Chemical potential of quadrupolar two-centre Lennard-Jones fluids by gradual insertion

The gradual insertion method for direct calculation of the chemical potential by molecular simulation is applied in the NpT ensemble to different quadrupolar two-centre Lennard-Jones fluids at high density state points. The results agree well with Widom's test particle insertion but show at very high densities significantly smaller statistical uncertainties. The gradual insertion method, which is coupled here with preferential sampling, extends the density range where reliable information on the chemical potential can be obtained. Application details are reported

Tempered Fermions in the Hybrid Monte Carlo Algorithm

Parallel tempering simulates at many quark masses simultaneously, by changing the mass during the simulation while remaining in equilibrium. The algorithm is faster than pure HMC if more than one mass is needed, and works better the smaller the smallest mass is.Comment: 4 pages, 2 figures, Combined proceedings for Lattice 97, Edinburgh and the International Workshop 'Lattice QCD on Parallel Computers', University of Tsukuba, Japa

McMillan–Mayer theory for solvent effects in inhomogeneous systems: Calculation of interaction pressure in aqueous electrical double layers

We demonstrate how to use the McMillan–Mayer theory to include solvent effects in effective solute–solute interactions for inhomogeneous systems, extending a recent derivation [S. Marčelja, Langmuir 16, 6081 (2000)] for symmetric planar double layers to the general case. In the exact treatment, the many-body potential of mean force between the solute molecules can be evaluated for an inhomogeneous reference system in equilibrium with pure bulk solvent. The reference system contains only solvent and a finite number, n, of fixed solute molecules and it has an external potential that in some cases is different from that of the original system. It is discussed how the n-body potential of mean force between the ions for the relevant cases of large n values can be approximated by a sum of effective singlet and pair interactions evaluated in the presence of, on average, all n ions, i.e., at finite concentration. In examples considered in this work we use effective interionic pair potentials evaluated from bulk electrolyte calculations at finite electrolyte concentrations. We calculate the contribution to the double layer interaction pressure arising from the interaction between ions dissolved in aqueous electrolyte. In cases of moderate or high surface charge, calculations show several new effects. At small surface separations one finds attractive and then strongly repulsive contributions. For surface charge density around one negative charge per 70 Å2 the full results for pressures resemble “secondary hydration force” measured in classical experiments in 1980s. When there is a tendency for ions to adsorb at the surfaces there is a marked change in behavior. The force is then oscillatory, reminiscent of results obtained with the surface force apparatus at low electrolyte concentration

Folding and Design in Coarse-Grained Protein Models

Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders are discussed. Similar patterns for non-randomness are found for real proteins. Dynamical parameter MC methods, such as the tempering and multisequence algorithms, are essential in order to obtain these results. Also, a new MC method for design, the inverse of folding, is presented. Here, one maximizes conditional probabilities rather than minimizing energies. By construction, this method ensures that the designed sequences represent good folders thermodynamically.Comment: LATTICE 99 (Spin Models), 3 pages, 1 figure, espcrc2.st

How would you integrate the equations of motion in dissipative particle dynamics simulations?

In this work we assess the quality and performance of several novel dissipative particle dynamics integration schemes that have not previously been tested independently. Based on a thorough comparison we identify the respective methods of Lowe and Shardlow as particularly promising candidates for future studies of large-scale properties of soft matter systems

Metal Ion-Induced Lateral Aggregation of Filamentous Viruses fd and M13

We report a detailed comparison between calculations of inter-filament interactions based on Monte-Carlo simulations and experimental features of lateral aggregation of bacteriophages fd and M13 induced by a number of divalent metal ions. The general findings are consistent with the polyelectrolyte nature of the virus filaments and confirm that the solution electrostatics account for most of the experimental features observed. One particularly interesting discovery is resolubilization for bundles of either fd or M13 viruses when the concentration of the bundle-inducing metal ion Mg2+ or Ca2+ is increased to large (\u3e100 mM) values. In the range of Mg2+ or Ca2+ concentrations where large bundles of the virus filaments are formed, the optimal attractive interaction energy between the virus filaments is estimated to be on the order of 0.01 kT per net charge on the virus surface when a recent analytical prediction to the experimentally defined conditions of resolubilization is applied. We also observed qualitatively distinct behavior between the alkali-earth metal ions and the divalent transition metal ions in their action on the charged viruses. The understanding of metal ions-induced reversible aggregation based on solution electrostatics may lead to potential applications in molecular biology and medicine