The generalized continuous multiple step (GCMS) potential: model systems and benchmarks.

The generalized continuous multiple step (GCMS) potential is presented in this work. Its flexible form allows forand/orcontributions to be encoded through adjustable energy and length scales. The GCMS interaction provides a continuous representation of square-well, square-shoulder potentials and their variants for implementation in computer simulations.

Defect-mediated colloidal interactions in a nematic-phase discotic solvent.

Interactions between colloidal inclusions dispersed in a nematic discotic liquid-crystalline solvent were investigated for different solute-solvent coupling conditions. The solvent was treated at the level of Gay-Berne discogens. Colloidal inclusions were coupled to the solvent with a generalized sphere-ellipsoid interaction potential.

Specific inter-domain interactions stabilize a compact HIV-1 Gag conformation.

HIV-1 Gag is a large multidomain poly-protein with flexible unstructured linkers connecting its globular subdomains. It is compact when in solution but assumes an extended conformation when assembled within the immature HIV-1 virion. Here, we use molecular dynamics (MD) simulations to quantitatively characterize the intra-domain interactions of HIV-1 Gag.

Influence of anchoring in the phase behaviour of discotic liquid crystals.

Molecular dynamics simulations were performed for a Gay-Berne discotic fluid confined in a slab geometry for two different anchorings: homeotropic (face-on) and planar (edge-on), and for two different confinement lengths. Our results show that the behaviour of the more confined system in the temperature region of the isotropic-nematic transition is critically influenced by the presence of the walls: the growth of the solid-liquid crystal interface spans over the entire width of the cell, and the character of the transition is changed from first order to continuous. For all the confined systems studied, we observe a higher nematic-columnar transition temperature and a smaller nematic phase region in the phase diagram, as compared with the behaviour of the infinite system.

Induced stabilization of columnar phases in binary mixtures of discotic liquid crystals.

Three discotic liquid-crystalline binary mixtures, characterized by their extent of bidispersity in molecular thickness, were investigated with molecular dynamics simulations. Each equimolar mixture contained A-type (thin) and B-type (thick) discogens. The temperature-dependence of the orientational order parameter reveals that A-type liquid samples produce ordered phases more readily, with the (hexagonal) columnar phase being the most structured variant.

Phase equilibria, fluid structure, and diffusivity of a discotic liquid crystal.

Molecular Dynamics simulations were performed for the Gay-Berne discotic fluid parameterized by GB(0.345, 0.2, 1.

Analytical equation of state with three-body forces: application to noble gases.

We developed an explicit equation of state (EOS) for small non polar molecules by means of an effective two-body potential. The average effect of three-body forces was incorporated as a perturbation, which results in rescaled values for the parameters of the two-body potential. These values replace the original ones in the EOS corresponding to the two-body interaction.

Modeling flows of confined nematic liquid crystals.

The flow of nematic liquid crystals in tightly confined systems was simulated using a molecular theory and an unsymmetric radial basis function collocation approach. When a nematic liquid crystal is subjected to a cavity flow, we find that moderate flows facilitate the relaxation of the system to the stable defect configuration observed in the absence of flow. Under more extreme flow conditions, e.

Phase and interfacial behavior of partially miscible symmetric Lennard-Jones binary mixtures.

We have carried out extensive equilibrium molecular-dynamics simulations to study quantitatively the topology of the temperature versus density phase diagrams and related interfacial phenomena in a partially miscible symmetric Lennard-Jones binary mixture. The topological features are studied as a function of miscibility parameter, alpha = epsilonAB/epsilonAA. Here epsilonAA = epsilonBB and epsilonAB stand for the parameters related to the attractive part of the intermolecular interactions for similar and dissimilar particles, respectively.

Metastable liquid lamellar structures in binary and ternary mixtures of Lennard-Jones fluids.

We have carried out extensive equilibrium molecular dynamics simulations to investigate the liquid-vapor coexistence in partially miscible binary and ternary mixtures of Lennard-Jones fluids. We have studied in detail the time evolution of the density profiles and the interfacial properties in a temperature region of the phase diagram where the condensed phase is demixed. The composition of the mixtures is fixed, 50% for the binary mixture and 33.