Multi-scale time-stepping in molecular dynamics

We introduce a modified molecular dynamics algorithm that allows one to freeze the dynamics of parts of a physical system, and thus concentrate the simulation effort on selected, central degrees of freedom. This freezing, in contrast to other multi-scale methods, introduces no approximations in the thermodynamic behaviour of the non-central variables while conserving the Newtonian dynamics of the region of physical interest.Comment: two figures, one tabl

Multiscale Monte Carlo for simple fluids

We introduce a multiscale Monte Carlo algorithm to simulate dense simple fluids. The probability of an update follows a power law distribution in its length scale. The collective motion of clusters of particles requires generalization of the Metropolis update rule to impose detailed balance. We apply the method to the simulation of a Lennard-Jones fluid and show improvements in efficiency over conventional Monte Carlo and molecular dynamics, eliminating hydrodynamic slowing down.Comment: 4 pages, 3 figures, revtex4. New figure added, labeling of figure 2 correcte

Auxiliary field Monte-Carlo for charged particles

This article describes Monte-Carlo algorithms for charged systems using constrained updates for the electric field. The method is generalized to treat inhomogeneous dielectric media, electrolytes via the Poisson-Boltzmann equation and considers the problem of charge and current interpolation for off lattice models. We emphasize the differences between this algorithm and methods based on the electrostatic potential, calculated from the Poisson equation.Comment: 11 pages 6 figures. Revtex

The Constitution and the Recovery Legislation: The Roles of Document, Doctrine, and Judges

Matlab is a proprietary, interactive, dynamically-typed language for technical computing. It is widely used for prototyping algorithms and applications of scientific computations. Since it is a dynamically typed language, the execution of programs has to be analyzed and interpreted which results in lower computational performance. In order to increase the performance and integrate with Modelica applications it is useful to be able to translate Matlab programs to statically typed Modelica programs. This project presents the design and implementation of Matlab to Modelica translator. The Lexical and Syntax analysis is done with the help of the OMCCp (OpenModelica Compiler Compiler parser generator) tool which generates the Matlab AST, which is later used by the translator for generating readable and reusable Modelica code

Two plateau moduli for actin gels

Conflicting experimental results have been reported for the plateau modulus in actin solutions: Analogies are often made with the viscoelastic behaviour of flexible polymers making use of the idea of entanglement as the source of the macroscopic storage modulus. We resolve apparent experimental and theoretical contradictions by pointing out the possibility of two distinct plateau regimes as a function of frequency in semidilute solutions of semiflexible polymers. We make the point that longitudinal and transverse hindrance can have very different effects at the macroscopic scale.Comment: Postscript file generated from Microsoft word. 4 figures, 13 pages. No TeX available. FIgures are packed in reverse order in file Some previewers have trouble with microsoft generated PS. The file should print correctl