The time duration for DNA thermal denaturation

Journal of Physics Condensed Matter

Volumn 20, Issue 3, 2008, Pages

  Calvo, Gabriel F ^a,c   Alvarez Estrada, Ramón F ^b  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

^c UNIVERSITY OF CASTILLA LA MANCHA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DENATURATION; DIFFERENTIAL EQUATIONS; DNA; MACROMOLECULES; MOLECULAR INTERACTIONS;

HYDRODYNAMIC INTERACTIONS; MEAN FIRST PASSAGE TIME (MFPT); SMOLUCHOWSKI EQUATION; THERMAL EQUILIBRIUM;

MOLECULAR DYNAMICS;

EID: 43049113205     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/20/03/035101     Document Type: Article

References (69)

1. Lehninger A L, Nelson D L and Cox M M 1993 Principles of Biochemistry 2nd edn (New York: Worth Publishers)
2. Volkenshtein M V 1983 Biophysics (Moscow: Mir)
3. Poland D and Scheraga H A 1970 Theory of Helix-Coil Transitions in Biopolymers (New York: Academic)
4. Grossberg A Y and Khokhlov A R 1994 Statistical Physics of Macromolecules (AIP Series in Polymers and Complex Materials) (New York: AIP)
5. Yakushevich L V 2004 Non-Linear Physics of DNA 2nd revised edn (Weinheim: Wiley-VCH)
6. Gotoh O 1983 Adv. Biophys. 16 1
7. Wartell R M and Benight A S 1985 Phys. Rep. 126 67
8. Prohofsky E 1995 Statistical Mechanics and Stability of Macromolecules (Cambridge: Cambridge University Press)
9. Frank-Kamenetskii M D 1997 Phys. Rep. 288 13
10. Peyrard M 2004 Nonlinearity 17 R1
11. Lifson S 1964 J. Chem. Phys. 40 3705
12. Peyrard M and Bishop A R 1989 Phys. Rev. Lett. 62 2755
13. Zhang Y, Zheng W, Liu J and Chen Y 1997 Phys. Rev. E 56 7100
14. Sung W and Jeon J-H 2004 Phys. Rev. E 69 031902
15. Alvarez-Estrada R F and Calvo G F 2002 Mol. Phys. 100 2957
16. Ritort F 2006 J. Phys.: Condens. Matter 18 R531
17. Zinchenko A A and Chen N 2006 J. Phys.: Condens. Matter 18 R453
18. Barbi M, Lepri S, Peyrard M and Theodorakopoulos N 2003 Phys. Rev. E 68 061909
19. Dauxois T, Peyrard M and Bishop A R 1993 Phys. Rev. E 47 684
20. Ares S, Voulgarakis N K, Rasmussen K O and Bishop A R 2005 Phys. Rev. Lett. 94 035504
21. Ambjörnsson T and Metzler R 2005 J. Phys.: Condens. Matter 17 S1841
22. Gompper G and Löwen H 2005 J. Phys.: Condens. Matter 17 S1827
23. Mohammad-Rafiee F and Golestanian R 2005 J. Phys.: Condens. Matter 17 S1165
24. Cherstvy A G 2005 J. Phys.: Condens. Matter 17 S1363
25. Lubensky D K and Nelson D R 2002 Phys. Rev. E 65 031917
26. Weber G, Haslam N, Whiteford N, Prugel-Bennett A, Essex J W and Neylon C 2006 Nat. Phys. 2 55
27. Calvo G F and Alvarez-Estrada R F 2005 J. Phys.: Condens. Matter 17 7755
28. Achter E K and Felsenfeld G 1971 Biopolymers 10 1625
29. Smith S B, Cui Y and Bustamante C 1996 Science 271 795
30. Rivetti C, Walker C and Bustamante C 1998 J. Mol. Biol. 280 41
31. Mills J B, Vacano E and Hagerman P J 1999 J. Mol. Biol. 285 245
32. Kuznetsov S V, Shen Y Q, Benight A S and Ansari A 2001 Biophys. J. 81 2864
33. Murphy M C, Rasnik I, Cheng W, Lohman T M and Ha T 2004 Biophys. J. 86 2530
34. Perkins T T, Quake S R, Smith D E and Chu S 1994 Science 264 822
35. Shusterman R, Alon S, Gavrinyov T and Krichevsky O 2004 Phys. Rev. Lett. 92 048303
36. Kuhn W 1957 Experientia 13 301
37. Longuet-Higgins H C and Zimm B H 1960 J. Mol. Biol. 2 1
38. Fixman M 1963 J. Mol. Biol. 6 39
39. Freese E B and Freese E 1963 Biochemistry 2 707
40. Crothers D M 1964 J. Mol. Biol. 9 712
41. Fong P 1964 Proc. Natl Acad. Sci. USA 52 239
42. Spatz H Ch and Crothers D M 1969 J. Mol. Biol. 42 191
43. Davison P F 1966 J. Mol. Biol. 22 97
44. Davison P F 1967 Biopolymers 5 715
45. Anshelevich V V and Vologodskii A V 1986 J. Biomol. Struct. Dyn. 4 251
46. Haenggi P, Talkner P and Borkovich M 1990 Rev. Mod. Phys. 62 251
47. Van Kampen N G 1985 Stochastic Processes in Physics and Chemistry (Amsterdam: North-Holland)
48. Risken H 1996 The Fokker-Planck Equation 2nd edn (Berlin: Springer)
49. Echenique P, Calvo I and Alonso J L 2006 J. Comput. Chem. 27 1733
50. Eyring H 1932 Phys. Rev. 39 746
51. Derrida B, Hakim V and Vannimenus J 1992 J. Stat. Phys. 66 1189
52. Kafri Y, Mukamel D and Peliti L 2000 Phys. Rev. Lett. 85 4988
53. Carlon E, Orlandini E and Stella A L 2002 Phys. Rev. Lett. 88 198101
54. Baiesi M et al 2003 Phys. Rev. E 67 021911
55. Theodarakopoulos N, Dauxois T and Peyrard M 2000 Phys. Rev. Lett. 85 6
56. Causo M S, Coluzzi B and Grassberger P 2000 Phys. Rev. E 62 3958
57. Garel T, Monthus C and Orland H 2001 Europhys. Lett. 55 132
58. Endres R G, Cox D L and Singh R R P 2004 Rev. Mod. Phys. 76 195
59. Roche S, Bicout D, Macia E and Kats E 2003 Phys. Rev. Lett. 91 228101
60. Murphy T J and Aguirre J L 1972 J. Chem. Phys. 57 2098
61. Pusey P N and Tough R J A 1983 Faraday Discuss. Chem. Soc. 76 123
62. Klein R and Hess W 1983 Faraday Discuss. Chem. Soc. 76 137
63. Doi M and Edwards S F 1986 The Theory of Polymer Dynamics (Oxford: Oxford University Press)
64. Kawakatsu T 2004 Statistical Physics of Polymers (Berlin: Springer)
65. Rubinstein M and Colby R H 2004 Polymer Physics (Oxford: Oxford University Press)
66. Calef D F and Deutch J M 1983 Annu. Rev. Phys. Chem. 34 493
67. Haken H 1975 Rev. Mod. Phys. 47 67
68. Calvo G F 2003 Non-Linear Propagation of Spatial Beams in Photorefractive media PhD Thesis Universidad Autonoma, Madrid
69. Wilde R E and Singh S 1998 Statistical Mechanics: Fundamentals and Modern Applications (New York: Wiley)