Barriers master equation dynamics

Proton transport in the gA channel was also simulated with a kinetic model (see section 16.3.5.3). " Each H2O molecule was allowed to take six orientations and each HsO molecule, four orientations, so that the chain of eleven H2O molecules could take 10 states. Three types of transitions were allowed rotation of H2O and HsO" proton transfer from HsO to a neighbouring H2O molecule when they form a hydrogen bond and proton uptake and release for water molecules located at the channel ends. The rate constants were taken of the TST type, with Ag values calculated by continuum electrostatics or deduced from data about proton transfer in water. For the proton uptake and release steps, the Ag value depended explicitly on the pH. The master equation was solved by a sequential dynamical Monte Carlo algorithm and the PMF was deduced from the probability of occupancy of the various sites. When no voltage was applied, the PMF was a symmetrical barrier with a maximum at 3.4 kcal mol . Stationary proton ffuxes calculated for various pH and voltages values were in reasonable agreement with the conductance data. Despite the simplified description of electrostatic interactions and the questionable... 

Most of the ingredients of the model described above have been formerly postulated in treatments of unimolecular reactions. In particular, the model for the barrier dynamics is inherent in the usual TST for unimolecular reactions involving polyatomic molecules, while taking the total molecular energy Ej as the important dynamic variable in the well is the underlying assumption in theories that use a master or a diffusion equation for Ej- as their starting point. 

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