Non-Markovian noise mediated through anomalous diffusion within ion channels

Abstract

It is evident from a wide range of experimental findings that ion channel gating is inherently stochastic. The issue of "memory effects" (diffusional retardation due to local changes in water viscosity) in ionic flow has been recently addressed using Brownian dynamics simulations. The results presented indicate such memory effects are negligible, unless the diffusional barrier is much higher than that of free solute. In this paper using differential stochastic methods we conclude that the Markovian property of exponential dwell times gives rise to a high barrier, resulting in diffusional memory effects that cannot be ignored in determining ionic flow through channels. We have addressed this question using a generalized Langevin equation that contains a combination of Markovian and non-Markovian processes with different time scales. This approach afforded the development of an algorithm that describes an oscillatory ionic diffusional sequence. The resulting oscillatory function behavior, with exponential decay, was obtained at the weak non-Markovian limit with two distinct time scales corresponding to the processes of ionic diffusion and drift. This will be analyzed further in future studies using molecular dynamics simulations. We propose that the rise of time scales and memory effects is related to differences of shear viscosity in the cytoplasm and extracellular matrix.