Influence of Interatomic Potentials in MD Investigation of Ordering in a-SiC

2000 ◽  
Vol 650 ◽  
Author(s):  
Xianglong Yuan ◽  
Linn W. Hobbs
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Interatomic Potentials ◽  
Chemical Ordering ◽  
Structure Ordering

ABSTRACTMolecular dynamics (MD) simulations of a-SiC using several Tersoff potentials have been performed and their influences on structure ordering were studied. It was found that using different potential cutoffs leads to remarkably different structures. An abrupt cutoff at 2.5 Å greatly increases the chemical ordering of a-SiC by disfavoring the formation of Si-Si bonds. In addition, annealing of SiC cascades embedded in β-SiC was simulated, and the final structures were compared. Again, much stronger topological and chemical ordering was observed in the structure modeled with the 2.5 Å potential cutoff.

Molecular Dynamics Simulations of Atoms Diffusion in Solid

2018 ◽  
Vol 15 ◽  
pp. 51-64
Author(s):  
Yu Lu Zhou ◽  
Xiao Ma Tao ◽  
Qing Hou ◽  
Yi Fang Ouyang
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Md Simulations ◽  
Einstein Relation ◽  
Interatomic Potentials ◽  
Body System ◽  
Many Body ◽  
Point Particles ◽  
Bulk Surface ◽  
Dynamics Simulations

Molecular dynamics (MD) simulations, which treat atoms as point particles and trace their individual trajectories, are always employed to investigate the transport properties of a many-body system. The diffusion coefficients of atoms in solid can be obtained by the Einstein relation and the Green-Kubo relation. An overview of the MD simulations of atoms diffusion in the bulk, surface and grain boundary is provided. We also give an example of the diffusion of helium in tungsten to illustrate the procedure, as well as the importance of the choice of interatomic potentials. MD simulations can provide intuitive insights into the atomic mechanisms of diffusion.

Choosing Appropriate Interatomic Potentials for Nanometric Molecular Dynamics (MD) Simulations

2016 ◽  
Vol 686 ◽  
pp. 194-199
Author(s):  
Akinjide O. Oluwajobi ◽  
Xun Chen
Keyword(s):  
Molecular Dynamics ◽  
Diamond Tool ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Interatomic Potentials ◽  
Embedded Atom ◽  
Pair Potentials ◽  
Empirical Potentials ◽  
Nanometric Machining ◽  
Cutting Processes

There is a need to choose appropriate interatomic empirical potentials for the molecular dynamics (MD) simulation of nanomachining, so as to represent chip formation and other cutting processes reliably. Popularly applied potentials namely; Lennard-Jones (LJ), Morse, Embedded Atom Method (EAM) and Tersoff were employed in the molecular dynamics simulation of nanometric machining of copper workpiece with diamond tool. The EAM potentials were used for the modelling of the copper-copper atom interactions. The pairs of EAM-Morse and EAM-LJ were used for the workpiece-tool (copper-diamond) atomic interface. The Tersoff potential was used for the carbon-carbon interactions in the diamond tool. Multi-pass simulations were carried out and it was observed that the EAM-LJ and the EAM-Morse pair potentials with the tool modelled as deformable with Tersoff potential were best suitable for the simulation. The former exhibit the lowest cutting forces and the latter has the lowest potential energy.

Molecular Dynamics simulations of displacement cascades: role of the interatomic potentials and of the potential hardening

2000 ◽  
Vol 650 ◽  
Author(s):  
C.S. Becquart ◽  
C. Domain ◽  
A. Legris ◽  
J.C. van Duysen
Keyword(s):  
Molecular Dynamics ◽  
Thermal Characteristics ◽  
Md Simulations ◽  
Interatomic Potentials ◽  
Static Properties ◽  
Displacement Cascades ◽  
Energy Transfers ◽  
Primary Damage ◽  
Dynamics Simulations

ABSTRACTThe role of the interatomic potentials on the primary damage has been investigated by Molecular Dynamics (MD) simulations of displacement cascades with three different interatomic potentials dedicated to α-Fe. The primary damage, caused by the neutron interaction with the matter, has been found to be potential sensitive. We have investigated the equilibrium parts of the potential as well as the “short distance interactions” which appear to have a strong influence on the cascade morphology and defects distribution at the end of the cascade. The static properties as well as dynamical (thermal) characteristics of the potentials have been considered; the kinetic and potential energy transfers during the collisions have also been studied.

