In many molecular dynamics simulation software packages and hardware implementations, piecewise polynomials are used to represent and compute pairwise potential functions efficiently.
Predicting thermal conductivity, k, of carbon nanotubes (CNTs) has been the focus of many molecular dynamics (MD) simulation studies reported in the literature.
Due to the difficulties in directly observing the cutting zone during the brittle ductile cutting mode transition by experimental techniques, many molecular dynamics (MD) studies have been conducted to investigate the atomicscale details of the phenomena, e.g. phase transformation, stress distribution and crack initiation, mostly under nanoscale undeformed chip thicknesses.
In this review, we have discussed the many roles that molecular dynamics simulations can play in drug discovery, including the identification of cryptic or allosteric binding sites, the enhancement of traditional virtual-screening methodologies, and the direct prediction of ligand binding energies.
The understanding of particle dynamics in N-body problems is of importance to many applications in astrophysics, molecular dynamics and cloud/plasma physics where the theoretical representation results in a coupled system of equations for a large number of entities.
Because so many calculations are required, molecular dynamics simulations are typically performed on computer clusters or supercomputers using dozens if not hundreds of processors in parallel.
We report the results of computational tensile and compressive tests for model bi-continuous nanoporous gold structures using atomistic simulations with empirical many-body potentials and molecular dynamics.
The redesigned Extensible Simulation Package for Research on Soft matter systems (ESPResSo++) is a free, open-source, parallelized, object-oriented simulation package designed to perform many-particle simulations, principally molecular dynamics and Monte Carlo, of condensed soft matter systems.
So far, it has been cited over 100 times [27], including applications in spectroscopy, catalysis, materials chemistry, theoretical chemistry, biochemistry, and molecular dynamics, among many others [28 47].
Availability: http://daweb.ism.ac.jp/yoshidalab/crest/ismb2014 Supplementary information: Supplementary data are available at http://daweb.ism.ac.jp/yoshidalab/crest/ismb2014 Contact: [email protected] Fluorescence microscopy imaging of live cells has been a powerful tool for studying cellular and molecular dynamics in many applications (Peng, 2008; Swedlow et al., 2009).
Nonetheless, considering that many other programs used for molecular dynamics such as GROMACS [ 41], NAMD [ 42], and CHARMM [ 43] do not have the same scalability on these architectures, the exploitation of parallel computing is still widely used for this kind of simulations.
