Charge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein model
We 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 phenomenolo...
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Peoples’ Friendship University of Russia (RUDN University)
2019-12-01
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doaj-f19f8a16e4c540189c078b0867979baa2020-11-25T03:43:54ZengPeoples’ Friendship University of Russia (RUDN University)Discrete and Continuous Models and Applied Computational Science2658-46702658-71492019-12-0127321723010.22363/2658-4670-2019-27-3-217-23018396Charge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein modelDmitry A Tikhonov0Egor V Sobolev1Victor D Lakhno2Institute of Mathematical Problems of Biology Branch of Keldysh Institute of Applied Mathematics of RAS; Institute of Theoretical and Experimental Biophysics of RASInstitute of Mathematical Problems of Biology Branch of Keldysh Institute of Applied Mathematics of RAS; European Molecular Biology Laboratory, Hamburg UnitInstitute of Mathematical Problems of Biology Branch of Keldysh Institute of Applied Mathematics of RASWe 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.http://journals.rudn.ru/miph/article/viewFile/22701/17708charge transfervelocity autocorrelation functiongeneralized frequency spectrumdnaholstein model |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Dmitry A Tikhonov Egor V Sobolev Victor D Lakhno |
spellingShingle |
Dmitry A Tikhonov Egor V Sobolev Victor D Lakhno Charge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein model Discrete and Continuous Models and Applied Computational Science charge transfer velocity autocorrelation function generalized frequency spectrum dna holstein model |
author_facet |
Dmitry A Tikhonov Egor V Sobolev Victor D Lakhno |
author_sort |
Dmitry A Tikhonov |
title |
Charge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein model |
title_short |
Charge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein model |
title_full |
Charge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein model |
title_fullStr |
Charge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein model |
title_full_unstemmed |
Charge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein model |
title_sort |
charge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the holstein model |
publisher |
Peoples’ Friendship University of Russia (RUDN University) |
series |
Discrete and Continuous Models and Applied Computational Science |
issn |
2658-4670 2658-7149 |
publishDate |
2019-12-01 |
description |
We 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. |
topic |
charge transfer velocity autocorrelation function generalized frequency spectrum dna holstein model |
url |
http://journals.rudn.ru/miph/article/viewFile/22701/17708 |
work_keys_str_mv |
AT dmitryatikhonov chargediffusioninhomogeneousmolecularchainsbasedontheanalysisofgeneralizedfrequencyspectraintheframeworkoftheholsteinmodel AT egorvsobolev chargediffusioninhomogeneousmolecularchainsbasedontheanalysisofgeneralizedfrequencyspectraintheframeworkoftheholsteinmodel AT victordlakhno chargediffusioninhomogeneousmolecularchainsbasedontheanalysisofgeneralizedfrequencyspectraintheframeworkoftheholsteinmodel |
_version_ |
1724517631174639616 |