We demonstrate the stochastic nature of cavitation in a binary metallic liquid Cu46Zr54 during hydrostatic expansion by employing molecular dynamics (MD) simulations using a quantum mechanics (QM)-derived potential. The activation volume is obtained from MD simulations and transition-state theory. Extrapolation of the pressure dependence of the activation volume from our MD simulations to low t...

Molecular dynamics (MD) simulation, in which the classical equations of motion for all particles of a system are integrated over finite period of time, is one of the theoretical methods to investigate dynamical properties of molecular systems [1]. The problem which arises in performing MD simulations of such systems is that only short simulations can be performed due to the high-frequency motio...

the purpose of the present study was to investigate the use of personal and impersonal metadiscourse (md) by persian- and english-speaking writers in academic writing. for this purpose, 80 abstracts were selected (40 written by persian-speaking writers and 40 by english-speaking ones) and analyzed. these abstracts were selected from endocrinology and metabolism journals published during 2010 to...

Coarse-grained (CG) molecular dynamics (MD) simulations are performed to study the insertion of cyclic peptide nanotubes into cell membranes and to examine whether cyclic peptide nanotubes can function as an ion channel and thereby as an antibacterial agent. To do so, the two coarse-grained (CG) models for lipid molecules and for proteins developed by Marrink et al. (J. Phys. Chem. B 2004, 108,...

We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in...

Computational methods can play a significant role in characterization of the carbon-based nanocomposites by providing simulation results. In this paper, we prepared a brief review of the mechanical properties of carbon nanotubes (CNTs), Graphene, and coiled carbon nanotube (CCNTs) reinforced nanocomposites. Varies simulation studies in mechanical properties of nanocomposites including represent...

Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not req...

It has been reported recently that classical, isothermal-isobaric molecular dynamics (NTP MD) simulations at a time step of 1.00 fs of the standard-mass time (Δt=1.00 fssmt) and a temperature of ≤340 K using uniformly reduced atomic masses by tenfold offers better configurational sampling than standard-mass NTP MD simulations at the same time step. However, it has long been reported that atomic...