scholarly journals Recent Developments in Using Molecular Dynamics Simulation Techniques to Study Biomolecules

2017 ◽  
Vol 33 (7) ◽  
pp. 1354-1365 ◽  
Author(s):  
Liao-Ran CAO ◽  
◽  
Chun-Yu ZHANG ◽  
Ding-Lin ZHANG ◽  
Hui-Ying CHU ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Simulation Techniques ◽  
Recent Developments

The Recent Developments of Molecular Dynamics Simulation

2013 ◽  
Vol 444-445 ◽  
pp. 1370-1373
Author(s):  
Wen Hai Gai ◽  
Ran Guo ◽  
Yuan Yuan Liu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Rapid Development ◽  
Equations Of Motion ◽  
Dynamics Simulation ◽  
Impact Factors ◽  
Lagrange Equations ◽  
Time Step ◽  
Basic Principles ◽  
Recent Developments

Based on the development of nanomaterials and the research on performance parameters of materials, molecular dynamics simulation has been rapid development and application. It is widely found that the material's physical, mechanical and other properties are both closely related to its macroscopic state and microstructure [. In order to explore and understand the nature of the material properties we need to analyze various impact factors including macroscopic, mesoscopic and microscopic. This paper describes the basic concepts and methods of molecular dynamics. The contents are comprised of time step, formulas such as Lagrange equations of motion and Hamiltonian equations of motion. The basic principles and recent developments of molecular dynamics were reviewed.

Molecular Dynamics Simulation on the Mechanism of Nanometric Machining of Single-Crystal Silicon

2004 ◽  
Vol 471-472 ◽  
pp. 144-148 ◽  
Author(s):  
Hui Wu ◽  
Bin Lin ◽  
S.Y. Yu ◽  
Hong Tao Zhu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Single Crystal ◽  
Single Crystal Silicon ◽  
Atomic Scale ◽  
Dynamics Simulation ◽  
Crystal Silicon ◽  
Nanometric Cutting ◽  
Simulation Techniques ◽  
Nanometric Machining

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.

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

2015 ◽  
Vol 11 (11) ◽  
pp. 3068-3080 ◽  
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.

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

2019 ◽  
Vol 15 ◽  
pp. 117693431985014 ◽  
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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