The stability of aqueous protein solutions is strongly affected by multivalent ions, which induce ion-ion correlations beyond the scope of classical mean-field theory. Using all-atom molecular dynamics (MD) and coarse grained Monte Carlo (MC) simulations, we investigate the interaction between a pair of protein molecules in 3:1 electrolyte solution. In agreement with available experimental find...

The properties of hot dense helium at megabar pressures are studied with two first principles computer simulation techniques: path integral Monte Carlo simulation and density functional molecular dynamics. The simulations predict that the compressibility of helium is substantially increased by electronic excitations that are present in the hot fluid at thermodynamic equilibrium. A maximum compr...

Molecular Dynamics (MD) and Monte Carlo (MC) simulations are the most popular simulation techniques for many-particle systems. Although they are often applied to similar systems, it is unclear to which extent one has to expect quantitative agreement of the two simulation techniques. In this work, we present a quantitative comparison of MD and MC simulations in the microcanonical ensemble. For t...

In light of an increasing awareness of environmental challenges, extensive research is underway to develop new light-weight materials. A problem arising with these materials is their increased response to vibration. This can be solved using a new composite material that contains embedded hollow spheres that are partially filled with particles. Progress on the adaptation of molecular dynamics to...

The behavior of hydronium and hydroxide ions at the water/alkane, water/vapor, and water/rigid wall interfaces was investigated by means of molecular dynamics simulations. All these interfaces exhibit a strong affinity for hydronium, which is in agreement with spectroscopic and low pH zeta-potential measurements. Except for the water/rigid wall interface, which strongly structures water and wea...

We present a Nested Markov chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, was used to substantially decorrelate configurations at which the potential of interest was evaluated, thereby dramatically reducing the number n...

Among the efficient numerical methods based on atomistic models, the quasicontinuum (QC) method has attracted growing interest in recent years. The QC method was first developed for crystalline materials with Bravais lattice and was later extended to multilattices (Tadmor et al, 1999). Another existing numerical approach to modeling multilattices is homogenization. In the present paper we revie...

A first-order liquid-liquid phase transition in high-pressure hydrogen between molecular and atomic fluid phases has been predicted in computer simulations using ab initio molecular dynamics approaches. However, experiments indicate that molecular dissociation may occur through a continuous crossover rather than a first-order transition. Here we study the nature of molecular dissociation in flu...

H. EID,1 G. G. ADAMS,1 N. E. MCGRUER,2 A. FORTINI,3 S. BULDYREV,4 and D. SROLOVITZ5 1Department of Mechanical and Industrial Engineering Northeastern University Boston, Massachusetts 2Department of Electrical and Computer Engineering Northeastern University Boston, Massachusetts 3Theoretische Physik II, Physikalisches Institut Universität Bayreuth Bayreuth, Germany 4Department of Physics Yeshiv...

Adaptation and implementation of the Generalized Shadow Hybrid Monte Carlo (GSHMC) method for molecular simulation at constant pressure in the NPT ensemble are discussed. The resulting method, termed NPT-GSHMC, combines Andersen barostat with GSHMC to enable molecular simulations in the environment natural for biological applications, namely, at constant pressure and constant temperature. Gener...