The reaction pathways characterizing macromolecular systems of biological interest are associated with high free energy barriers. Resorting to the standard all-atom molecular dynamics (MD) to explore such critical regions may be inappropriate as the time needed to observe the relevant transitions can be remarkably long. In this paper, we present a new method called Extended Diffusion-Map-direct...

Several heat transfer problems related to singlewalled carbon nanotubes (SWNTs) are considered through molecular dynamics (MD) simulations. MD simulations of thermal conductivity along a nanotube, isotope effect in longitudinal thermal conductivity, and thermal boundary resistance in a junction of nanotubes are reviewed. Then, the heat transfer from an SWNT to various surrounding materials is s...

A universal character of molecular dynamics (MD) method is discussed. Contrary to the classical area of MD applications in microscopic world investigations, MD simulation of mesoscopic phenomena is considered. Sample results of MD simulations of the Rayleigh-Taylor instability are shown and discussed briefly. To cover the larger time-and-space scale either simplified MD model or more sophistica...

Peptides are frequently used model systems for protein folding. They are also gaining increased importance as therapeutics. Here, the ability of molecular dynamics (MD) simulation for describing the structure and dynamics of β-hairpin peptides was investigated, with special attention given to the impact of a single interstrand sidechain to sidechain interaction. The MD trajectories were compare...

This communication reports the first example of spontaneous lipid bilayer formation in unbiased all-atom molecular dynamics (MD) simulations. Using two different lipid force fields we show simulations started from random mixtures of lipids and water in which four different types of phospholipids self-assemble into organized bilayers in under 1 microsecond.

The overall aim of this study is to calculate some water properties in the single wall carbon naotubes (SWCNT) and compare them to the bulk water properties to investigate the deviation of water properties inside the SWCNT from those in the bulk. Here some physical and transport properties of water molecules in the single wall carbon nanotube were reported by performing molecular dynamics (MD) ...

Molecular dynamics (MD) simulation plays an effective role in predicting the critical properties and explaining macroscale phenomenon at nanoscale. This review summarized application cases of MD simulations various bitumen systems, considering aging, modification, rejuvenation factors. Meanwhile, potential relationships between nanoscale parameters predicted from measured experimental tests wer...

We present state-of-the-art molecular dynamics (MD) simulations of high-density plasma-bombardment of carbon, mimicking plasma–wall interactions at the fusion reactor first wall. Bare and hydrogenated amorphous carbon surfaces with temperatures in the range of 300–800 K are bombarded by a distribution of neutral hydrogen molecules representing well-defined center-of-mass and rovibrational tempe...

Molecular dynamics (MD) and volume of fluid (VOF) are powerful methods for the simulation dynamic wetting at nanoscale macroscale, respectively, but massive computational cost MD sensitivity uncertainty boundary conditions in VOF limit their applications to other scales. In this work, we propose a multiscale strategy by enhancing simulations using self-consistent derived from MD. Specifically, ...

Today Molecular Dynamics (MD) Simulations are a key tool in many research and industry areas: Biochemistry, solid state physics, chemical engineering, to just mention some. While in the past MD was a playground for some very simple problems, the ever-increasing compute power of super computers lets handle more and more complex problems: It allows increasing number of particles and more sophisti...