Recent Advances in Ion Channel Modeling and Simulation Tools

Many ion channel models have been developed by using either the Poisson-Boltzmann (PB) equation or a system of Poisson–Nernst–Planck (PNP) equations through considering volume-exclusion entropy effects, hard sphere interactions, Leonard Jones' interactions, and electric charge correlations, etc. Even so, how to let PB/PNP ion channel models reflect charge effect from membrane and membrane influence from the outside of a simulation box domain remains an interesting research topic. In this talk, I will report the recent advances that we made toward the solution of this research problem. In particular, a PNP ion channel model using periodic boundary value conditions for mimicking an infinitely large ion channel membrane, denoted by PNPic, and a size modified Poisson-Boltzmann ion channel model using a membrane surface charge density and Neumann boundary conditions, denoted by SMPBic, will be reported. I then will describe our PNPic and SMPBic finite element algorithms, and introduce the related software packages, which work for an ion channel protein in a solvent of multiple ionic species with distinct ion sizes. Moreover, I will discuss some important mathematical and numerical issues arisen from the study of PNPic and SMPBic. Finally, numerical results will be reported to demonstrate the performance and application of our PNPic and SMPBic software packages.

Event Topic

Stochastic & Multiscale Modeling and Computation