Predicting XAFS scattering path cumulants and XAFS spectra for metals (Cu, Ni, Fe, Ti, Au) using molecular dynamics simulations

2013 ◽  
Vol 20 (4) ◽  
pp. 555-566 ◽  
Author(s):  
M. A. Karolewski ◽  
R. G. Cavell ◽  
R. A. Gordon ◽  
C. J. Glover ◽  
M. Cheah ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Embedded Atom Method ◽  
Interatomic Potentials ◽  
Embedded Atom ◽  
Scaling Parameters ◽  
Order Of Magnitude ◽  
Experimental Errors ◽  
Dynamics Simulations ◽  
X Ray Absorption

The ability of molecular dynamics (MD) simulations to support the analysis of X-ray absorption fine-structure (XAFS) data for metals is evaluated. The low-order cumulants (ΔR, σ2,C3) for XAFS scattering paths are calculated for the metals Cu, Ni, Fe, Ti and Au at 300 K using 28 interatomic potentials of the embedded-atom method type. The MD cumulant predictions were evaluated within a cumulant expansion XAFS fitting model, using global (path-independent) scaling factors. Direct simulations of the corresponding XAFS spectra, χ(R), are also performed using MD configurational data in combination with theFEFFab initiocode. The cumulant scaling parameters compensate for differences between the real and effective scattering path distributions, and for any errors that might exist in the MD predictions and in the experimental data. The fitted value of ΔRis susceptible to experimental errors and inadvertent lattice thermal expansion in the simulation crystallites. The unadjusted predictions of σ2vary in accuracy, but do not show a consistent bias for any metal except Au, for which all potentials overestimate σ2. The unadjustedC3predictions produced by different potentials display only order-of-magnitude consistency. The accuracy of direct simulations of χ(R) for a given metal varies among the different potentials. For each of the metals Cu, Ni, Fe and Ti, one or more of the tested potentials was found to provide a reasonable simulation of χ(R). However, none of the potentials tested for Au was sufficiently accurate for this purpose.

Molecular Dynamics Simulations of Thermal Conductivity of Bi2Te3 Nanowires

2009 ◽  
Author(s):  
Bo Qiu ◽  
Lin Sun ◽  
Xiulin Ruan
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Surface Roughness ◽  
Smooth Surface ◽  
Lattice Thermal Conductivity ◽  
Phonon Scattering ◽  
Md Simulations ◽  
Interatomic Potentials ◽  
Phonon Confinement ◽  
Dynamics Simulations

In this paper, by employing the previously developed two-body interatomic potentials for bismuth telluride, molecular dynamics (MD) simulations are used to describe the thermoelectric properties, namely the lattice thermal conductivity, of Bi2Te3 nanowires. Cylindrical nanowires with both smooth surface and sawtooth surface roughness are studied, aiming at revealing the effects of phonon confinement in 1-D structures, phonon boundary scatterings and surface roughness on the lattice thermal conductivity of Bi2Te3 nanowires. In the end, the influence of various phonon scattering mechanisms on the nanostructures under study are summarized, possible paths to reduce lattice thermal conductivity in nanostructured Bi2Te3, which is favorable for enhancing thermoelectric performance, are pointed out.

Meta-Atom Molecular Dynamics for Studying Material Property Dependent Deformation Mechanisms of Alloys

2017 ◽  
Vol 84 (11) ◽  
Author(s):  
Peng Wang ◽  
Hongtao Wang
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Dislocation Motion ◽  
Deformation Mechanisms ◽  
Massively Parallel ◽  
Interatomic Potentials ◽  
Strengthening Effect ◽  
Face Centered Cubic ◽  
Embedded Atom ◽  
Meta Atom

Massively parallel molecular dynamics (MD) simulations have been performed to understand the plastic deformation of metals. However, the intricate interplay between the deformation mechanisms and the various material properties is largely unknown in alloy systems for the limited available interatomic potentials. We adopt the meta-atom method proposed by Wang et al., which unifies MD simulations of both pure metals and alloys in the framework of the embedded atom method (EAM). Owing to the universality of EAM for metallic systems, meta-atom potentials can fit properties of different classes of alloys. Meta-atom potentials for both aluminum bronzes and hypothetic face-centered-cubic (FCC) metals have been formulated to study the parametric dependence of deformation mechanisms, which captures the essence of competitions between dislocation motion and twinning or cleavage. Moreover, the solid-solution strengthening effect can be simply accounted by introducing a scaling factor in the meta-atom method. As the computational power enlarges, this method can extend the capability of massively parallel MD simulations in understanding the mechanical behaviors of alloys. The calculation of macroscopic measurable quantities for engineering oriented alloys is expected to be possible in this way, shedding light on constructing materials with specific mechanical properties.

Efficient Treatment of Fixed and Induced Dipolar Interactions

2000 ◽  
Vol 653 ◽  
Author(s):  
Celeste Sagui ◽  
Thoma Darden
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Lagrangian Formalism ◽  
Dipolar Interactions ◽  
Time Step ◽  
Efficient Treatment ◽  
Particle Mesh Ewald ◽  
Fixed Charges ◽  
Self Consistency ◽  
Induced Dipoles

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.

Split the Charge Difference in Two! a Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Molecular Dynamics ◽  
Ionic Strength ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Good Practices ◽  
Rule Of Thumb ◽  
Ionic Concentrations

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>

Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations

2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Tylophora Indica ◽  
Multidrug Resistance Protein 1 ◽  
Receptor Complexes ◽  
Resistance Protein ◽  
Dynamics Simulations ◽  
Stable Trajectory

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.

scholarly journals On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 99
Author(s):  
Cristian Privat ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Jaime Rubio-Martínez
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Md Simulations ◽  
Point Of View ◽  
Conformational Space ◽  
Conformational Sampling ◽  
Protonation State ◽  
Constant Ph ◽  
Biochemical Systems ◽  
Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

Sign in / Sign up

Export Citation Format

Share Document