Abstract: TlBr is promising for g- and x- radiation detection, but suffers from rapid performance degradation under the operating external electric fields. To enable molecular dynamics (MD) studies of this degradation, we have developed a Stillinger-Weber type of TlBr interatomic potential. During this process, we have also addressed two problems of wider interests. First, the conventional Stillinger-Weber potential format is only applicable for tetrahedral structures (e.g., diamond-cubic, zinc-blende, or wurtzite). Here we have modified the analytical functions of the Stillinger-Weber potential so that it can now be used for other crystal structures. Second, past modifications of interatomic potentials cannot always be applied by a broad community because any new analytical functions of the potential would require corresponding changes in the molecular dynamics codes. Here we have developed a polymorphic potential model that simultaneously incorporates Stillinger-Weber, Tersoff, embedded-atom method, and any variations (i.e., modified functions) of these potentials. We have implemented this polymorphic model in MD code LAMMPS, and demonstrated that our TlBr potential enables stable MD simulations under external electric fields. read less

Abstract: The first-principles modeling of biomaterials has made tremendous advances over the last few years with the ongoing growth of computing power and impressive developments in the application of density functional theory (DFT) codes to large systems. One important step forward was the development of dispersion corrections for DFT methods, which account for the otherwise neglected dispersive van der Waals (vdW) interactions. Approaches at different levels of theory exist, with the most often used (semi-)empirical ones based on pair-wise interatomic C6R(-6) terms. Similar terms are now also used in connection with semiempirical QM (SQM) methods and density functional tight binding methods (SCC-DFTB). Their basic structure equals the attractive term in Lennard-Jones potentials, common to most force field approaches, but they usually use some type of cutoff function to make the mixing of the (long-range) dispersion term with the already existing (short-range) dispersion and exchange-repulsion effects from the electronic structure theory methods possible. All these dispersion approximations were found to perform accurately for smaller systems, but error estimates for larger systems are very rare and completely missing for really large biomolecules. We derive such estimates for the dispersion terms of DFT, SQM and MM methods using error statistics for smaller systems and dispersion contribution estimates for the PDBbind database of protein-ligand interactions. We find that dispersion terms will usually not be a limiting factor for reaching chemical accuracy, though some force fields and large ligand sizes are problematic. read less

Abstract: The structure and energetics of coincidence site lattice grain boundaries (GB) in CdTe are investigated by mean of molecular statics simulations, using the Cd–Zn–Te bond-order potential (second iteration) developed by Ward et al (2012 Phys. Rev. B 86 245203; 2013 J. Mol. Modelling 19 5469–77). The effects of misorientation (Σ value) and interface plane are treated separately, complying with the critical need for full five-parameter characterization of GB. In addition, stoichiometric shifts, occurring between the inner interfaces and their adjacent atomic layers, are also predicted, revealing the energetic preference of Te-rich boundaries, opening opportunities for crystallography-based intrinsic interface doping. Our results also suggest that the intuitive assumption that Σ3 boundaries with low-indexed planes are more energetically favorable is often unfounded, except for coherent twins developing on {111} boundary planes. Therefore, Σ5, 7 or 9 boundaries, with lower interface energy than that of twin boundaries lying on different facets, are frequently encountered. read less

Abstract: A Stillinger-Weber potential is computationally very efficient for molecular dynamics simulations. Despite its simple mathematical form, the Stillinger-Weber potential can be easily parameterized to ensure that crystal structures with tetrahedral bond angles (e.g., diamond-cubic, zinc-blende, and wurtzite) are stable and have the lowest energy. As a result, the Stillinger-Weber potential has been widely used to study a variety of semiconductor elements and alloys. When studying an A-B binary system, however, the Stillinger-Weber potential is associated with two major drawbacks. First, it significantly overestimates the elastic constants of elements A and B, limiting its use for systems involving both compounds and elements (e.g., an A/AB multilayer). Second, it prescribes equal energy for zinc-blende and wurtzite crystals, limiting its use for compounds with large stacking fault energies. Here, we utilize the polymorphic potential style recently implemented in LAMMPS to develop a modified Stillinger-Weber potential for InGaN that overcomes these two problems.A Stillinger-Weber potential is computationally very efficient for molecular dynamics simulations. Despite its simple mathematical form, the Stillinger-Weber potential can be easily parameterized to ensure that crystal structures with tetrahedral bond angles (e.g., diamond-cubic, zinc-blende, and wurtzite) are stable and have the lowest energy. As a result, the Stillinger-Weber potential has been widely used to study a variety of semiconductor elements and alloys. When studying an A-B binary system, however, the Stillinger-Weber potential is associated with two major drawbacks. First, it significantly overestimates the elastic constants of elements A and B, limiting its use for systems involving both compounds and elements (e.g., an A/AB multilayer). Second, it prescribes equal energy for zinc-blende and wurtzite crystals, limiting its use for compounds with large stacking fault energies. Here, we utilize the polymorphic potential style recently implemented in LAMMPS to develop a modified Stillinger-Weber... read less

