatomic potential in first-order, time-dependent perturbation theory. In molecular dynamics?(MD) simulations, linewidths are obtained from appropriate correlation functions and include the fully anharmonic contribution of the interaction potential. Surface relaxations and phonon frequencies calculated in the harmonic approximation, using selected many-body interatomic potentials, are found to be in good agreement with results from experimental data and ab initio calculations. At 300?K, the surface phonon linewidths range approximately between?1 and 0.1?THz, and are found to be in reasonable agreement with the values deduced from experiments. Some disagreement is found between results from perturbative methods and MD simulations. For the low-Miller-index surfaces of Ni, available results from MD simulations also summarized. 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) D. Alfé, M. Gillan, and G. D. Price, “Complementary approaches to the ab initio calculation of melting properties,” Journal of Chemical Physics. 2001. link Times cited: 79 Abstract: Several research groups have recently reported ab initio cal… read moreAbstract: Several research groups have recently reported ab initio calculations of the melting properties of metals based on density functional theory, but there have been unexpectedly large disagreements between results obtained by different approaches. We analyze the relations between the two main approaches, based on calculation of the free energies of solid and liquid and on direct simulation of the two coexisting phases. Although both approaches rely on the use of classical reference systems consisting of parametrized empirical interaction models, we point out that in the free energy approach the final results are independent of the reference system, whereas in the current form of the coexistence approach they depend on it. We present a scheme for correcting the predictions of the coexistence approach for differences between the reference and ab initio systems. To illustrate the practical operation of the scheme, we present calculations of the high-pressure melting properties of iron using the corrected coexis... read less NOT USED (high confidence) J. B. Adams, L. Hector, D. J. Siegel, H. Yu, and J. Zhong, “Adhesion, lubrication and wear on the atomic scale,” Surface and Interface Analysis. 2001. link Times cited: 50 Abstract: This paper reviews three important aspects of tribology (adh… read moreAbstract: This paper reviews three important aspects of tribology (adhesion, lubrication and wear) on the atomic scale with a focus on our work on aluminum surfaces. Adhesion is critical to the success of many applications but there is no simple analytical model available to predict adhesion between different materials, so we discuss the use of electronic structure methods to investigate adhesion between Al and various ceramics to determine the factors that control adhesion. Lubricants used to control friction usually include ‘boundary additives’ to bind the lubricant more strongly to the surface, so that higher stresses can be employed and wear can be reduced. Little is known about how boundary additives bond to Al surfaces, so we used electronic structure methods to investigate that phenomenon. Regarding wear, we review the literature on molecular dynamics simulations to investigate nanoindentation and wear. We discuss our molecular dynamics simulations of nanoindentation and asperity–asperity shear and the effect of temperature, loading rate, interaction strength and geometry. Copyright © 2001 John Wiley & Sons, Ltd. read less NOT USED (high confidence) M. Baskes, M. Asta, and S. G. Srinivasan, “Determining the range of forces in empirical many-body potentials using first-principles calculations,” Philosophical Magazine A. 2001. link Times cited: 26 Abstract: A computationally efficient and accurate description of inte… read moreAbstract: A computationally efficient and accurate description of interatomic interactions is indispensable to the fidelity of atomistic simulations. In the development of popular empirical potentials, it is assumed that atoms separated beyond a certain cut-off distance have negligible interatomic forces and hence may be safely ignored in the force calculations. This arbitrary, and yet common, practice of force truncation is undoubtedly ad hoc and is not grounded in the physics of the interactions. With the advent of fast computers and accurate first-principles calculations, it is now feasible to determine what this cut-off distance should be. In this work, employing a first-principles calculation based on density functional theory and the local density approximation (LDA) we probe the extent of interatomic forces in aluminium caused by a variety of defect types. The forces on neighbours to these defects, obtained from first-principles calculations, were then compared with the corresponding values from many short- and long-range semiempirical literature potentials. It is clear that none of these semiempirical potentials can reproduce the LDA results, although the newest potentials that use LDA force data for potential determination come close. The results also indicate that nearest-neighbour forces are dominant for zero- and one-dimensional defects. Only for a free surface did we find forces at more distant neighbours to be comparable in magnitude. Using the new LDA force data for the single vacancy, we modify a literature potential to improve significantly the agreement with the first-principles calculations. read less NOT USED (high confidence) C. S. Liu, Z.-jie Zhu, J. Xia, and D. Sun, “Cooling rate dependence of structural properties of aluminium during rapid solidification,” Journal of Physics: Condensed Matter. 2001. link Times cited: 34 Abstract: Constant-pressure molecular dynamics simulations and a syste… read moreAbstract: Constant-pressure molecular dynamics simulations and a systematic analysis of the local atomic structures have been performed to study the structural evolution of aluminium on different cooling runs. The regular and defective icosahedral atomic configurations depend strongly on the cooling rate, which is responsible for the cooling rate dependence of the enthalpy. In the simulated amorphous aluminium there exist three kinds of microstructure unit that do not depend on the cooling rate. Two of them are similar to those in the fcc crystal containing interstitialcy and hardly change with decreasing temperature after the glass formation. The third can be considered as crystal germs. Our results also suggest that there exists a critical cooling rate below which the icosahedra form a percolating cluster and the glass exhibits high stability. At a certain quenching rate that is slower than this critical cooling rate, the strength of the icosahedron clusters infinite network may have a saturation value, i.e. a maximum. This may be the origin of the existence of an ideal quenching rate at which the glass exhibits the highest structural stability. 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) 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 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) R. Phillips, D. Rodney, V. Shenoy, E. Tadmor, and M. Ortiz, “Hierarchical models of plasticity: dislocation nucleation and interaction,” Modelling and Simulation in Materials Science and Engineering. 1999. link Times cited: 52 Abstract: One avenue being pursued in the development of dislocation-b… read moreAbstract: One avenue being pursued in the development of dislocation-based models of plasticity is the explicit simulation of the dynamics of dislocations, based on the recognition that such dislocations are the carriers of plasticity. The construction of models of dislocation dynamics requires insights into both the nucleation and interaction of dislocations, many of the details of which fall outside the domain of validity of the linear theory of elasticity. The aim of the present paper is to show how preliminary steps have been made to elucidate the mechanisms of dislocation nucleation and interaction, and to illustrate how such information can be imported into explicit models of dislocation dynamics. This effort reflects, in part, the research program of Gilles Canova, to whom the present volume is dedicated and to whom the authors dedicate this paper. read less NOT USED (high confidence) M. Sarychev, Y. Zhitnikov, L. Borucki, C. Liu, and T. Makhviladze, “General model for mechanical stress evolution during electromigration,” Journal of Applied Physics. 