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What are the physical laws of the diffusive search of proteins for their specific binding sites on DNA in the presence of the macromolecular crowding in cells? We performed extensive computer simulations to elucidate the protein target search on DNA. The novel feature is the viscoelastic non-Brownian protein bulk diffusion recently observed experimentally. We examine the influence of the protein-DNA binding affinity and the anomalous diffusion exponent on the target search time. In all cases an optimal search time is found. The relative contribution of intermittent three-dimensional bulk diffusion and one-dimensional sliding of proteins along the DNA is quantified. Our results are discussed in the light of recent single molecule tracking experiments, aiming at a better understanding of the influence of anomalous kinetics of proteins on the facilitated diffusion mechanism. [ABSTRACT FROM AUTHOR]

The COMPASS (condensed-phase optimized molecular potentials for atomistic simulation studies) force field with two sets of partial atomic charges of water was used to simulate adsorption and diffusion behavior of water/methanol and water/ethanol mixtures in zeolite 4A at 298 K. The adsorption of alcohol first increased and then decreased with increasing pressure, whereas the adsorption of water increased progressively until an adsorption equilibrium was reached. Both the adsorbed molecules and the zeolite framework were treated as a fully flexible model in MD simulations. The simulation results show that the effects of the size and steric hindrance of the diffusing molecules on diffusivity are significant. The diffusivity of water, methanol, and ethanol molecules decreases by 1 order of magnitude in the order of water > methanol > ethanol. The diffusivity of water molecules depends on the mass fraction and the partial charges of water in zeolite 4A. The ethanol and methanol molecules have restricted motion through the α-cages, whereas the water molecules can easily pass through the α-cages window at low feed alcohol concentrations. And the extent of hydrogen bonding increased with increasing water concentration. [ABSTRACT FROM AUTHOR]

Molecular dynamics (MD) simulations have been used to study the transport properties of oxygen and nitrogen in the para-substituted polystyrenes which possess one to four Si atoms in each substituent. The Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies (COMPASS) force field was used to construct the polymers. Diffusion coefficients were obtained from molecular dynamics (NVT ensemble) with up to 3 ns simulation times. After molecular dynamic simulation, the trajectories of the small molecules in the polymer matrix were obtained. Then diffusion coefficients have been calculated from the Einstein relationship revealing a considerable agreement between the simulated and the experimental data. And solubility coefficients have been calculated by the Grand Canonical Monte Carlo (GCMC) method. The solubility of oxygen increased with increasing Si content in the polymer membrane. The para-substituted polystyrenes with a branched substituent at the -position showed higher permeability than those of the nonbranched ones. The higher the glass transition temperature (Tg) of the membrane, the larger the diffusion coefficients of oxygen and nitrogen obtained. [ABSTRACT FROM AUTHOR]