The Improvement of Generalized Particle Method for Nano-Materials Molecular Dynamics Simulation

2010 ◽  
Vol 97-101 ◽  
pp. 2159-2162 ◽  
Author(s):  
Zhen Qing Wang ◽  
Zeng Jie Yang ◽  
Yong Jun Wang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Particle Method ◽  
Potential Energy Function ◽  
Simulation Software ◽  
Dynamics Simulation ◽  
Nano Materials ◽  
Multi Scale ◽  
Structural Details

A generalized particle molecular dynamics simulation (GP) method has been proposed by J. Fan to solve the multi-scale problems in nano-materials. Although the method has attractive features, its acceleration equivalency hypothesis doesn’t meet the actual situation. In this paper an improved GP method is proposed. It assumes that the potential energy of generalized particles is equal to the potential energy of corresponding atomic groups in nano-materials. The parameters of improved GP method rest with the atomic structural details and corresponding atomic potential energy function. And by using open-source molecular simulation software DL-POLY, an example to compare the MD and the improved GP methods has been proposed, in which the Improved GP method presents sufficient accuracy

MOLECULAR-DYNAMICS SIMULATION OF RADIATION DAMAGE ON COPPER CLUSTERS

2000 ◽  
Vol 11 (05) ◽  
pp. 1025-1032
Author(s):  
ŞAKIR ERKOÇ
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Kinetic Energy ◽  
Potential Energy ◽  
Radiation Damage ◽  
Potential Energy Function ◽  
Dynamics Simulation ◽  
External Radiation ◽  
Empirical Potential ◽  
Copper Clusters

The effect of radiation damage on copper clusters has been investigated by performing molecular-dynamics simulation using empirical potential energy function for interaction between copper atoms. The external radiation is modeled by giving extra kinetic energy in the range of 5–50 eV to initially chosen atom in the cluster. It has been found that the atom having extra kinetic energy dissociates independently from the amount of given energy in the studied range.

scholarly journals Molecular dynamics simulation study of the diamond D5 substructures

2012 ◽  
Vol 10 (4) ◽  
pp. 1028-1033 ◽  
Author(s):  
Anahita Kyani ◽  
Mircea Diudea
Keyword(s):  
Heat Treatment ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Potential Energy Function ◽  
Dynamics Simulation ◽  
Type Ii ◽  
Many Body ◽  
Higher Temperature ◽  
Body Potential

AbstractDiamond D5 is the name proposed by Diudea for hyper-diamonds having their rings mostly pentagonal. Within D5, in crystallographic terms: the mtn structure, known in clathrates of type II, several substructures can be defined. In the present work, the structural stability of such intermediates/fragments appearing in the construction/destruction of D5 net was investigated using molecular dynamics simulation. Calculations were performed using an empirical many-body potential energy function for hydrocarbons. It has been found that, at normal temperature, the hexagonal hyper-rings are more stable while at higher temperature, the pentagonal ones are relatively more resistant against heat treatment.

scholarly journals Inverse Boltzmann Iterative Multi-Scale Molecular Dynamics Study between Carbon Nanotubes and Amino Acids

2021 ◽  
Author(s):  
Wanying Huang ◽  
Xinwen Ou ◽  
JunYan Luo
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Coarse Graining ◽  
Simulation Method ◽  
Potential Of Mean Force ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Multi Scale

Our work uses Iterative Boltzmann Inversion (IBI) to study the coarse-grained interaction between 20 amino acids and the representative carbon nanotube CNT55L3. IBI is a multi-scale simulation method that has attracted the attention of many researchers in recent years. It can effectively modify the coarse-grained model derived from the Potential of Mean Force (PMF). IBI is based on the distribution result obtained by All-Atom molecular dynamics simulation, that is, the target distribution function, the PMF potential energy is extracted, and then the initial potential energy extracted by the PMF is used to perform simulation iterations using IBI. Our research results have gone through more than 100 iterations, and finally, the distribution obtained by coarse-grained molecular simulation (CGMD) can effectively overlap with the results of all-atom molecular dynamics simulation (AAMD). In addition, our work lays the foundation for the study of force fields for the simulation of the coarse-graining of super-large proteins and other important nanoparticles.

Nonadiabatic molecular dynamics simulation for the ultrafast photoisomerization of dMe-OMe-NAIP based on TDDFT on-the-fly potential energy surfaces

2021 ◽  
Vol 23 (9) ◽  
pp. 5236-5243
Author(s):  
Ying Hu ◽  
Chao Xu ◽  
Linfeng Ye ◽  
Feng Long Gu ◽  
Chaoyuan Zhu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Dynamics Simulation ◽  
Surface Hopping ◽  
Nonadiabatic Molecular Dynamics ◽  
Energy Surfaces

Global switching on-the-fly trajectory surface hopping molecular dynamics simulation was performed on the accurate TD-B3LYP/6-31G* potential energy surfaces for E-to-Z and Z-to-E photoisomerization of dMe-OMe-NAIP up to S1(ππ*) excitation.

A multi-scale molecular dynamics simulation of PMAL facilitated delivery of siRNA

RSC Advances ◽  
2015 ◽  
Vol 5 (83) ◽  
pp. 68227-68233 ◽  
Author(s):  
Jipeng Li ◽  
Yiyun Ouyang ◽  
Xian Kong ◽  
Jingying Zhu ◽  
Diannan Lu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Lipid Bilayer ◽  
Dynamics Simulation ◽  
Lipid Bilayer Membranes ◽  
Bilayer Membranes ◽  
Multi Scale

PMAL as a novel carrier for the delivery of siRNA into lipid bilayer membranes.

scholarly journals Study on Interface Structure of Cu/Al Clad Plates by Roll Casting

Metals ◽  
2018 ◽  
Vol 8 (10) ◽  
pp. 770 ◽  
Author(s):  
Qinghua Chang ◽  
Jingpei Xie ◽  
Aixia Mao ◽  
Wenyan Wang
Keyword(s):  
Molecular Dynamics ◽  
Electron Microscope ◽  
Molecular Dynamics Simulation ◽  
Large Scale ◽  
Aluminum Atom ◽  
Simulation Software ◽  
Dynamics Simulation ◽  
Aluminum Composite ◽  
Atom Diffusion ◽  
Heating And Cooling

Large scale Atomic/Molecular dynamic Parallel Simulator (LAMMPS) molecular dynamics simulation software was used to simulate the copper and aluminum atom diffusion and changes of interface during heating and cooling process of copper and aluminum composite panels. The structures of the interface were characterized through scanning electron microscope (SEM), X-ray diffraction (XRD), and transmission electron microscope (TEM), and the mechanical properties were also tested. The simulation results show that the diffusion rate of copper atom is higher than that of aluminum atom, and that the CuAl2 radial distribution function of the interface at 300 K is consistent with that of pure CuAl2 at room temperature. At 930 K, t = 50 ps Cu atoms spread at a distance of approximately four Al lattice constants around the Al layer, and Al atoms spread to about half a lattice constant distance to the Cu layer. The experimental results show that the thickness of the interface in copper–aluminum composite plate is about 1 μm, and only one kind of CuAl2 with tetragonal phase structure is generated in the interface, which corresponds with the result of molecular dynamics simulation.

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