1999. link Times cited: 158 Abstract: A model is presented for the development of stress during el… read moreAbstract: A model is presented for the development of stress during electromigration. Formally similar to a thermal stress model, it provides a method of calculating all of the components of the stress tensor and clearly couples vacancy transport and stress evolution with the boundary conditions that apply to the metal. Analytic solutions are discussed for electromigration either normal or parallel to a plate. The solution parallel to a plate is used to reinterpret x-ray microdiffraction experiments from the literature. We find that the effective charge for vacancies in pure polycrystalline aluminum at 533 K is about 0.84. Using parameters that were either measured or calculated with the embedded atom method, our model displays good agreement with both transient electromigration data and drift data. read less NOT USED (high confidence) D. Sun, Y. Xiang, and X. Gong, “Interatomic potential fitted for lead,” Philosophical Magazine. 1999. link Times cited: 2 Abstract: By using the recently improved generalized-simulated-anneali… read moreAbstract: By using the recently improved generalized-simulated-annealing algorithm and the molecular dynamics method, we numerically fit an interatomic potential for lead. The potential obtained can correctly reproduce many physical properties of lead in crystalline and non-crystalline phases. The surface energy and surface relaxation obtained are in good agreement with the experimental results. The melting point predicted by this potential is very close to the experimental data. The present potential is used to study the surface melting and liquid structure; good agreement with experimental results is observed. read less NOT USED (high confidence) M. López and J. Jellinek, “On the problem of fitting many-body potentials. I. The minimal maximum error scheme and the paradigm of metal systems,” Journal of Chemical Physics. 1999. link Times cited: 34 Abstract: Issues involved in fitting a semiempirical potential, such a… read moreAbstract: Issues involved in fitting a semiempirical potential, such as the choice of a goodness criterion, selection of fitting quantities (properties), ascription of the degree of importance to the individual members of a fitting set, etc., all of which affect the outcome of a fitting procedure, are addressed and analyzed. The minimal maximum error fitting scheme is implemented to obtain the values of the parameters of the Gupta-type potential for nickel. The subtleties of this potential, one of which is that only four of its five parameters are independent, and their implications are pointed out and discussed. The resulting values of the parameters for nickel are analyzed and compared with those obtained in earlier studies. read less NOT USED (high confidence) I. Garzón, I. Kaplan, R. Santamaria, and O. Novaro, “Molecular dynamics study of the Ag6 cluster using an ab initio many-body model potential,” Journal of Chemical Physics. 1998. link Times cited: 21 Abstract: A general approach to construct a model potential with param… read moreAbstract: A general approach to construct a model potential with parameters fitted to ab initio energy surfaces, including many-body nonadditive effects, developed in our previous works is applied to the Ag6 cluster. A molecular dynamics study of structural and dynamical properties of this cluster is performed using such a potential. Two new stable two-dimensional isomers with C2v and C2h symmetries are identified as local minima of the potential surface using the simulated quenching technique. An analysis of the thermal stability as a function of the cluster temperature reveals interesting features in the meltinglike transition of Ag6. A two-step isomerization phenomenon is observed: at temperatures around 300 K, the cluster structures fluctuate among two-dimensional isomers, at higher temperatures (500 K), fast transitions occur between two- and three-dimensional cluster configurations. The simulation was extended up to the cluster fragmentation which is observed through dimer evaporation. read less NOT USED (high confidence) R. Hyland, M. Asta, S. Foiles, and C. L. Rohrer, “Al(F.C.C.) :Al3Sc (L12) interphase boundary energy calculations,” Acta Materialia. 1998. link Times cited: 43 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) W. King, G. Campbell, S. Foiles, D. Cohen, and K. Hanson, “Quantitative HREM observation of the Σ11(113)/[1¯10] grain‐boundary structure in aluminium and comparison with atomistic simulation,” Journal of Microscopy. 1998. link Times cited: 25 Abstract: Quantitative high‐resolution electron microscopy (QHREM) inv… read moreAbstract: Quantitative high‐resolution electron microscopy (QHREM) involves the detailed comparison of experimental high‐resolution images with image simulation based on a model and weighted by the estimated uncertainty in the experimental results. For simple metals, such as Al, models have been systematically improved using nonlinear least‐squares methods to obtain simulated images that are indistinguishable from experimental images within the experimental error. QHREM has been used to study the atomic structure of the Σ11(113)/[1¯10] in Al. In this paper, we focus on the method of refining electron‐optical imaging parameters and atomic structure to bring the simulated HREM image into agreement with the experimental result to within the experimental error and thus yield a result more useful to the materials scientist. Uncertainties in fitted parameters are studied using the conditional probability distribution function. We discuss experimental results for atomic column locations compared with atomistic simulations of the structure of the grain boundary. read less NOT USED (high confidence) R. E. Miller, R. Phillips, G. Beltz, and M. Ortiz, “A non-local formulation of the peierls dislocation model,” Journal of The Mechanics and Physics of Solids. 1996. link Times cited: 53 NOT USED (high confidence) C.-L. Liu, “Diffusion mechanisms at metallic grain boundaries,” Journal of Computer-Aided Materials Design. 1996. link Times cited: 0 NOT USED (high confidence) I. Robertson, D. I. Thomson, V. Heine, and M. Payne, “A database of structural energies of aluminium from ab initio calculations,” Journal of Physics: Condensed Matter. 1994. link Times cited: 9 Abstract: We present a database of 171 aluminium structures with coord… read moreAbstract: We present a database of 171 aluminium structures with coordination number ranging from 0 to 12 and nearest-neighbour distance from 2.0 AA to 5.7 AA. The purpose of the database is further to test and refine empirical and semi-empirical models of metallic bonding. Each structure is specified by the atomic positions and the unit cell used and a total energy per atom is given. Full details of the first-principles total energy calculations are given along with the estimated errors involved. Examples of densities of states are also given for a few of the structures. read less NOT USED (high confidence) T. Tsuru, “Descriptions of Dislocation via First Principles Calculations,” The Plaston Concept. 2022. link Times cited: 0 NOT USED (high confidence) S. Koch, “Development of RF-MEAM interaction potentials for Fe-Y.” 2019. link Times cited: 0 Abstract: Der Fokus dieser Arbeit lag zunachst auf einer simulationsge… read moreAbstract: Der Fokus dieser Arbeit lag zunachst auf einer simulationsgestutzen Untersuchung uber die Entsteh- ungsmechanismen von Oxidteilchen in ODS-Stahlen. Hierbei bilden empirische Wechselwirkungs- potenziale von Eisen-Yttrium-Sauerstoff (Fe-Y-O) die Grundlage fur eine Beschreibung dieser Oxid- teilchen-Bildungs-Prozesse in Molekulardynamik (MD) Simulationen, die auch Eigenschaften von Versetzungen und anderen Bestrahlungs-Panomenen detailiert zur weiteren Aufklarung behandeln konnen.
Zu diesem Zweck ist das speziell auf die Simulation zugeschnittene Anfitten der o.g. MD Potenziale (hier fur Fe-Y-O) notwendig. Hierzu dienen die zuvor durchgefuhrten ab-initio (DFT) Rechnungen als Daten- referenzgrundlage (z.B. von Phasen oder Defekten) zur Optimierung der Potenzialparameter wahrend des Anfittens, um ein moglichst exaktes MD Potenzial zu erzeugen, dass die ab-initio Daten auf groseren MD Skalen detailgetreu abbildet. Im ersten Drittel dieses Projektes wurden mehrere Potenziale fur die einzelnen Metall-Komponenten, Fe-Fe und Y-Y, erzeugt. Dabei stellte sich heraus, dass etablierte Standardmethoden nicht in der Lage sind genaue Fe-Y Potenziale als Teillosung fur das Fe-Y-O Problem zu erzeugen. Dabei wurde eine Kombination aus dem (M)EAM Modell und zur Optimierung eine LSM gestutzte Software (POTFIT) genutzt. Die Komplexitat des Problems liegt in den richtungsabhangigen Atombindungen, die die hier entwickelten fortgeschrittenen Simulations- und Fitmethoden benotigen.
