Using Correlated Monte Carlo Sampling for Efficiently Solving the Linearized Poisson-Boltzmann Equation Over a Broad Range of Salt Concentration.

Journal of Chemical Theory and Computation
Marcia O FenleyNikolai A Simonov

Abstract

Dielectric continuum or implicit solvent models provide a significant reduction in computational cost when accounting for the salt-mediated electrostatic interactions of biomolecules immersed in an ionic environment. These models, in which the solvent and ions are replaced by a dielectric continuum, seek to capture the average statistical effects of the ionic solvent, while the solute is treated at the atomic level of detail. For decades, the solution of the three-dimensional Poisson-Boltzmann equation (PBE), which has become a standard implicit-solvent tool for assessing electrostatic effects in biomolecular systems, has been based on various deterministic numerical methods. Some deterministic PBE algorithms have drawbacks, which include a lack of properly assessing their accuracy, geometrical difficulties caused by discretization, and for some problems their cost in both memory and computation time. Our original stochastic method resolves some of these difficulties by solving the PBE using the Monte Carlo method (MCM). This new approach to the PBE is capable of efficiently solving complex, multi-domain and salt-dependent problems in biomolecular continuum electrostatics to high precision. Here we improve upon our novel stocha...Continue Reading

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Citations

Nov 14, 2012·Physical Chemistry Chemical Physics : PCCP·Xingping LiuRay Luo
Nov 29, 2014·Journal of Computational Chemistry·Marcia O FenleyAlexander H Boschitsch
Jun 15, 2016·Physical Review. E·Zebo Li, Dallas R Trinkle
Sep 3, 2013·Journal of Chemical Theory and Computation·Robert C HarrisMarcia O Fenley
Jan 31, 2018·Journal of Chemical Theory and Computation·Saeed IzadiAlexey V Onufriev

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