Bubble merging in breathing DNA as a vicious walker problem in opposite potentials

Journal of Chemical Physics

Volumn 130, Issue 16, 2009, Pages

  Pedersen, Jonas Nyvold ^a   Hansen, Mikael Sonne ^b   Novotný, Tomáš ^c,d   Ambjörnsson, Tobias ^a,e   Metzler, Ralf ^f  

^a LUND UNIVERSITY   (Sweden)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^c CHARLES UNIVERSITY   (Czech Republic)

^d UNIVERSITY OF COPENHAGEN   (Denmark)

^e MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^f TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BARRIER CROSSINGS; BASE PAIRS; BUBBLE COALESCENCES; BUBBLE DYNAMICS; CHARACTERISTIC TIME; DNA BUBBLES; DNA STABILITIES; DOUBLE-STRANDED DNAS; DRIFT DIFFUSIONS; FOKKER-PLANCK APPROACHES; HIGH TEMPERATURES; MASTER EQUATIONS; MELTING TEMPERATURES; NUMERICAL EVALUATIONS; QUANTITATIVE INVESTIGATIONS; SINGLE MOLECULE FLUORESCENCES; STOCHASTIC SIMULATIONS;

DNA; DYNAMICS; GENES; MELTING POINT; NUCLEIC ACIDS; RATE CONSTANTS; SYSTEMS ANALYSIS; THERMODYNAMIC STABILITY;

COALESCENCE;

DNA;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; KINETICS; THERMODYNAMICS;

BASE PAIRING; COMPUTER SIMULATION; DNA; KINETICS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; THERMODYNAMICS;

EID: 65149095479     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3117922     Document Type: Article

References (72)