Im ersten Schritt von drei Schritten (chapter 3) wurden zunachst einmal die Defizite der Standard-Fittechniken evaluiert, indem die wahrend des Fitting-Prozesses gefundenen Parametersets im EAM Formalismus mit der flexiblen Software POTFIT auf ihre Eignung hin grundlich untersucht worden sind. Die hierfur genutzten Fitfunktionen wurden ursprunglich Anfang 2000 von Zhou und Wadley entwickelt. Hierbei liegt die Ursache fur die dann entdeckte Parameterset-Problematik darin, dass zur Beschreibung des Fe-Y Systems das Model aus drei Potentialkomponenten besteht: Fe-Fe, Y-Y und Fe-Y. Fur diese einzelnen Komponenten sind die Potentialparameter erfolgreich angefittet worden mit Bezug zur Gitterkonstante und Bindungs- bzw. Kohasionsenergie (beides mit 1% Genauigkeit bezgl. DFT Rechnungen) sowie zu allen elastischen Konstanten (5% Genauigkeit bezgl. Experimente). All dies unter Zuhilfenahme von Parametersuchraum-beschrankenden Techniken, die zur Einhaltung der oben genannten Eigenschaften dienen und urspurnglich von Johnson & Oh sind. Selbst kompliziertere Defekteigenschaften, wie Zwischengitter- und Leerstellenbildungsenergien wurden erfolgreich angefittet. Das hier entwickelte EAM Potenzial fur Y-Y ist z.B. in der Lage bei Eigenzwischengitteratomen die basal oktaedrische Position von Zwischengitteratomen (ZA) im Yttrium hcp-Gitter als Grundzustand und die Transition eines jeden ZAs aus einer anderen Position, wie zuvor in DFT berechnet, zu reproduzieren.
Zur Bildung des angestrebten Fe-Y Potenzials wurden diese beiden Komponenten, Fe-Fe und Y-Y, zum weiteren Fitten in dem weitgefacherten und komplexen Fe-Y Potzenzialsuchraum genutzt. Die Parametersets wurden mit sogenannten hier entwickelten Hauptparameter (Key Driver) systematisch untersucht. Ein flexibleres Konzept statt der starreren Universal Binding Relations in Abhangigkeit von der Rose Gleichung. Dieser Hauptparameter zeigte eindeutig, dass die Nutzung der Rose Gleichung zur Parametersuchraum-Minimierung den Suchraum dahingehend einschrankt, sodass ein akkurates Anfitten der hier genutzten 900 DFT Datensets nicht mehr moglich ist. Allerdings ist die Orientierung im Parametersuchraum mit dieser Rose Gleichung bei standardmasigen Optimierungsmethoden (wie LSM) unabdingbar, da ohne diese die benotigten globalen Optima fur die Parameter nicht auffindbar sind.
Als aufklarendes Testverfahren zur weiteren Ergrundung dieser Problematik und Prufung zur Eignung fur Fe-Y Potenziale und den anschliesenden Simulationen diente der Versuch, 9 verschiedene Bindungs-energien von Yttrium-Leerstellenclustern mit ansteigender Leerstellenzahl zu reproduzieren. Dieser Test konnte von diesen Potenzialen nur teilweise erfullt werden und wurde auf die fehlende Beschreibung der Bindungswinkelabhangigkeit im Modell zuruckgefuhrt. Die Erweiterung von EAM durch MEAM mit Winkelabhangigkeit ist jedoch keineswegs eine zufriedenstellende Losung, da MEAM alternativlos auf der irrefuhrenden Rose Gleichung beruht. Daher war die Benutzung des ubersichtlicheren EAM Typs aus zwei Grunden nutzlich: 1. MEAM braucht die Rose Gleichung um diesen komplexen Formalismus zu beherrschen mit denselben Problemen wie in EAM, aber dieses grundlegende Problem ist in MEAM deutlich schwerer zu identifizieren als in EAM. 2. Die mit EAM gefundenen, angefitteten Parameter sind eine hervorragende Startparameter-Grundlage fur den verbesserten darauffolgenden RF-MEAM Typ.
Im zweiten Schritt wurde das Problem aus dem ersten Schritt gelost, indem ein modifizierter MEAM Spezialtyp im referenzlosen Format (RF-MEAM) angewandt worden ist. Im Gegensatz zum herkommlichen MEAM wird hier die Rose Gleichung durch mehr DFT Daten und insbesondere einer intelligenteren Machine Learning ahnlichen Genetic Algorithmus (GA) Optimiertechnik ersetzt, die allerdings eine bedachte Startparameterwahl vorraussetzt, womit Schritt 1 wieder ins Spiel kommt. Die genutzte fortgeschrittene MEAMfit Software, die per GA funktioniert, wurde zwischen 2016 und 2017 funktionierend eigens dafur implementiert. Mit den in Schritt 1 gefitteten Parametern und Set-Auswahltechniken konnten die weiterfuhrenden Fits mit optimalen Startparametern durchgefuhrt werden.
Auf dieser Stufe waren diese Fits mit der speziell verbesserten Technik in der Lage ein detailgetreues Fe-Y Potenzial zu generieren, das sowohl alle Phasen (Fe2Y, Fe3Y, Fe5Y, Fe23Y6 und Fe17Y2 sowohl als auch reines Fe und Y) als auch die gesamte Defektdatenbasis mit einer durchschnittlichen Abweichung von ≈11% erfolgreich abbildet. Zusatzlich bestatigend zu dieser allgemeinen Ubereinstimmung wurde konsequenterweise der in Schritt 1 entwickelte Test hervorragend mit einmaliger Genauigkeit bestanden, mit max. 5% Abweichung von den komlexen o.g. Y-Leerstellen Bildungsenergien. Allerdings konnte ein systematischer Fehlertrend aufgespurt werden, der Schwachen in der Fe-Fe Komponente offenbarte. Als Folge dessen wurde umgehend diese Komponente durch ein anderes etabliertes Fe-Fe Potenzial von G. Ackland mit einer extrem genauen Schmelztemperatur (nur 3% Abweichung vom Exp.) ausgetauscht. Mit diesem genauen Potenzial konnte zum ersten Mal die Clusterbildung von gelosten Yttrium Atomen in einer Eisenschmelze erfolgreich per MD Simulation auf atomarer Ebene nachgestellt werden oberhalb von 1750 K. Temperaturen darunter hatten eine Ausscheidungsbildung von Y mit sehr geringer Y-Loslichkeit (<0.1%) in Ubereinstimmung mit den Experimenten zur Folge. Dies wurde durch den Pot. Typ A ermoglicht, der aber die energetische Reihenfolge bei den Fe-Y Phasen nicht ganz genau einhalt. Typ B hingegen halt diese ein, dort fehlt aber die Y-Clusterbildungsneigung. Durch den gebotenen Praxisbezug zur Metallurgie mussen die Loslichkeit und Clusterbildung gleichzeitig in der Simulation genau reproduzierbar sein, was aber weder Typ A noch B kann, was zum Typ A/B Dilemma fuhrt.
