We present a methodology for the efficient calculation of the shock Hugoniot using standard molecular simulation techniques. The method is an extension of an equation of state methodology proposed by Erpenbeck [J. J. Erpenbeck, Phys. Rev. A 46, 6406 (1992)] and is considered as an alternative to other methods that generate Hugoniot properties. We illustrate the methodology for shocked liquid N2...

Neutrinos in core collapse supernovae are likely trapped by neutrino-nucleus elastic scattering. Using molecular dynamics simulations, we calculate neutrino mean free paths and ion-ion correlation functions for heterogeneous plasmas. Mean free paths are systematically shorter in plasmas containing a mixture of ions compared to a plasma composed of a single ion species. This is because neutrinos...

We examine the nonideal behavior of real vapor in the context of the theory of nonin-teracting molecular clusters. The vapor is treated as a perfect mixture of clusters, which in equilibrium attain a distribution in size determined by formation energies G i , where G i is the energy required to form a cluster of i molecules from i molecules in bulk saturated liquid. A theory for the G i gives a...

We present a simple method for calculating a continuum temperature field directly from a molecular dynamics (MD) simulation. Using the idea of a projection matrix previously developed for use in the bridging scale, we derive a continuum temperature equation which only requires information that is readily available from MD simulations, namely the MD velocity, atomic masses and Boltzmann constant...

Motivated by some numerical observations on molecular dynamics simulations, we analyze metastable trajectories in a very simple setting, namely paths generated by a one-dimensional overdamped Langevin equation for a double well potential. Specifically, we are interested in so-called reactive paths, namely trajectories which leave definitely one well and reach the other one. The aim of this pape...

Nonequilibrium molecular dynamics ~NEMD! simulations are performed for argon at different strain rates using accurate two-body and three-body intermolecular potentials. The contributions of twoand three-body interactions to the configurational energy of argon at different strain rates are reported. The NEMD data indicate that there is the same simple relationship between twoand three-body inter...

We investigate picosecond laser ablation of metals using a hybrid simulation scheme. Laser energy input into the electron system and heat conduction within it are modeled using a finite-difference scheme for solving the heat conduction equation. Atom motion in the near-surface part ~72 nm! of the sample is modeled using molecular dynamics. Energy transfer between the electronic and atomic subsy...

In this article we use the recently developed perturbed matrix method (PMM) to investigate the effect of conformational fluctuations on the electronic properties of heme in Myoglobin. This widely studied biomolecule has been chosen as a benchmark for evaluating the accuracy of PMM in a large and complex system. Using a long, 80-ns, molecular dynamics simulation and unperturbed Configuration Int...

Monte Carlo and molecular dynamics computer simulations are now able to provide detailed information concerning the structure, dynamics, and thermodynamics of pore fluids in 2:1 clays. This article will discuss interparticle interaction potentials currently available for atomistic simulations of clay-water systems, and will describe how computational techniques can be applied to modelling of cl...

An analytic method of smearing link variables in lattice QCD is proposed and tested. The differentiability of the smearing scheme with respect to the link variables permits the use of modern Monte Carlo updating methods based on molecular dynamics evolution for gauge-field actions constructed using such smeared links. In examining the smeared mean plaquette and the static quark-antiquark potent...