The glass transition is usually regarded as a kinetic phenomenon but it can be treated in a purely thermodynamic way when physical constraints, rather than lack of time, are applied to prevent a liquid from sampling its many glasses. Simulations of Lennard Jones fluids show that they can be made glassy at any density or temperature and that the glass transition is accompanied by a decrease in t...

The Lennard-Jones potential for an atom inside a conducting spherical cavity is derived. The interest is in possible anomalous effects near the focal point of a cavity viewed as a spherical mirror. We find a smooth dependence of the potential on the distance of the atom from the surface of the cavity. 1 Plane Mirror and the C3 coefficient Let us consider first a plane mirror, assumed to lie in ...

Atomistic simulations of nucleic acids are prohibitively expensive and, consequently, reduced models of these compounds are of great interest in the field. In this work, we propose a physics-based coarse-grained model of nucleic-acid bases in which each base is represented by several (3-5) interaction centers. van der Waals interactions are modeled by Lennard-Jones spheres with a 12-6 potential...

We develop computational tools for spectral analysis of stochastic networks representing energy landscapes of atomic and molecular clusters. Physical meaning and some properties of eigenvalues, left and right eigenvectors, and eigencurrents are discussed. We propose an approach to compute a collection of eigenpairs and corresponding eigencurrents describing the most important relaxation process...

HIV-1 capsid proteins (CAs) assemble into a capsid that encloses the viral RNA. The binding between a pair of C-terminal domains (CTDs) constitutes a major interface in both the CA dimers and the large CA assemblies. Here, we attempt to use a general residue-level coarse-grained model to describe the interaction between two isolated CTDs in Monte Carlo simulations. With the standard parameters ...

The Enskog theory for the self-diffusion coefficient for fluids with continuous potentials, such as the Lennard-Jones, is developed. Starting from the Green–Kubo formula ~rather than the conventional kinetic equation! and introducing the similar assumptions upon which the Boltzmann equation is based, we derived a general expression for the memory kernel and the self-diffusion coefficient. The n...