Dieses Typ A/B Dilemma (Phasen oder Defekt Genauigkeit) fuhrt zum letzten dritten Schritt (chapter 5). Darin ist zusatzlich die Strukturaufklarung von der Fe17Y2 Phase mit Vergleichen zu exp. EXAFS Spektren unserer Kollaborationspartner vom ISSP (Riga) enthalten. Diese Aufklarung dient auch dazu die fehlenden magnetischen Abhangigkeiten im Potenzial zu kompensieren, da die Phasenreihenfolge mit sehr feinen Energieunterschieden wohl stark von magnetischen Wechselwirkungen gepragt ist. Obwohl Potenzial Typ B diesen (Magnetismus) nicht direkt beachtet, ist es in der Lage das tatsachlich gemessene EXAFS Spektrum grostenteils genau wiederzugeben. Allerdings offenbart eine einzige ausgepragte Phasenverschiebung, dass die angenommene hcp Struktur durch eine unterschwellige rhombohedrale Komponente, die sporadisch in der c-Gitterrichtung auftritt, korrigiert werden muss. AIMD (DFT) Berechnungen in Kooperation mit der University of Edinburgh bestatigen dies und zeigen sogar, dass magnetische Wechselwirkungen diese Strukturmischung stabilisieren. Endgultig bestatigt werden konnte dies mit der genauen EXAFS Spektren Reproduktion mit dem durch AIMD verbesserten nochmals gefitteten Potenzialtyp B, der als neuer Typ C durch AIMD indirekt den Einfluss der magnetischen Wechselwirkungen mit einschliest. Diese erstmalige nahezu deckungsgleiche MD Simulation eines EXAFS Spektrums von einem komplexen metallischen Alloy, hier Fe-Y, stellt eine bisher unerreichte Verbesserung dar. Schlieslich lost Typ C das Typ A/B Dilemma und ernoglicht eine genaue gleichzeitige MD Modellierung von Phasen- und Defekten in Fe-Y – ein Durchbruch in der MD-Potenzialentwicklung. read less NOT USED (high confidence) N. Hackney, D. Tristant, A. Cupo, C. Daniels, and V. Meunier, “Shell model extension to the valence force field: application to single-layer black phosphorus.,” Physical chemistry chemical physics : PCCP. 2018. link Times cited: 4 Abstract: We propose an extension of the traditional valence force fie… read moreAbstract: We propose an extension of the traditional valence force field model to allow for the effect of electronic polarization to be included in the inter-atomic potential. Using density functional theory as a reference, this model is parameterized for the specific case of single-layer black phosphorus by fitting the phonon dispersion relation over the entire Brillouin zone. The model is designed to account for the effect of induced dipole interaction on the long-wavelength (|q[combining right harpoon above]| → 0) modes for the case of homopolar covalent crystals. We demonstrate that the near Γ-point frequencies of the IR-active modes are substantially damped by the inclusion of the induced dipole interaction, in agreement with experiment. The fitting procedure outlined here allows for this model to be adapted to other materials, including but not limited to two-dimensional crystals. read less NOT USED (high confidence) C. Wu, “Multiscale Modeling Scheme for Simulating Polymeric Melts: Application to Poly(Ethylene Oxide),” Macromolecular Theory and Simulations. 2018. link Times cited: 19 NOT USED (high confidence) T. Bonnell, S. Henzi, and L. Barrett, “Direction matching for sparse movement data sets: determining interaction rules in social groups,” Behavioral Ecology. 2017. link Times cited: 12 Abstract: It is generally assumed that high-resolution movement data a… read moreAbstract: It is generally assumed that high-resolution movement data are needed to extract meaningful decision-making patterns of animals on the move. Here we propose a modified version of force matching (referred to here as direction matching), whereby sparse movement data (i.e., collected over minutes instead of seconds) can be used to test hypothesized forces acting on a focal animal based on their ability to explain observed movement. We first test the direction matching approach using simulated data from an agent-based model, and then go on to apply it to a sparse movement data set collected on a troop of baboons in the DeHoop Nature Reserve, South Africa. We use the baboon data set to test the hypothesis that an individual’s motion is influenced by the group as a whole or, alternatively, whether it is influenced by the location of specific individuals within the group. Our data provide support for both hypotheses, with stronger support for the latter. The focal animal showed consistent patterns of movement toward particular individuals when distance from these individuals increased beyond 5.6 m. Although the focal animal was also sensitive to the group movement on those occasions when the group as a whole was highly clustered, these conditions of isolation occurred infrequently. We suggest that specific social interactions may thus drive overall group cohesion. The results of the direction matching approach suggest that relatively sparse data, with low technical and economic costs, can be used to test between hypotheses on the factors driving movement decisions. read less NOT USED (high 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 (high confidence) X. Bian, Z. Li, and N. Adams, “A note on hydrodynamics from dissipative particle dynamics,” Applied Mathematics and Mechanics. 2017. link Times cited: 5 NOT USED (high confidence) Y. Zhou, P. Ojeda-May, M. Nagaraju, and J. Pu, “Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path-Force Matching QM/MM Method.,” Methods in enzymology. 2016. link Times cited: 11 NOT USED (high confidence) T. Heinemann, “Systematic coarse-graining procedures for molecular systems.” 2016. link Times cited: 1 Abstract: In this thesis, we present two fundamental strategies to mod… read moreAbstract: In this thesis, we present two fundamental strategies to model systems comprising many molecules in a more abstract or coarse-grained manner. The goal is to reduce the number of the degrees of freedom for computing many-particle simulations of large systems over long time scales. A challenging feature of coarse-grained systems is implicitly including the dynamics of the microscopic degrees of freedom characterized by small lengthand time-scales. In particular, the typical time scale of electronic wave functions is in the order of attoseconds, while for large molecules it is several femtoseconds. The first strategy illustrates the systematic abstraction of the atomic level of detail of a system consisting of two coronene molecules, which possess a discotic shape. We force a coarse-grained configuration in an equilibrium ensemble to occur equally frequently, regardless of the level of detail. This frequency directly leads to the effective potential between these molecules. For phase-space sampling at the atomic level, we use Langevin dynamics results with modifications based on umbrella sampling or steered dynamics techniques. We treat the complex electrostatics of these molecules which is essential for the molecular orientation in the crystalline phase separately from the main coarse-graining procedure. To fit our temperature and angle-dependent effective molecule-molecule potential, we use several models with a different number of parameters. We additionally investigate the applicability of these models through molecular dynamics simulations in systems with constant temperature and mostly constant pressure. We also consider the structure and melting behavior of the system in the isotropic and condensed phases. We conclude that a model with an extended charge distribution is required, particularly to reproduce the correct temperature. In our second strategy, we introduce a model for the interaction in two dimensions, where the electrostatics is approximated through a linear point quadrupole. For this purpose, we consider monodisperse systems of purely repulsive ellipses with different aspect ratios and an embedded linear point quadrupole along one main axis. Using molecular dynamics simulations, we examine the partly quite complex structure of the systems and their melting temperatures at a constant pressure. We deduce that the crystalline phases of the molecules with high eccentricity melt at higher temperatures than crystalline phases of more isotropically-shaped molecules. We also discuss the applicability of our results to systems with different parameter settings. In principle, both strategies presented here can be applied at various orders of magnitude. Further possible fields of application are colloidal systems or even cosmic objects, provided relativistic effects are considered. read less NOT USED (high confidence) D. J. Förster, S. Scharring, J. Roth, and H. Eckel, “Molecular Dynamics Simulations of Laser Induced Ablation for Micro Propulsion,” International Conference on High Performance Computing. 2015. link Times cited: 1 NOT USED (high 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 (high confidence) K. L. Baker and D. Warner, “An atomistic investigation into the nature of near threshold fatigue crack growth in aluminum alloys,” Engineering Fracture Mechanics. 2014. link Times cited: 18 NOT USED (high confidence) M. Griebel, J. Hamaekers, and F. Heber, “A Bond Order Dissection ANOVA Approach for Efficient Electronic Structure Calculations.” 2014. link Times cited: 2 NOT USED (high confidence) P. Posocco, S. Pricl, and M. Fermeglia, “Modelling and Simulation of Sol-Gel Nanocomposites.” 2014. link Times cited: 1 NOT USED (high confidence) P. Carbone and C. Avendaño, “Coarse‐grained methods for polymeric materials: enthalpy‐ and entropy‐driven models,” Wiley Interdisciplinary Reviews: Computational Molecular Science. 