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Volume 14   Issue 1   Year 2019
Nadezhda S. Fialko, Victor D. Lakhno

Numerical Simulation of Small Radius Polaron in a Chain with Random Perturbations

Mathematical Biology & Bioinformatics. 2019;14(1):126-136.

doi: 10.17537/2019.14.126.

References

 

  1. Nanobioelectronics – for Electronics, Biology, and Medicine. Eds. Offenhausser A., Rinaldi R. New York: Springer; 2009. 337 p. doi: 10.1007/978-0-387-09459-5
  2. Lakhno V.D. DNA nanobioelectronics. International Journal of Quantum Chemistry. 2008;108(11):1970–1981. doi: 10.1002/qua.21717
  3. Charge Migration in DNA. Perspectives from Physics, Chemistry, and Biology. Ed. Chakraborty T. Berlin: Springer; 2007. 288 p. doi: 10.1007/978-3-540-72494-0
  4. Long-Range Charge Transfer in DNA II. Ed. Schuster G.B. Topics in Current Chemistry, Vol. 237. Springer; 2004. 245 p.
  5. Modern Methods for Theoretical Physical Chemistry of Biopolymers. Eds. Starikov E.B., Tanaka S., Lewis J.P. Amsterdam: Elsevier Scientific; 2006. 461 p.
  6. Alexandre S.S., Artacho E., Soler J., Chacham H. Small polarons in dry DNA. Physical Review Letters. 2003;91:108105. doi: 10.1103/PhysRevLett.91.108105
  7. Wang Y., Fu L., Wang K.-L. Extended Holstein small polaron model for charge transfer in dry DNA. Biophysical Chemistry. 2006;119:107–114. doi: 10.1016/j.bpc.2005.09.008
  8. Starikov E. Electron-phonon coupling in DNA: A systematic study. Philosophical Magazine. 2005;85:3435–3462. doi: 10.1080/14786430500157110
  9. Fialko N., Lakhno V. Nonlinear dynamics of excitations in DNA. Physical Letters A. 2000;278:108–112. doi: 10.1016/S0375-9601(00)00755-6
  10. Lakhno V.D. Davydov' solitons in DNA. In: Self-Organization of Molecular Systems – From Molecules and Clusters to Nanotubes and Proteins. Eds. Russo N., Antonchenko V.Y., Kryachko E.S. Netherlands: Springer; 2009. P. 255–273. ISBN: 978-90-481-2482-4.
  11. Lakhno V.D., Fialko N.S. Glass Phys. Chem. 2011;37:51–59. doi: 10.1134/S1087659611010068
  12. Grozema F.C., Berlin Y.A., Siebbeles L.D.A. Sequence-dependent charge transfer in donor-DNA-acceptor systems: A theoretical study. International Journal of Quantum Chemistry. 1999;75:1009–1016. doi: 10.1002/(SICI)1097-461X(1999)75:6<1009::AID-QUA5>3.0.CO;2-A
  13. Jortner J., Bixon M., Langenbacher T., Michel-Beyerle M.E. Charge transfer and transport in DNA. PNAS USA. 1998;95:12759–12765. doi: 10.1073/pnas.95.22.12759
  14. Jortner J., Bixon M., Voityuk A.A., Roesh N. Superexchange Mediated Charge Hopping in DNA. J. Phys. Chem. A. 2002;106(33):7599–7606. doi: 10.1021/jp014232b
  15. Basko D.M., Conwell E.M. Effect of Solvation on Hole Motion in DNA. Phys. Rev. Lett. 2002;88(9):098102. doi: 10.1103/PhysRevLett.88.098102
  16. Genereux J.C., Barton J.K. Mechanisms for DNA Charge Transport. Chem. Rev. 2010;110(3):1642–1662. doi: 10.1021/cr900228f
  17. Holstein T. Studies of polaron motion: Part I. The molecular-crystal model. Annals of Physics. 1959;8(3):325–342.
  18. Lomdahl P.S., Kerr W.C. Do Davydov solitons exost at 300K? Phys. Rev. Lett. 1985;55(11):1235–1238. doi: 10.1103/PhysRevLett.55.1235
  19. Helfand E. Brownian dynamics study of transitions in a polymer chain of bistable oscillators. J. Chem. Phys. 1978;69(3):1010–1018. doi: 10.1063/1.436694
  20. Greenside H.S., Helfand E. Numerical integration of stochastic differential equations-II. Bell System Technical Journal. 1981;60:1927–1940. doi: 10.1002/j.1538-7305.1981.tb00303.x
  21. Voityuk A.A., Rosch N., Bixon M., Jortner J. Electronic Coupling for Charge Transfer and Transport in DNA. J. Phys. Chem. B. 2000;104(41):9740–9745. doi: 10.1021/jp001109w
  22. Lewis F.D., Wu Ya. Dynamics of superexchange photoinduced electron transfer in duplex DNA. J. Photochem. Photobiol. C. 2001;2(1):1–16. doi: 10.1016/S1389-5567(01)00008-9
  23. Fialko N.S., Sobolev E.V., Lakhno V.D. On the calculation of thermodynamic quantities in the Holstein model for homogeneous polynucleotides. Journal of Experimental and Theoretical Physics. 2017;124(4):635-642. doi: 10.1134/S1063776117040124
  24. Holstein T. Studies of polaron motion: Part II. The “small” polaron. Annals of Physics. 1959;8(3):343–389. doi: 10.1016/0003-4916(59)90003-X
  25. Lakhno V.D., Fialko N.S. On the dynamics of a polaron in a classical chain with finite temperature. Journal of Experimental and Theoretical Physics. 2015;120(1):125-131. doi: 10.7868/S0044451015010125
  26. Chetverikov A.P., Ebeling W., Velarde M.G. Local electron distributions and diffusion in anharmonic lattices mediated by thermally excited solitons. Eur. Phys. J. B. 2009;70:217–227. doi: 10.1140/epjb/e2009-00224-2
  27. Chetverikov A.P., Ebeling W., Velarde M.G. On the temperature dependence of fast electron transport in crystal lattices. Eur. Phys. J. B. 2015;88:202–207. doi: 10.1140/epjb/e2015-60495-4
  28. Chandrasekhar S. Stokhasticheskie problemy v fizike i astronomii. Ed. Bogoliubova N.N. Moscow; 1947. 168 p.(Translation of: Chandrasekhar S. Stochastic Problems in Physics and Astronomy. Rev. Mod. Phys. 1943. V. 15).
  29. Yoo K.-H., Ha D.H., Lee J.-O., Park J.W., Kim Jinhee, Kim J.J., Lee H.-Y., Kawai T., Choi H.Y. Electrical Conduction through Poly(dA)-Poly(dT) and Poly(dG)-Poly(dC) DNA Molecules. Physical Review Letters. 2001;87(19):198102. doi: 10.1103/PhysRevLett.87.198102
  30. Voityuk A. Charge transfer in DNA: Hole charge is confined to a single base pair due to solvation effects. J. Chem. Phys. 2005;122:204904. doi: 10.1063/1.1924551
  31. Fialko N., Pyatkov M., Lakhno V. On the Thermodynamic Equilibrium Distribution of a Charge in a Homogeneous Chain with a Defect. EPJ Web of Conferences. 2018;173:06004. doi: 10.1051/epjconf/201817306004
Table of Contents
Original Article
Math. Biol. Bioinf.
2019;14(1):126-136
doi: 10.17537/2019.14.126
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 
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