Publications on Modeling of electron transfer in DNA

A.Yu.Aponin, V.D.Lakhno. Excitation transfer in DNA and parallel processing // Preprint. – Pushchino : Pushchino Research Center RAS, 1999 ( in Russian )

V.D.Lakhno. A possible mechanism of the nonexponential electron transfer in DNA // Doklady Biophysics, 2000, Vol.372, №1, P.18-20

V.D.Lakhno. Soliton-like solutions and electron transfer in DNA // J. of Biol. Phys., 2000, Vol.26, P.133-147

V.D.Lakhno, N.S.Fialko. The model of the excitation transfer in DNA // XIII All-Russia Conference on “Theoretical foundations and constructing of numerical algorithms for the solution of mathematical physics problems”, Pushchino, 2000 : Proceedings. – Pushchino : Pushchino Research Center RAS, 2000, P.42-44 ( in Russian )

N.S.Fialko, V.D.Lakhno. Nonlinear dynamics of excitations in DNA // Phys. Lett. A, 2000, Vol.278, P.108-111

N.S.Fialko. Computations of excitation transfer in DNA // Master’s thesis. – Pushchino: IMPB RAS, 2001 ( in Russian )

V.D.Lakhno. Clusters in physics, chemistry, biology // Izhevsk : Scientific Publisher’s Center “Regular and Chaotic Dynamics”, 2001 ( in Russian )

V.D.Lakhno, N.S.Fialko. Long-range charge transfer in DNA // V International congress of mathematical modeling, 30 September – 6 October 2002, Dubna : Abstracts. – Moscow: Janus-K, 2002, Vol.2, P.206

A.A.Zimin, V.D.Lakhno, N.N.Nazipova. Biological macromolecules: structure, shapes and functions // Computer and supercomputers in biology // Eds. V.D.Lakhno, M.N.Ustinin. – Moscow: Institute of Computer Investigations, 2002, Vol.1, P.35-54 ( in Russian )

V.D.Lakhno. Dynamics of hole transfer in nucleotide sequences // Computer and supercomputers in biology // Eds. V.D.Lakhno, M.N.Ustinin. – Moscow: Institute of Computer Investigations, 2002, Vol.1, P.137-171 ( in Russian )

V.D.Lakhno, N.S.Fialko. Long-range charge transfer in DNA // Computer and supercomputers in biology // Eds. V.D.Lakhno, M.N.Ustinin. – Moscow: Institute of Computer Investigations, 2002, Vol.1, P.172-194 ( in Russian )

V.D.Lakhno, N.S.Fialko. Numerical modeling of charge transfer in polynucleotides // The XIV-th All-Russia Conference on “Theoretical backgrounds and construction of numerical algorithms to solve the problems of mathematical physics”, 15-22 September 2002, Dyurso : Abstracts. – Ekaterinburg: Ural Department RAS, 2002, P.135-136 ( in Russian )

N.S.Fialko, V.D.Lakhno. Long-range charge transfer in DNA (draft) // Regular & Chaotic Dynamics, 2002, Vol.7, №3, P.299-313

V.D.Lakhno, E.V.Sobolev, N.S.Fialko, V.V.Baryshnikov, L.А.Kirzhemanov. Database on charge transfer in DNA // The 10-th International Conference on “Mathematics. Computer. Education”, 20-25 Jan. 2003, Pushchino : Abstracts, 2003 ( in Russian )

V.D.Lakhno, N.S.Fialko. Hole mobility in a homogeneous nucleotide chain // JETP Letters, 2003, Vol.78, №5, P.336-338

N.S.Fialko, V.D.Lakhno. Charge transfer in DNA-metal-ligand complexes. Polynucleotides // N.Russo et al. (eds.), Metal-Ligand Interactions, Kluwer Academic Publishers, 2003, P.453-459

V.D.Lakhno. Charge transfer in DNA-metal-ligand complexes. Oligonucleotides // N.Russo et al. (eds.), Metal-Ligand Interactions, Kluwer Academic Publishers, 2003, P.571-584

V.D.Lakhno, V.B.Sultanov. Hopping and superexchange mechanisms of charge transfer in DNA // Biophysics, 2003, Vol.48, №5, P.741-745

V.D.Lakhno. Mathematical cell. Concepts of constructing mathematical models for charge transfer in a living cell // Vestnik RUDN, Seriya Prikladnaya i komputernaya matematika, 2003, Vol.2, №2, P.77-84

