Crystal structures of acetylcholinesterase complexed with ligands are compared with side-chain conformations accessed by native acetylcholinesterase in molecular dynamics (MD) simulations. Several crystallographic conformations of a key residue in a specific binding site are accessed in a simulation of native acetylcholinesterase, although not seen in rotomer plots. Conformational changes upon ...

in this study the operations of melting of au15ag40 nanoalloy have been studied using the molecular dynamic simulations through the gupta multiparticle potential and the nonergodicity of simulations is eliminated by the multiple histogram method. the melting characteristics are determined by the analysis of variations in the potential energy. the calculations indicate that the melting of au15ag...

In the past decades, several mesoscale simulation techniques have emerged as tools to study hydrodynamic flow phenomena on scales in the range of nanoto micrometers. Examples are Dissipative Particle Dynamics (DPD), Multiparticle Collision Dynamics (MPCD), or Lattice Boltzmann (LB) methods. These methods allow one to access time and length scales which are not yet within reach of atomistic Mole...

Molecular dynamics (MD) simulations provide a molecular-resolution physical description of the folding and assembly processes, but the size and the timescales of simulations are limited because the underlying algorithm is computationally demanding. We recently introduced a parallel neighbor list algorithm that was specifically optimized for MD simulations on GPUs. In our present study, we analy...

A hierarchical procedure bridging the gap between atomistic and mesoscopic simulation for polymer-clay nanocomposite (PCN) design is presented. The dissipative particle dynamics (DPD) is adopted as the mesoscopic simulation technique, and the interaction parameters of the mesoscopic model are estimated by mapping the corresponding energy values obtained from atomistic molecular dynamics (MD) si...

We have developed a parallel program for molecular dynamics (MD) simulation on clusters of personal computers (PCs). The program implements the Split Integration Symplectic Method (SISM) for MD integration that analytically treats high-frequency motions in molecules, allowing the simulation time step to be longer than in standard methods. The program is designed to run on parallel clusters of p...

The aim of this research was to calculate the mechanical properties of Pd3Rh and PdRh3 ordered alloys. The molecular dynamics (MD) simulation technique was used to obtain temperature dependence of the energy, the Yong modulus, the shear modulus, the bulk modulus, Poisson’s ratio and the elastic stiffness constants at the isobaric-isothermal (NPT) ensemble in the range of 100-325 K. The interato...

Molecular Dynamics(MD) is computational study through simulating in detail the interatomic interactions in protein. Currently, there is no better simulating algorithm due to the demand on accuracy. However, a ensemble/distributed dynamics method is developed to run the simulation in parallel on many distributed computers on the internet. The objective of this research is to design and code a re...

In this paper, the stability characteristics of single-walled carbon nanotubes (SWCNTs) under the action of axial load are investigated. To this end, a nonlocal Flügge shell model is developed to accommodate the small length scale effects. The analytical Rayleigh-Ritz method with beam functions is applied to the variational statement derived from the Flügge-type buckling equations. Molecular dy...

We show that arbitrary phase space vector fields can be used to generate phase functions whose ensemble averages give the thermodynamic temperature. We describe conditions for the validity of these functions in periodic boundary systems and the Molecular Dynamics (MD) ensemble, and test them with a short-ranged potential MD simulation. 05.20.-y 05.20.Gd Typeset using REVTEX 1