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DIRECT SIMULATION OF POLARON DYNAMICS IN BIOPOLIMER 1-D CHAINS
Abstract
The possibility of applying biological macromolecules, especially DNA, in nanobioelectronics currently attracts attention of researchers. For example, DNA can be used when designing electronic microarrays and as a molecular wire. Therefore, the study of the conducting properties of polynucleotide chains is of great interest. In a number of publications about biophysical experiments on the charge transfer along DNA it is assumed that a charge is transferred via a super-exchange mechanism at short distances of 2?3 nucleotide pairs, and the charge forms a polaron in large DNA fragments, that moves along the chain under the influence of temperature fluctuations. Using numerical simulation, we investigate the dynamics of small radius polaron in a homogeneous chain placed in constant electric field at a finite temperature. We studied the model based on the semiclassical Holstein Hamiltonian for a discrete sites chain. In case of DNA, the site is a complementary base pair. Taking into account the temperature fluctuations, the classical subsystem of equations becomes the Langevin-type equations. It is shown that in the chains with parameter values corresponding to small radius polaron, there is no charge transfer by the polaron mechanism. That is no sequential polaron moving from site to site, e.g., in homogeneous adenine or cytosine DNA fragments. Results of numerical simulation demonstrate that without electric field, there is a mode of switching between the states "immobile polaron - delocalized state", and a new polaron arises at a random site of the chain. In the chain placed in electric field with constant intensity, the averaged time-dependences show that charge moves in the direction of the field, but the transfer occurs in a delocalized state.
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