V.D.Lakhno, N.S.Fialko. Bloch oscillations in a homogeneous nucleotide chain // Pisma v ZhETF, 2004, Vol.79, №10, P.575-578

V.D.Lakhno, N.S.Fialko. Dynamics of charge transfer along the oligonucleotide at a finite temperature // Biophysics, 2004, Vol.49, №1, P.8-12

V.D.Lakhno, V.V.Sychyov. Modeling of the hole transfer dynamics in the tetramer GAGG // Biophysics, 2004, Vol.49, №3, P.430-433

V.D.Lakhno, V.B.Sultanov and B.Montgomery Pettitt. Combined hopping-superexchange model of a hole transfer in DNA // Chemical Physics Letters, 2004, Vol.400, №1-3, P.47-53

V.D.Lakhno. Sequence dependent hole evolution in DNA // Journal of Biological Physics, 2004, Vol.30, P.123-138

V.D.Lakhno. The problem of reversibility and irreversibility in quantum mechanics and charge transfer in DNA // Proceedings of the Seminar “Time, chaos, and mathematical problems”, 2004, P.3 ( in Russian )

V.D.Lakhno, N.S.Fialko. Is DNA an ideal conductor? // 8-th School-Conference of Young Scientists, 17-21 May 2004, Pushchino : Abstracts. – Pushchino, 2004, P.245 ( in Russian )

V.D.Lakhno, N.S.Fialko. A computer modelling study of the hole mobility in polynucleotides // VI International congress of mathematical modeling, 20-26 September 2004, Dubna : Abstracts, 2004, P.501

V.D.Lakhno, N.S.Fialko. Hole mobility in G-C polynucleotides // The XV-th All-Russia Conference on “Theoretical backgrounds and construction of numerical algorithms to solve the problems of mathematical physics”, 8-11 September 2004, Abstracts, 2004, P.43-44 ( in Russian )

V.D. Lakhno, N.S. Fialko. HSSH-model of Hole transfer in DNA // The European Physical Journal B, 2005, Vol.43, P.279-281

N.S.Fialko. Temperature dependance of the hole mobility in homogeneous polynucleotides // 9-th School-Conference of Young Scientists, 18-22 April 2005, Pushchino : Abstracts. – Pushchino, 2005, P.333 ( in Russian )

N.S. Fialko, V.D. Lakhno, A. Zaytsev. Application of GRID resource for modeling charge transfer in DNA // EGEE User Forum 01-03 March 2006, CERN, Switzerland. Book of abstracts, 2006, P.6

V.D.Lakhno, N.S.Fialko. Hole mobility in nucleotide chain and disputable migration of charge in DNA // 10-th School-Conference of Young Scientists, 18-22 April 2006, Pushchino : Abstracts. – Pushchino, 2006 ( in Russian )

V.D.Lakhno, N.S.Fialko. Hole mobility in polynucleotides and the problem of charge transfer in DNA // International School of Crystallography, 38-th Course: Structure and Functions of Large Molecular Assemblies. Erice, Italy, 9-18 June 2006. Book of abstracts, 2006, P.79

V.D. Lakhno. The problem of DNA conductivity. // International Conference on Mathematical Modeling and Computational Physics, Tatranska Strba, Slovakia, August 28 – Septemper 1 2006. Book of abstracts, 2006, P.25

N.S. Fialko, V.D. Lakhno. Dynamics of Charge Transfer in Ordered and Chaotic Nucleotide Sequences // Mathematical Biology and Bioinformatics, 2006, Vol.1, №1, P.1-7

V.D. Lakhno, N.S. Fialko. Hole mobility in (GC)n polynucleotides // Mathematical Biology and Bioinformatics, 2006, Vol.1, №1, P.8-11

V.D. Lakhno, V.B. Sultanov. The DNA-based electronic logical gate XOR // Mathematical Biology and Bioinformatics, 2006, Vol.1, №1, P.123-126 ( in Russian )

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V.D. Lakhno, N.S. Fialko. Soliton disruption in DNA through temperature fluctuations // Proceedings of the 1th International Conference on Mathematical Biology and Bioinformatics, Pushchino, Russia, 2006, P.27-28 ( in Russian )

