An improved Poisson‐Nernst‐Planck ion channel model and numerical studies on effects of boundary conditions, membrane charges, and bulk concentrations

Abstract

In this paper, an improved Poisson‐Nernst‐Planck ion channel (PNPic) model is presented, along with its effective finite element solver and software package for an ion channel protein in a solution of multiple ionic species. Numerical studies are then done on the effects of boundary value conditions, membrane charges, and bulk concentrations on electrostatics and ionic concentrations for an ion channel protein, a gramicidin A (gA), and five different ionic solvents with up to four species. Numerical results indicate that the cation selectivity property of gA occurs within a central portion of ion channel pore, insensitively to any change of boundary value condition, membrane charge, or bulk concentration. Moreover, a numerical scheme for computing the electric currents induced by ion transports across membrane via an ion channel pore is presented and implemented as a part of the PNPic finite element package. It is then applied to the calculation of current–voltage curves, well validating the PNPic model and finite element package by electric current experimental data.In this study, we added 0.3 and 0.1 mol of KCl, respectively, to the bottom and top water compartments connected by a voltage‐dependent anion channel (VDAC with PDB ID: 3EMN) as the conduit of ions. We then generated the concentrations of K+ and Cl− and visualized them in color mappings and two‐dimensional curves by the Poisson‐Nernst‐Planck finite element package of this paper, clearly validating the anion selectivity of VDAC.