Condensed Matter/Biological Physics Seminar: Dr. Fangqiang Zhu, IUPUI
Title: Calculating Ion Channel Conductance from All-atom Simulations
Abstract: Ion channels facilitate the passage of ions across cell membranes, and play important roles in biology. The single-channel conductance, defined as the ratio of the ionic current to the transmembrane voltage, is a major biophysical quantity for ion channels. In this talk, I will present methods for calculating the ion channel conductance from all-atom simulations. For channels with large conductance, the ionic currents can be directly determined in simulations with applied voltages. Complementary to this approach, I will introduce a new method, the collective diffusion model, to obtain the conductance at small voltages from the spontaneous fluctuation of ion permeation at equilibrium. For channels with low conductance, I will present an approach to calculate the conductance from the single-ion free energy and diffusion coefficients. Having their roots in the classical statistical mechanics, these computational methods rigorously connect atomic simulations to experimental observation. I will also discuss the role of water molecules in the ion conduction in a hydrophobic channel.