Central in a variational implicit-solvent description of biomolecular solvation is an effective free-energy functional of the solute atomic positions and the solute-solvent interface (i.e., the dielectric boundary). The free-energy functional couples together the solute molecular mechanical interaction energy, the solute-solvent interfacial energy, the solute-solvent van der Waals interaction e...

2014 We propose a model for describing electrostatic interactions in the aqueous core of a spherical reversed micelle. Some counterions are located at the surface of the aqueous core, the others are distributed inside the core following a Boltzmann law. The nonlinearized Poisson-Boltzmann equation is solved in spherical geometry; an asymptotic expansion of its solution is found near a logarithm...

phenomena, overstating the need for simulational tools that can handle multiple space and time scales is hard. The capability of addressing problems across several length and time scales is a hallmark of modern computational science, the goal of which is to tackle issues that straddle various traditional disciplines of science and engineering. Some interesting examples of such phenomena that ha...

An accurate prediction of the ligand-receptor binding free energies (ΔG) is a critical step in early stages rational drug design. The Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) method popular
 
 approach to estimate ΔG. However, correlations between predicted and experimental ΔG are variable. goal this study investigate various approaches optimize accuracy MM-GBSA met...

Recently, the combination of state-of-the-art molecular mechanical force fields with continuum solvation models enables us to make relatively accurate predictions of both structures and free energies for macromolecules from molecular dynamics trajectories. The first part of this review is focused on the history and basic theory of free energy calculations based on physically effective energy fu...

We study discrete solvent effects on the interaction of two parallel charged surfaces in ionic aqueous solution. These effects are taken into account by adding a bilinear nonlocal term to the free energy of Poisson–Boltzmann theory. We study numerically the density profile of ions between the two plates, and the resulting interplate pressure. At large plate separations the two plates are decoup...

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treat...

The main purpose of this note is to present a new approach to Poisson Approximations. Some bounds in Poisson Approximations in term of classical Le Cam’s inequalities for various row-wise triangular arrays of independent Poisson-binomial distributed random variables are established via probability distances based on Trotter-Renyi operators. Some analogous results related to random sums in Poiss...