Numerical considerations in the computation of the electrostatic free energy of interaction within the Poisson-Boltzmann theory (Q1371981)

The aim of this paper is the calculation of the approximate electrostatic free energy of interaction arising from hydrogen bonds between DNA strands. First general aspects of discretization methods applied to the nonlinear Poisson-Boltzmann equation are presented and two ways how the electrostatic free energy can be integrated. The discretization methods used are: finite element methods and the finite difference methods. At the end some applications are discussed.