Bubbles and denaturation in DNA

European Physical Journal E

Volumn 20, Issue 4, 2006, Pages 421-434

  Van Erp, T S ^a   Cuesta Lopez S ^b,c   Peyrard, M ^b  

^a UNIVERSITY OF LEUVEN   (Belgium)

^b UNIVERSITÉ DE LYON   (France)

^c UNIVERSITY OF ZARAGOZA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; MOLECULAR DYNAMICS; PHASE TRANSITIONS; PROTEINS; STATISTICAL METHODS; STRESSES;

BIOLOGICAL ACTIVITIES; GENETIC CODES; MESOSCOPIC MODELS; THERMAL FLUCTUATIONS;

DNA;

DNA;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; DNA DENATURATION; DNA SEQUENCE; METHODOLOGY; ULTRASTRUCTURE;

COMPUTER SIMULATION; DNA; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; SEQUENCE ANALYSIS, DNA;

EID: 33748675685     PISSN: 12928941     EISSN: 1292895X     Source Type: Journal    
DOI: 10.1140/epje/i2006-10032-2     Document Type: Article

References (52)

1. C.H. Choi et al., Nucl. Acid Res. 32, 1584 (2004).
2. G. Kalosakas et al., Europhys. Lett. 68, 127 (2004).
3. T.S. van Erp, S. Cuesta-López, J.-G. Hagmann, M. Peyrard, Phys. Rev. Lett. 95, 218104 (2005).
4. R.B. Inman, R.L. Baldwin, J. Mol. Biol. 8, 452 (1964).
5. R.M. Wartell, A.S. Benight, Phys. Rep. 126, 67 (1985).
6. U. Dornberger, M. Leijon, H. Fritzsche, J. Biol. Chem. 274, 6957 (1999).
7. H. Urabe, Y. Tominaga, Biopolymers 21, 2477 (1982).
8. L. Movileanu, J.M. Benevides, G.J. Thomas, Biopolymers 63, 181 (2002).
9. H. Grimm, A. Rupprecht, in Nonlinear Excitations in Biornolecules, Les Editions de Physique, edited by M. Peyrard (Springer-Verlag, Berlin, 1995), p. 101.
10. G. Altan-Bonnet, A. Libchaber, O. Krichevsky, Phys. Rev. Lett. 90, 138101 (2003).
11. M.Y. Azbel, Phys. Rev. A 20, 1671 (1979).
12. J. Santa Lucia jr, Proc. Natl. Acad. Sci. U.S.A. 95, 1460 (1998).
13. D. Poland, H.A. Scheraga, J. Chem. Phys. 45, 1456 (1966).
14. C. Kittel, Am. J. Phys. 37, 917 (1969).
15. M. Peyrard, A.R. Bishop, Phys. Rev. Lett. 62, 2755 (1989).
16. T. Dauxois, M. Peyrard, A.R. Bishop, Phys. Rev. E 47, R44 (1993).
17. A. Campa, A. Giansanti, Phys. Rev. E 58, 3585 (1998).
18. C.J. Benham, Proc. Natl. Acad. Sci. U.S.A. 90, 29995 (1993).
19. C.J. Benham, J. Mol. Biol. 255, 425 (1996).
20. R.M. Fye, C.J. Benham, Phys. Rev. E 59, 3408 (1999).
21. C.J. Benham, C.-P. Bi, J. Comput. Biol. 11, 519 (2004).
22. C.-P. Bi, C.J. Benham, Bioinformatics 20, 1477 (2004).
23. A. Montrichok, G. Gruner, G. Zocchi, Europhys. Lett. 62, 452 (2003).
24. Y. Zheng, A. Montrichok, G. Zocchi, J. Mol. Biol. 339, 67 (2004).
25. Y. Zheng, A. Montrichok, G. Zocchi, Phys. Rev. Lett. 91, 148101 (2003).
26. M. Peyrard, T. Dauxois, Math. Comput. Simul. 40, 305 (1996).
27. M. Joyeux, S. Buyukdagli, Phys. Rev. E 72, 051902 (2005).
28. A. Campa, A. Giansanti, J. Biol. Phys. 24, 141 (1999).
29. L.A. Marky, K.J. Breslauer, Biopolymers 21, 2185 (1982).
30. K.J. Breslauer, R. Frank, H. Blocker, L.A. Marky, Proc. Natl. Acad. Sci. U.S.A. 83, 3746 (1986).
31. J. SantaLucia, H.T. Allawi, P.A. Seneviratne, Biochemistry 35, 3555 (1996).
32. R.L. Ornstein, R. Rein, D.L. Breen, R.D. Macelroy, Biopolymers 17, 2341 (1978).
33. W. Saenger, Principles of Nucleic Acid Structure (Springer-Verlag, Berlin, 1984).
34. P. Mignon, S. Loverix, J. Steyaert, P. Geerlings, Nucl. Acid Res. 33, 1779 (2005).
35. P. Hobza, J. Sponer, Chem. Rev. 99, 3247 (1999).
36. J. Sponer, J. Leszczynski, P. Hobza, Theochem-J. Mol. Struct. 573, 43 (2001).
37. M. Peyrard, Nonlinearity 17, R1 (2004).
38. N. Theodorakopoulos, M. Peyrard, Phys. Rev. Lett. 85, 6 (2000).
39. T. Dauxois, M. Peyrard, A.R. Bishop, Phys. Rev. E 47, 684 (1993).
40. S. Ares, N.K. Voulgarakis, K.O. Rasmussen, A.R. Bishop, Phys. Rev. Lett. 94, 035504 (2005).
41. Y. I. Zhang, W.-M. Zheng, J.-X. Liu, Y. Z. Chen, Phys. Rev. E 56, 7100 (1997).
42. R.A. Neher, U. Gerland, Phys. Rev. E 73, 030902 (2006).
43. G. Pólya, Math. Ann. 84, 149 (1921).
44. S. Buyukdagli, M. Sanrey, M. Joyeux, Chem. Phys. Lett. 419, 434 (2006).
45. K.S. Murakami et al., Science 296, 1285 (2002).
46. Z. Rapti, A. Smerzi, K.O. Rasmussen, A.R. Bishop, Europhys. Lett. 74, 540 (2006).
47. Z. Rapti et al., Phys. Rev. E 73, 051902 (2006).
48. D.J. Galas, M. Eggert, M.S. Waterman, J. Mol. Biol. 186, 117 (1985).
49. S. Cuesta-López et al., in preparation.
50. G. Boole, J.F. Moulton, A Treatise on the Calculus of Finite Differences, 2nd rev. ed. (Dover Publications, New York, 1960).
51. A.M. Abramowitz, I.A. Stegun, Handbook of Mathematical Functions (Dover Publications, New York, 1972).
52. G.M. Torrie, J.P. Valleau, Chem. Phys. Lett. 28, 578 (1974).