2014. link Times cited: 31 Abstract: Polymers are multiscale systems by construction. They are fo… read moreAbstract: Polymers are multiscale systems by construction. They are formed by several monomeric units connected by covalent bonds whose chemical nature defines the rigidity of the chain. The interconnection between the monomeric units determines the interdependence of the motion of the different chain segments and the intrinsic multiscale nature of polymeric materials. This characteristic is reflected on the different modeling techniques that can be used to simulate polymeric materials. Because of the large conformational space that needs to be sampled when simulating polymers, coarse‐grained (CG) models are commonly used and depending on which part of the system free energy (enthalpy, entropy, or both) is relevant for the properties of interest, the appropriate modeling techniques should be used. Each model is characterized by advantages and limitations that can have a great impact on the quality of the results obtained. In this overview, we address some of the more common CG techniques presented in the literature for the modeling of polymeric materials at different length scales. WIREs Comput Mol Sci 2014, 4:62–70. doi: 10.1002/wcms.1149 read less NOT USED (high confidence) M. M. Schneider, “A Study of Solid/Liquid Interfacial Phenomena in Hypereutectic Al-Si with High Resolution in situ Transmission Electron Microscopy.” 2014. link Times cited: 1 Abstract: Department of Materials Science and Engineering Master of Sc… read moreAbstract: Department of Materials Science and Engineering Master of Science, Materials Science and Engineering by Matthew M. Schneider Solid-liquid interfaces are extensively encountered in materials processing and applications. The structure and properties of these interfaces a↵ect solidification, wetting behavior, and crystalline growth mechanisms, including epitaxial growth. The exact structural, dynamic, and chemical nature of these interfaces have been historically di cult to study at high resolution due to the fact that one phase is a liquid. Recently, advances in in situ high-resolution transmission electron microscopy experimental methods have progressed to enable the study of solidliquid interfaces in metals with resolution on the atomic scale. Reported results thus far include direct observation of step/ledge growth, the presentation of various crystallographic facets during growth/dissolution, ordering of liquid layers adjacent to crystalline solids, and chemical segregation at interfaces. This work reports the first observations of a number of new interfacial phenomena associated with the dynamic behavior of the solid/liquid phase boundary at equilibrium. The structural dynamics of silicon {111}-type planes were tracked near the vapor/liquid/solid triple-point as the solid/liquid interface fluctuated between roughened, smoothly faceted, and smoothly rounded morphologies. Both the roughened and smoothly faceted configurations were unstable from frame-to-frame while the faceted configuration was observed to persist for as many as three consecutive time-steps. Adjacent to the triple-point, the facets {100}, {112}, {117}, and {113} were observed along the interface between with the solid and liquid phases. In contrast to previous experimental and theoretical work at disordered solid/solid interfaces, no characteristic length between interfacial fluctuations was observed. The magnitude of the planar motion of individual {111} planes at the interface between a stable {113} silicon facet and liquid-phase aluminum alloy showed a bias to quantize changes in lengths corresponding to multiples of the {113} inter-planar spacing. This bias towards quantized fluctuation magnitudes has not been shown in previous work modelling the fluctuations present at solid/liquid interfaces in metallic systems; this quantization is likely a result of the strong directional nature of the covalent bonds present in the silicon lattice. In contrast to previous experimental and theoretical work at disordered solid/solid interfaces, no characteristic length between interfacial fluctuations was observed. Finally, a metastable copper precursor phase was observed to heterogeneously nucleate at the boundary between the solid and liquid phases. These copper islands ranged widely in length along the interface, from 4–132 Å; the range of distances that they extended o↵ of the interface into the liquid phase ranged from 2–13 Å. Each copper island observed shared the same (11̄3)Sik(076)Cu;[110]Sik(100)Cu orientation relationship with the silicon substrate below. read less NOT USED (high confidence) M. Dömer, “Approaches to Increase the Accuracy of Molecular Dynamics Simulations.” 2013. link Times cited: 0 Abstract: Keywords: Molecular Dynamics ; Molecular Mechanics ; Tight B… read moreAbstract: Keywords: Molecular Dynamics ; Molecular Mechanics ; Tight Binding ; Density Functional Theory ; QM/MM ; Force Matching ; Iterative Boltzmann Inversion ; Dispersion Interactions These Ecole polytechnique federale de Lausanne EPFL, n° 5833 (2013)Programme doctoral Chimie et Genie chimiqueFaculte des sciences de baseInstitut des sciences et ingenierie chimiquesLaboratoire de chimie et biochimie computationnellesJury: K. Johnsson (president), M. Dal Peraro, T. Frauenheim, A.P. Seitsonen Public defense: 2013-7-30 Reference doi:10.5075/epfl-thesis-5833Print copy in library catalog Record created on 2013-07-25, modified on 2017-05-12 read less 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) T. Steinbrecher and M. Elstner, “QM and QM/MM simulations of proteins.,” Methods in molecular biology. 2013. link Times cited: 24 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) P. Beck, “Molecular dynamics of metal oxides with induced electrostatic dipole moments.” 2012. link Times cited: 1 Abstract: Metal oxides belong to the most important material classes i… read moreAbstract: Metal oxides belong to the most important material classes in industrial technology. These high-tech ceramics are irreplacable in lots of modern microelectronic devices due to their excellent insulating properties, high melting points and high degrees of hardness. In the theoretical study of these systems, the atomistic modelling with molecular dynamics simulations and classical effective interaction force fields is a very powerful tool. There, fundamental properties can be uncovered and understood due to the atomic resolution. Both force field generation and simulation of oxide systems are computationally much more demanding than those of metals or covalent materials due to long-range electrostatic interactions. Furthermore, it is often not sufficient to only take Coulomb interactions into account, but to include electrostatic dipole moments. The latter can be integrated with the Tangney Scandolo polarizable force field model, where dipole moments are determined by a self-consistent iterative solution during each simulation time step. Applying the direct, pairwise Wolf summation to interactions between charges and its extension to dipole moments avoids high computational effort due to its linear scaling properties in the number of particles. Three relevant metal oxides have been selected to apply the new high-performance force field generation model. Therewith, a detailed investigation of crack propagation was possible. Both crack propagation insights and the influence of cracks on the dipole field are shown. Finally, the coupling of strain and – even more meaningful – strain gradient with the dipole moments is presented, which gives rise to flexoelectric effects in non-piezoeletric materials.
Die vorliegende Arbeit vertieft die breit angelegte Modellierungs-Studie dreier wichtiger Metalloxide. Detaillierte Untersuchungen durch Molekulardynamik- Simulationen mit Kraftfeldern fur Siliziumdioxid, Magnesiumoxid und Alpha-Aluminiumoxid werden dargestellt. Speziell angepasste Visualisierungs-Techniken erweitern die numerischen Einblicke und verhelfen zu neuen Erkenntnissen in den untersuchten ionischen Systemen. Im Wesentlichen leistet die Arbeit einen dreistufigen Beitrag zur numerischen Erforschung ionischer kondensierter Materie:
1. Zunachst wird die neue Art der Kraftfelderstellung dargestellt, welche
das Potenzial-Modell von Tangney und Scandolo mit der direkten Wolfsummation verknupft. Gezeigt wird die gewissenhafte Prufung, dass die Vereinigung der Vorteile des TS Modells, welches elektrostatische Dipolmomente mit einbezieht, mit den linearen Skalierungs-Eigenschaften der Wolfsumme gelungen ist. Die Implementierung der Kraftfelderstellung in potfit durch den Autor gibt anderen Simulations-Gruppen die Moglichkeit, diese prazise, effiziente und flexible
Methode fur ihre individuellen Studien ionischer Materie einzusetzen.
2. Weiterhin werden die mithilfe der neuen Methodik generierten Kraftfelder fur Siliziumdioxid, Magnesiumoxid und Alpha-Aluminiumoxid vorgestellt. Neben ihrer Erstellung wird in jedem Einzelfall die sorgfaltige Validierung gezeigt. Die neuen Kraftfelder werden nicht nur fur eigene Simulationen eingesetzt, sondern anderen Gruppen offentlich zuganglich gemacht. Dadurch konnen nun vielerorts Simulationen durchgefuhrt werden, die bisher aufgrund von Beschrankungen bezuglich Zeit-, Langenskalen oder Randbedingungen nicht annehmbar realisierbar waren.
