Finite Volume Element Method for Predicting Electrostatics of a Biomolecule Immersed in an Ionic Solvent

Abstract

Poisson-Boltzmann equation (PBE) is a classic implicit continuum model to predict the electrostatic potentials of a solvated biomolecule. In this paper, we present a finite volume element method specific to the elliptic interface problem with a non-homogeneous flux condition for solving PBE and provide a follow-up analysis. The new PBE solver is fulfilled through both Fortran and Python, afterwards the local Poisson test model coupled with an analytical solution is adopted to well validate the program. Lastly, an application of the new solver to the prediction of solvation free energies of the proteins is made.