Computation of the Onset of Point Defect Aggregation in Crystalline Silicon Using an Empirical Interatomic Potential

1995 ◽  
Vol 378 ◽  
Author(s):  
T. Sinno ◽  
R.A. Brown
Keyword(s):  
Point Defects ◽  
Interatomic Potential ◽  
Driving Forces ◽  
Crystalline Silicon ◽  
Single Point ◽  
Binding Energies ◽  
Single Vacancy ◽  
Single Defect ◽  
Equilibrium Configurations ◽  
Dynamics Simulations

AbstractThe Stillinger-Weber interatomic potential is used in molecular dynamics simulations to investigate the equilibrium, transport and aggregation properties of self-interstitials and vacancies in crystalline silicon at temperatures ranging from 500K to the melting point. The simulations predict equilibrium configurations of a < 110 > dumbbell for the single self-interstitial and an inwardly relaxed structure for the single vacancy. Both single-defect structures exhibit significant derealization at high temperatures resulting in strongly temperature dependent entropies of formation, as suggested by diffusion experiments. Diffusion coefficients and mechanisms for the single defects are predicted as a function of temperature. The results for the single point defects are discussed in the context of the existing literature values. Aggregation of two point defects is investigated by the computation of binding energies and entropies for these structures. Interstitials exhibit significant aggregation driving forces across the entire temperature range under simulation conditions, while vacancies aggregate less readily.

scholarly journals Tight-Binding Molecular Dynamics Simulations on Point Defects Diffusion and Interactions in Crystalline Silicon

1995 ◽  
Vol 396 ◽  
Author(s):  
M. tang ◽  
L. colombo ◽  
T. Diaz De La Rubia
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Point Defects ◽  
Crystalline Silicon ◽  
Tight Binding ◽  
Diffusion Path ◽  
Binding Energies ◽  
Defect Clusters ◽  
Dynamics Simulations

AbstractTight-binding molecular dynamics (TBMD) simulations are performed (i) to evaluate the formation and binding energies of point defects and defect clusters, (ii) to compute the diffusivity of self-interstitial and vacancy in crystalline silicon, and (iii) to characterize the diffusion path and mechanism at the atomistic level. In addition, the interaction between individual defects and their clustering is investigated.

scholarly journals Assessing the capability ofin silicomutation protocols for predicting the finite temperature conformation of amino acids

2018 ◽  
Vol 20 (40) ◽  
pp. 25901-25909 ◽  
Author(s):  
Rodrigo Ochoa ◽  
Miguel A. Soler ◽  
Alessandro Laio ◽  
Pilar Cossio
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulations ◽  
Point Mutation ◽  
Finite Temperature ◽  
Single Point ◽  
Single Point Mutation ◽  
Equilibrium Configurations ◽  
Dynamics Simulations

Single-point mutation protocols based on backbone-dependent rotamer libraries show the best performance in predicting equilibrium configurations from molecular dynamics simulations.

Length-scale Effects in Cascade Damage Production in Iron

2008 ◽  
Vol 1125 ◽  
Author(s):  
R. E. Stoller ◽  
P. J. Kamenski ◽  
Yu. N. Osetsky
Keyword(s):  
Single Crystal ◽  
Point Defects ◽  
Interatomic Potential ◽  
Scale Effects ◽  
Atomic Displacement ◽  
Nanocrystalline Iron ◽  
Cooling Phase ◽  
Primary Damage ◽  
Dynamics Simulations ◽  
Cascade Damage

ABSTRACTMolecular dynamics simulations provide an atomistic description of the processes that control primary radiation damage formation in atomic displacement cascades. An extensive database of simulations describing cascade damage production in single crystal iron has been compiled using a modified version of the interatomic potential developed by Finnis and Sinclair. This same potential has been used to investigate primary damage formation in nanocrystalline iron in order to have a direct comparison with the single crystal results. A statistically significant number of simulations were carried out at cascade energies of 10 keV and 20 keV and temperatures of 100 and 600K to make this comparison. The results demonstrate a significant influence of nearby grain boundaries as a sink for mobile defects during the cascade cooling phase. This alters the residual primary damage that survives the cascade event. Compared to single crystal, substantially fewer interstitials survive in the nanograined iron, while the number of surviving vacancies is similar or slightly greater than the single crystal result. The fraction of the surviving interstitials contained in clusters is also reduced. The asymmetry in the survival of the two types of point defects is likely to alter damage accumulation at longer times.

scholarly journals Accuracy and Reproducibility of Host-Guest Interactions in Zeolites

2020 ◽  
Author(s):  
Daniel Schwalbe-Koda ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Density Functional ◽  
Single Point ◽  
Cost Effective ◽  
Binding Energies ◽  
Binding Affinities ◽  
Computationally Efficient ◽  
Zeolite Framework ◽  
Functional Theory ◽  
Organic Structure ◽  
Dynamics Simulations

