Molecular Dynamics Simulations of Thin Film Diamond Growth

1991 ◽  
Vol 223 ◽  
Author(s):  
Bernard A. Pailthorpe ◽  
Peter Knight
Keyword(s):  
Molecular Dynamics ◽  
High Stress ◽  
Distribution Functions ◽  
Film Stress ◽  
Diamond Growth ◽  
Vacuum Arc ◽  
Hartree Fock ◽  
Intermediate Energies ◽  
Dynamics Simulations ◽  
Weber Potential

ABSTRACTThe growth of synthetic diamond thin films is studied by molecular dynamics computer simulations of low energy carbon atom deposition onto a low temperature diamond (111) surface. A previously reported Stillinger Weber potential, reparameterised for sp3 bonding in carbon using Hartree-Fock calculations for small carbon clusters, is used to model the interatomic interactions. The penetration of 1-100eV neutral carbon atoms into a (111) surface of carbon at 100K and the resultant surface atom rearrangements and induced film stress are studied. For intermediate energies (20-60eV) the incident atoms penetrate beneath the exposed (111) surface and increase the lateral compressive stress in the diamond film. It is suggested that diamond films grow from below the exposed surface in a region of locally high stress and tetrahedral coordination. The predicted radial distribution functions agree reasonably with electron diffraction studies of vacuum arc deposited amorphous diamond.

scholarly journals Origin and control of ionic hydration patterns in nanopores

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Miraslau L. Barabash ◽  
William A. T. Gibby ◽  
Carlo Guardiani ◽  
Alex Smolyanitsky ◽  
Dmitry G. Luchinsky ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Water Molecules ◽  
Surrounding Water ◽  
Ionic Hydration ◽  
Hydration Shells ◽  
Water Layers ◽  
Dynamics Simulations ◽  
And Control

AbstractIn order to permeate a nanopore, an ion must overcome a dehydration energy barrier caused by the redistribution of surrounding water molecules. The redistribution is inhomogeneous, anisotropic and strongly position-dependent, resulting in complex patterns that are routinely observed in molecular dynamics simulations. Here, we study the physical origin of these patterns and of how they can be predicted and controlled. We introduce an analytic model able to predict the patterns in a graphene nanopore in terms of experimentally accessible radial distribution functions, giving results that agree well with molecular dynamics simulations. The patterns are attributable to a complex interplay of ionic hydration shells with water layers adjacent to the graphene membrane and with the hydration cloud of the nanopore rim atoms, and we discuss ways of controlling them. Our findings pave the way to designing required transport properties into nanoionic devices by optimising the structure of the hydration patterns.

scholarly journals Effects of temperatures on pressure-induced structural changes in amorphous Si: A molecular-dynamics study

10.29007/6kp3 ◽  
2020 ◽  
Author(s):  
Renji Mukuno ◽  
Manabu Ishimaru
Keyword(s):  
Molecular Dynamics ◽  
Phase Transformation ◽  
Amorphous Phase ◽  
Structural Changes ◽  
Interatomic Potential ◽  
Activation Barrier ◽  
Distribution Functions ◽  
High Density ◽  
Angle Distribution ◽  
Dynamics Simulations

The structural changes of amorphous silicon (a-Si) under compressive pressure were examined by molecular-dynamics simulations using the Tersoff interatomic potential. a-Si prepared by melt-quenching methods was pressurized up to 30 GPa under different temperatures (300K and 500K). The density of a-Si increased from 2.26 to 3.24 g/cm3 with pressure, suggesting the occurrence of the low-density to high-density amorphous phase transformation. This phase transformation occurred at the lower pressure with increasing the temperature because the activation barrier for amorphous-to-amorphous phase transformation could be exceeded by thermal energy. The coordination number increased with pressure and time, and it was saturated at different values depending on the pressure. This suggested the existence of different metastable atomic configurations in a-Si. Atomic pair-distribution functions and bond-angle distribution functions suggested that the short-range ordered structure of high-density a-Si is similar to the structure of the high-pressure phase of crystalline Si (β-tin and Imma structures).

Molecular dynamics simulation of the solidification process of multicrystalline silicon from homogeneous nucleation to grain coarsening

CrystEngComm ◽  
2018 ◽  
Vol 20 (25) ◽  
pp. 3569-3580 ◽  
Author(s):  
Xiaoxiao Sui ◽  
Yongjian Cheng ◽  
Naigen Zhou ◽  
Binbing Tang ◽  
Lang Zhou
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Homogeneous Nucleation ◽  
Solidification Process ◽  
Dynamics Simulation ◽  
Multicrystalline Silicon ◽  
Solidification Processes ◽  
Dynamics Simulations ◽  
Weber Potential

Based on the Stillinger–Weber potential, molecular dynamics simulations of the solidification processes of multicrystalline silicon were carried out.

scholarly journals Molecular Dynamics Simulations of CO2Molecules in ZIF-11 Using Refined AMBER Force Field

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
W. Wongsinlatam ◽  
T. Remsungnen
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Binding Energies ◽  
Hydrogen Atoms ◽  
Amber Force Field ◽  
Bonding Parameters ◽  
Flexible Framework ◽  
Dynamics Simulations

Nonbonding parameters of AMBER force field have been refined based onab initiobinding energies of CO2–[C7H5N2]−complexes. The energy and geometry scaling factors are obtained to be 1.2 and 0.9 forεandσparameters, respectively. Molecular dynamics simulations of CO2molecules in rigid framework ZIF-11, have then been performed using original AMBER parameters (SIM I) and refined parameters (SIM II), respectively. The site-site radial distribution functions and the molecular distribution plots simulations indicate that all hydrogen atoms are favored binding site of CO2molecules. One slight but notable difference is that CO2molecules are mostly located around and closer to hydrogen atom of imidazolate ring in SIM II than those found in SIM I. The Zn-Zn and Zn-N RDFs in free flexible framework simulation (SIM III) show validity of adapting AMBER bonding parameters. Due to the limitations of computing resources and times in this study, the results of flexible framework simulation using refined nonbonding AMBER parameters (SIM IV) are not much different from those obtained in SIM II.

scholarly journals Molecular Dynamics Analysis of Mg2+-dependent Cleavage of a Pistol Ribozyme Reveals a Fail-safe Secondary Ion for Catalysis

2019 ◽  
Author(s):  
Newlyn N. Joseph ◽  
Raktim N. Roy ◽  
Thomas A. Steitz
Keyword(s):  
Molecular Dynamics ◽  
Metal Ion ◽  
Conformational Stability ◽  
Genomic Analysis ◽  
Distribution Functions ◽  
Comparative Genomic ◽  
Magnesium Ions ◽  
Trajectory Data ◽  
Dynamics Simulations ◽  
Fail Safe

Pistol ribozymes comprise a class of small, self-cleaving RNAs discovered via comparative genomic analysis. Prior work in the field has probed the kinetics of the cleavage reaction, as well as the influence of various metal ion cofactors that accelerate the process. In the current study we perform unbiased and unconstrained molecular dynamics simulations from two current high-resolution pistol crystal structures, and we analyzed trajectory data within the context of the currently accepted ribozyme mechanistic framework. Root-mean-squared deviations (RMSDs), radial distribution functions (RDFs), and distributions of nucleophilic angle-of-attack reveal insights into the potential roles of three magnesium ions with respect to catalysis and overall conformational stability of the molecule. A series of simulation trajectories containingin-silicomutations reveal the relatively flexible and partially interchangeable roles of two particular magnesium ions within solvated hydrogen-bonding distances from the catalytic center.

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