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.

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.

THE ROLE OF SUBSTRATE IN PACKING STRUCTURES OF SEXITHIOPHENES ON AG (111) SURFACE: MOLECULAR DYNAMICS SIMULATIONS AND QUANTUM CHEMICAL CALCULATIONS

2009 ◽  
Vol 08 (04) ◽  
pp. 677-690 ◽  
Author(s):  
JIN WEN ◽  
JING MA
Keyword(s):  
Molecular Dynamics ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Density Functional ◽  
Md Simulations ◽  
Site Preference ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Dynamics Simulations

Packing structures and orientation of sexithiophene (6T) molecules on Ag (111) surface are investigated by molecular dynamics (MD) simulations and quantum chemical calculations. Both the cluster and the slab models are employed. The density functional theory and molecular mechanism calculations demonstrate a weak physisorption and little site-preference in thiophene/ Ag (111) system. The MD simulations show that in the first layer close to the surface, the nearly coplanar 6T strips lie parallel with long axes deviating from [Formula: see text] direction about 20° – 30° and 75° – 90°. The average adsorption height of the monolayer is about 3.2 Å with most of the sulfur atoms in thienyl rings sitting on the bridge site of Ag (111) surface. The 6T molecules tend to take tilted orientations when they are far away from the surface. The packing structures of 6T layers deposited on the surface resulted from the competition between the molecule–substrate and intermolecular interactions.

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.

scholarly journals On the Use of Molecular Dynamics Simulations for Elucidating Fine Structural, Physico-Chemical and Thermomechanical Properties of Lignocellulosic Systems: Historical and Future Perspectives

2021 ◽  
Vol 5 (2) ◽  
pp. 55
Author(s):  
Krishnamurthy Prasad ◽  
Mostafa Nikzad ◽  
Shammi Sultana Nisha ◽  
Igor Sbarski
Keyword(s):  
Molecular Dynamics ◽  
High Performance ◽  
Molecular Mechanisms ◽  
Md Simulations ◽  
Thermomechanical Properties ◽  
Current State ◽  
Physico Chemical ◽  
Carbohydrate Complex ◽  
Dynamics Simulations

The use of Molecular Dynamics (MD) simulations for predicting subtle structural, thermomechanical and related characteristics of lignocellulosic systems is studied. A historical perspective and the current state of the art are discussed. The use of parameterised MD force fields, scaling up simulations via high performance computing and intrinsic molecular mechanisms influencing the mechanical, thermal and chemical characteristics of lignocellulosic systems and how these can be predicted and modelled using MD is shown. Individual discussions on the MD simulations of the lignin, cellulose, lignin-carbohydrate complex (LCC) and how MD can elucidate the role of water on the surface and microstructural characteristics of these lignocellulosic systems is shown. In addition, the use of MD for unearthing molecular mechanisms behind lignin-enzyme interactions during precipitation processes and the deforming/structure weakening brought about by cellulosic interactions in some lignocellulosic systems is both predicted and quantified. MD results from relatively smaller systems comprised of several hundred to a few thousand atoms and massive multi-million atom systems are both discussed. The versatility and effectiveness of MD based on its ability to provide viable predictions from both smaller and massive starting systems is presented in detail.

Role of CSL Boundaries on Displacement Cascades in β-SiC

2013 ◽  
Vol 1514 ◽  
pp. 43-48
Author(s):  
Prithwish K. Nandi ◽  
V. Ajay Annamareddy ◽  
Jacob Eapen
Keyword(s):  
Molecular Dynamics ◽  
Grain Boundary ◽  
Grain Boundaries ◽  
Neutron Irradiation ◽  
Md Simulations ◽  
Atomic Mobility ◽  
Statistical Nature ◽  
Displacement Cascades ◽  
Tilt Grain Boundary

ABSTRACTMolecular dynamics (MD) simulations are carried out to understand the mechanisms of damage production and recovery near grain boundaries in β-SiC under neutron irradiation. Our investigations show that the damage generated by radiation is reduced by the presence of a ∑9{122}[110] tilt grain boundary. Directional displacements which are averaged over an isoconfigurational ensemble are used to characterize the statistical nature of atomic mobility near the grain boundary.

Isolating the role of hydrogen bonding in hydroxyl-functionalized ionic liquids by means of vaporization enthalpies, infrared spectroscopy and molecular dynamics simulations

2019 ◽  
Vol 21 (36) ◽  
pp. 20308-20314 ◽  
Author(s):  
Dzmitry H. Zaitsau ◽  
Jan Neumann ◽  
Thomas Niemann ◽  
Anne Strate ◽  
Dietmar Paschek ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Infrared Spectroscopy ◽  
Ir Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Dispersion Interaction ◽  
Dynamics Simulations

Hydrogen bonding in hydroxyl-functionalized ionic liquids (right) prevents favourable dispersion interaction between cation and anion (left). We analyze this subtle balance of interactions by combining calorimetry, IR spectroscopy and MD simulations.

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.

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