Molecular dynamics (MD) simulation has been carried out to study dynamical stability of intra-protein hydrogen bonds based on two set of atomic charges, the standard AMBER charge and the polarized protein-specific charge (PPC). The latter is derived from quantum mechanical calculation for protein in solution using a recently developed molecular fractionation with conjugate caps-Poisson-Boltzman...

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...

The advances in theory and computing technology over the last decade have led to enormous progress in applying atomistic molecular dynamics (MD) methods to the characterization, prediction, and design of chemical, biological, and material systems. MD simulation of very large systems are currently being performed by using massively parallel architectures. However, there is a fundamental difficul...

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...

Establishing the neighbor list to efficiently calculate the inter-atomic forces consumes the majority of computation time in molecular dynamics (MD) simulation. Several algorithms have been proposed to improve the computation efficiency for short-range interaction in recent years, although an optimized numerical algorithm has not been provided. Based on a rigorous definition of Verlet radius wi...

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...

We have simulated the heat conduction characteristics of finite length single walled carbon nanotubes (SWNTs) with the molecular dynamics method [1-3] with Tersoff-Brenner bond order potential. Temperature at each end of a SWNT was controlled by the phantom technique, and the thermal conductivity was calculated with Fourier’s law from the measured temperature gradient and the energy budgets in ...

A general statistical approach is described to couple the continuum with molecular dynamics in fluid simulation. Arbitrary thermodynamic field boundary conditions can be imposed on an MD system while minimally disturbing the particle dynamics of the system. And by acting away from the region of interest through a feedback control mechanism, across a buffer zone where the disturbed dynamics are ...

Abstract The microscopic mechanism of metal ablation induced by ultrashort laser pulse irradiation is investigated. A two-temperature model scheme combined with molecular dynamics (TTM-MD) developed to incorporate electronic entropy effects into the simulation while satisfying energy conservation law. Simulation TTM-MD reveals that near threshold causes high-energy atom/ion emission and sub-nan...

We report self-assembly and phase transition behavior of lower diamondoid molecules and their primary derivatives using molecular dynamics (MD) simulation and density functional theory (DFT) calculations. Two lower diamondoids (adamantane and diamantane), three adamantane derivatives (amantadine, memantine and rimantadine) and two artificial molecules (ADM·Na and DIM·Na) are studied separately ...