Molecular modeling plays an important role in the discovery of organic structure-directing agents (OSDAs) for zeolites. By quantifying the intensity of host-guest interactions, it is possible to select cost-effective molecules that maximize binding towards a given zeolite framework. Over the last decades, a variety of methods and levels of theory have been used to calculate these binding energies. Nevertheless, no benchmark examining these calculation strategies has been reported. In this work, we compare binding affinities from density functional theory (DFT) and force field calculations for 272 zeolite-OSDA pairs obtained from static and time-averaged simulations. We show that binding energies from the frozen pose method correlate best with DFT time-averaged energies. They are also less sensitive to the choice of initial lattice parameters and optimization algorithms, as well as less computationally expensive. Furthermore, we demonstrate that a broader exploration of the conformation space from molecular dynamics simulations does not provide significant improvements in binding energy trends over single-point calculations. The code and benchmark data are open-sourced and together with the reported results, provide robust, reproducible, and computationally-efficient guidelines to calculating binding energies in zeolite-OSDA pairs.

scholarly journals Accuracy and Reproducibility of Host-Guest Interactions in Zeolites

2020 ◽  
Author(s):  
Daniel Schwalbe-Koda ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Density Functional ◽  
Single Point ◽  
Cost Effective ◽  
Binding Energies ◽  
Binding Affinities ◽  
Computationally Efficient ◽  
Zeolite Framework ◽  
Functional Theory ◽  
Organic Structure ◽  
Dynamics Simulations

Molecular modeling plays an important role in the discovery of organic structure-directing agents (OSDAs) for zeolites. By quantifying the intensity of host-guest interactions, it is possible to select cost-effective molecules that maximize binding towards a given zeolite framework. Over the last decades, a variety of methods and levels of theory have been used to calculate these binding energies. Nevertheless, no benchmark examining these calculation strategies has been reported. In this work, we compare binding affinities from density functional theory (DFT) and force field calculations for 272 zeolite-OSDA pairs obtained from static and time-averaged simulations. We show that binding energies from the frozen pose method correlate best with DFT time-averaged energies. They are also less sensitive to the choice of initial lattice parameters and optimization algorithms, as well as less computationally expensive. Furthermore, we demonstrate that a broader exploration of the conformation space from molecular dynamics simulations does not provide significant improvements in binding energy trends over single-point calculations. The code and benchmark data are open-sourced and together with the reported results, provide robust, reproducible, and computationally-efficient guidelines to calculating binding energies in zeolite-OSDA pairs.

scholarly journals Isochronal Annealing of Electron-Irradiated Tungsten Modelled by CD Method: 1D and 3DModel of SIA Diffusivity

2018 ◽  
Vol 19 (1) ◽  
pp. 5-13
Author(s):  
M. S. Kondria ◽  
A. R. Gokhman
Keyword(s):  
Experimental Data ◽  
Carbon Atom ◽  
Electron Irradiation ◽  
Binding Energies ◽  
Isochronal Annealing ◽  
Multiscale Approach ◽  
Single Vacancy ◽  
Vacancy Clusters ◽  
Energy Formation ◽  
Dynamics Simulations

The evolution of the microstructure of tungsten under electron irradiation and post-irradiation annealing hasbeen modeled using a multiscale approach based on Cluster Dynamics simulations. In these simulations, bothself-interstitials atoms (SIA) and vacancies, carbon atoms isolated or in clusters, are considered. Isochronal annealing has been simulated in carbon free tungsten and tungsten with carbon, focusing on the recovery stages I and II. The carbon atom, single SIA, single vacancy and vacancy clusters with sizes up to four are treated as the mobile pieces. Their diffusivities as well as the energy formation and binding energies are based on the  experimental data and ab initio predictions and some of these parameters have been slightly  adjusted, without modifying the interaction character, on isochronal annealing experimental data. The both models with assumption on 1D as well as 3D dimensionality of diffusivity of SIA are treated. The advantage of the model with 1D diffusivity of SIA is found.

Study of Oxygen Diffusion and Clustering in Silicon Using an Empirical Interatomic Potential

1995 ◽  
Vol 378 ◽  
Author(s):  
Z. Jiang ◽  
R. A. Brown
Keyword(s):  
Interatomic Potential ◽  
Crystalline Silicon ◽  
Diffusion Path ◽  
Rate Theory ◽  
Free Energies ◽  
Silicon Crystals ◽  
Oxygen Precipitation ◽  
Dynamics Simulations ◽  
Small Clusters ◽  
Oxygen Atoms

AbstractThe diffusion path and diffusivity of oxygen in crystalline silicon are computed using an empirical interatomic potential which was recently developed [1] for modelling the interactions between oxygen and silicon atoms. The diffusion path is determined by constrained energy minimization, and the diffusivity is computed using jump rate theory. The calculated diffusivity D=0.025 exp(-2.43eV/kBT) cm2/sec is in excellent agreement with experimental data. The same interatomic potential also is used to study the formation of small clusters of oxygen atoms in silicon. The structures of these clusters are found by NPT molecular dynamics simulations, and their free energies are calculated by thermodynamic integration. These free energies are used to predict the temperature dependence of the equilibrium partitioning of oxygen atoms into clusters of different sizes. The calculations show that, for given total oxygen concentration, most oxygen atoms are in clusters at temperature below 1300K, and that the average cluster size increases with decreasing temperature. These results are in qualitative agreement with the effects of thermal annealing on oxygen precipitation in silicon crystals.

