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Numerical Modeling of the Charge Transfer Along 1D Molecular Chain “Donor-Bridge-Acceptor” at T = 300 K

  • Nadezhda FialkoEmail author
  • Victor D. Lakhno
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11386)

Abstract

We consider charge transfer along homogeneous chain of sites (such as DNA fragment) with the ends which imitate a donor and an acceptor. We performed direct numerical experiments based on the semi-classical Holstein model. To take into account the temperature, Langevin thermostat is used. Recently it has been shown that in homogeneous chains the charge distribution in thermodynamic equilibrium state (TDE) depends on the thermal energy of the lattice subsystem. Here, we have calculated dynamics of the system from the initial state “the charge is localized at the donor” over time intervals to the attainment of the TDE. The time intervals dependence on the length of the chain at fixed temperature is estimated. Part of parameter values are chosen as for DNA fragments of the GA...AGGG type. The results of the calculations are compared with the data of biophysical experiments on the hole transfer in DNA sequences.

Keywords

Holstein model Langevin equation Time to the attainment of the thermodynamic equilibrium state DNA fragment 

Notes

Acknowledgements

The work is partially supported by Russian Foundation for Basic Research, grants 16-07-00305 and 17-07-00801, and Russian Science Foundation, grant 16-11-10163.

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Institute of Mathematical Problems of Biology - The Branch of KIAM RASPushchinoRussia

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