Theoretical study of collective modes in DNA at ambient temperature

Journal of Chemical Physics

Volumn 112, Issue 22, 2000, Pages 10017-10033

  Cocco, Simona ^a,b,c   Monasson, Rémi ^c  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b Laboratoire de Physique UMR CNRS ENSL   (France)

^c LABORATOIRE DE PHYSIQUE STATISTIQUE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

COMPRESSIVE STRESS; DAMPING; GIBBS FREE ENERGY; HYDROGEN BONDS; MATHEMATICAL MODELS; MATRIX ALGEBRA; MOLECULAR VIBRATIONS; NEUTRON SCATTERING; RAMAN SPECTROSCOPY; THERMAL EFFECTS;

GIBBS AVERAGE SOLVENT; REPLICATED TRANSFER MATRIX;

DNA;

EID: 0033684417     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.481646     Document Type: Article

References (57)

1. H. Grimm, H. Stiller, C. F. Majkrazak, A. Rupprecht, and U. Dahlborg, Phys. Rev. Lett. 59, 1780 (1987).
2. H. Grimm and A. Rupprecht, Physica B 174, 291 (1991).
3. H. Grimm and A. Rupprecht, Physica B 234-236, 183 (1997).
4. J. F. Marko and B. M. Pettitt, Fluctuations of DNA Double Helix Structure, preprint.
5. D. P. Millar, R. J. Robbins, and A. H. Zewail, J. Chem. Phys. 76, 2080 (1982).
6. P. Painter, L. Mosher, and C. Rhoads, Biopolymers 20, 243 (1981).
7. H. Urabe and Y. Tominaga, J. Phys. Soc. Jpn. 50, 3543 (1981).
8. H. Urabe, Y. Tominaga, and K. Kubota, J. Chem. Phys. 78, 5937 (1983).
9. H. Urabe, H. Hayashi, Y. Tominaga, Y. Nishimura, K. Kubota, and M. Tsuboi, J. Chem. Phys. 82, 531 (1985).
10. S. M. Lindsay, S. A. Lee. J. W. Powell, T. Weidlich, C. Demarco, G. D. Lewen, N. J. Tao, and A. Rupprecht, Biopolymers 27, 1015 (1988).
11. H. Urabe, Y. Sugawara, M. Tsukakoshi, and T. Kasuya, J. Chem. Phys. 95, 5519 (1991).
12. E. W. Prohofsky, Statistical Mechanics and Stability of Macromolecules (Cambridge University Press, Cambridge, 1995).
13. J.M. Eyster and E. W. Prohofsky, Biopolymers 13, 2505 (1974); 13, 2527 (1974).
14. J.M. Eyster and E. W. Prohofsky, Biopolymers 13, 2505 (1974); 13, 2527 (1974).
15. Y. Gao, K. V. Devi-Prasad, and E. W. Prohofsky, J. Chem. Phys. 80, 6291 (1984).
16. Y. Z. Chen and E. W. Prohofsky, Phys. Rev. E 49, 873 (1993).
17. Y. Z. Chen and E. W. Prohofsky, Phys. Rev. E 49, 3444 (1993).
18. Y. Z. Chen, Y. Zhang, and E. W. Prohofsky, Phys. Rev. E 55, 5843 (1997).
19. V. Lisy, P. Miskovsky, and P. Schreiber, J. Biomol. Struct. Dyn. 13, 707 (1996).
20. C. Kittel, Introduction to Solid State Physics (Wiley, New York, 1986).
21. V. V. Prabhu, W. K. Schroll, L. L. Van Zandt, and E. W. Prohofsky, Phys. Rev. Lett. 60, 1587 (1988); H. Grimm and H. Stiller, ibid. 60, 1588 (1988).
22. V. V. Prabhu, W. K. Schroll, L. L. Van Zandt, and E. W. Prohofsky, Phys. Rev. Lett. 60, 1587 (1988); H. Grimm and H. Stiller, ibid. 60, 1588 (1988).
23. R. Shuker and R. Gammon, Phys. Rev. Lett. 25, 222 (1970).
24. A. J. Martin and W. Brenig, Phys. Status Solidi B 64, 163 (1974).
