Dynamics of ions in the selectivity filter of the KcsA channel

The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications

Noise-induced failures of chaos stabilization: Large fluctuations and their control.

Noise-induced failures in the stabilization of an unstable orbit in the one-dimensional logistic map are considered as large fluctuations from a stable state. The properties of the large fluctuations are examined by determination and analysis of the optimal path and the optimal fluctuational force corresponding to the stabilization failure. The problem of controlling noise-induced large fluctuations is discussed, and methods of control have been developed