An Efficient Finite Element Iterative Method for Solving a Nonuniform Size Modified Poisson-Boltzmann Ion Channel Model

TL;DR

This paper introduces an efficient finite element iterative method for solving a complex nonlinear ion channel model that accounts for nonuniform ion sizes and membrane charges, demonstrating fast convergence and validation with biological data.

Contribution

It develops a novel iterative solver and finite element implementation for the nonuniform size modified Poisson-Boltzmann ion channel model, improving numerical efficiency and biological relevance.

Findings

Fast convergence of the iterative method.

High performance of the software package.

Validation with biological ion channel data.

Abstract

In this paper, a nonuniform size modified Poisson-Boltzmann ion channel (nuSMPBIC) model is presented as a nonlinear system of an electrostatic potential and multiple ionic concentrations. It mixes nonlinear algebraic equations with a Poisson boundary value problem involving Dirichlet-Neumann mixed boundary value conditions and a membrane surface charge density to reflect the effects of ion sizes and membrane charges on electrostatics and ionic concentrations. To overcome the difficulties of strong singularities and exponential nonlinearities, it is split into three submodels with a solution of Model 1 collecting all the singular points and Models 2 and 3 much easier to solve numerically than the original nuSMPBIC model. A damped two-block iterative method is then presented to solve Model 3, along with a novel modified Newton iterative scheme for solving each related nonlinear algebraic system. To this end, an effective nuSMPBIC finite element solver is derived and then implemented as a program package that works for an ion channel protein with a three-dimensional molecular structure and a mixture solution of multiple ionic species. Numerical results for a voltage-dependent anion channel (VDAC) in a mixture of four ionic species demonstrate a fast convergence rate of the damped two-block iterative method, the high performance of the software package, and the importance of considering nonuniform ion sizes. Moreover, the nuSMPBIC model is validated by the anion selectivity property of VDAC.