A series of molecular dynamics (MD) simulations of nonlinear molecules has been performed to test the efficiency of newly introduced semianalytical second-order symplectic time-reversible MD integrators that combine MD and the standard theory of molecular vibrations. The simulation results indicate that for the same level of accuracy, the new algorithms allow significantly longer integration ti...

A new algorithm for calculating intermolecular pair forces in Molecular Dynamics (MD) simulations on a distributed parallel computer is presented. The Arbitrary Interacting Cells Algorithm (AICA) is designed to operate on geometrical domains defined by an unstructured, arbitrary polyhedral mesh, which has been spatially decomposed into irregular portions for parallelisation. It is intended for ...

Both atomic force microscopy (AFM) experiments and molecular dynamics (MD) simulation are carried out to investigate atomic stick-slip friction by sliding a Pt tip on an Au substrate. Efforts are taken to match the conditions for AFM experiment and MD simulation as closely as possible. The results show that AFM and MD provide consistent energetic parameters, which suggests that MD simulations c...

The new Arbitrary Interacting Cells Algorithm (AICA) for calculating intermolecular pair forces for Molecular Dynamics (MD) on a distributed parallel computer is presented. AICA is designed to operate on geometrical domains defined by an unstructured, arbitrary polyhedral mesh, which has been spatially decomposed into irregular portions for parallelisation. It is intended for nano scale fluid m...

GRAPE (GRavity PipE) processors are special purpose computers for simulation of classical particles. The performance of MD-GRAPE, one of the GRAPEs developed for molecular dynamics, was investigated. The effective speed of MD-GRAPE was equivalent to approximately 6 Gflops. The precision of MD-GRAPE was good judging from the acceptable fluctuation of the total energy. Then a software named PEACH...

The mechanical properties including elastic stiffness constants as well as bulk modulus of Palladium (Pd) nanowire were calculated in the constant temperature and pressure (NPT), ensemble by molecular dynamics (MD) simulation technique. The quantum Sutton-Chen (Q-SC) many-body potential was used to calculate the cohesive energy as well as forces experience by every atoms. The temperature and pr...

author(s): forouzanfar mh, (md, phd) mohammad k, (phd) majdzadeh r, (phd) malekzadeh r, (md) abolhasani f, (md) mohammadnejad m, (md) holakouie naeini k, (phd) hosseini m, (phd) naghavi m, (phd). introduction: hepatitis b is a common problem in many countries. due to high efficacy, safety and low cost of vaccine, mass immunization has become a favorite strategy to improve population health. in ...

Ž . The canonical molecular dynamics MD simulation was accelerated by the integrated method of the multiple time-step Ž . integrator algorithm combined with the particle mesh Ewald method PMEM applied not only to the calculation of the Coulomb interaction but also of the Van der Waals interaction. Although the previous integrated method, in which the PMEM was used in the calculation only for th...

In this article, dynamic modeling of double walled cylindrical functionally graded (FG) microshell is studied. Size effect of double walled cylindrical FG microshell are investigated using modified couple stress theory (MCST). Each layer of microshell is embedded in a viscoelastic medium. For the first time, in the present study, has been considered, FG length scale parameter in double walled c...

We combine molecular dynamics (MD) and Monte Carlo (MC) simulations to study the properties of gas molecules confined between two hard walls of a microchannel or nanochannel. The coupling between MD and MC simulations is introduced by performing MD near the boundaries for accuracy and MC in the bulk because of the low computational cost. We characterize the influence of different densities and ...