1. J. D. Watson and F. H. C. Crick, Nature (London) 0028-0836 171, 737 (1953). 10.1038/171737a0
2. C. R. Cantor and P. R. Schimmel, Biophysical Chemistry (Freeman, New York, 1980).
3. A. Kornberg, DNA Synthesis (Freeman, San Francisco, 1974).
4. A. Kornberg and T. A. Baker, DNA Replication (Freeman, New York, 1992).
5. M. D. Frank-Kamenetskii, Phys. Rep. 0370-1573 288, 13 (1997). 10.1016/S0370-1573(97)00020-3
6. S. G. Delcourt and R. D. Blake, J. Biol. Chem. 0021-9258 266, 15160 (1991).
7. R. D. Blake, J. W. Bizzaro, J. D. Blake, G. R. Day, S. G. Delcourt, J. Knowles, K. A. Marx, and J. SantaLucia, Jr., Bioinformatics 1367-4803 15, 370 (1999). 10.1093/bioinformatics/15.5.370
8. A. Krueger, E. Protozanova, and M. D. Frank-Kamenetskii, Biophys. J. 0006-3495 90, 3091 (2006). 10.1529/biophysj.105.078774
9. D. Poland and H. A. Scheraga, Theory of Helix-Coil Transitions in Biopolymers (Academic, New York, 1970).
10. M. Peyrard, Nat. Phys. 1745-2473 2, 13 (2006). 10.1038/nphys197
11. R. M. Wartell and A. S. Benight, Phys. Rep. 0370-1573 126, 67 (1985). 10.1016/0370-1573(85)90060-2
12. C. Richard and A. J. Guttmann, J. Stat. Phys. 0022-4715 115, 925 (2004). 10.1023/B:JOSS.0000022370.48118.8b
13. E. Yeramian, Gene 0378-1119 255, 139 (2000) 10.1016/S0378-1119(00)00301- 2; E. Yeramian, Gene 0378-1119 255, 151 (2000). 10.1016/S0378-1119(00)00300-0
14. E. Carlon, M. L. Malki, and R. Blossey, Phys. Rev. Lett. 0031-9007 94, 178101 (2005). 10.1103/PhysRevLett.94.178101
15. M. Gúron, M. Kochoyan, and J. -L. Leroy, Nature (London) 0028-0836 328, 89 (1987). 10.1038/328089a0
16. G. Altan-Bonnet, A. Libchaber, and O. Krichevsky, Phys. Rev. Lett. 0031-9007 90, 138101 (2003). 10.1103/PhysRevLett.90.138101
17. R. Metzler, T. Ambjörnsson, A. Hanke, Y. Zhang, and S. Levene, J. Comput. Theor. Nanosci. 1546-1955 4, 1 (2007). 10.1166/jctn.2007.001a
18. K. Pant, R. L. Karpel, and M. C. Williams, J. Mol. Biol. 0022-2836 327, 571 (2003). 10.1016/S0022-2836(03)00153-0
19. K. Pant, R. L. Karpel, I. Rouzina, and M. C. Williams, J. Mol. Biol. 0022-2836 336, 851 (2004) 10.1016/j.jmb.2003.12.025; K. Pant, R. L. Karpel, I. Rouzina, and M. C. Williams, J. Mol. Biol. 349, 317 (2005). 10.1016/j.jmb.2005. 03.065 0006-3495
20. I. M. Sokolov, R. Metzler, K. Pant, and M. C. Williams, Biophys. J. 0006-3495 89, 895 (2005). 10.1529/biophysj.104.057612
21. T. Ambjörnsson and R. Metzler, Phys. Rev. E 1063-651X 72, 030901 (R) (2005). 10.1103/PhysRevE.72.030901
22. C. H. Choi, G. Kalosakas, K. . Rasmussen, M. Hiromura, A. R. Bishop, and A. Usheva, Nucleic Acids Res. 0305-1048 32, 1584 (2004). 10.1093/nar/gkh335
23. S. Ares and G. Kalosakas, Nano Lett. 1530-6984 7, 307 (2007). 10.1021/nl062304a
24. T. Ambjörnsson, S. K. Banik, O. Krichevsky, and R. Metzler, Phys. Rev. Lett. 0031-9007 97, 128105 (2006). 10.1103/PhysRevLett.97.128105
25. T. Ambjörnsson, S. K. Banik, O. Krichevsky, and R. Metzler, Biophys. J. 0006-3495 92, 2674 (2007). 10.1529/biophysj.106.095935
26. M. Peyrard and A. R. Bishop, Phys. Rev. Lett. 0031-9007 62, 2755 (1989). 10.1103/PhysRevLett.62.2755
27. T. Dauxois, M. Peyrard, and A. R. Bishop, Phys. Rev. E 1063-651X 47, R44 (1993). 10.1103/PhysRevE.47.R44
28. B. S. Alexandrov, L. T. Wille, K. . Rasmussen, A. R. Bishop, and K. B. Blagoev, Phys. Rev. E 1063-651X 74, 050901 (2006). 10.1103/PhysRevE.74.050901
29. A. Campa and A. Giansanti, Phys. Rev. E 1063-651X 58, 3585 (1998). 10.1103/PhysRevE.58.3585
30. M. Peyrard, Nonlinearity 0951-7715 17, R1 (2004). 10.1088/0951-7715/17/2/ R01
31. A. Hanke and R. Metzler, J. Phys. A 0305-4470 36, L473 (2003). 10.1088/0305-4470/36/36/101
32. A. Bar, Y. Kafri, and D. Mukamel, Phys. Rev. Lett. 0031-9007 98, 038103 (2007). 10.1103/PhysRevLett.98.038103
33. H. C. Fogedby and R. Metzler, Phys. Rev. Lett. 0031-9007 98, 070601 (2007) 10.1103/PhysRevLett.98.070601; H. C. Fogedby and R. Metzler, Phys. Rev. E 1063-651X 76, 061915 (2007). 10.1103/PhysRevE.76.061915
34. D. J. Bicout and E. Kats, Phys. Rev. E 1063-651X 70, 010902 (R) (2004). 10.1103/PhysRevE.70.010902
35. T. Ambjörnsson and R. Metzler, J. Phys.: Condens. Matter 0953-8984 17, S1841 (2005). 10.1088/0953-8984/17/20/013
