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International Conference on Finite Difference Methods

FDM 2018: Finite Difference Methods. Theory and Applications pp 225–232Cite as

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

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,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.

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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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Authors and Affiliations

  1. Institute of Mathematical Problems of Biology - The Branch of KIAM RAS, 142290, Pushchino, Russia

    Nadezhda Fialko & Victor D. Lakhno

Authors
  1. Nadezhda Fialko
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  2. Victor D. Lakhno
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Correspondence to Nadezhda Fialko .

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Editors and Affiliations

  1. IICT, Bulgarian Academy of Sciences, Sofia, Bulgaria

    Ivan Dimov

  2. Eötvös Loránd University, Budapest, Hungary

    István Faragó

  3. University of Rousse, Rousse, Bulgaria

    Lubin Vulkov

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Fialko, N., Lakhno, V.D. (2019). Numerical Modeling of the Charge Transfer Along 1D Molecular Chain “Donor-Bridge-Acceptor” at T = 300 K. In: Dimov, I., Faragó, I., Vulkov, L. (eds) Finite Difference Methods. Theory and Applications. FDM 2018. Lecture Notes in Computer Science(), vol 11386. Springer, Cham. https://doi.org/10.1007/978-3-030-11539-5_24

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  • DOI: https://doi.org/10.1007/978-3-030-11539-5_24

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-11538-8

  • Online ISBN: 978-3-030-11539-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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