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V.D. Lakhno, M.M. Olshevetz. Calculation of a uniform soliton velocity in homogeneous nucleotide chain with applied electric field // Proceedings of the 1th International Conference on Mathematical Biology and Bioinformatics, Pushchino, Russia, 2006, P.31-32 ( in Russian )

V.D.Lakhno, V.B.Sultanov. Charge transfer in single and double chains of DNA // Proceedings of the 1th International Conference on Mathematical Biology and Bioinformatics, Pushchino, Russia, 2006, P.33-34 ( in Russian )

V.D. Lakhno. Nonlinear models in DNA conductivity // Chapter 24 in “Modern Methods for Theoretical Physical Chemistry of Biopolymers”, Eds. E.B. Starikov, J.P. Lewis, S. Tanaka; Elsevier Science Ltd. 604 pp. ISBN: 0-444-52220-4., 2006, P.461-481

V.D. Lakhno, A.N. Korshunova. Bloch oscillations of a soliton in a molecular chain // The European Physical Journal B, 2007, Vol.55, P.85-87

V.D. Lakhno, V.B. Sultanov. Combined Hopping-Superexchange Mechanism of Charge Transfer in DNA: Consideration of Nearest Interactions // Biophysics, 2007, Vol.52, №1, P.24-29

A.N. Korshounova, V.D. Lakhno. Simulation of soliton formation in a uniform chain // Mathematical Modeling, 2007, Vol.19, P.3-13 ( in Russian )

V.D. Lakhno, V.B. Sultanov. On the Possibility of Electronic DNA Nanobiochips // J. Chem. Theory Comput., 2007, Vol.3, P.703-705

V. Lakhno , N. Nazipova, V. Kim, S. Filippov, A. Zaitsev, N. Fialko, G. Tyulbasheva, D. Ustinin, A. Teplukhin, M. Ustinin. Integrated Mathematical Model of the Living Cell // Mathematical Biology and Bioinformatics, 2007, Vol.2, №2, P.361-376 ( in Russian )

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V.D. Lakhno, A.N. Korshunova. The modelling of selftrapped state formation in homogeneous polynucleotide chain // Nonlinear Dynamics, 2008, Vol.4, №2, P.193-214 ( in Russian )

. Molecular motors based on DNA charge transfer // White book on nanotechnology, 2008, P.197-198 ( in Russian )

. Biosensors based on DNA charge transfer // White book on nanotechnology, 2008, P.198 ( in Russian )

V.D. Lakhno. On the path length of an excess electron interacted with optical phonons in a molecular chain // Physics Letters A, 2008, Vol.372, №35, P.5725-5726

V.D. Lakhno, A.N. Korshunova. Instability of a uniform distribution over a molecular chain // II International Conference on Mathematical Biology and Bioinformatics (September 7-13, 2008, Pushchino, Russia) : Proceedings of the Conference. — Moscow: MAKS Press, 2008. 256 p. (in Russian). ISBN 978-5-317-02503-8, 2008, P.12-14 ( in Russian )

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V.D. Lakhno, N.I. Kashirina . Solvated hole mobility in a Poly G/Poly C nucleotide chain // II International Conference on Mathematical Biology and Bioinformatics (September 7-13, 2008, Pushchino, Russia) : Proceedings of the Conference. — Moscow: MAKS Press, 2008. 256 p. (in Russian). ISBN 978-5-317-02503-8, 2008, P.21 ( in Russian )

V.D. Lakhno, V.B. Sultanov. Charge distribution in DNA at finite temperature // II International Conference on Mathematical Biology and Bioinformatics (September 7-13, 2008, Pushchino, Russia) : Proceedings of the Conference. — Moscow: MAKS Press, 2008. 256 p. (in Russian). ISBN 978-5-317-02503-8, 2008, P.24-25 ( in Russian )

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V.D. Lakhno, N.S. Fialko. Mechanism of soliton stopping in a molecular chain without dispersion // Computer Research and Modeling, 2009, Vol.1, №1, P.93-99 ( in Russian )

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Lakhno V.D., Korshunova A.N.. Formation of stationary electronic states in finite homogeneous molecular chains // Mathematical biology and bioinformatics (arXiv:1305.5732 [cond-mat.other]), 2010, Vol.5, №1, P.1-29

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V.D. Lakhno, N.S. Fialko. Disrupting of polaron in homogeneous polynucleotide by temperature fluctuations // III International Conference on Mathematical Biology and Bioinformatics, ICMBB-3 (October 10-15, 2010, Pushchino, Russia):Proceedings of the Conference. — Moscow: MAKS Press, 2010. 288 p. (in Russian). ISBN 978-5-317-03411-5, 2010, P.20-21 ( in Russian )

