Computational Issues in Modeling Ion Transport in Biological Channels: Self-Consistent Particle-Based Simulations

In this work, a self-consistent Langevin dynamics simulator will be presented, and computational issues unique to the simulation of charge transport through ion channels will be addressed. The simulation approach is divided into two parts; the first is the development of an efficient model to account for the charge transport in bulk electrolyte solutions, while the second is the accurate representation of the channel protein and lipid structure. A cavity is made in the interior of a phospholipid bilayer and an ion channel is inserted, where the atomic coordinates of the protein are obtained from experimental work. The electrostatic potential felt by a potassium ion along the center of the channel is then calculated and comparisons are made between two types of potassium channels, KcsA and MthK.