Modern simulation and modeling approaches to investigation of biomolecular structure and
function rely heavily on a variety of methods—water models—to approximate the influence …

▪ Abstract It would often be useful in computer simulations to use a simple description of
solvation effects, instead of explicitly representing the individual solvent molecules …

Implicit solvation models provide, for many applications, a reasonably accurate and
computationally effective way to describe the electrostatics of aqueous solvation. Here, a …

Understanding protein–inorganic surface interactions is central to the rational design of new
tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant …

Electrostatics plays a fundamental role in virtually all processes involving biomolecules in
solution. The Poisson–Boltzmann equation constitutes one of the most fundamental …

A new method, weighted-ensemble Brownian dynamics, is proposed for the simulation of
protein-association reactions and other events whose frequencies of outcomes are …

This study compares generalized Born (GB) and Poisson (PB) methods for calculating
electrostatic solvation energies of proteins. A large set of GB and PB implementations from …

We report here an efficient implementation of the finite difference Poisson–Boltzmann
solvent model based on the Modified Incomplete Cholsky Conjugate Gradient algorithm …

Generalized Born (GB) models provide, for many applications, an accurate and
computationally facile estimate of the electrostatic contribution to aqueous solvation. The GB …

The use of Ewald and related methods to handle electrostatic interactions in explicit-solvent
simulations of solutions imposes an artificial periodicity on systems which are inherently …