A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules

JOURNAL OF COMPUTATIONAL PHYSICS

卷:322

Article

Xie, Dexuan¹  Jiang, Yi¹ 

[1] Univ Wisconsin, Dept Math Sci, Milwaukee, WI 53201 USA

关键词: Nonlocal dielectric model;    Poisson-Boltzmann equation;    Finite element method;    Newton method;    Electrostatics;   

DOI  :  10.1016/j.jcp.2016.06.028

来源: Elsevier

【 摘 要 】

The nonlocal dielectric approach has been studied for more than forty years but only limited to water solvent until the recent work of Xie et al. (2013) [20]. As the development of this recent work, in this paper, a nonlocal modified Poisson-Boltzmann equation (NMPBE) is proposed to incorporate nonlocal dielectric effects into the classic Poisson-Boltzmann equation (PBE) for protein in ionic solvent. The focus of this paper is to present an efficient finite element algorithm and a related software package for solving NMPBE. Numerical results are reported to validate this new software package and demonstrate its high performance for protein molecules. They also show the potential of NMPBE as a better predictor of electrostatic solvation and binding free energies than PBE. (C) 2016 Elsevier Inc. All rights reserved.

【 授权许可】

Free