Study of the amorphous phase of silicon using molecular dynamics simulation techniques

Molecular dynamics (MD) simulation can play a significant role in addressing a number of machining problems at the atomic scale. This simulation, unlike other simulation techniques, can provide new data and insights on nanometric machining; which cannot be obtained readily in any other theory or experiment. In this paper, some fundamental problems of mechanism are investigated in the nanometric cutting with the aid of molecular dynamics simulation, and the single-crystal silicon is chosen as the material. The study showed that the purely elastic deformation took place in a very narrow range in the initial stage of process of nanometric cutting. Shortly after that, dislocation appeared. And then, amorphous silicon came into being under high hydrostatic pressure. Significant change of volume of silicon specimen is observed, and it is considered that the change occur attribute to phase transition from a diamond silicon to a body-centered tetragonal silicon. The study also indicated that the temperature distributing of silicon in nanometric machining exhibited similarity to conventional machining.

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Investigation into the interaction of losartan with human serum albumin and glycated human serum albumin by spectroscopic and molecular dynamics simulation techniques: A comparison study

Chemico-Biological Interactions ◽

10.1016/j.cbi.2016.07.025 ◽

2016 ◽

Vol 257 ◽

pp. 4-13 ◽

Cited By ~ 7

Author(s):

Farid Moeinpour ◽

Fatemeh S. Mohseni-Shahri ◽

Bizhan Malaekeh-Nikouei ◽

Hooriyeh Nassirli

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Human Serum Albumin ◽

Serum Albumin ◽

Human Serum ◽

Dynamics Simulation ◽

Comparison Study ◽

Simulation Techniques

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Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding

Molecular BioSystems ◽

10.1039/c5mb00465a ◽

2015 ◽

Vol 11 (11) ◽

pp. 3068-3080 ◽

Cited By ~ 12

Author(s):

A. Tomić ◽

M. Berynskyy ◽

R. C. Wade ◽

S. Tomić

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulation ◽

Ligand Binding ◽

Long Range ◽

Dynamics Simulation ◽

Structure And Dynamics ◽

Simulation Techniques ◽

Conformational Landscape ◽

Protein Structure And Dynamics

A range of molecular dynamics simulation techniques were applied to investigate the DPP III conformational landscape and the influence of ligand binding on the protein structure and dynamics.

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[10] Molecular dynamics simulation techniques for determination of molecular structures from nuclear magnetic resonance data

Methods in Enzymology - Nuclear Magnetic Resonance Part B Structure and Mechanism ◽

10.1016/0076-6879(89)77012-9 ◽

1989 ◽

pp. 204-218 ◽

Cited By ~ 75

Author(s):

R.M. Scheek ◽

W.F. van Gunsteren ◽

R. Kaptein

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Molecular Dynamics Simulation ◽

Magnetic Resonance ◽

Molecular Structures ◽

Dynamics Simulation ◽

Magnetic Resonance Data ◽

Simulation Techniques ◽

Resonance Data

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Are Gaming-Enabled Graphic Processing Unit Cards Convenient for Molecular Dynamics Simulation?

Evolutionary Bioinformatics ◽

10.1177/1176934319850144 ◽

2019 ◽

Vol 15 ◽

pp. 117693431985014 ◽

Cited By ~ 3

Author(s):

Tommaso Biagini ◽

Francesco Petrizzelli ◽

Mauro Truglio ◽

Roberto Cespa ◽

Alessandro Barbieri ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Small Molecules ◽

Graphic Processing Unit ◽

Dynamics Simulation ◽

Processing Unit ◽

Market Prices ◽

Simulation Techniques ◽

Scientific Skills ◽

Graphic Processing

In several fields of research, molecular dynamics simulation techniques are exploited to evaluate the temporal motion of particles constituting water, ions, small molecules, macromolecules, or more complex systems over time. These techniques are considered difficult to setup, computationally demanding and require high specialization and scientific skills. Moreover, they need specialized computing infrastructures to run faster and make the simulation of big systems feasible. Here, we have simulated 3 systems of increasing sizes on scientific- and gaming-enabled graphic processing unit (GPU) cards with Amber, GROMACS, and NAMD and measured their performance accounting also for the market prices of the GPU cards where they were run on.

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