Numerical evidence for relevance of disorder in a Poland-Scheraga DNA denaturation model with self-avoidance: Scaling behavior of average quantities

European Physical Journal B

Volumn 56, Issue 4, 2007, Pages 349-365

  Coluzzi, B ^a   Yeramian, E ^b  

^a ECOLE NORMALE SUPÉRIEURE   (France)

^b INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

FINITE SIZE BEHAVIOR; HETEROGENEITY; POLAND-SCHERAGA MODELS; PURE SYSTEMS;

ALGORITHMS; DENATURATION; MATHEMATICAL MODELS; MONTE CARLO METHODS; PARAMETER ESTIMATION; PROBABILITY DISTRIBUTIONS; THERMODYNAMIC PROPERTIES;

DNA;

EID: 34249721370     PISSN: 14346028     EISSN: 14346036     Source Type: Journal    
DOI: 10.1140/epjb/e2007-00140-5     Document Type: Article

References (75)

1. R.M. Warteil, A.S. Benight, Phys. Rep. 126, 67 (1985)
2. Theory of Helix-Coil Transitions in Biopolymers, edited by D. Poland, H.A. Scheraga (Academic, New York, 1970)
3. For a recent review in which the effects of self-avoidance in Poland-Scheraga models are critically discussed see C. Richard, A.J. Guttman, J. Stat. Phys. 115, 943 (2004)
4. M. Fixman, J.J. Freire, Biopolymers 16, 2693 (1977)
5. E. Yeramian, F. Schaeffer, B. Caudron, P. Claverie, H. Buc, Biopolymers 30, 481 (1990)
6. D. Poland, H.A. Scheraga, J. Chem. Phys. 45, 1456, 1464 (1966)
7. M.E. Fisher, J. Chem Phys. 45, 1469 (1966)
8. S. Cocco, R. Monasson, Phys. Rev. Lett. 83, 5178 (1999)
9. N. Theodarakopoulos, T. Dauxois, M. Peyrard, Phys. Rev. Lett. 85, 6 (2000), references therein
10. Y. Kafri, D. Mukamel, L. Peliti, Phys. Rev. Lett. 85, 4988 (2000)
11. A. Hanke, R. Metzler, Phys. Rev. Lett. 90, 159801 (2003);
12. Y. Kafri, D. Mukamel, L. Peliti, Phys. Rev. Lett. 90, 159802 (2003)
13. Y. Kafri, D. Mukamel, L. Peliti, Eur. Phys. J. B 27, 135 (2002)
14. M.S. Causo, B. Coluzzi, P. Grassberger, Phys. Rev. E 62, 3958 (2000)
15. E. Carlon, E. Orlandini, A.L. Stella, Phys. Rev. Lett. 88, 198101. (2002)
16. M. Baiesi, E. Carlon, Y. Kafri, D. Mukamel, E. Orlandini, A.L. Stella, Phys. Rev. E 67, 021911 (2003)
17. T. Garel, C. Monthus, H. Orland, Europhys. Lett. 55, 132 (2001);
18. S.M. Bhattacharjee, Europhys. Lett. 57, 772 (2002);
19. T. Garel, C. Monthus, H. Orland, Europhys. Lett. 57, 774 (2002)
20. S. Buyukdagli, M. Joyeux, Phys. Rev. E 73, 051910 (2006)
21. M.E. Fisher, J. Stat. Phys. 34, 667 (1984)
22. P. Belohorec, B. Nickel, Accurate Universal and Two-parameter Model Results from a Monte-Carlo Renormalization Group Study, Preprint - University of Guelph (1997)
23. D. Poland, Biopolymers 13, 1859 (1974)
24. G. Steger, Nucleic Acids Res. 22, 2760 (1994)
25. R.D. Blake et al., Bioinformatics 15, 370 (1999)
26. E. Yeramian, Europhys. Lett. 25, 49 (1994)
27. T. Garel, H. Orland, Biopolymers 75, 453 (2004)
28. E. Yeramian, Gene 255, 139 (2000);
29. E. Yeramian, Gene 255, 151 (2000)
30. E. Yeramian, S. Bonnefoy, G. Langsley, Bioinfomatics 18, 1.90 (2002)
31. E. Yeramian, L. Jones, Nucl. Acid Res. 31, 3843 (2003)
32. E. Carlon, M.L. Malki, R. Blossey, Phys. Rev. Lett. 94, 178101 (2005)
33. T. Garel, C. Monthus, J. Stat. Mech., P06004 (2005)
34. C. Monthus, T. Garel, Eur. Phys. J. B 48, 393 (2005)
35. B. Coluzzi, Phys. Rev. E T3, 011911 (2006)