V.D. Lakhno, E.V. Sobolev, N.S. Fialko. Parallelization of calculations in task of modeling of charge transfer in DNA at prescribed temperature // III International Conference on Mathematical Biology and Bioinformatics, ICMBB-3 (October 10-15, 2010, Pushchino, Russia):Proceedings of the Conference. — Moscow: MAKS Press, 2010. 288 p. (in Russian). ISBN 978-5-317-03411-5, 2010, P.22-23 ( in Russian )

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V.D. Lakhno, A.N. Korshunova. Electron motion in a Holstein molecular chain in an electric field // Eur. Phys. J. B, 2011, Vol.79, P.147-151

V.D. Lakhno. sf(d) Exchange mechanism of magnon generation by slow spinpolarons // International Journal of Modern Physics B, 2011, Vol.25, №5, P.619-627

V.D. Lakhno. Translation-invariant bipolarons and the problem of high-temperature superconductivity // Solid State Communications, 2012, Vol.152, №7, P.621-623

N.I. Kashirina, V.D. Lakhno, A.V. Tulub. The Virial Theorem and the Ground State Problem in Polaron Theory // Journal of Experimental and Theoretical Physics (arXiv:1310.0246 [cond-mat.other]), 2012, Vol.114, №5, P.867-869

V.D. Lakhno. On the cutoff parameter in the translation-invariant theory of the strong coupling polaron. (response to comments [8] on the paper V.D. Lakhno, SSC, 152, (2012), 621) // Solid State Communications, 2012, Vol.152, №19, P.1855-1856

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V.D. Lakhno. On the inconsistency of Porsch-Roeseler cutoff theory. (Reply to [arXiv:1208.1166v2]). // arXiv:1211.0382 [cond-mat.other], 2012

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V.D. Lakhno. Mathematical modeling of charge dynamics in molecular chains // The International Conference MATHEMATICAL MODELING AND COMPUTATIONAL PHYSICS (MMCP 2013, Dubna, Russia, July 8 – July 12, 2013) — Dubna:JINR, 2013; ISBN 978-5-9530-0362-9, 2013, P.121-122

A. Volokhova, E. Zemlyanaya, V. Lakhno, I. Amirkhanov, I. Puzynin, T. Puzynina. Numerical simulation of the hydrated electron formation // The International Conference MATHEMATICAL MODELING AND COMPUTATIONAL PHYSICS (MMCP 2013, Dubna, Russia, July 8 – July 12, 2013) — Dubna:JINR, 2013; ISBN 978-5-9530-0362-9, 2013, P.180

A.N. Korshunova, V.D.Lakhno. A new type of localized fast moving electronic excitations in molecular chains // Physica E (arXiv:1404.2093), 2014, Vol.60, P.206-209

V.D. Lakhno. Large-radius Holstein polaron and the problem of spontaneous symmetry breaking // Progress of Theoretical and Experimental Physics, 2014, P.073I01

A.V. Volokhova, E.V. Zemlyanaya, V.D. Lakhno, I.V. Amirkhanov, I.V. Puzynin, T.P. Puzynina. Numerical Simulation of the Hydrated Electron Formation // Bulletin of Peoples’ Friendship University of Russia (PFUR Bulletin, Vestnik RUDN). Mathematics, informatics, physics, 2014, №2, P.244-247 ( in Russian )

A.V. Volokhova, E.V. Zemlyanaya, V.D. Lakhno, I.V. Amirkhanov, I.V. Puzynin, T.P. Puzynina. Numerical investigation of photoexcited polaron states in water // Computer Research and Modeling, 2014, Vol.6, №2, P.253-261 ( in Russian )

V.D. Lakhno, A.V. Volokhova, E.V. Zemlyanaya, I.V. Amirkhanov, I.V. Puzynin, T.P. Puzynina. Polaron Model of the Hydrated Electron States Formation // Preprint of the Joint Institute for Nuclear Research. Dubna, 2014, 15 рр, 2014, Vol.P11-2014-19 ( in Russian )

