Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees freedom multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular solvation is such a framework, its initial success has been demonstrated consistently. In VISM, an effective free-energy functional solute-solvent interfaces minimi...

The interaction between the solute and the solsent molecules play a crucial role in understanding the various molecular processes involved in chemistry and biochemistry, so in this work the potential energy of active site of azurin have been calculated in solvent by the Monte Carlo simulation. In this paper we present quantitative results of Monte Carlo calculations of potential energies of ...

A diffusion-influenced pseudo-first order reversible reaction A + B ↔C + B is investigated by the molecular dynamics (MD) simulation method. Theoretical finding that the temporal evolution of reactants [conditional probabilities] in the reversible system can be expressed by the irreversible survival probability with an effective rate parameter is confirmed even in the presence of solvent partic...

The aggregation and solubility of asphaltenes are studied by classical molecular dynamics simulations. Average three-dimensional atomistic models are built on the basis of experimental data for the asphaltenes from a series of crude oil samples. The simulation of two such asphaltene models in four different solvents puts into evidence the formation of oligomeric clusters and gives clues to the ...

Accurate simulation and control of nanoparticle aggregation in chemical reactors requires that population balance equations be solved by using realistic expressions for aggregation and breakage rate kernels. Obtaining such expressions requires that atomistic simulation approaches that can account for microscopic details of particle collisions be used. In principle, molecular dynamics simulation...