Abstract: We have modeled laser-induced transient current waveforms in radiation coplanar grid detectors. Poisson's equation has been solved by finite element method and currents induced by photo-generated charge were obtained using Shockley-Ramo theorem. The spectral response on a radiation flux has been modeled by Monte-Carlo simulations. We show 10$\times$ improved spectral resolution of coplanar grid detector using differential signal sensing. We model the current waveform dependence on doping, depletion width, diffusion and detector shielding and their mutual dependence is discussed in terms of detector optimization. The numerical simulations are successfully compared to experimental data and further model simplifications are proposed. The space charge below electrodes and a non-homogeneous electric field on a coplanar grid anode are found to be the dominant contributions to laser-induced transient current waveforms. read less

Abstract: For colloidal quantum dots to transition from research laboratories to deployment as optical and electronic products, there will be a need to scale-up their production to large-scale manufacturing processes. This demand increases the need to understand their formation via a molecular representation of the nucleation of lead sulfide (PbS) quantum dot systems passivated by lead oleate complexes. We demonstrate the effectiveness of a new type of reactive potential, custom-made for this system, that is drawn from simple Morse, Lennard-Jones, and Coulombic components, which can reproduce reactions across a broad range of PbS quantum dot sizes with good accuracy. We validate the capability of this model to capture reactive systems by comparison to ab initio calculations for a reaction between two dots. read less

Abstract: The aim of the study described in this thesis is to obtain a profound understanding of transformations in NCs at the atomic level, by performing molecular simulations for such transformations, and by comparing the simulation results with available experimental high resolution transmission electron microscopy (HRTEM) data to validate the simulations and to reveal underlying physical mechanisms. These transformations include structural and morphological transitions and cation exchange processes in ionic nanocrystals (II-VI and IV-VI semiconductors). The main simulation method used is classical Molecular Dynamics (MD) simulation. First principles density functional theory (DFT) calculations were used to develop empirical force fields that are able to accurately reproduce phase transitions. Using these newly developed force fields, large scaled classical MD simulations were carried out and linked to HRTEM experiments. The partially charged rigid ion model (PCRIM) was chosen for the force fields. This PCRIM approach has a simple functional form with a few number of parameters and has a clear physical meaning for ionic crystals. To simulate cation exchange in colloidal NC systems at the NC/solution interface, we used a combination of all-atom force fields and a coarse-grained model. In Chapter 2, an ab-initio based force field for ZnO is developed within the framework of the PCRIM approach. The values of the partial charges were determined by Bader charge analysis of DFT calculations on various ZnO phases. Beside Coulombic interactions, only short-ranged pairwise interatomic interactions were included. An initial guess of the parameters of the short-ranged pair potentials were first obtained by the lattice inversion method. The parameters were further adjusted by an ab-initio potential surface fitting procedure. The new ZnO force field has a very simple functional form is able to accurately reproduce several important physical properties of ZnO materials. These physical properties include the lattice parameters and phase stability of several ZnO polymorphs, as well as the elastic constants, bulk moduli, phonon dispersion, and melting points of wurtzite ZnO. The transition pressure of the wurtzite-to-rocksalt transition calculated with the force field equals 12.3 GPa, in agreement with experimental measurements and DFT calculations. A wurtzite-to-honeycomb phase transition is predicted at an uniaxial pressure of 8.8 GPa. We found a rational and effective way to derive force fields with simple functional forms for accurate simulations of phase transitions in ionic crystals. In Chapter 3, we developed a transferable force field for CdS-CdSe-PbSPbSe solid systems. The selection of the force field and the fitting procedure are similar to that of the ZnO force field in Chapter 2. The challenges when developing this force field were to maintain the transferability of this force field for four materials (CdS, CdSe, PbS, and PbSe) and to describe their mixed phases. This was solved by assuming that different cations/anions have the same values of the partial charges, and that shortranged interatomic interactions between two cations/anions are the same in different materials. For the mixed phases, DFT calculations of the mixed phases were included in both the training and validation sets. This work is the first step for further simulation studies of these II-VI and IV-VI semiconductor NCs and heteronanocrystals (HNCs). In Chapter 4, a thermally induced morphological and structural transition of CdSe NCs was investigated using MD simulations. In MD simulations, a CdSe nanosphere with the ZB structure transforms into a tetrapodlike morphology at 800 K. In a CdSe tetrapod, four WZ legs attach to the {111} facets of a tetrahedral ZB core. This transformation is achieved by a layer-by-layer slip of the ZB-{111} bilayer. Simulations show that the slips are mediated by the formation of Cd vacancies on the surface of the NCs to overcome the potentially large energy barriers associated with slip. The morphology of the annealed NCs is found to be temperature and size-dependent. An octapod-like morphology is found in NCs with a relatively large NC size and in a certain range of the heating temperature. Surprisingly, nanoscale transformations of CdSe NCs have been directly observed in HRTEM in situ heating experiments. Our findings provide a simple method to modify the morphology of ionic NCs and can potentially be used in the synthesis of branched NCs. The cation exchange process of PbSe/CdSe HNCs has been investigated by HRTEM in situ heating experiments in combination with MD simulations and DFT calculations in Chapter 5. In the HRTEM experiments, we bserved that Cd atoms in PbSe/CdSe nanodumbbells (CdSe rods with one or two PbSe tip(s)) are replaced by Pb atoms. The exchange rate depends on the heating temperature and the amount of Pb atoms present in the system. Sometimes, fully converted PbSe nanodumbells can be observed. MD simulations were performed to investigate the mechanism of this cation exchange process. It was found that the the CdSe domains near the PbSe/CdSe interfaces have significant structural disorder. These findings are in line with the experimental observation that the exchange process proceeds in a layer-by-layer fashion along the WZ- direction. We concluded that cation exchange in PbSe/CdSe HNCs is mediated by the local structural disorder which enables the formation of vacancies and accelerated the motion of cations. In Chapter 6, a coarse-grained psuedoligand model was introduced to simulate cation exchange in PbS colloidal NCs taking into account the cation-solvent interactions. Modelling colloidal NC systems including interactions with the solvent has long been a challenge due to the large system size and long time scales. Here, we incorporated the effects of ligands and solvents into negatively charged large spherical coarse-grained psuedoligands. MD simulations combining coarse-grained and all-atom models can successfully reproduce the cation exchange process in PbS colloidal NCs. Simulations show that the exchange rate and system equilibrium can be controlled by the temperature and by changing ligands. The exchange process is directly related to vacancy formation and the high mobility of Cd ions at the PbS/CdS interface. Our simulations also predict that high-pressure conditions will be beneficial for achieving fast exchange at elevated temperatures. Our coarse-grained model can be easily extended to other systems for the computational investigation of transformations in nanostructures. read less