25. B. Souillard, "Waves and Electrons in Random Media," Chance and Matter, Les Houches session XLVI (Elsevier, New York, 1986).
26. S. R. Elliott, Physics of Amorphous Materials (Longman Scientific and Technical, London, 1990).
27. T. Keyes, J. Phys. Chem. A 101, 2921 (1997).
28. Y. Wan and R. Stratt, J. Chem. Phys. 100, 5123 (1994).
29. G. Biroli and R. Monasson, J. Phys. A 32, L255 (1999).
30. A. Cavagna, I. Giardina, and G. Parisi, Phys. Rev. Lett. 83, 108 (1999).
31. S. Cocco and R. Monasson, Phys. Rev. Lett. 83, 5178 (1999).
32. S. B. Smith, L. Finzi, and C. Bustamante, Science 258, 1122 (1992).
33. R. H. Austin, J. P. Brody, E. C. Cox, T. Duke, and W. Volkmuth, Phys. Today 32 (1997) and references therein.
34. T. R. Strick, J.-F. Allemand, D. Bensimon, A. Bensimon, and V. Croquette, Science 271, 1835 (1996).
35. T. R. Strick, J.-F. Allemand, D. Bensimon, R. Lavery, and V. Croquette. Physica A 263, 392 (1999).
36. R. Monasson, Eur. Phys. J. B 12, 555 (1999).
37. D. J. Thouless, Phys. Rep., Phys. Lett. 13, 93 (1974); Mesoscopic Quantum Physics, Les Houches session LXI (Elsevier, New York, 1995).
38. D. J. Thouless, Phys. Rep., Phys. Lett. 13, 93 (1974); Mesoscopic Quantum Physics, Les Houches session LXI (Elsevier, New York, 1995).
39. M. Barbi, S. Cocco, and M. Peyrard, Phys. Lett. A 253, 358 (1999).
40. Vibrations of the sugar puckering modes that could be in the frequency range of interest will not be considered here.
41. M. Peyrard and A. R. Bishop, Phys. Rev. Lett. 62, 2755 (1989).
42. T. Dauxois and M. Peyrard, Phys. Rev. E 51, 4027 (1995).
43. J. A. McCammon and S. C. Harvery, Dynamic of Proteins and Nucleic Acids (Cambridge University Press, Cambridge, 1987).
44. Y. Zang, W. Zheng, J. Liu, and Y. Z. Chen, Phys. Rev. E 56, 7100 (1997).
45. W. Saenger, Principles of Nucleic Acid Structure (Springer-Verlag, New York, 1984); C. R. Calladine and H. R. Drew, Understanding DNA (Academic, San Diego, 1997).
46. W. Saenger, Principles of Nucleic Acid Structure (Springer-Verlag, New York, 1984); C. R. Calladine and H. R. Drew, Understanding DNA (Academic, San Diego, 1997).
47. G. Parisi, Statistical Field Theory (Addison-Wesley, Redwood City, CA, 1988).
48. H. Urabe, Y. Sugawara, M. Ataka, and A. Rupprecht, Biophys. J. 74, 1533 (1998).
49. S. N. Volkov and A. M. Kosevich, J. Biomol. Struct. Dyn. 8, 1069 (1991).
50. Y. Tominaga, K. Kubota, H. Urabe, Y. Nishimura, and M. Tsuboi, J. Chem. Phys. 83, 5972 (1985).
51. V. K. Malinovsky, V. N. Novikov, P. P. Parshin, A. P. Sokolov, and M. G. Zemlyanov, Europhys. Lett. 11, 43 (1990).
52. A. P. Sokolov, A. Kisliuk, D. Quitmann, and E. Duval, Phys. Rev. B 48, 7692 (1993).
53. J. M. Luck, Systèmes Désordonnés Unidimensionels (Aléa Saclay, 1992).
54. S. Cocco and R. Monasson (unpublished).
55. A. Leburn and R. Lavery, J. Biomol. Struct. Dyn. 16, 593 (1998).
56. J. F. Marko and E. Siggia, Science 265, 506 (1994).
57. C. Bouchiat and M. Mézard, Phys. Rev. Lett. 80, 1556 (1997).