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

Metropolis Monte Carlo (MC) Brownian dynamics simulations are performed to determine values of the anisotropy of the electrical polarizability of a mo del 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 counte rions in increasing order of the sum of their distances from both ends of t he polyion and calculate the contribution to the dipole moment of the first it counterions in the sorting list. According to the fluctuation-dissipati on theorem, partial polarizability is calculated from the fluctuation of th is quantity. The anisotropy of the electrical polarizability de! is determi ned by cutting off the contribution from the Debye-Huckel ion atmosphere wh ich shows large statistical uncertainties assuming that this contribution t o the polarizability tensor is isotropic as a first approximation. (C) 1999 Elsevier Science B.V. All rights reserved.