Abstract: By using the interatomic potential derived from ab initio simulations, equilibrium molecular dynamics simulations using the Green–Kubo relation were carried out to study the elastic constants and thermal conductivity of a layered organic–inorganic hybrid crystal β-ZnTe(en)0.5, whose inorganic ZnTe monolayers are connected by organic ligands ethylenediamine (en) with covalent bonds. As compared to inorganic ZnTe, the results of elastic constants showed that β-ZnTe(en)0.5 is much more flexible, especially in terms of the shearing stiffness. Low thermal conductivity values are found in β-ZnTe(en)0.5. At 300 K, the thermal conductivities are kST = 1.2 W/m·K in the stacking direction normal to the ZnTe monolayers, kAM = 0.8 W/m·K in the armchair direction, and kZZ = 1.8 W/m·K in the zigzag direction parallel to the ZnTe monolayers, respectively. The low thermal conductivity across the ZnTe monolayers is determined by the mismatch of phonon spectra between the organic ligands and ZnTe monolayers. The anisotropi... read less

Abstract: Carbon is the most widely studied material today because it exhibits special properties not seen in any other materials when in nano dimensions such as nanotube and graphene. Reduction of material defects created during synthesis has become critical to realize the full potential of carbon structures. Molecular dynamics (MD) simulations, in principle, allow defect formation mechanisms to be studied with high fidelity, and can, therefore, help guide experiments for defect reduction. Such MD simulations must satisfy a set of stringent requirements. First, they must employ an interatomic potential formalism that is transferable to a variety of carbon structures. Second, the potential needs to be appropriately parameterized to capture the property trends of important carbon structures, in particular, diamond, graphite, graphene, and nanotubes. Most importantly, the potential must predict the crystalline growth of the correct phases during direct MD simulations of synthesis to achieve a predictive simulation of defect formation. Because an unlimited number of structures not included in the potential parameterization are encountered, the literature carbon potentials are often not sufficient for growth simulations. We have developed an analytical bond order potential for carbon, and have made it available through the public MD simulation package LAMMPS. We demonstrate that our potential reasonably captures the property trends of important carbon phases. Stringent MD simulations convincingly show that our potential accounts not only for the crystalline growth of graphene, graphite, and carbon nanotubes but also for the transformation of graphite to diamond at high pressure. © 2015 Wiley Periodicals, Inc. read less

