Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed wit...

Density Functional Theory (DFT) which is based on quantum mechanics theory has been broadly used to compute the energy and the structure of molecules and solids. However, the DFT method is limited when running calculations for a large system and only thousands of atoms can be solved. Alternatively, Molecular Dynamics (MD) simulation can be used to investigate the properties of the atomic system...

The present study involves a novel computational technique, regarding simultaneous use of the pseudo particle method, Poisson integral method and a special-purpose computer originally designed for molecular dynamics simulations (MDGRAPE-3). In the present calculations, the dynamics of two colliding vortex rings have been studied using the vortex method. The present acceleration technique allows...

Developing an understanding of the mechanism of voltage-gated ion channels in molecular terms requires knowledge of the structure of the active and resting conformations. Although the active-state conformation is known from x-ray structures, an atomic resolution structure of a voltage-dependent ion channel in the resting state is not currently available. This has motivated various efforts at us...

Based on the fact the manipulation of fine nanoclusters calls for more precise modeling, the aim of this paper is to conduct an atomistic investigation for interaction analysis of particle-substrate system for pushing and positioning purposes. In the present research, 2D molecular dynamics simulations have been used to investigate such behaviors. Performing the planar simulations can provide a ...

Important questions exist regarding the quality of force fields used in molecular dynamics (MD) simulations and their interoperable use with other available MD implementations. NAMD is one of the most efficient and scalable parallel molecular dynamics codes for large-scale biomolecular simulations in the open source domain. It is the aim of this article to analyze and compare the dynamics of a ...

In Förster resonance energy transfer (FRET) experiments, extracting accurate structural information about macromolecules depends on knowing the positions and orientations of donor and acceptor fluorophores. Several approaches have been employed to reduce uncertainties in quantitative FRET distance measurements. Fluorophore-position distributions can be estimated by surface accessibility (SA) ca...

We propose a symmetry reduction technique whereby molecular dynamics (MD) simulations for spherically symmetric gas bubbles can be accelerated. Results for an imploding Xenon bubble containing fifty million particles — the smallest measured sonoluminescing system — are presented.

The use of nanoscopic fibres for acoustic absorption can potentially result in thinner liners than for conventional acoustic materials. Modelling acoustic mechanisms at the nanoscale requires molecular simulations as the flow behaviour at the nanoscale is in the transition regime (based on Knudsen number). Molecular Dynamics (MD) was identified as a suitable method for simulating the physical p...