Quasi-two-dimensional dispersions of Brownian particles with competitive interactions: phase behavior and structural properties.

Competing short-range attractive (SA) and long range repulsive (LR) particle interactions can be used to describe three-dimensional charge-stabilized colloid or protein dispersions at low added salt concentrations, as well as membrane proteins with interaction contributions mediated by lipid molecules. Using Langevin dynamics (LD) simulations, we determine the generalized phase diagram, cluster shapes and size distributions of a generic quasi-two-dimensional (Q2D) dispersion of spherical SALR particles confined to in-plane motion inside a bulk fluid. The SA and LR interaction parts are modelled by a generalized Lennard-Jones potential and a screened Coulomb potential, respectively.

Subdiffusive-Brownian crossover in membrane proteins: a generalized Langevin equation-based approach.

In this work, we propose a generalized Langevin equation-based model to describe the lateral diffusion of a protein in a lipid bilayer. The memory kernel is represented in terms of a viscous (instantaneous) and an elastic (noninstantaneous) component modeled through a Dirac δ function and a three-parameter Mittag-Leffler type function, respectively. By imposing a specific relationship between the parameters of the three-parameter Mittag-Leffler function, the different dynamical regimes-namely ballistic, subdiffusive, and Brownian, as well as the crossover from one regime to another-are retrieved.

Hydrodynamics of immiscible binary fluids with viscosity contrast: a multiparticle collision dynamics approach.

We present a multiparticle collision dynamics (MPC) implementation of layered immiscible fluids A and B of different shear viscosities separated by planar interfaces. The simulated flow profile for imposed steady shear motion and the time-dependent shear stress functions are in excellent agreement with our continuum hydrodynamics results for the composite fluid. The wave-vector dependent transverse velocity auto-correlation functions (TVAF) in the bulk-fluid regions of the layers decay exponentially, and agree with those of single-phase isotropic MPC fluids.

Open-Boundary Molecular Mechanics/Coarse-Grained Framework for Simulations of Low-Resolution G-Protein-Coupled Receptor-Ligand Complexes.

G-protein-coupled receptors (GPCRs) constitute as much as 30% of the overall proteins targeted by FDA-approved drugs. However, paucity of structural experimental information and low sequence identity between members of the family impair the reliability of traditional docking approaches and atomistic molecular dynamics simulations for in silico pharmacological applications. We present here a dual-resolution approach tailored for such low-resolution models.

Molecular Dynamics Simulations of the [2Fe-2S] Cluster-Binding Domain of NEET Proteins Reveal Key Molecular Determinants That Induce Their Cluster Transfer/Release.

The NEET proteins are a novel family of iron-sulfur proteins characterized by an unusual three cysteine and one histidine coordinated [2Fe-2S] cluster. Aberrant cluster release, facilitated by the breakage of the Fe-N bond, is implicated in a variety of human diseases, including cancer. Here, the molecular dynamics in the multi-microsecond timescale, along with quantum chemical calculations, on two representative members of the family (the human NAF-1 and mitoNEET proteins), show that the loss of the cluster is associated with a dramatic decrease in secondary and tertiary structure.