Mixed algorithm for modeling of charge transfer in DNA on long time intervals
Charge transfer in DNA is simulated by a discrete Holstein model «quantum particle + classical site chain + interaction». Thermostat temperature is taken into account as stochastic force, which acts on classical sites (Langevin equation). Thus dynamics of charge migration along the chain is describe...
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| Format: | Article |
| Language: | Russian |
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Institute of Computer Science
2010-03-01
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| Series: | Компьютерные исследования и моделирование |
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| Online Access: | http://crm.ics.org.ru/uploads/crm/crm2010-1/crm10108.pdf |
| _version_ | 1828522323796295680 |
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| author | Nadejda S. Fialko |
| author_facet | Nadejda S. Fialko |
| author_sort | Nadejda S. Fialko |
| collection | DOAJ |
| description | Charge transfer in DNA is simulated by a discrete Holstein model «quantum particle + classical site chain + interaction». Thermostat temperature is taken into account as stochastic force, which acts on classical sites (Langevin equation). Thus dynamics of charge migration along the chain is described by ODE system with stochastic right-hand side. To integrate the system numerically, algorithms of order 1 or 2 are usually applied. We developed «mixed» algorithm having 4th order of accuracy for fast «quantum» variables (note that in quantum subsystem the condition «sum of probabilities of charge being on site is time-constant» must be held), and 2nd order for slow classical variables, which are affecting by stochastic force. The algorithm allows us to calculate trajectories on longer time intervals as compared to standard algorithms. Model calculations of polaron disruption in homogeneous chain caused by temperature fluctuations are given as an example. |
| first_indexed | 2024-12-11T20:05:39Z |
| format | Article |
| id | doaj.art-432d6619da2f4fdaa51099637e8219cd |
| institution | Directory Open Access Journal |
| issn | 2076-7633 2077-6853 |
| language | Russian |
| last_indexed | 2024-12-11T20:05:39Z |
| publishDate | 2010-03-01 |
| publisher | Institute of Computer Science |
| record_format | Article |
| series | Компьютерные исследования и моделирование |
| spelling | doaj.art-432d6619da2f4fdaa51099637e8219cd2022-12-22T00:52:24ZrusInstitute of Computer ScienceКомпьютерные исследования и моделирование2076-76332077-68532010-03-0121637210.20537/2076-7633-2010-2-1-63-721651Mixed algorithm for modeling of charge transfer in DNA on long time intervalsNadejda S. FialkoCharge transfer in DNA is simulated by a discrete Holstein model «quantum particle + classical site chain + interaction». Thermostat temperature is taken into account as stochastic force, which acts on classical sites (Langevin equation). Thus dynamics of charge migration along the chain is described by ODE system with stochastic right-hand side. To integrate the system numerically, algorithms of order 1 or 2 are usually applied. We developed «mixed» algorithm having 4th order of accuracy for fast «quantum» variables (note that in quantum subsystem the condition «sum of probabilities of charge being on site is time-constant» must be held), and 2nd order for slow classical variables, which are affecting by stochastic force. The algorithm allows us to calculate trajectories on longer time intervals as compared to standard algorithms. Model calculations of polaron disruption in homogeneous chain caused by temperature fluctuations are given as an example.http://crm.ics.org.ru/uploads/crm/crm2010-1/crm10108.pdfDNAHolstein modelLangevin equationintegration algorithm for ODE with stochastic right-hand side |
| spellingShingle | Nadejda S. Fialko Mixed algorithm for modeling of charge transfer in DNA on long time intervals Компьютерные исследования и моделирование DNA Holstein model Langevin equation integration algorithm for ODE with stochastic right-hand side |
| title | Mixed algorithm for modeling of charge transfer in DNA on long time intervals |
| title_full | Mixed algorithm for modeling of charge transfer in DNA on long time intervals |
| title_fullStr | Mixed algorithm for modeling of charge transfer in DNA on long time intervals |
| title_full_unstemmed | Mixed algorithm for modeling of charge transfer in DNA on long time intervals |
| title_short | Mixed algorithm for modeling of charge transfer in DNA on long time intervals |
| title_sort | mixed algorithm for modeling of charge transfer in dna on long time intervals |
| topic | DNA Holstein model Langevin equation integration algorithm for ODE with stochastic right-hand side |
| url | http://crm.ics.org.ru/uploads/crm/crm2010-1/crm10108.pdf |
| work_keys_str_mv | AT nadejdasfialko mixedalgorithmformodelingofchargetransferindnaonlongtimeintervals |