Implicit Water Simulations of Non-Equilibrium Charge Transport in Ion Channels

Abstract

Ion channels are natural nano-channels found in the membranes of all living cells, which exhibit a broad range of specific device-like functions to help regulate cell physiology. The study of charge transport in ion channels is imperative to understand how charge regulation is accomplished at the molecular level if one is to develop nanoscale artificial systems that mimic biological function and detection. Although Molecular Dynamics is the most popular approach to simulate ion channel behavior, the computational cost of representing all water molecules and ions in the system is prohibitive to study the timescales required to resolve ionic current and lead to structure design. A hierarchy of models of decreasing complexity is needed to address simulation of different time and space scales, similar to the set of models developed to study transport in semiconductors. This paper discusses the application of Monte Carlo and Drift-diffusion methods to simulate transport in ion channels, using the ompF porin channel as a prototype.