Appearing as a computational microscope, MD simulation can ‘zoom in’ to atomic resolution to assess detailed interactions of a membrane protein with its surrounding lipids, which play important roles in the stability and function of such proteins. This study has employed the molecular dynamics (MD) simulations, to determine the effect of added DMPC or DMTAP molecules on the structure of D...

Molecular Dynamics (MD) simulations are an important technique for studying the conformational dynamics of proteins in Computational Structural Biology. Traditional methods for the analysis of MD simulation assumes a single conformational state underlying the data. With recent developments in MD simulation technologies, MD simulation now can produce massive and long time-scale trajectories acro...

As is known from molecular dynamics simulation, lysozyme oligomers in crystallization solutions are most stable when taking into account as many precipitant ions possible embedded the corresponding crystal structure. Therefore, number of associated with crystallographic oligomer models can play a role during modeling small-angle X-ray scattering (SAXS) data. This hypothesis has been tested pres...

A study has been initiated to investigate interactions between low-energy xenon ions and molybdenum using molecular dynamics (MD) simulation. An MD code, Simulation Kit, designed for simulation of atomic collisions in solid lattices was used in this study. The ion energies ranged from 150 to 500 eV. The ions impinged on the target normal to the (110) plane. The target consisted of 6 layers, eac...

Accurate simulation and control of nanoparticle aggregation in chemical reactors requires that population balance equations be solved by using realistic expressions for aggregation and breakage rate kernels. Obtaining such expressions requires that atomistic simulation approaches that can account for microscopic details of particle collisions be used. In principle, molecular dynamics simulation...

A universal character of molecular dynamics (MD) method is discussed. Contrary to the classical area of MD applications in microscopic world investigations, MD simulation of mesoscopic phenomena is considered. Sample results of MD simulations of the Rayleigh-Taylor instability are shown and discussed briefly. To cover the larger time-and-space scale either simplified MD model or more sophistica...

Classical molecular dynamics (MD) has been successfully applied to model radiation-induced dynamics of highly ionized assemblies of atoms, including the dynamics of electrons, released during ionization processes. Here we test the applicability of a classical molecular dynamics scheme in a yet unexplored regime: for a strongly bound molecular system represented by buckminsterfullerene, C60, sin...

The binding interaction between gallic acid (GA) and lysozyme (LYS) was investigated and compared by molecular dynamics (MD) simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are ...

a novel computational fluid dynamics and molecular kinetic theory (cfd-mk) method was developed to simulate the impingement of a nanodroplet onto a solid surface. a numerical solution of the navier–stokes equation using a volume-of-fluid (vof) technique was used to model nanodroplet deformation. dynamic contact angle during droplet impact was obtained by molecular kinetic theory. this dynamic c...

in the current study, five different atomistic water models (awms) are implemented, in order to investigate the impact of awms treatment on the water velocity profile and density number. for this purpose, molecular dynamics simulation (mds) of poiseuille flow in a nano-channel is conducted. considered awms are spc/e, tip3p, tip4p, tip4pfq and tip5p. to assessment of the ability of each model in...