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 ...

We discuss the phenomenon of physical aging in a well studied atomic model liquid, a binary mixture of particles interacting with Lennard-Jones potentials. We put emphasis on the different dynamical behaviours of the model as well as on the relations between the experimental and numerical timescales. The physics of aging is discussed within a well characterized thermodynamic framework, based on...

We study, through molecular dynamics, a conservative two-dimensional Lennard-Jones-like gas (with attractive potential ∝ r−α). We consider the effect of the range index α of interactions, number of particles, total energy and particle density. We detect negative specific heat when the interactions become long-ranged (0 ≤ α/d < 1). PACS: 05.20.-y, 05.20.Jj, 64.60.Fr

The previous paper [A. A. Veldhorst et al., J. Chem. Phys. 141, 054904 (2014)] demonstrated that the isomorph theory explains the scaling properties of a liquid of flexible chains consisting of ten Lennard-Jones particles connected by rigid bonds. We here investigate the same model with harmonic bonds. The introduction of harmonic bonds almost completely destroys the correlations in the equilib...

We report a numerical study of saddles properties of the potential energy landscape for soft spheres with different softness, i.e. different power n of the interparticle repulsive potential. We find that saddle-based quantities rescale into master curves once energies and temperatures are scaled by mode-coupling temperature TMCT , confirming and generalizing previous findings obtained for Lenna...

The Particle Swarm Optimization method has proven quite successful in treating a variety of applied problems. Here we further test its capabilities by studying its behavior when applied to a challenging problem, namely the search for energy conformations of atomic clusters. In its simplest form this is known as the Lennard-Jones Problem. Results are compared with those achieved using simple Gen...

We investigate numerically the structure, thermodynamics, and relaxation behavior of a family of (n, 6) Lennard-Jones-like glass-forming binary mixtures interacting via pair potentials with variable softness, fixed well depth, and fixed well depth location. These constraints give rise to progressively more negative attractive tails upon softening, for separations greater than the potential ener...

Covering the solid lattice with a finite-element mesh produces a coarse-grained system of mesh nodes as pseudoatoms interacting through an effective potential energy that depends implicitly on the thermodynamic state. Use of the pseudoatomic Hamiltonian in a Monte Carlo simulation of the two-dimensional Lennard-Jones crystal yields equilibrium thermomechanical properties (e.g., isotropic stress...

The influence of the unlike Lennard-Jones (LJ) parameters on vapor-liquid equilibria of mixtures is investigated and the performance of eleven combining rules is assessed. In the first part of the work, the influence of the unlike LJ size and energy parameter on vapor pressure, bubble density and dew point composition is systematically studied for the mixtures CO+C2H6 and N2+C3H6, respectively....

We examine the performance of several molecular simulation techniques aimed at evaluation of the surface tension through its thermodynamic definition. For all methods explored, the surface tension is calculated by approximating the change in Helmholtz free energy associated with a change in interfacial area through simulation of a liquid slab at constant particle number, volume, and temperature...