A First Passage Time Analysis of Atomic-Resolution Simulations of the Ionic Transport in a Bacterial Porin - Condensed Matter > Soft Condensed MatterReport as inadecuate




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Abstract: We have studied the dynamics of chloride and potassium ions in the interiorof the OmpF porin under the influence of an external electric field. From theresults of extensive all-atom molecular dynamics simulations of the system wecomputed several first passage time FPT quantities to characterize thedynamics of the ions in the interior of the channel. Such FPT quantitiesobtained from MD simulations demonstrate that it is not possible to describethe dynamics of chloride and potassium ions inside the whole channel with asingle constant diffusion coefficient. However, we showed that a valid,statistically rigorous, description in terms of a constant diffusioncoefficient D and an effective deterministic force Feff can be obtained afterappropriate subdivison of the channel in different regions suggested by theX-ray structure. These results have important implications for popularsimplified descriptions of channels based on the 1D Poisson-Nernst-Planck PNPequations. Also, the effect of entropic barriers on the diffusion of the ionsis identified and briefly discussed.



Author: Carles Calero, Jordi Faraudo, Marcel Aguilella-Arzo

Source: https://arxiv.org/







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