Discrete 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)2270110.22363/2658-4670-2019-27-3-217-230Research ArticleCharge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein modelTikhonovDmitry ACandidate 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 VCandidate of Physical and Mathematical Sciences, Postdoctoral fellow, European Molecular Biology Laboratory, Hamburg Unitegor@embl-hamburg.deLakhnoVictor DDoctor 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 RASInstitute of Theoretical and Experimental Biophysics of RASEuropean Molecular Biology Laboratory, Hamburg Unit1512201927321723022012020Copyright © 2019, Tikhonov D.A., Sobolev E.V., Lakhno V.D.2019We 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. 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