1st Reading February 18, 2012 15:26 WSPC/S0219-4775 167-FNL 00083 Fluctuation and Noise Letters 1 Vol. 11, No. 1 (2012) 00083 (10 pages) 2 c  World Scientific Publishing Company 3 DOI: 10.1142/S0219477512000837 4 5 NONEQUILIBRIUM RATE THEORY FOR CONDUCTION 6 IN OPEN ION CHANNELS 7 R. TINDJONG ∗ , I. KAUFMAN † and P. V. E. McCLINTOCK ‡ 8 Department of Physics 9 Lancaster University, Lancaster, LA1 4YB, UK 10 ∗ r.tindjong@lancaster.ac.uk 11 † i.kaufman@lancaster.ac.uk 12 ‡ p.v.e.mcclintock@lancaster.ac.uk 13 D. G. LUCHINSKY 14 Mission Critical Technologies Inc., 2041 Rosecrans 15 Ave. Suite 225 El Segundo, CA 90245, USA 16 Department of Physics 17 Lancaster University, Lancaster, LA1 4YB, UK 18 dmitry.g.luchinsky@nasa.gov 19 R. S. EISENBERG 20 Department of Molecular Biophysics and Physiology 21 Rush Medical College 22 1750 West Harrison, Chicago, IL 60612, USA 23 beisenbe@rush.edu 24 Received 25 Revised 26 Published 27 We present a nonequilibrium reaction rate model of the ionic transition through an 28 open ion channel, taking account of the interaction between an ion at the entrance of 29 the channel and an ion at the binding site in a self-consistent way. The electrostatic 30 potential is calculated by solution of the Poisson equation for a channel modeled as a 31 cylindrical tube. The transition rate, and the binding site occupancy as a function of 32 the left bulk concentration are compared to 1D Brownian dynamics simulations. The 33 analysis is performed for a single binding site of high-affinity, with the exit rate influenced 34 by barrier fluctuations at the channel exit. The results are compared with experimental 35 data for the permeation of the Na + ion through the Gramicidin A channel, with which 36 they are shown to be in good agreement. 37 Keywords : Ion channels; permeation; nonequilibrium rate; stochastic dynamics; fluctu- 38 ating barrier. 39 00083-1