Radiation damage to the steel material of reactor pressure vessels is a major threat nuclear safety. It caused by metal atom cascade collision, initialized when atoms are struck high-energy neutron. The paper presents MISA-MD, new implementation molecular dynamics, simulate such collision with EAM potential. MISA-MD realizes (1) hash-based data structure efficiently store an and find its neighb...

In order to understand the response of conductive materials to high-frequency electrical or optical excitations, the interplay between carrier transport and electrodynamics must be captured. We present our recent work on developing EMC/FDTD/MD, a self-consistent coupled simulation of semiclassical carrier transport, described by ensemble Monte Carlo (EMC), with full-wave electrodynamics, descri...

In most of the cases, the experimental study of Nanotechnology involves high cost for Laboratory set-up and the experimentation processes were also slow. So, one cannot rely on experimental nanotechnology alone. As such, the Computer-Based molecular simulations and modeling are one of the foundations of computational nanotechnology. The computer based modeling and simulations were also referred...

Depending on the pH-value and salt concentration of Al2O3 suspensions different microstructures can form. Especially the clustered one is of major interest for industrial purposes as found in the production of ceramics. In this paper we investigate the clustered microstructure by means of a coupled Stochastic Rotation Dynamics (SRD) and Molecular Dynamics (MD) simulation. In order to gain stati...

Electron paramagnetic resonance (EPR) spectroscopy using site-directed spin-labeling is an appropriate technique to analyze the structure and dynamics of flexible protein regions as well as protein-protein interactions under native conditions. The analysis of a set of protein mutants with consecutive spin-label positions leads to the identification of secondary and tertiary structure elements. ...

The evaluation of molecular dynamics models incorporating temperature control methods is of great importance for molecular dynamics practitioners. In this paper, we study the way in which biomolecular systems achieve thermal equilibrium. In unthermostatted (constant energy) and Nosé-Hoover dynamics simulations, correct partition of energy is not observed on a typical MD simulation timescale. We...

Recent studies of catalysis have highlighted the importance heat-driven reaction enhancement, suggesting need for improved understanding heat transfer in vicinity catalyst particles process. Specifically, it is essential and necessary to understand transferred surrounding gas molecules surface. In present study, we developed a method estimate ratio particle framework ReaxFF. A molecular dynamic...

The influence of temperature on the surface structure of the octadecylsilica (ODS) bonded phase was investigated with a molecular dynamics (MD) simulation. The MD simulation was applied to a molecular model consisting of three parts: amorphous silica base, dimethyloctadecylsilyl ligands and n-hexane as a mobile phase solvent. More detailed information on the effect of temperature was obtained a...

Over the past 20 years, molecular simulation methods have been applied to the modeling of reversed-phase liquid chromatography (RPLC). The purpose of these simulations was to provide a molecular-level understanding of: (i) the structure and dynamics of the bonded phase and its interface with the mobile phase, (ii) the interactions of analytes with the bonded phase, and (iii) the retention mecha...