Abstract: Cd1-xZnxTe/CdS solar cells are currently limited by material defects. While nano-structuring promises further defect reductions, the materials synthesis and characterization become more challenging. Molecular dynamics models capable of growth simulations enable defects to be explored without assumptions, and can therefore guide nanoscale experiments. Such models are difficult to develop, and are not routinely available in literature for semiconductor compounds. To fill this gap, we have developed growth simulation enabling Stillinger-Weber and bond-order potentials. These new models begin to enable molecular dynamics to be used to explore nano-structured Cd1-xZnxTe/CdS solar cells with reduced defects. read less

Abstract: Recently developed molecular dynamics models have been applied to study the formation of defects during growth of ZnTe-on-CdS multilayers. Our studies indicated that misfit dislocations are formed during growth, and the dislocation density can be reduced if the ZnTe layer is grown in a nano island configuration as opposed to a continuous film. These results highlight the use of molecular dynamics methods in providing valuable defect formation mechanism insight and guiding experimental efforts to produce high efficiency Cd1-xZnxTe solar cells. read less

Abstract: We have carried out density functional theory based calculations for understanding the structural, electronic and magnetic properties of pristine and transition metal (TM) doped ZnTe nanowires. Pristine ZnTe nanowires (NWs) turn out to be semiconducting in nature, with the band gap varying with the diameter of the NWs. In Mn-doped ZnTe NWs, the Mn atoms retain a magnetic moment of 5 μB each and couple anti-ferromagnetically. A half metallic ferromagnetic state, although energetically not favorable, is observed arising from a strong hybridization between the d-states of Mn atoms and p-states of Te atoms. Further studies of V- and Sc-doped ZnTe NWs reveal the systems to be anti-ferromagnetic. read less

Abstract: The ternary semiconductor CuYS2 is studied by using the first-principles methods in the density functional theory (DFT) framework. The structural, electronic, optical and elastic properties were calculated at the ambient and elevated hydrostatic pressures. The compound was shown to have an indirect band gap of about 1.342/1.389 eV (in the generalized gradient and local density approximations, respectively). The anisotropy of the optical properties was studied by calculating the absorption spectra, dielectric function and index of refraction for different polarizations. The anisotropy of the elastic properties was visualized by plotting the three-dimensional dependence of the Young’s moduli on the direction in the crystal lattice. The obtained results, which are reported for the first time to the best of the author’s knowledge, can facilitate assessment of possible applications of the title material. read less

Abstract: Reducing defects in InGaN films deposited on GaN substrates has been critical to fill the “green” gap for solid-state lighting applications. To enable researchers to use molecular dynamics vapor deposition simulations to explores ways to reduce defects in InGaN films, we have developed and characterized a Stillinger-Weber potential for InGaN. We show that this potential reproduces the experimental atomic volume, cohesive energy, and bulk modulus of the equilibrium wurtzite / zinc-blende phases of both InN and GaN. Most importantly, the potential captures the stability of the correct phase of InGaN compounds against a variety of other elemental, alloy, and compound configurations. This is validated by the potential’s ability to predict crystalline growth of stoichiometric wurtzite and zinc-blende InxGa1-xN compounds during vapor deposition simulations where adatoms are randomly injected to the growth surface. read less

Abstract: Central-force decompositions are fundamental to the calculation of stress fields in atomic systems by means of Hardy stress. We derive expressions for a central-force decomposition of the spline-based modified embedded atom method (s-MEAM) potential. The expressions are subsequently simplified to a form that can be readily used in molecular-dynamics simulations, enabling the calculation of the spatial distribution of stress in systems treated with this novel class of empirical potentials. We briefly discuss the properties of the obtained decomposition and highlight further computational techniques that can be expected to benefit from the results of this work. To demonstrate the practicability of the derived expressions, we apply them to calculate stress fields due to an edge dislocation in bcc Mo, comparing their predictions to those of linear elasticity theory. read less

Abstract: A transferable force field for the PbSe-CdSe solid system using the partially charged rigid ion model has been successfully developed and was used to study the cation exchange in PbSe-CdSe heteronanocrystals [A. O. Yalcin et al., "Atomic resolution monitoring of cation exchange in CdSe-PbSe heteronanocrystals during epitaxial solid-solid-vapor growth," Nano Lett. 14, 3661-3667 (2014)]. In this work, we extend this force field by including another two important binary semiconductors, PbS and CdS, and provide detailed information on the validation of this force field. The parameterization combines Bader charge analysis, empirical fitting, and ab initio energy surface fitting. When compared with experimental data and density functional theory calculations, it is shown that a wide range of physical properties of bulk PbS, PbSe, CdS, CdSe, and their mixed phases can be accurately reproduced using this force field. The choice of functional forms and parameterization strategy is demonstrated to be rational and effective. This transferable force field can be used in various studies on II-VI and IV-VI semiconductor materials consisting of CdS, CdSe, PbS, and PbSe. Here, we demonstrate the applicability of the force field model by molecular dynamics simulations whereby transformations are initiated by cation exchange. read less