Concentration dependence of the anisotropy of the electrical polarizability of a model DNA fragment in salt-free aqueous solution studied by Monte Carlo simulations

Abstract

Metropolis Monte Carlo (MC) Brownian dynamics simulations are performed to determine values of the anisotropy of the electrical polarizability of a model DNA fragment in salt-free aqueous solutions. A 64 base-pair fragment of the double-stranded DNA is modeled as an impenetrable cylinder and placed in a spherical MC cell. At every simulation step we numerically sort counterions in increasing order of the sum of their distances from both ends of the polyion and calculate the contribution to the dipole moment of the first n counterions in the sorting list. According to the fluctuation–dissipation theorem, partial polarizability is calculated from the fluctuation of this quantity. The anisotropy of the electrical polarizability Δ α is determined by cutting off the contribution from the Debye–Hückel ion atmosphere which shows large statistical uncertainties assuming that this contribution to the polarizability tensor is isotropic as a first approximation.