Enriched Gradient Recovery for Interface Solutions of the Poisson-Boltzmann Equation
arXiv:2006.14617 · doi:10.1016/j.jcp.2020.109725
Abstract
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.
References in corpus (6)
- Adaptive Finite Element Methods with Inexact Solvers for the Nonlinear Poisson-Boltzmann Equation
- Gradient recovery for elliptic interface problem: II. immersed finite element methods
- Continuum Electromechanical Modeling of Protein-Membrane Interaction
- An implicit boundary integral method for computing electric potential of macromolecules in solvent
- Gradient recovery for elliptic interface problem: III. Nitsche's method
- A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces