Simulation of the charge transfer process in the DNA molecule

Zakir'yanov F.K., Mel'nikov V.Yu.

Bashkir State University

Currently, there are many different experiments on charge transfer in DNA, the interpretation of which is devoted to a large number of theoretical works. In particular, it was shown in [1] that conformational perturbations in the form of breathers, excited in the so-called PB-model of DNA, interact with charges. In this case, the characteristic length of the displacement of the bound state "breather charge" amounted to about 20 sites in this model.

We propose to consider the dynamics of charge transfer in the Y-model of the DNA molecule, which differs from the PB-model in that the change in conformation occurs not due to lateral displacement of nucleotides, but due to their rotation around the sugar-phosphate backbone. The initial conformational perturbation is given in the form of a kink-antikink soliton pair, the center of which falls approximately at the 50th site of the DNA molecule (see Fig. 1). The main charge density was within this perturbation. After the kink-antikink pair is transformed into a moving breather, information about the charge density loses its meaning. As can be seen from fig. 1, the distance traveled by a soliton carrying a charge before it becomes a breather increases with a decrease in the interaction coefficient between the conformational perturbation and charge density, and can reach a value of about 80 sites.

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