M.G. Velarde, A.P. Chetverikov, W.Ebeling, V. Lakhno. Wave Motions Along Lattices with Nonlinear On-Site and Inter-Site Potentials. Cooperation and/or Competition Leading to Lattice Solitons and/or Discrete Breathers. // IUTAM Symposium on Complexity of Nonlinear Waves, 8-12 September, Tallinn, 2014. Book of Abstracts, 2014, P.133-134

V.D. Lakhno. Pekar’s ansatz and the strong coupling problem in polaron theory // Phys. Usp. (draft version arXiv:1505.01699 [cond-mat.other]), 2015, Vol.58, P.295

V.D. Lakhno, A.V. Volokhova, E.V. Zemlyanaya, I.V. Amirkhanov, I.V. Puzynin, T.P. Puzynina. Polaron Model of the Formation of Hydrated Electron States // Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques, 2015, Vol.9, P.75-80

V.D. Lakhno. Superconducting properties of 3D low-density TI-bipolaron gas. // arXiv:1507.08510 [cond-mat.supr-con], 2015

Manuel G. Velarde, Alexander P. Chetverikov, Werner Ebeling, Sergey V. Dmitriev, and Victor D. Lakhno. Wave motions along lattices with nonlinear on-site and inter-site potentials. Cooperation and/or competition leading to lattice solitons and/or discrete breathers // Proceedings of the Estonian Academy of Sciences, 2015, Vol.64, P.396-404

V.D. Lakhno. TI-bipolaron theory of superconductivity // arXiv:1510.04527 [cond-mat.supr-con], 2015

V.D. Lakhno. Phonon interaction of electron in the translation-invariant strong-coupling theory // arXiv:1510.05812 [cond-mat.other]; Modern Physics Letters B, accepted, 2015

V.D. Lakhno. On the term of the 4-th order with respect to the field operators in the translation-invariant polaron theory // arXiv:1510.05865 [cond-mat.other], 2015

Kashirina N.I., Lakhno V.D.. Bipolaron in anisotropic crystals (arbitrary coupling) // Math. Biol. Bioinf., 2015, Vol.10, №1, P.283-293 ( in Russian )

E.V. Zemlyanaya, A.V. Volokhova, V.D. Lakhno, I.V. Amirkhanov, I.V. Puzynin, T.P. Puzynina, V.S. Rikhvitskiy, P. Kh. Atanasova. Numerical simulation of photoexcited polaron states in water // AIP Conference Proceedings, 2015, Vol.1684, P.100006

V.D. Lakhno. Phonon interaction of electrons in the translation-invariant strong-coupling theory // Mod. Phys. Lett. B, 2016, Vol.30, №04, P.1650031

Victor Lakhno . A translation invariant bipolaron in the Holstein model and superconductivity // SpringerPlus, 2016, Vol.5, P.1277

Manuel G. Velarde, Alexander P. Chetverikov, Werner Ebeling, Sergey V. Dmitriev, and Victor D. Lakhno. From solitons to discrete breathers // Eur. Phys. J. B, 2016, Vol.89, P.233

V.D. Lakhno. Cooper pairs and bipolarons // Mod. Phys. Lett. B, 2016, Vol.30, №31, P.1650365

Kashirina N.I., Lakhno V.D.. The single-center and two-center model of Holstein bipolaron // VI International conference «Mathematical biology and bioinformatics», Pushchino, Russia, October 16-21, 2016. Book of Abstracts., 2016, P.10-11 ( in Russian )

Fialko N.S., Pyatkov M.I., Lakhno V.D.. On the calculations of delocalization parameter in the Holstein model with solvation effect // VI International conference «Mathematical biology and bioinformatics», Pushchino, Russia, October 16-21, 2016. Book of Abstracts., 2016, P.20-21 ( in Russian )

Kashirina N.I., Lakhno V.D.. Application of Gaussian basis with correlation factors for calculating of the energy spectrum of localized and auto-localized states in polar environments // VI International conference «Mathematical biology and bioinformatics», Pushchino, Russia, October 16-21, 2016. Book of Abstracts., 2016, P.92-93 ( in Russian )

Kashirina N.I., Lakhno V.D.. Exponentially Correlated Gaussians for Simulating Of Localized and Autolocalized States in Polar Media // Math. Biol. Bioinf., 2017, Vol.12, №2, P.273 ( in Russian )

V.D. Lakhno. Peculiarities in the concentration dependence of the superconducting transition temperature in the bipolaron theory of Cooper pairs // Modern Physics Letters B, 2017, Vol.31, №11, P.1750125