Biophysical implications of the Peyrard-Bishop-Dauxois model of DNA dynamics

Journal of Computational and Theoretical Nanoscience

Volumn 1, Issue 2, 2004, Pages 169-179

  Zdravkovic S ^a   Sataric M ^b   Tuszynski J ^c  

^a UNIVERSITY OF PRI TINA   (Serbia)

^b UNIVERSITY OF NOVI SAD   (Serbia)

^c UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Breather modes; DNA; PBD model; Regulatory proteins

Indexed keywords

DNA; MATHEMATICAL MODELS; MOLECULAR STRUCTURE; PROTEINS; SOLITONS;

BREATHER MODES; PEYRARD-BISHOP-DAUXOIS MODEL; REGULATORY PROTEINS;

MOLECULAR DYNAMICS;

EID: 8544225062     PISSN: 15461955     EISSN: None     Source Type: Journal    
DOI: 10.1166/jctn.2004.013     Document Type: Article

References (37)

1. J. Darnell, H. Lodish, and D. Baltimore, [i Molecular Cell Biology i], Scientific American Books, New York ([b 1990 b]), pp. 68-72.
2. J. F. Marko and E. D. Siggia, [i Phys. Rev. E i] 52, 2912 ([b 1995 b])
3. P. R. Selvin, D. N. Cook, N. G. Pon, N. R. Bauer, M. P. Klein, and J. E. Hearst, [i Science i] 255, 82 ([b 1992 b]).
4. J. F. Marko, [i Phys. Rev. E i] 57, 2134 ([b 1998 b]).
5. S. W. Englander, N. R. Kalenbach, A. J. Heeger, J. A. Krumhansl, and S. Litwin, [i Proc. Natl. Acad. Sci. USA i] 77, 7222 ([b 1980 b]).
6. S. Homa and S. Takeno, [i Prog. Theor. Phys. i] 72, 679 ([b 1984 b]).
7. V. Muto, A. C. Scott, and P. L. Christiansen, [i Phys. Lett. A i] 136, 33 ([b 1989 b]).
8. M. Peyrard and A. R. Bishop, [i Phys. Rev. Lett. i] 62, 2755 ([b 1989 b] ).
9. M. Salerno, [i Phys. Rev. A i] 44, 5292 ([b 1991 b]).
10. S. N. Volkov, [i J. Theor. Biol. i] 143, 485 ([b 1990 b]).
11. S. Yamosa, [i Phys. Rev. A i] 30, 474 ([b 1984 b]).
12. G. F. Zhou and C. T. Zhang, [i Phys. Scripta i] 43, 347 ([b 1991 b]).
13. L. V. Yakushevich, [i Nonlinear Physics of DNA i], Wiley series in Nonlinear Science, John Wiley, Chichester ([b 1980 b]).
14. T. Dauxois, [i Phys. Lett. A i] 159, 390 ([b 1991 b]).
15. T. Dauxois and M. Peyrard, [i Phys. Rev. Lett. i] 70, 3935 ([b 1993 b]).
16. K. Forinash, M. Peyrard, and B. Malomed, [i Phys. Rev. E i] 49, 3400 ([b 1994 b]).
17. G. Gaeta, [i Phys. Lett. A i] 172, 365 ([b 1993 b]).
18. S. Zdravković and M. V. Satarić, [i Phys. Scripta i] 64, 612 ([b 2001 b]).
19. T. Dauxois, M. Peyrard, and A. R. Bishop, [i Phys. Rev. E i] 47, 684 ([b 1993 b]).
20. S. Zdravković, M. V. Satarić, and J. A. Tuszyński, Peyrard-Bishop-Dauxois Model of DNA Dynamics: Parameter Selection and Impact of Viscosity ([b 2003 b]), submitted to [i Int. J. Mod. Phys. B. i]
21. A. C. Scott, [i Phys. Rev. A i] 26, 578 ([b 1982 b]).
22. M. Peyrard, [i J. Biol. Phys. i] 27, 217 ([b 2001 b]).
23. G. Carreri, M. Geraci, A. Giansanti, and J. A. Ruply, [i Proc. Natl. Acad. Sci. USA i] 82, 5342 ([b 1985 b]).
24. N. N. Bogoliubov and Y. A. Mitropolskii, [i The Asymptotic Method in the Theory of Non- Linear Vibrations i], Nauka, Moscow ([b 1974 b]), (in Russian)
25. D. M. Crothers and M. Fried, in [i Cold Spring Harbour Symposia on Quantitative Biology i], 19, 47 ([b 1983 b]).
26. M. Ptashene, [i Nature i] 332, 697 ([b 1986 b]).
27. R. R. Sinden, [i DNA Structure and Function i], Chap. 8, Academic Press ([b 1994 b]).
28. D. N. Zubarev, [i Nonequilibrium Statistical Thermodynamics i], Consultants Bureau ([b 1974 b]).
29. M. V. Satarić and J. A. Tuszyński, [i Phys. Rev. E i] 65, 1 ([b 2002 b]).
30. M. V. Satarić, [i Physica D i] 126, 60 ([b 1999 b]).
31. R. Hölcel and I. Lamprecht, [i Neural Net. World i] 4, 327 ([b 1994 b]).
32. B. Trpišová and J. A. Tuszyński, [i Phys. Rev. E i] 55, 3288 ([b 1997 b]).
33. J. J. Ladik, [i Journ. of Molec. Structure i] 277, 109 ([b 1992 b]).
34. T. Dauxois and M. Peyrard, [i Phys. Rev. E i] 51, 4027 ([b 1995 b]).
35. K. Forinash, T. Cretegny, and M. Peyrard, [i Phys. Rev. E i] 55, 4740 ([i 1997 i]).
36. M. Peyrard, [i Physica D i] 119, 184 ([b 1998 b]).
37. B. Essevaz-Roulet, U. Bockelmann, and F. Heslot, [i Proc. Natl. Acad. Sci. USA i] 94, 11935 ([b 1997 b]).