3. Unter Einsatz der neuen Kraftfelder wurden verschiedene Simulationen durchgefuhrt, die – auch mithilfe der speziell angepassten Visualisierung der fraktionalen Anisotropie – zu neuen Entdeckungen und grundlegenden Erkenntnissen gefuhrt haben:
• Das fur Alpha-Aluminiumoxid erstellte Kraftfeld wurde zur MD Simulation von sich ausbreitenden Rissen verwendet, welche die vor zwei Jahren elektronenmikroskopisch untersuchten Verlaufs-Richtungen von in verschiedenen kristallinen Ebenen existierenden Rissen vollstandig reproduzieren konnte. Daruberhinaus konnte – erstmalig in atomistischen Simulationen von Metalloxiden – der Einfluss von sich ausbreitenden Rissen auf die Orientierung der elektrostatischen Dipolmomente beobachtet und analysiert werden.
• Derartige flexoelektrische Phanomene wurden schlieslich sowohl in MD Simulationen als auch mithilfe der Darstellungstheorie untersucht. Die Kombination liefert eine konsistente Vorhersage flexoelektrischen Verhaltens in Alpha-Aluminiumoxid und auch in Periklas, obwohl beide Materialien aufgrund ihrer inversionssymmetrischen Kristallstruktur keine Piezoelektrizitat aufweisen. Die analytisch angenommene und experimentell vorhergesagte lineare Kopplung zwischen Spannungsgradient und flexoelektrischer Polarisation wurde von MD Simulationen bestatigt. Erstmalig wurde flexoelektrische Domanenausbildung modelliert. In Periklas zeigt sich, dass flexoelektrische Domanen exakt von Neel-Wanden abgetrennt werden. read less NOT USED (high confidence) M. A. González, “Force fields and molecular dynamics simulations.” 2011. link Times cited: 170 Abstract: The objective of this review is to serve as an introductory … read moreAbstract: The objective of this review is to serve as an introductory guide for the non-expert to the exciting field of Molecular Dynamics (MD). MD simulations generate a phase space trajectory by integrating the classical equations of motion for a system of N particles. Here I review the basic concepts needed to understand the technique, what are the key elements to perform a simulation and which is the information that can be extracted from it. I will start defining what is a force field, which are the terms composing a classical force field, how the parameters of the potential are optimized, and which are the more popular force fields currently employed and the lines of research to improve them. Then the Molecular Dynamics technique will be introduced, including a general overview of the main algorithms employed to integrate the equations of motion, compute the long-range forces, work on different thermodynamic ensembles, or reduce the computational time. Finally the main properties that can be computed from a MD trajectory are briefly introduced. 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) J. Roth, C. Trichet, H. Trebin, and S. Sonntag, “Laser Ablation of Metals,” High Performance Computing in Science and Engineering. 2010. link Times cited: 16 NOT USED (high confidence) B. Eidel, A. Hartmaier, and P. Gumbsch, “Atomistic Simulation Methods and their Application on Fracture.” 2010. link Times cited: 6 NOT USED (high confidence) A. Lyubartsev, A. Mirzoev, L. J. Chen, and A. Laaksonen, “Systematic coarse-graining of molecular models by the Newton inversion method.,” Faraday discussions. 2010. link Times cited: 133 Abstract: Systematic construction of coarse-grained molecular models f… read moreAbstract: Systematic construction of coarse-grained molecular models from detailed atomistic simulations, and even from ab initio simulations is discussed. Atomistic simulations are first performed to extract structural information about the system, which is then used to determine effective potentials for a coarse-grained model of the same system. The statistical-mechanical equations expressing the canonical properties in terms of potential parameters can be inverted and solved numerically according to the iterative Newton scheme. In our previous applications, known as the Inverse Monte Carlo, radial distribution functions were inverted to reconstruct pair potential, while in a more general approach the targets can be other canonical averages. We have considered several examples of coarse-graining; for the united atom water model we suggest an easy way to overcome the known problem of high pressure. Further, we have developed coarse-grained models for L- and D-prolines, dissolved here in an organic solvent (dimethylsulfoxide), keeping their enantiomeric properties from the corresponding all-atom proline model. Finally, we have revisited the previously developed coarse-grained lipid model based on an updated all-atomic force field. We use this model in large-scale meso-scale simulations demonstrating spontaneous formation of different structures, such as vesicles, micelles, and multi-lamellar structures, depending on thermodynamical conditions. read less NOT USED (high confidence) M. Engel, “Dynamics and defects of complex crystals and quasicrystals : perspectives from simple model systems.” 2008. link Times cited: 5 Abstract: Komplexe Kristalle und Quasikristalle sind geordnete Festkor… read moreAbstract: Komplexe Kristalle und Quasikristalle sind geordnete Festkorperstrukturen mit sehr grosen beziehungsweise unendlichen grosen Einheitszellen. Ihre Teilchendynamik unterscheidet sich grundlegend von derjenigen der einfachen Kristalle: Aufgrund der strukturellen Komplexitat treten lokale Umordnungen, sogenannte Phasonflips, und neueartige Versetzungen auf. Um das Verhalten auf einer elementaren Ebene zu verstehen, werden drei ein- und zweidimensionale Modellsysteme eingefuhrt. Die Systeme werden sowohl analytisch, als auch mit numerischen Simulationen untersucht.
(i) Die Strukturfaktoren der dynamischen Fibonacci-Kette wurden in hoher Auflosung berechnet. Sie zeigen eine charakteristische Verbreiterung der Phonondispersionsrelation. Die Teilchendynamik im Realraum zeichnet sich durch Soliton- und Breathermoden aus, welche zusammen mit Phasonflips auftreten.
(ii) Mit Hilfe eines Tilingmodells wurde die experimentelle Beobachtung von Metaversetzungen im intermetallischen System AlPdMn und die damit verbundene kollektive strukturelle Umordnung erklart. Die Burgersvektoren der Versetzungen konnen aus Energieuberlegungen abgeleitet werden.
(iii) Im Lennard-Jones-Gaus-System treten eine uberaschende Vielzahl an zweidimensionalen komplexen Kristallen, ein dekagonaler und zwei dodekagonale Quasikristalle auf. Bei Temperaturen nahe des Schmelzpunktes ordnen sich die Teilchen per Phasonflips um. Wahrend des Abkuhlens transformieren sich die entropisch stabilisierten Quasikristalle reversibel in komplexe Kristalle. Mit dem Lennard-Jones-Gaus-System ist es zum ersten Mal moglich, das Wachstum, die Gleichgewichtsdynamik und die Defekte von Quasikristallen und komplexen Kristallen in Simulationen zu untersuchen.
Complex crystals and quasicrystals are ordered states of matter with very large or even infinite unit cells. Their particle dynamics and defects differ significantly from what is known for simple crystals: Local rearrangements, phason flips, and new types of dislocations are consequences of the structural complexity. In order to understand their behavior at an elementary level, we introduce three model systems in one and two dimensions. The systems are studied analytically and with numerical simulations.
(i) The structure factors of the dynamic Fibonacci chain are computed with high resolution. They show a characteristic broadening of the phonon dispersion relation. The particle motion in real space reveals soliton and breather modes, closely connected to phason flips.
(ii) Using a tiling model for the intermetallic system AlPdMn, experimental observations of metadislocations and the collective particle dynamics are explained. The Burgers vectors of stable dislocations are derived from energy considerations.
