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Molecular dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been developed for continuous potential systems, software for discrete potential systems based on event-driven algorithms are(More)
We present Monte Carlo simulation results for square-well homopolymers at a series of bond lengths. Although the model contains only isotropic pairwise interactions, under appropriate conditions this system shows spontaneous chiral symmetry breaking, where the chain exists in either a left- or a right-handed helical structure. We investigate how this(More)
We investigate the low density behaviour of fluids that interact through a short-ranged attraction together with a long-ranged repulsion (SALR potential) by developing a molecular thermodynamic model. The SALR potential is a model of effective solute interactions where the solvent degrees of freedom are integrated-out. For this system, we find that clusters(More)
greater than the bulk value, depending on the deposition temperature. There is no signifi cant change in density and cationic ratio of the oxide so the effect is attributed to Sr/Ti antisite defects, an attribution supported by density functional theory calculations. It was found that the bandgap enhancement signifi cantly changes the electronic and(More)
The dynamics of sheared inelastic-hard-sphere systems is studied using nonequilibrium molecular-dynamics simulations and direct simulation Monte Carlo. In the molecular-dynamics simulations Lees-Edwards boundary conditions are used to impose the shear. The dimensions of the simulation box are chosen to ensure that the systems are homogeneous and that the(More)
Many separation processes are related to the behavior of ions close to charged surfaces. In this work, we examine uranyl ions, which can be considered as rod-like molecular ions with a spatially distributed charge, embedded in a system of like charged surfaces. The analysis of the system is based on an approximate field theory which is accurate from the(More)
The static and dynamic properties of binary mixtures of hard spheres with a diameter ratio of sigma(B)/sigma(A)=0.1 and a mass ratio of m(B)/m(A)=0.001 are investigated using event driven molecular dynamics. The contact values of the pair correlation functions are found to compare favorably with recently proposed theoretical expressions. The transport(More)
The densities of states are evaluated for very short chain molecules made up of overlapping monomers, using a model which has previously been shown to produce helical structure. The results of numerical calculations are presented for tetramers and pentamers. We show that these models demonstrate behaviors relevant to the behaviors seen in longer,(More)
We have studied the competition between helix formation and aggregation for a simple polymer model. We present simulation results for a system of two such polymers, examining the potential of mean force, the balance between intermolecular and intramolecular interactions, and the promotion or disruption of secondary structure brought on by the proximity of(More)
We have performed parallel tempering Monte Carlo simulations using a simple continuum heteropolymer model for proteins. All 10 heteropolymer sequences which we have studied have shown first-order transitions at low temperature to ordered states dominated by single chain conformations. These results are in contrast with the theoretical predictions of the(More)
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