Theory of DNA melting based on the Peyrard-Bishop model

Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics

Volumn 56, Issue 6, 1997, Pages 7100-7115

  Zhang, Yong li ^a   Zheng, Wei Mou ^a   Liu, Ji Xing ^a   Chen, Y Z ^a,b  

^a INSTITUTE OF THEORETICAL PHYSICS   (China)

^b PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0001040631     PISSN: 1063651X     EISSN: None     Source Type: Journal    
DOI: 10.1103/PhysRevE.56.7100     Document Type: Article

References (36)

1. R. M. Wartell and A. S. Benight, Phys. Rep. 126, 67 (1985).PRPLCM
2. Gen-fa Zhou and Chun-Ting Zhang, Phys. Scr. 43, 347 (1991).PHSTBO
3. Y. Z. Chen and E. W. Prohofsky, Phys. Rev. E 49, 3444 (1994).PLEEE8
4. Y. Z. Chen and E. W. Prohofsky, Phys. Rev. E 51, 5048 (1995).PLEEE8
5. G. S. Manning, Q. Rev. Biophys. II, 179 (1978).QURBAW
6. G. Ramachandran and T. Schlick, Phys. Rev. E 51, 6188 (1995).PLEEE8
7. J. D. Watson, N. H. Hopkins, J. W. Roberts, J. A. Steitz, and A. M. Weiner, Molecular Biology of the Gene (The Benjamin/Cummings Publishing Company, Inc., Reading, MA, 1988).
8. S. M. Lindsay, J. Powell, E. W. Prohofsky, and K. V. Devi-Prasad, in Structure & Motion: Membranes, Nucleic Acids & Proteins, edited by E. Clementi, G. Corongiu, M. H. Sarma, and R. H. Sarma (Adenine Press, New York, 1985).
9. H. Grimm, H. Stiller, C. F. Majkrzak, A. Rupprecht, and U. Dahlborg, Phys. Rev. Lett. 59, 1780 (1987).PRLTAO
10. M. Peyrard and A. R. Bishop, Phys. Rev. Lett. 62, 2755 (1989).PRLTAO
11. P. G. Wolynes, in Spin Glasses and Biology, edited by D. L. Stein (Academic Press, London, 1993).
12. D. Poland and H. A. Scheraga, Theory of Helix-coil Transitions in Biopolymers (Academic Press, New York, 1970).
13. E. W. Prohofsky, Statistical Mechanics and Stability of Macromolecules (Cambridge University Press, Cambridge, 1995).
14. T. Dauxois, M. Peyrard, and A. R. Bishop, Phys. Rev. E 47, 684 (1993).PLEEE8
15. T. Dauxois and M. Peyrard, Phys. Rev. Lett. 70, 3935 (1993).PRLTAO
16. T. Dauxois and M. Peyrard, Phys. Rev. E 51, 4027 (1995).PLEEE8
17. T. Dauxois, M. Peyrard, and A. R. Bishop, Phys. Rev. E 47, R44 (1993).PLEEE8
18. A. C. Pipkin, A Course on Integral Equations (Springer, Berlin, 1991).
19. M. Peyrard and T. Dauxois, in Proceedings of the 6th Joint EPS-APS International Conference on Physics Computing PC ’94, edited by R. Gruber and M. Tomassini (European Physical Society, Petit-Lancy, 1994).
20. J. R. Morris and R. J. Gooding, Phys. Rev. B 43, 6057 (1991).PRBMDO
21. J. A. Krumhansl and J. R. Schrieffer, Phys. Rev. B 11, 3535 (1975).PLRBAQ
22. G. Parisi, Statistical Field Theory (Addison-Wesley, New York, 1988).
23. D. J. Scalapino, M. Sears, and R. A. Ferrell, Phys. Rev. B 6, 3409 (1972).PLRBAQ
24. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes in C (Cambridge University Press, Cambridge, 1992).
25. In this case, the upper limit (Formula presented) is set to 30 Å. The number of points to discretize the integral will increase with the enlargement of integral range. In Dauxois and Peyrard’s calculations, the (Formula presented) is chosen to be 190 Å. With this value of (Formula presented), the dimension of the matrix will be (Formula presented) using Gauss-Legendre node.
26. Landau and Lifshitz, Statistical Physics (Pergamon Press, Oxford, 1980).
27. R. Peierls, Surprises in Theoretical Physics (Princeton University Press, Princeton, 1979).
28. M. Techera, L. L. Daemen, and E. W. Prohofsky, Phys. Rev. A 40, 6636 (1989).PLRAAN
29. T. Dauxois, M. Peyrard, and C. R. Willis, Phys. Rev. E 48, 4768 (1993).PLEEE8
30. J. R. Morris and R. J. Gooding, J. Stat. Phys. 67, 471 (1992).JSTPBS
31. Yong-li Zhang and Wei-Mou Zheng, Phys. Rev. E 55, 4531 (1997).PLEEE8
32. R. D. Wells, J. E. Larson, R. C. Grant, B. E. Shortle, and C. R. Cantor, J. Mol. Biol. 54, 465 (1970).JMOBAK
33. W. Saenger, Principles of Nucleic Acid Structure (Springer-Verlag, Berlin, 1984).
34. S. C. Hardies, W. Hillen, T. C. Goodman, and R. D. Wells, J. Biol. Chem. 254, 10 128 (1979).JBCHA3
35. Y. Z. Chen, Yong-li Zhang, and E. W. Prohofsky, Phys. Rev. E 55, 5843 (1997).PLEEE8
36. M. Peyrard and T. Dauxois, Math. Comput. Simul. 40, 305 (1996).