(iii) In the Lennard-Jones-Gauss system a surprising variety of two-dimensional complex crystals as well as a decagonal and two dodecagonal quasicrystals are grown. The particles reorder by phason flips at elevated temperatures. During annealing, the entropically stabilized quasicrystals undergo reversible phase transitions into complex crystals. Competing interparticle distances seem to favor structural complexity. With the Lennard-Jones-Gauss system the growth, equilibrium dynamics, and defects of quasicrystals and complex crystals can be studied in simulations for the first time. read less NOT USED (high confidence) P. Brommer, “Development and test of interaction potentials for complex metallic alloys.” 2008. link Times cited: 8 Abstract: Complex metallic alloys and quasicrystals show extraordinary… read moreAbstract: Complex metallic alloys and quasicrystals show extraordinary physical properties relevant for technological applications, for example hardness at low density. In the study of these systems, atomistic simulation with classical interaction potentials is a very promising tool. Such simulations require classical effective potentials describing the cohesive energy as a function of the atomic coordinates. The quality of the simulation depends crucially on the accuracy with which this potential describes the real interactions. One way to generate physically relevant potentials is the force matching method, where the parameters of a potential are adjusted to optimally reproduce the forces on individual atoms determined from quantum-mechanical calculation. The programme package potfit developed as part of this thesis implements the force matching method efficiently. Potentials are generated for a number of complex metallic alloy systems. A potential for the decagonal basic Ni-rich Al-Co-Ni quasicrystal is used to simulate diffusion processes and melting. In the CaCd6 system built from multishelled clusters, the shape and orientation of the innermost cluster shell is studied. Finally, phonon dispersion in the Mg-Zn system is determined and compared to experiment. The programme potfit is shown to be an effective tool for generating physically justified effective potentials. Potentials created with potfit can greatly improve the understanding of complex metallic alloys through atomistic simulations.
Komplexe intermetallische Verbindungen und Quasikristalle zeigen ausergewohnliche physikalische Eigenschaften, wie z.B. Harte bei geringer Dichte. Bei der Untersuchung dieser Systeme sind atomistische Simulationen mit klassischen Wechselwirkungspotenzialen ein wichtiges Werkzeug. Fur solche Simulationen benotigt man klassische effektive Potenziale, die die Bindungsenergie als eine Funktion der Atomkoordinaten beschreiben. Die Qualitat der Simulation hangt entscheidend von der Genauigkeit ab, mit der diese Potenziale die echten Wechselwirkungen wiedergeben. Eine Moglichkeit, physikalisch relevante Potenziale zu erzeugen, ist die Force-Matching-Methode. Dabei werden die Parameter eines Potenzials so angepasst, dass die mit quantenmechanischen Methoden bestimmten Krafte auf die einzelnen Atome bestmoglich reproduziert werden. Das als Teil dieser Arbeit entwickelte Programmpaket potfit implementiert die Force-Matching-Methode effizient. Fur einige komplexe intermetallische Verbindungen werden Potenziale bestimmt. In dekagonalen Al-Co-Ni-Quasikristallen werden mit Hilfe eines Potenzials Diffusionsprozesse und Schmelzvorgange simuliert. In der aus mehrschaligen Clustern bestehenden CaCd6-Verbindung wird die Struktur der innersten Clusterschale untersucht. Schlieslich wird die Phononendispersion im Mg-Zn-System bestimmt und mit experimentellen Ergebnissen verglichen. Es wird gezeigt, dass das Programm potfit ein effektives Werkzeug zur Erzeugung physikalisch gerechtfertigter Wechselwirkungen ist. Potenziale, die mit potfit erzeugt werden, konnen zum Verstandnis komplexer metallischer Verbindungen durch atomistische Simulationen viel beitragen. read less NOT USED (high confidence) S. Hocker, “Molekulardynamiksimulation der Diffusion in dekagonalen Quasikristallen mit optimierten Wechselwirkungspotentialen.” 2007. link Times cited: 1 Abstract: Die etwa 25 Jahre zuruckliegende Entdeckung der Quasikristal… read moreAbstract: Die etwa 25 Jahre zuruckliegende Entdeckung der Quasikristalle erweiterte das Gebiet der Festkorperphysik um einen neuen Strukturtyp. In der Erforschung dieser geordneten, jedoch nicht periodischen Strukturen wurden seither bedeutende Erfolge erzielt. Von verschiedenen Quasikristalltypen konnten zunehmend detaillierte Strukturmodelle erstellt werden. Zunachst wurden in der numerischen Simulation einfache binare Modellsysteme untersucht, inzwischen sind realistische ternare Strukturen Gegenstand der numerischen Forschung.
Fur die Molekulardynamiksimulation solcher Strukturen ist, neben einem geeigneten Strukturmodell, eine gute Modellierung der atomaren Wechselwirkungen erforderlich. Besonders fur Simulationen nahe der Schmelztemperatur besteht Bedarf nach einem realistischen Wechselwirkungspotential. Da herkommliche Potentiale ublicherweise an Parameter der Grundzustandsstruktur angepasst wurden, tendieren diese dazu, bei hohen Temperaturen zu versagen.
Die numerische Exploration in diesem Temperaturbereich kann einen wichtigen Beitrag zum Verstandnis der Quasikristalle liefern. Diffusionsprozesse, die bedeutend fur die Entstehung von quasikristallinen Hochtemperaturphasen sind, konnen im Fall von Aluminium nur in der Simulation erforscht werden, weil fur das ubliche Messverfahren kein geeignetes Radioisotop existiert. Da Aluminium ein wesentlicher Bestandteil vieler Quasikristalle ist, ist das Verstandnis der Aluminiumdiffusion von groser Bedeutung.
Ziel dieser Arbeit ist die Untersuchung der Aluminiumdiffusion in den dekagonalen Quasikristallen AlNiCo und AlCoCu mittels Molekulardynamiksimulation. Dazu werden zunachst, durch Anpassung an Ab-initio-Daten, Wechselwirkungspotentiale fur die Strukturen entwickelt. Mit diesen Potentialen werden Simulationen bei hohen Temperaturen durchgefuhrt. Die dabei auftretende Diffusion wird ausgewertet und mit Daten aus Ab-initio-Rechnungen verglichen.
Die in der vorliegenden Arbeit konstruierten EAM-Potentiale fur Hochtemperatursimulationen an dekagonalen Quasikristallen erwiesen sich als geeignet, um grundlegende Eigenschaften der Systeme richtig zu modellieren. Der Vergleich mit der Ab-initio-Rechnung lieferte fur alle Atomsorten eine sehr gute Ubereinstimmung in den aus der thermischen Bewegung resultierenden Atomaufenthaltswahrscheinlichkeiten der Strukturen. Auch einzelne mit den EAM-Potentialen untersuchten Al-Diffusionsprozesse konnten in der Ab-initio-MD-Simulation bestatigt werden.
In den quasikristallinen Strukturen wurde in der klassischen Molekulardynamiksimulation weit reichende Aluminiumdiffusion beobachtet. Die durch Ab-initio-Rechnungen bestatigten Al-Diffusionsprozesse wurden detailliert untersucht. Dabei wurde deutlich, dass die Diffusion in der dekagonalen Ebene uber quasikristallspezifische Mechanismen verlauft. Bedeutend ist hierbei die Besonderheit, dass Gebiete existieren, die zur Atomabgabe neigen, wahrend andere ein zusatzliches Atom aufnehmen konnen. Es finden Kettenprozesse statt, an deren Start- und Endpositionen sich diese Regionen befinden. Charakterisch fur diese Gebiete ist, dass die Al-Positionen nicht scharf lokalisiert sind, sondern innerhalb eines Bereichs eine kontinuierliche Al-Aufenthaltswahrscheinlichkeit besteht. In der periodischen Richtung existieren durchgangige Kanale kontinuierlicher Al-Aufenthaltswahrscheinlichkeit. Durch diese Kanale verlauft die Al-Diffusion in periodischer Richtung. Der Diffusionsmechanismus ist hierbei die direkte, synchron verlaufende, Bewegung innerhalb einer Reihe von Atomen. Dabei befinden sich immer drei Atome pro Schicht im Kanal. Bei mehr als drei Schichten findet meist eine Kopplung mit einem Prozess der dekagonalen Ebene statt, wobei ein Atom aus der dekagonalen Ebene in den Diffusionskanal springt, wahrend ein anderes diesen verlasst. In diesem Fall diffundieren nur die sich dazwischen befindenden Atome entlang des Kanals.
