ISSN 0869-6632 (Print)
ISSN 2542-1905 (Online)

For citation:

Yakushevich L. V. Modeling of the nonlinear dynamics of DNA. Izvestiya VUZ. Applied Nonlinear Dynamics, 1996, vol. 4, iss. 3, pp. 107-111.

This is an open access article distributed under the terms of Creative Commons Attribution 4.0 International License (CC-BY 4.0).
Full text PDF(Ru):
PDF icon 1996no3p107.pdf
(downloads: 0)
Language: 
Russian
Heading: 
Journal in the journal
Article type: 
Article
UDC: 
531.391;577.323

Modeling of the nonlinear dynamics of DNA

Autors: 
Yakushevich Ludmila Vladimirovna, Institute of Cell Biophysics RAS\
Abstract: 

The DNA molecule is considered as a nonlmear dynamic system. We discuss here one of the methods of theoretical studying the molecule, which is based on the math- ematical modeling of the DNA nonlinear properties. The main pomts of the method and two examples illustrating its application are presented.

Key words: 
-
Reference: 
  1. Watson JD, Crick FNC. Molecular structure of nucleic acids. A structure for deoxyribose nucleic acid. Nature. 1953;171(4356):737-738. DOI: 10.1038/171737a0.
  2. Saenger W. Principles of Nucleic Acid Structure. N.Y.: Springer; 1987. 556 p. DOI: 10.1007/978-1-4612-5190-3.
  3. McCammon JA, Harvey SС. Dynamics of Proteins and Nucleic Acids. Cambridge: Cambridge University Press; 1988. 234 p.
  4. Yakushevich LV. DNA dynamics. Mol. Biol. 1989;23(3):652-662.
  5. Scott A.C. A nonlinear Klein - Gordon equation. Am. J. Phys. 1969;37(1):52-61. DOI: 10.1119/1.1975404.
  6. Englander SW, Kallenbach NR, Heeger AJ, Krumhansl JA, Litwin S. Nature of the open state in long polynucleotide double helices: possibility of soliton excitations. Proc. Natl. Acad. Sci. USA. 1980;77(12):7222-7226. DOI: 10.1073/pnas.77.12.7222.
  7. Yakushevich LV. Nonlinear dynamics of biopolymers: theoretical models, experimental data. Quart. Rev. Biophys. 1993;26(2):201-223. DOI: 10.1017/S0033583500004078.
  8. Yakushevich LV. Nonlinear DNA dynamics: hierarchy of the models. Physica D. 1994;79(1):77-86. DOI: 10.1016/0167-2789(94)90038-8.
  9. Scott AC, Chu FY, McLaughlin DW. The soliton: а new concept in applied science. Рrос. IEEE. 1973;61(10):1443-1483. DOI: 10.1109/PROC.1973.9296.
  10. Yomosa S. Solitary excitations in deoxyribonucleic acid (DNA) double helices. Phys. Rev. A. 1984;30(1):474-480. DOI: 10.1103/PhysRevA.30.474.
  11. Takeno S, Homma S. Topological solitons and modulated structure of bases in DNA double helices. Prog. Theor. Phys. 1983;70(1):308-311. DOI: 10.1143/PTP.70.308.
  12. Homma S, Takeno S. A coupled base-rotator model for structure and dynarnics of DNA. Prog. Theor. Phys. 1984;72(4):679-693. DOI: 10.1143/PTP.72.679.
  13. Fedyanin VK, Gochev L, Lisy V. Nonlinear dynamics of bases in а continual model of DNA double helices. Stud. biophys. 1986;116:59-64.
  14. Fedyanin VK, Lisy V. Soliton conformational excitations in DNA. Stud. biophys. 1986;116:65-71.
  15. Zhang Ch-T. Soliton excitations in deoxyribonucleic acid (DNA) double helices. Phys. Rev. А. 1987;35(2):886-891. DOI: 10.1103/physreva.35.886.
  16. Yakushevich LV. Investigation of a system of nonlinear equations simulating DNA torsional dynamics. Stud. biophys. 1991;140:163-170.
  17. Hai W. Kink couples in deoxyribonucleic acid (DNA) double helices. Phys. Lett. A. 1994;186(4):309-316. DOI: 10.1016/0375-9601(94)91176-2.
  18. Yakushevich LV. Bulletin of the Russian Academyof Sciences: Physics. (In the press).
  19. Yakushevich LV. Hierarchy of dynamic DNA models. Rus. J. Phys. Chem. A. 1995;69(1):180-185.
  20. Salerno M. Discrete model for DNA-promoter dynamics. Phys. Rev. А. 1991;44(8):5292-5297. DOI: 10.1103/physreva.44.5292.
Received: 
09.10.1995
Accepted: 
30.05.1996
Published: 
15.12.1996
  • 76 reads