36. S. K. Banik, T. Ambjörnsson, and R. Metzler, Europhys. Lett. 0295-5075 71, 852 (2005). 10.1209/epl/i2005-10144-9
37. T. Hwa, E. Marinari, K. Sneppen, and L. -H. Tang, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 100, 4411 (2003). 10.1073/pnas.0736291100
38. J. -H. Jeon, P. J. Park, and W. Sung, J. Chem. Phys. 0021-9606 125, 164901 (2006). 10.1063/1.2359724
39. T. Ambjörnsson, S. K. Banik, M. A. Lomholt, and R. Metzler, Phys. Rev. E 1063-651X 75, 021908 (2007). 10.1103/PhysRevE.75.021908
40. R. Metzler and T. Ambjörnsson, J. Comput. Theor. Nanosci. 1546-1955 2, 389 (2005). 10.1166/jctn.2005.209
41. T. Ambjörnsson and R. Metzler, J. Phys.: Condens. Matter 0953-8984 17, S4305 (2005). 10.1088/0953-8984/17/49/022
42. D. Poland and H. A. Scheraga, J. Chem. Phys. 0021-9606 45, 1464 (1966). 10.1063/1.1727786
43. M. E. Fisher, J. Chem. Phys. 0021-9606 45, 1469 (1966). 10.1063/1.1727787
44. Y. Kafri, D. Mukamel, and L. Peliti, Phys. Rev. Lett. 0031-9007 85, 4988 (2000). 10.1103/PhysRevLett.85.4988
45. A. Hanke and R. Metzler, Phys. Rev. Lett. 0031-9007 90, 159801 (2003) 10.1103/PhysRevLett.90.159801; Y. Kafri, D. Mukamel, and L. Peliti, Phys. Rev. Lett. 0031-9007 90, 159802 (2003). 10.1103/PhysRevLett.90.159802
46. A. Hanke, M. G. Ochoa, and R. Metzler, Phys. Rev. Lett. 0031-9007 100, 018106 (2008). 10.1103/PhysRevLett.100.018106
47. R. Blossey and E. Carlon, Phys. Rev. E 1063-651X 68, 061911 (2003). 10.1103/PhysRevE.68.061911
48. G. Bonnet, O. Krichevsky, and A. Libchaber, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 95, 8602 (1998) 10.1073/pnas.95.15.8602; G. Bonnet, S. Tyagi, A. Libchaber, and F. R. Kramer, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 96, 6171 (1999). 10.1073/pnas.96.11.6171
49. O. Krichevsky and G. Bonnet, Rep. Prog. Phys. 0034-4885 65, 251 (2002). 10.1088/0034-4885/65/2/203
50. M. E. Fisher, J. Stat. Phys. 0022-4715 34, 667 (1984). 10.1007/BF01009436
51. A. J. Bray and K. Winkler, J. Phys. A 0305-4470 37, 5493 (2004). 10.1088/0305-4470/37/21/001
52. M. Fixman and J. J. Freire, Biopolymers 0006-3525 16, 2693 (1977). 10.1002/bip.1977.360161209
53. Also, tL+ (X=- NL -1,Y) =0 and tR- (X,Y=N+ NR +1) =0 for completeness.
54. E. A. Di Marzio, C. M. Guttman, and J. D. Hoffman, Faraday Discuss. 0301-7249 68, 210 (1979). 10.1039/dc9796800210
55. T. Novotn, J. N. Pedersen, M. S. Hansen, T. Ambjörnsson, and R. Metzler, Europhys. Lett. 0295-5075 77, 48001 (2007). 10.1209/0295-5075/77/48001
56. H. Risken, The Fokker-Planck Equation (Springer, Berlin, 1989).
57. N. G. van Kampen, Stochastic Processes in Physics and Chemistry, 2nd ed. (North-Holland, Amsterdam, 1992).
58. C. W. Gardiner, Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences (Springer, Berlin, 1989).
59. R. F. Pawula, Phys. Rev. 0096-8250 162, 186 (1967). 10.1103/PhysRev.162. 186
60. J. Marcinkiewicz, Math. Z. 0025-5874 44, 612 (1939). 10.1007/BF01210677
61. The name vicious stems from Ref.
62. S. Redner, A Guide to First-Passage Processes (Cambridge University Press, Cambridge, UK, 2001).
63. T. Novotn and P. Chvosta, Phys. Rev. E 1063-651X 63, 012102 (2000). 10.1103/PhysRevE.63.012102
64. T. Novotn and R. Metzler (unpublished).
65. C. Aslangul, J. Phys. A 0305-4470 32, 3993 (1999). 10.1088/0305-4470/32/ 22/301
66. T. Ambjörnsson and R. J. Silbey, J. Chem. Phys. 0021-9606 129, 165103 (2008). 10.1063/1.2999602
67. M. D. Frank-Kamenetskii, Biopolymers 0006-3525 10, 2623 (1971). 10.1002/bip.360101223
68. P. Yakovchuk, E. Protozanova, and M. D. Frank-Kamenetskii, Nucleic Acids Res. 0305-1048 34, 564 (2006). 10.1093/nar/gkj454
69. E. Protozanova, P. Yakovchuk, and M. D. Frank-Kamenetskii, J. Mol. Biol. 0022-2836 342, 775 (2004). 10.1016/j.jmb.2004.07.075
70. C. Schildkraut and S. Lifson, Biopolymers 0006-3525 3, 195 (1965). 10.1002/bip.360030207
71. B. van den Broek, M. A. Lomholt, S. -M. J. Kalisch, R. Metzler, and G. J. L. Wuite, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 105, 15738 (2008). 10.1073/pnas.0804248105
72. D. T. Gillespie, J. Comput. Phys. 0021-9991 22, 403 (1976). 10.1016/0021-9991(76)90041-3