Discrete and Continuous Models and Applied Computational ScienceDiscrete and Continuous Models and Applied Computational ScienceDiscrete and Continuous Models and Applied Computational Science2658-46702658-7149Peoples' Friendship University of Russia named after Patrice Lumumba (RUDN University)2270110.22363/2658-4670-2019-27-3-217-230Modeling and SimulationМатематическое моделированиеResearch ArticleCharge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein modelО диффузии заряда в однородных молекулярных цепочках на основе анализа обобщенных частотных спектров в рамках модели ХолстейнаTikhonovDmitry AТихоновД АCandidate of Physical and Mathematical Sciences, Senior researcher, Institute of Mathematical Problems of Biology Branch of Keldysh Institute of Applied Mathematics Russian Academy of Sciencesdmitry.tikhonov@gmail.comSobolevEgor VСоболевЕ ВCandidate of Physical and Mathematical Sciences, Postdoctoral fellow, European Molecular Biology Laboratory, Hamburg Unitegor@embl-hamburg.deLakhnoVictor DЛахноВ ДDoctor of Physical and Mathematical Sciences, Scientific Director, Institute of Mathematical Problems of Biology Branch of Keldysh Institute of Applied Mathematics Russian Academy of Scienceslak@impb.ruInstitute of Mathematical Problems of Biology Branch of Keldysh Institute of Applied Mathematics of RASИнститут математических проблем биологии (ИМПБ РАН)Institute of Theoretical and Experimental Biophysics of RASИнститут теоретической и экспериментальной биофизики РАНEuropean Molecular Biology Laboratory, Hamburg UnitЕвропейская лаборатория молекулярной биологии, отделение в Гамбурге15122019273VOL 27, NO3 (2019)ТОМ 27, №3 (2019)21723022012020Copyright ©; 2019, Tikhonov D.A., Sobolev E.V., Lakhno V.D.Copyright ©; 2019, Тихонов Д.А., Соболев Е.В., Лахно В.Д.2019Tikhonov D.A., Sobolev E.V., Lakhno V.D.Тихонов Д.А., Соболев Е.В., Лахно В.Д.http://creativecommons.org/licenses/by/4.0https://journals.rudn.ru/miph/article/view/22701We analyzed numerically computed velocity autocorrelation functions and generalized frequency spectra of charge distribution in homogeneous DNA sequences at finite temperature. The autocorrelation function and generalized frequency spectrum (frequency-dependent diffusion coefficient) are phenomenologically introduced based on the functional of mean-square displacement of the charge in DNA. The charge transfer in DNA was modeled in the framework of the semi-classical Holstein model. In this model, DNA is represented by a chain of oscillators placed into thermostat at a given temperature that is provided by the additional Langevin term. Correspondence to the real DNA is provided by choice of the force parameters, which are calculated with quantum-chemical methods. We computed the diffusion coefficient for all homogenous DNA chains with respect to the temperature and found a special scaling of independent variables that the temperature dependence of the diffusion coefficient for different homogenous DNA is almost similar. Our calculations suggest that for all the sequences, only one parameter of the system is mainly responsible for the charge kinetics. The character of individual motions contributing to the charge mobility and temperature-dependent regimes of charge distribution is determined.В статье проведён анализ автокорреляционных функций скорости и обобщённых частотных спектров распространения заряда в однородных последовательностях ДНК при конечной температуре. Функции рассчитаны численно в рамках квазиклассической модели Холстейна. Показано, что в системе только один параметр главным образом определяет кинетику заряда для всех последовательностей. Анализ позволил определить характер отдельных движений, вносящих вклад в подвижность заряда, и выделить различные режимы распространения заряда в зависимости от температуры.charge transfervelocity autocorrelation functiongeneralized frequency spectrumDNAHolstein modelперенос зарядаавтокорреляционная функция скоростиобобщённый частотный спектрДНКмодель Холстейна1.P. Maniadis, G. Kalosakas, K. Ø. Rasmussen, and A. R. 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