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 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 one-dimensional PoissonNernst-Planck equations. Also, the effect of entropic barriers on the diffusion of the ions is identified and briefly discussed.

Cooperative rectification in confined Brownian ratchets

“…Modulations in the available explored region lead to gradients in the system effective free energy, inducing a local bias in its diffusion that can promote a macroscopic net velocity for asymmetric channel profiles [7] or due to applied alternating fields [8]. Geometric barriers constitue a common feature at small scales; they are found in a variety of systems, including molecular transport in zeolites [9], ionic channels [10], or in microfluidic devices [11,12], where their shape explains, for example, the magnitude of the rectifying electric signal observed experimentally [13].…”

Confined Brownian ratchets

“…This restriction can be understood as an effective change of the entropy of the Brownian ratchet as it displaces along the confined environment. 12 The relevance of entropic barriers to promote entropic transport 13,14 in confined environments has been recognized in a variety of situations that include molecular transport in zeolites, 15 ionic channels, 16 or in microfluidic devices, 17,18 where their shape explains, for example, the magnitude of the rectifying electric signal observed experimentally. 19 In fact, spatially varying geometric constraints provide themselves an alternative means to rectify thermal fluctuations.…”

Tracer diffusion of hard-sphere binary mixtures under nano-confinement

“…Recent studies have shown that the coupling between the system and the geometrical constraints overimposed by the environment can be relevant in situations such as molecular transport in zeolites, 3 ionic channels, 4 or in microfluidic devices. 5,6 Moreover, geometrical constraints can induce novel dynamical scenarios, such as particle separation, 7 cooperative rectification, 8,9 and negative mobility 10,11 that are absent in the behavior of the corresponding systems in bulk.…”