Applied Math Seminar: Framework Models of Ion Permeation
3:10 PM, Webster B8
Framework models are designed to incorporate information from molecular dynamics simulations of ion channels in order to calculate their conductance properties on much longer time scales than can be achieved by the simulations. They provide a comparison between the simulations and conductance data. This talk describes three different steady state framework models. The single particle model was originally developed by Levitt, and describes a channel whose pore can be occupied by only one ion at a time. It has been used to model Na+ conduction through gramicidin. Transport is described by a Smoluchowski equation with non-local boundary conditions enforcing the single occupancy constraint. The Grotthuss conduction model describes proton conduction through gramicidin. It incorporates potentials of mean force for proton occupation and water reorientation calculated by Pomès and Roux. Model parameters were optimized against an extensive set of conductance data taken by Busath and his colleagues. Bernèche and Roux developed a framework model for conduction through the narrow pore of the KcsA potassium channel, using a potential of mean force for occupation of the pore by two or three potassium ions. Finally, the problem of constructing time-dependent framework models is addressed. This is practice for a talk I will give at the Mathematical Biosciences Institute, at Ohio State University, on Feb. 19.