title: Framework model for single proton conduction through gramicidin.
abstract: This paper describes a framework model for proton conduction through gramicidin; a model designed to incorporate information from molecular dynamics and use this to predict conductance properties. The state diagram describes both motion of an excess proton within the pore as well as the reorientation of waters within the pore in the absence of an excess proton. The model is constructed as the diffusion limit of a random walk, allowing control over the boundary behavior of trajectories. Simple assumptions about the boundary behavior are made, which allow an analytical solution for the proton current and conductance. This is compared with corresponding expressions from statistical mechanics. The random walk construction allows diffusing trajectories underlying the model to be simulated in a simple way. Details of the numerical algorithm are described.
authors.affiliation: Department of Pure and Applied Mathematics, Washington State University, Pullman, Washington 99164-3113, USA. schumaker@wsu.edu
authors.forename: M F
authors.initials: MF
authors.lastname: Schumaker
authors.forename: R
authors.initials: R
authors.lastname: Pomès
authors.forename: B
authors.initials: B
authors.lastname: Roux
mesh_terms: D000465:Algorithms; D055592:Biophysical Phenomena; D001703:Biophysics; D004058:Diffusion; D004553:Electric Conductivity; D006096:Gramicidin / Q000737:chemistry / Q000378:metabolism*; D007473:Ion Channels / Q000737:chemistry / Q000378:metabolism*; D008954:Models, Biological; D011522:Protons; D013816:Thermodynamics
chemical_list: D007473:Ion Channels; D011522:Protons; D006096:Gramicidin