36. G. Giacomin, F.L. Toninelli, Commun. Math. Phys. 266, 1 (2006)
37. G. Giacomin, F.L. Toninelli, Phys. Rev. Lett. 96, 060702 (2006)
38. F.L. Toninelli, J. Stat. Phys. 126, 1025 (2007)
39. A.B. Harris, J. Phys. C 7, 1671 (1974)
40. M. Aizenman, J. Wehr, Phys. Rev. Lett. 62, 2503 (1989);
41. M. Aizenman, J. Wehr, Phys. Rev. Lett. 64, 1311 (E) (1990)
42. A.N. Berker, Physica A 194, 72 (1993)
43. C. Monthus, Random walks and polymers in the presence of quenched disorder, e-print arXiv: cond-mat/0601332, Proceedings of the conference Mathematics and Physics, I.H.E.S., Paris (France), November 2005
44. C. Monthus, T. Garel, Random polymers and delocalization transition, e-print arXiv:cond-mat/0605448, Proceedings of the conference Inhomogeneous Random Systems, I.H.P., Paris (France), January 2006
45. B. Coluzzi, E. Yeramian, Numerical evidence for the relevance of disorder in a Poland-Scheraga model for DNA denaturation with self-avoidance: An analysis in terms of pseudo-critical temperatures, work in progress
46. B. Duplantier, Phys. Rev. Lett. 57, 941 (1986);
47. B. Duplantier, J. Stat. Phys. 54, 581 (1989)
48. L. Schäfer, Can Finite Size Effects in the Poland-Scheraga Model Explain Simulations of a Simple Model for DNA Denatumtion?, e-print arXiv:cond-mat/0502668
49. D. Cule, T. Hwa, Phys. Rev. Lett. 79, 2375 (1997)
50. D.K. Lubensky, D.R. Nelson, Phys. Rev. Lett. 85, 1575 (2000);
51. D.K. Lubensky, D.R. Nelson, Phys. Rev. E 65, 031917 (2002)
52. S. Ares, A. Sánchez, Disorder Universality: the case of DNA denaturation, e-print arXiv: cond-mat/0511532
53. L.-H. Tang, H. Chaté, Phys. Rev. Lett. 86, 830 (2001)
54. Y. Kafri, D. Mukamel, Phys. Rev. Lett. 91, 055502 (2003)
55. V. Ivanov, Y. Zeug, G. Zocchi, Phys. Rev. E 70, 051907 (2004);
56. V. Ivanov, D. Piontkovski, G. Zocchi, Phys. Rev. E 71, 041909 (2005)
57. J.T. Chayes, L. Chayes, D.S. Fisher, T. Spencer, Phys. Rev. Lett. 57, 2999 (1986)
58. A. Aharoriy, A.B. Harris, S. Wiseman, Phys. Rev. Lett. 81, 252 (1998)
59. F. Pázmándi, R.T. Scalettar, G.T. Zimanyi, Phys. Rev. Lett. 79, 5130 (1997)
60. S. Wiseman, E. Domany, Phys. Rev. E 52, 3469 (1995);
61. S. Wiseman, E. Domany, Phys. Rev. Lett. 81, 22 (1998);
62. S. Wiseman, E. Domany, Phys. Rev. E 58, 2938 (1998)
63. T. Garel, G. Monthus, Eur. Phys. J. B 46, 117 (2005)
64. C. Monthus, T. Garel, J. Stat. Mech., P12011 (2005)
65. R. Blossey, E. Carlon, Phys. Rev. E 68, 061911 (2003)
66. E. Yeramian, P. Claverie, Nature 326, 169 (1987)
67. Z. Bay, Phys. Rev. 77, 419 (1950);
68. P. Wahl, H. Land, Biochem. Biophys. Acta 133, 233 (1967);
69. I. Isenberg, R.D. Dyson, Biophys. J. 9, 1337 (1969)
70. A. Bar, Y. Kafri, D. Mukamel, Phys. Rev. Lett. 98, 038103 (2007)
71. T. Ambjörnsson, S.K. Banik, O. Krichevsky, R. Metzler, Phys. Rev. Lett. 97, 128105 (2006)
72. T. Ambjörnsson, S.K. Banik, M.A. Lomholt, R. Metzler, Phys. Rev. E 75, 021908 (2007)
73. T. Novotný, J.N. Pedersen, T. Ambjörnsson, M.S. Hansen, R. Metzler, Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials, e-print arXiv:cond-mat/0610752
74. B. Coluzzi, E. Yeramian, On the disordered SAW model for DNA denaturation, Proceedings of the X International Workshop on Disordered Systems, Andalo (Italy), 18-21 March 2006.
75. Phil. Mag. 87, 517 (2007)