Enriched gradient recovery for interface solutions of the Poisson-Boltzmann equation

JOURNAL OF COMPUTATIONAL PHYSICS

卷:421

Article

Borleske, George¹  Zhou, Y. C.¹ 

[1] Colorado State Univ, Dept Math, Ft Collins, CO 80523 USA

关键词: Biomolecular electrostatics;    Poisson-Boltzmann equation;    Numerical solution;    Interface methods;    Gradient recovery;    High accuracy;   

DOI  :  10.1016/j.jcp.2020.109725

来源: Elsevier

【 摘 要 】

Accurate calculation of electrostatic potential and gradient on the molecular surface is highly desirable for the continuum and hybrid modeling of large scale deformation of biomolecules in solvent. In this article a new numerical method is proposed to calculate these quantities on the dielectric interface from the numerical solutions of the Poisson-Boltzmann equation. Our method reconstructs a potential field locally in the least square sense on the polynomial basis enriched with Green's functions, the latter characterize the Coulomb potential induced by charges near the position of reconstruction. This enrichment resembles the decomposition of electrostatic potential into singular Coulomb component and the regular reaction field in the Generalized Born methods. Numerical experiments demonstrate that the enrichment recovery produces drastically more accurate and stable potential gradients on molecular surfaces compared to classical recovery techniques. (C) 2020 Elsevier Inc. All rights reserved.

【 授权许可】

Free