Distribution and dynamics of mobile ions in systems of ordered B-DNA

Abstract

The distribution and dynamics of monovalent counterions in systems of hexagonally packed B-DNA molecules are studied using a continuum solvent model with an atomic description of the solute species. The properties of the model are evaluated using the brownian dynamics computer simulation method. The aim of the work is to investigate a detailed model which can be used to describe the system on the long timescales, and over the large distances, that are characteristic of polyelectrolytes. The properties of the proposed continuum solvent model are related to results from a molecular dynamics simulation study of a fully molecular description of the same system, as well as to the predictions of simpler models. We find that the continuum solvent model is able to reproduce the molecular dynamics results for the distribution of those counterions that do not lose their hydration shells; while in dilute systems, the counterion distribution in regions away from the macroions is similar to that given by the Poisson-Boltzmann equation. We present results for some aspects of the static distribution of counterions in ordered systems of four different macroion concentrations. The dynamic behaviour of the counterions are discussed in terms of average residence times and macroscopic diffusion coefficients.