The peculiarities of charge motion in the molecular polynucleotide chains of finite length. The rapid formation of a moving polaron state

A. N. Korshounova ; V. D. Lakhno

Matematičeskaâ biologiâ i bioinformatika, Tome 13 (2018) no. 2, pp. 534-550.

Résumé

The numerical experiments which demonstrate the possibility of charge transfer in a homogeneous G/C DNA chain in the absence of an electric field have been carried out. As a model, which describes the dynamics of a DNA molecule, was considered the nonlinear Peyrard–Bishop–Dauxois–Holstein model. It is commonly supposed that the main electric current carrier in homogeneous synthetic polynucleotide chains is the polaron. We have previously studied the peculiarities of polaron motion in molecular polynucleotide chains of finite length. It was shown that a polaron placed at the initial moment of time not in the center of the chain acquires the ability to move in the absence of an electric field and in the absence of any additional excitations in the chain. The numerical experiments which demonstrate the possibility of polaron charge transfer in a homogeneous finite unclosed G/C DNA chain due to the interaction with localized excitations have been carried out in the absence of an electric field. In this study, at the initial moment of time, a polaron is not added to the chain, but a charge localized in the region of a certain number of neighboring sites displaced from the equilibrium positions. The motion of the charge in the chain is caused by choice of these specified initial conditions, which ensure the rapid formation of the polaron state and, as a consequence, charge transfer along the chain. For the assignment of the external nonlinear excitations, we used nonzero values of the displacements of particles and/or their velocities at the initial instant of time. Non-zero values of chain sites velocities at the initial time were used to stimulate the motion of the charge. It is shown that for the rapid formation of the polaron state, the initial conditions must correspond to the parameters of the polaron, which is formed in the chain under the chosen parameters. It is shown that, depending on the parameters of the chain and on the parameters of the selected initial conditions, the charge can be transferred along the chain over long distances.

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