title: First-passage-time analysis of atomic-resolution simulations of the ionic transport in a bacterial porin.
abstract: We have studied the dynamics of chloride and potassium ions in the interior of the Outer membrane porin F (OmpF) under the influence of an external electric field. From the results of extensive all-atom molecular dynamics (MD) simulations of the system, we computed several first-passage-time (FPT) quantities to characterize the dynamics of the ions in the interior of the channel. Such FPT quantities obtained from MD simulations demonstrate that it is not possible to describe the dynamics of chloride and potassium ions inside the whole channel with a single constant diffusion coefficient. However, we showed that a valid, statistically rigorous description in terms of a constant diffusion coefficient D and an effective deterministic force F(eff) can be obtained after appropriate subdivision of the channel in different regions suggested by the x-ray structure. These results have important implications for popular simplified descriptions of channels based on the one-dimensional Poisson-Nernst-Planck equations. Also, the effect of entropic barriers on the diffusion of the ions is identified and briefly discussed.
authors.affiliation: Institut de Ciència dels Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Spain. ccalero@icmab.es
authors.forename: Carles
authors.initials: C
authors.lastname: Calero
authors.forename: Jordi
authors.initials: J
authors.lastname: Faraudo
authors.forename: Marcel
authors.initials: M
authors.lastname: Aguilella-Arzo
mesh_terms: D003198:Computer Simulation; D004574:Electromagnetic Fields; D015640:Ion Channel Gating / Q000528:radiation effects*; D017136:Ion Transport / Q000528:radiation effects*; D008954:Models, Biological; D008956:Models, Chemical; D018272:Porins / Q000737:chemistry* / Q000528:radiation effects*; D011829:Radiation Dosage
chemical_list: C109237:OmpF protein; D018272:Porins