Two-level system with a thermally fluctuating transfer matrix element: application to the problem of DNA charge...

Charge transfer along the base-pair stack in DNA is modeled in terms of thermally assisted tunneling between adjacent base pairs. The key element of the approach in this paper is the notion that this tunneling between base pairs that fluctuate significantly from their nominal orientation is rate limited by the requirement of optimal alignment. We focus on this aspect of the process by modeling two adjacent base pairs in terms of a classical damped oscillator subject to thermal fluctuations as described by a Fokker-Planck equation. We find that the process is characterized by two time scales, a result that is in accord with the experimental findings.