scholarly journals Benchmarking binding energy calculations for organic structure-directing agents in pure-silica zeolites

2021 ◽  
Author(s):  
Daniel Schwalbe-Koda ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Binding Energy ◽  
Density Functional ◽  
Single Point ◽  
Cost Effective ◽  
Binding Energies ◽  
Computationally Efficient ◽  
Organic Structure ◽  
Pure Silica ◽  
Structure Directing Agents ◽  
Dynamics Simulations

Molecular modeling plays an important role in the discovery of organic structure-directing agents (OSDAs) for zeolites. By quantifying the intensity of host-guest interactions, it is possible to select cost-effective molecules that maximize binding towards a given zeolite framework. Over the last decades, a variety of methods and levels of theory have been used to calculate these binding energies. Nevertheless, there is no consensus on the best calculation strategy for high-throughput virtual screening undertakings. In this work, we compare binding affinities from density functional theory (DFT) and force field calculations for 272 zeolite-OSDA pairs obtained from static and time-averaged simulations. Enabled by automation software, we show that binding energies from the frozen pose method correlate best with DFT time-averaged energies. They are also less sensitive to the choice of initial lattice parameters and optimization algorithms, as well as less computationally expensive. Furthermore, we demonstrate that a broader exploration of the conformation space from molecular dynamics simulations does not provide significant improvements in binding energy trends over single-point calculations. The code and benchmark data are open-sourced and provide robust and computationally-efficient guidelines to calculating binding energies in zeolite-OSDA pairs.

On the Adsorption of Aspartate Derivatives to Calcite Surfaces in Aqueous Environment

2020 ◽  
Author(s):  
Robert Stepic ◽  
Lara Jurković ◽  
Ksenia Klementyeva ◽  
Marko Ukrainczyk ◽  
Matija Gredičak ◽  
...  
Keyword(s):  
Active Sites ◽  
Realistic Model ◽  
Binding Energies ◽  
Inhibition Mechanism ◽  
Aqueous Environment ◽  
Binding Modes ◽  
Carboxylate Groups ◽  
Dissolved Ions ◽  
Living Organisms ◽  
Dynamics Simulations

In many living organisms, biomolecules interact favorably with various surfaces of calcium carbonate. In this work, we have considered the interactions of aspartate (Asp) derivatives, as models of complex biomolecules, with calcite. Using kinetic growth experiments, we have investigated the inhibition of calcite growth by Asp, Asp2 and Asp3.This entailed the determination of a step-pinning growth regime as well as the evaluation of the adsorption constants and binding free energies for the three species to calcite crystals. These latter values are compared to free energy profiles obtained from fully atomistic molecular dynamics simulations. When using a flat (104) calcite surface in the models, the measured trend of binding energies is poorly reproduced. However, a more realistic model comprised of a surface with an island containing edges and corners, yields binding energies that compare very well with experiments. Surprisingly, we find that most binding modes involve the positively charged, ammonium group. Moreover, while attachment of the negatively charged carboxylate groups is also frequently observed, it is always balanced by the aqueous solvation of an equal or greater number of carboxylates. These effects are observed on all calcite features including edges and corners, the latter being associated with dominant affinities to Asp derivatives. As these features are also precisely the active sites for crystal growth, the experimental and theoretical results point strongly to a growth inhibition mechanism whereby these sites become blocked, preventing further attachment of dissolved ions and halting further growth.

scholarly journals Interfacial Strengthening of Graphene/Aluminum Composites through Point Defects: A First-Principles Study

Nanomaterials ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 738
Author(s):  
Xin Zhang ◽  
Shaoqing Wang
Keyword(s):  
Mechanical Properties ◽  
Metal Matrix Composites ◽  
Point Defects ◽  
Metal Matrix ◽  
Interfacial Bonding ◽  
Theoretical Research ◽  
Matrix Composites ◽  
Aluminum Composites ◽  
Single Vacancy ◽  
Design Guideline

The relationship between point defects and mechanical properties has not been fully understood yet from a theoretical perspective. This study systematically investigated how the Stone–Wales (SW) defect, the single vacancy (SV), and the double vacancy (DV) affect the mechanical properties of graphene/aluminum composites. The interfacial bonding energies containing the SW and DV defects were about twice that of the pristine graphene. Surprisingly, the interfacial bonding energy of the composites with single vacancy was almost four times that of without defect in graphene. These results indicate that point defects enhance the interfacial bonding strength significantly and thus improve the mechanical properties of graphene/aluminum composites, especially the SV defect. The differential charge density elucidates that the formation of strong Al–C covalent bonds at the defects is the most fundamental reason for improving the mechanical properties of graphene/aluminum composites. The theoretical research results show the defective graphene as the reinforcing phase is more promising to be used in the metal matrix composites, which will provide a novel design guideline for graphene reinforced metal matrix composites. Furthermore, the sp3-hybridized C dangling bonds increase the chemical activity of the SV graphene, making it possible for the SV graphene/aluminum composites to be used in the catalysis field.

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