Abstract
We have studied the dynamics of chloride and potassium ions in the interior of the OmpF porin under the influence of an external electric field. From the results of extensive all-atom molecular dynamics 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 Feff can be obtained after appropriate subdivison 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 1D Poisson-Nernst-Planck (PNP) equations. Also, the effect of entropic barriers on the diffusion of the ions is identified and briefly discussed.
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