Fialko N.S., Olshevets M.M., Lakhno V.D.
Equilibrium Charge Distribution in a Finite Chain with a Trapping Site
Mathematical Biology & Bioinformatics. 2021;16(1):152-168.
doi: 10.17537/2021.16.152.
References
- Modern Methods for Theoretical Physical Chemistry of Biopolymers. Eds. Starikov E., Tanaka S., Lewis J. Amsterdam: Elsevier Scientific, 2006. 604 p. doi: 10.1016/B978-0-444-52220-7.X5062-X
- Polarons in Advanced Materials. Ed. Alexandrov A. Springer; 2007. 672 p. (Springer Series in Materials Science; V. 103). doi: 10.1007/978-1-4020-6348-0
- Nanobioelectronics – for Electronics, Biology, and Medicine. Eds. Offenhäusser A., Rinaldi R. New York: Springer, 2009. 337 p. doi: 10.1007/978-0-387-09459-5
- Seeman N.C. Nanotechnology and the double helix. Sci. Am. 2004;290(6):64-9, 72-5. doi: 10.1038/scientificamerican0604-64
- 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
- Long-Range Charge Transfer in DNA II. Ed. Schuster G.B. Topics in Current Chemistry;237. Springer; 2004. 245 p. doi: 10.1007/b14032
- Conwell E.M. Charge transport in DNA in solution: The role of polarons. PNAS USA. 2005;102(25):795–8799. doi: 10.1073/pnas.0501406102
- Davydov A.S. The theory of contraction of proteins under their excitation. J. Theor. Biology. 1973;38:559–569. doi: 10.1016/0022-5193(73)90256-7
- Su W.P., Schrieffer J.R. Soliton dynamics in polyacetylene. PNAS USA. 1980;77(10):5626–5629. doi: 10.1073/pnas.77.10.5626
- Landau L.D., Lifshitz E.M. Quantum Mechanics. Non-relativistic Theory. Elsevier; 1977. (Course of Theoretical Physics, V. 3).
- Holstein T. Studies of polaron motion: Part I. The molecular-crystal model. Annals of Physics. 1959;8(3):325–342. doi: 10.1016/0003-4916(59)-90002-8
- Kalosakas G., Rasmussen K., Bishop A. Charge trapping in DNA due to intrinsic vibrational hot spots. J. Chem. Phys. 2003;118(8):3731–3735. doi: 10.1063/1.1539091
- Qu Z., Kang D., Jiang H., Xie S. Temperature effect on polaron dynamics in DNA molecule: The role of electron-base interaction. Physica B. 2010;405:S123–S125. doi: 10.1016/j.physb.2009.12.020
- Patwardhan S., Tonzani S., Lewis F., Siebbeles L., Schatz G., Grozema F. Effect of structural dynamics and base pair sequence on the nature of excited states in DNA hairpins. J. Phys. Chem. B. 2012;116:11447–11458. doi: 10.1021/jp307146u
- Lomdahl P.S., Kerr W.C. Do Davydov solitons exist at 300K? Phys. Rev. Lett. 1985;55(11):1235–1238. doi: 10.1103/PhysRevLett.55.1235
- 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
- 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
- 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
- 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
- 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
- Voityuk A.A., Rösch 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
- Jortner J., Bixon M., Voityuk A.A., Röcsh N. Superexchange mediated charge hopping in DNA. J. Phys. Chem. A. 2002;106(33):7599–7606. doi: 10.1021/jp014232b
- 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
- Chandrasekhar S. Stochastic Problems in Physics and Astronomy. Rev. Mod. Phys. 1943;15:1. doi: 10.1103/RevModPhys.15.1
- Yakushevich L.V. Nonlinear Physics of DNA. Wiley; 1998.
- Fialko N.S., Lakhno V.D. Numerical Simulation of Small Radius Polaron in a Chain with Random Perturbations. Mathematical Biology and Bioinformatics. 2019;14(1):126–136 (in Russ.). doi: 10.17537/2019.14.126
- Cheng K.C., Cahill D.S., Kasai H., Nishimura S., Loeb L.A. 8-Hydroxyguanine, an abundant form of oxidative DNA damage, causes G→T and A→C substitutions. J. Biol. Chem. 1992;267(1):166–172. doi: 10.1016/S0021-9258(18)48474-8
- 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. Article No. 06004. doi: 10.1051/epjconf/201817306004
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