A multi-scale method for the calculation of charge transfer rates through the Pi-stack of DNA: application to DNA dynamics

We describe an ultra-fast, multi-scale method for calculating charge transfer rates through the alpha-stack of DNA using a simple charge hopping model in conjunction with the Marcus equation. The calculation of the parameters required as input to the Marcus equation, such as the electronic coupling and the driving force, are calculated with a combination of quantum mechanical methods and conformations sampled from classical molecular dynamics (MD) simulations. The resulting set of time dependent rate equations are then solved stochastically using Monte Carlo (MC) methods. We have applied this model to investigate the importance of thermal fluctuations in DNA conformation over picosecond and nanosecond timescales, and have identified the timescales of most relevance to hole transfer through DNA.