The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulation...

Over the last 15 years molecular dynamics (MD) simulations have become one of the important tools to tackle many of the complex problems that are faced by rheologists and engineers. The advent of modern areas of science such as nanotechnology and the need to understand physical phenomena including rheology and tribology at the molecular scale have helped the growth of research both experimental...

The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulation...

We present a Bayesian probabilistic framework for quantifying and propagating the uncertainties in the parameters of force fields employed in molecular dynamics (MD) simulations. We propose a highly parallel implementation of the transitional Markov chain Monte Carlo for populating the posterior probability distribution of the MD force-field parameters. Efficient scheduling algorithms are propo...

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 finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-ar...

   This paper explores the mechanical properties and fracture analysis of C2N-h2D single-layer sheets using classical molecular dynamics (MD) simulations. Simulations are carried out based on the Tersoff potential energy function within Nose-Hoover thermostat algorithm at the constant room temperature in a canonical ensemble. The influences of boron (B) doping on the mechanical properties, ...

We consider tracer diffusion in colloidal suspensions under solid loading conditions, where hydrodynamic interactions play an important role. To this end, we carry out computer simulations based on the hybrid stochastic rotation dynamics-molecular dynamics (SRD-MD) technique. Many details of the simulation method are discussed in detail. In particular, our choices for the SRD-MD parameters and ...

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...

A computational strategy for calibrating, validating and analyzing molecular dynamics (MD) simulations to predict dynamic nuclear polarization (DNP) coupling factors and relaxivities of proton spins is presented. Simulations of the polarizing agent TEMPOL in liquid acetone and DMSO are conducted at low (infinite dilution) and high (1 M) concentrations of the free radical. Because DNP coupling f...