Low-frequency localized oscillations of the DNA double strand

Abstract

The results of the molecular dynamic study on the low-energy elementary linear and nonlinear excitations of DNA macromolecule obtained within the framework of the coarse-grain model of the DNA double strand are presented. The characteristics of the basic states of the model agree well with the experimental parameters of both A and B conformations of the DNA double strand. The correlation between the directly calculated dispersion curves and density distribution of the frequency spectrum obtained in the simulation experiments is found. Special attention is focused on the soliton type of nonlinear localized excitations (breathers). These excitations are shown to exist in several frequency gaps in which the propagation of harmonic linear waves is prohibited. The types of motions corresponding to all calculated breathers are identified. The correlation between the two types of breathers and their analogs studied in terms of unidimensional models and treated as elementary excitations responsible for the initial stage of the opening of the DNA double strand is established.