Zur Diffusion in der dekagonalen Ebene konnen deutlich mehr Al-Atome beitragen als zu jener in der periodischen Richtung, welche auf die Diffusionskanale beschrankt ist. Da jedoch die Mobilitat der Al-Atome in den Diffusionskanalen deutlich hoher ist, liegen die Diffusionskoeffizienten fur die periodische Richtung uber jenen der dekagonalen Ebene. Die geringe Energiebarriere innerhalb der Diffusionskanale wurde mit Ab-initio-Rechnungen bestatigt.
With the discovery of quasicrystals in 1982, condensed matter physics was extended by a new kind of structure. Since then, the exploration of these ordered, but nonperiodic structures has lead to significant new results. There was an increase of detailed structure models of several quasicrystals. For a long time, in numerical simulations only binary model systems were studied, but real quasicrystals are mostly ternary or even quaternary. Nowadays these structures can be explored in numerical simulations.
Molecular dynamics simulations of such realistic structures require, apart from an appropriate model of the structure, a well adjusted model of the atomic interactions. Especially for simulations at temperatures near the melting point, there is demand for realistic potentials. Since conventional potentials were usually constructed by adjustment to the ground state structure, these potentials tend to fail at high temperatures.
Simulations at high temperatures provide an important contribution to the understandig of quasicrystals. Diffusion processes are fundamental in the formation of high temperature phases and the motion of defects. In the case of aluminium the diffusion cannot be measured experimentally, due to the lack of suitable radiotracers. Therefore numerical simulation is the sole possibilty to study the Al diffusion processes. Since aluminium is a basic component of many quasicrystals, the understanding of aluminum diffusion is of great importance.
The goal of this thesis is the exploration of diffusion in the decagonal AlNiCo and AlCoCu quasicrystals via molecular dynamics simulation. For this purpose, atomic interaction potentials for these structures are developed by adjusting them to ab initio data.
The newly developed EAM potentials for molecular dynamics simulations at high temperatures in AlNiCo and AlCoCu quasicrystals turned out to be well adapted for modelling the basic properties of these decagonal quasicrystals. The comparison with ab initio calculations shows very good agreement in the atom density maps of both structures. Similarly some specific diffusion processes, which were found in the simulations with EAM potentials, were validated in ab initio calculations.
In the molecular dynamics simulation, long range Al diffusion was observed in both decagonal quasicrystal structures. Al diffusion processes, which were validated by ab initio calculations, were studied in detail. It was found that the diffusion in the decagonal plane proceeds via mechanisms which are specific to quasicrystals. Of great importance are sites which tend to emit atoms, whereas other sites can absorb atoms. Chain processes occur, where the initial and the final positions are at these sites. The important characteristic of these sites is that the Al positions are not localized, but there is a continuous Al density in these regions. In the periodic direction, channels of continuous Al density extend through the structure. The diffusion in this direction runs via such channels. The diffusion mechanism is a synchronous motion of atoms within a column. In each layer there are three atoms which are part of this column. With more than three layers there is usually a coupling with a jump process in the decagonal plane. An atom of the decagonal plane jumps into the diffusion channel, whereas another atom leaves the channel. In this case, only the atoms in-between diffuse along the channel.
There are clearly more Al atoms which contribute to the diffusion in the decagonal plane than in the periodic direction, in which the diffusion is limited to the channels. However, since the mobility of Al atoms in the diffusion channels is significantly higher, the diffusion coefficients in the periodic direction are larger than those in the decagonal plane. The small energy barriers in the diffusion channels were validated in ab inito calculations. read less NOT USED (high confidence) D. A. Drabold, “Defects in Amorphous Semiconductors: Amorphous Silicon.” 2007. link Times cited: 7 NOT USED (high confidence) F. Gähler and K. Benkert, “Atomistic Simulations on Scalar and Vector Computers.” 2006. link Times cited: 6 NOT USED (high confidence) M. Buehler and H. Gao, “MODELING DYNAMIC FRACTURE USING LARGE-SCALE ATOMISTIC SIMULATIONS.” 2005. link Times cited: 9 Abstract: We review a series of large-scale molecular dynamics studies… read moreAbstract: We review a series of large-scale molecular dynamics studies of dynamic fracture in brittle materials, aiming to clarify questions such as the limiting speed of cracks, crack tip instabilities and crack dynamics at interfaces. This chapter includes a brief introduction of atomistic modeling techniques and a short review of important continuum mechanics concepts of fracture. We find that hyperelasticity, the elasticity of large strains, can play a governing role in dynamic fracture. In particular, hyperelastic deformation near a crack tip provides explanations for a number of phenomena including the “mirror-misthackle” instability widely observed in experiments as well as supersonic crack propagation in elastically stiffening materials. We also find that crack propagation along interfaces between dissimilar materials can be dramatically different from that in homogeneous materials, exhibiting various discontinuous transition mechanisms (mother-daughter and mother-daughter-granddaughter) to different admissible velocity regimes. read less NOT USED (high confidence) D. Datta, R. C. Picu, and M. Shephard, “Composite Grid Atomistic Continuum Method: An Adaptive Approach to Bridge Continuum with Atomistic Analysis,” International Journal for Multiscale Computational Engineering. 2004. link Times cited: 42 Abstract: The Composite Grid Atomistic Continuum Method (CACM), a meth… read moreAbstract: The Composite Grid Atomistic Continuum Method (CACM), a method to couple continuum and atomistic models is proposed in a three dimensional setting. In this method, atomistic analysis is used only at places where it is needed in order to capture the intrinsically non-linear/non-local behavior of the material at the atomic scale, while continuum analysis is used elsewhere for efficiency. The atomistic model is defined on a separate grid that overlaps the continuum in selected regions. The atomistic and the smallest scale continuum model are connected by appropriately defined operators. The continuum model provides boundary conditions to the discrete model while the atomistic model returns correcting eigenstrains. The adaptive selection of the spatial regions where the atomistic correction is needed is made based on error indicators developed to capture the non-linearity and non-locality modeling errors. The method is applied to represent dislocation nucleation from crack tips and nanoindentation in aluminum. read less NOT USED (high confidence) D. Zhang and R. C. Picu, “Solute clustering in Al–Mg binary alloys,” Modelling and Simulation in Materials Science and Engineering. 2004. link Times cited: 18 Abstract: Clustering of Mg in Al–Mg binary alloys is studied by means … read moreAbstract: Clustering of Mg in Al–Mg binary alloys is studied by means of atomistic simulations. The phenomenon is analysed in the undistorted Al lattice, as well as in the presence of dislocations. In the undistorted lattice, Mg has a tendency to cluster in a coherent phase. The binding energy of this structure is rather low and it dissolves at room temperature, and only dynamic associations of doublets or triples of solute atoms are observed. Increasing the temperature above 100°C inhibits the formation of any solute short range order. The application of a homogeneous hydrostatic strain has no effect on clustering. In the presence of dislocations and at room temperature, Mg clusters at cores forming the coherent phase observed in the undistorted lattice at low temperatures. Clustering at the cores of all types of dislocations is discussed. It is shown that the size, shape and structure of the cluster cannot be predicted using elementary calculations based on the pressure field generated by the unclustered dislocation. Furthermore, the field of the clustered dislocation is observed to differ from that of the unclustered defect, even at distances as large as 20 Burgers vectors from the core. The variation of the stacking fault due to clustering is determined by simply monitoring the distance between partials, which is observed to decrease upon clustering. read less NOT USED (high 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 (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
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