Ionic motion in the bulk solution away from the mouth of a biological ion channel, and inside the channel, is
analyzed using Poisson-Nernst-Planck (PNP) equation. The one-dimensional method allows us to connect in
a self-consistent way ion dynamics in the bulk solution and inside the channel by taking into account access
resistance to the channel. In order to glue the PNP solution in the bulk to that inside the channel, a continuity
condition is used for the concentration and the current near the channel mouth at the surface of the hemisphere.
The resulting one dimensional (1D) current-voltage characteristics are compared with the Kurnikova16 results
which are in good agreement with experimental measurement on the channel, by using a filling factor as the
only fitting parameter. The filling factor compensates the fact that the radial charge distribution is non-uniform
in a real channel as compared to the cylindrically symmetrical channel used in the 1D approximation.
A novel conceptual model is introduced in which ion permeation is coupled to the protein wall vibration and the
later in turn modulates exponentially strongly the permeation via radial oscillations of the potential of mean
force. In the framework of this model of ion-wall-water interaction we discuss problems of selectivity between
alike ions and coupling of ion permeation to gating.
Ionic motion through an open ion channel is analyzed within the framework of self-consistent Brownian dynamics formalism. A novel conceptual model of coupling of the ion's motion to the vibrations of the pore walls is introduced. The model allows one to include into simulations an important additional mechanism of energy dissipation and the effects of self-induced strong modulation of the channel conductivity.