Hydration of a B-DNA Fragment in the Method of Atom-atom Correlation Functions with the Reference Interaction Site Model Approximation

TL;DR

This paper introduces an efficient numerical algorithm for solving integral equations in liquid theory, specifically applied to calculating solvent-solute correlations in a B-DNA fragment, with results validated against experiments and simulations.

Contribution

The paper presents a novel, efficient iterative algorithm for solving RISM integral equations for large macromolecules in dilute solutions.

Findings

Calculated solvent-solute correlation functions for B-DNA fragment

Results agree with experimental data

Results align with computer simulation outcomes

Abstract

We propose an efficient numerical algorithm for solving integral equations of the theory of liquids in the Reference Interaction Site Model (RISM) approximation for infinitely dilute solution of macromolecules with a large number of atoms. The algorithm is based on applying the nonstationary iterative methods for solving systems of linear algebraic equations. We calculate the solvent-solute atom-atom correlation functions for a fragment of the B-DNA duplex d(GGGGG).d(CCCCC) in infinitely dilute aqueous solution. The obtained results are compared with available experimental data and results from computer simulations.