Denaturation of circular DNA: Supercoil mechanism

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 84, Issue 4, 2011, Pages

  Bar, Amir ^a   Kabakçoǧlu, Alkan ^b   Mukamel, David ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b KOÇ UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

CONDENSATION TRANSITION; CONTINUOUS TRANSITIONS; CRITICAL TEMPERATURES; DOUBLE-STRANDED HELICES; FIRST ORDER TRANSITIONS; HIGH ORDER; LINKING NUMBERS; PS-MODEL; SECOND ORDER TRANSITION; WINDING NUMBER;

DENATURATION; PHASE TRANSITIONS; WINDING;

DNA;

EID: 81555200678     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.84.041935     Document Type: Article

References (33)

1. D. Dixon, R. Simpson-White, and L. Dixon, J. Mar. Biol. Assoc. U.K. JMBAAK 0025-3154 10.1017/S0025315400059312 72, 519 (1992).
2. D. Hickey and G. Singer, Genome Biol. JMBAAK 1465-6906 10.1186/gb-2004-5-10-117 5, 117 (2004). (Pubitemid 39485397)
3. R. M. Wartell and A. S. Benight, Phys. Rep. PRPLCM 0370-1573 10.1016/0370-1573(85)90060-2 126, 67 (1985).
4. H. Hiasa and K. J. Marians, J. Biol. Chem. 269, 32655 (1994).
5. H. Hiasa and K. Marians, J. Biol. Chem. JBCHA3 0021-9258 10.1074/jbc.271.35.21529 271, 21529 (1996). (Pubitemid 26293020)
6. E. Carlon and T. Heim, Physica A PHYADX 0378-4371 10.1016/j.physa.2005. 09.067 362, 433 (2006). (Pubitemid 43234066)
7. M. Peyrard and A. R. Bishop, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.62.2755 62, 2755 (1989).
8. M. E. Fisher, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1727787 45, 1469 (1966).
9. D. Poland and H. A. Scheraga, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1727785 45, 1456 (1966).
10. T. Dauxois, M. Peyrard, and A. R. Bishop, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.47.684 47, 684 (1993).
11. Y. Kafri, D. Mukamel, and L. Peliti, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.85.4988 85, 4988 (2000). (Pubitemid 32871686)
12. R. Wartell and E. Montroll, Adv. Chem. Phys. PRLTAO 0065-2385 10.1002/9780470143728.ch2 22, 129 (1972).
13. C. J. Benham, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.439625 72, 3633 (1980).
14. C. J. Benham, J. Mol. Biol. JMOBAK 0022-2836 10.1016/0022-2836(92)90404-8 225, 835 (1992).
15. C. Bouchiat and M. Mezard, Eur. Phys. J. E EPJSFH 1292-8941 10.1007/s101890050020 2, 377 (2000).
16. J. Palmeri, M. Manghi, and N. Destainville, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.99.088103 99, 088103 (2007). (Pubitemid 47331091)
17. J. F. Marko and E. D. Siggia, Macromolecules MAMOBX 0024-9297 10.1021/ma00082a015 27, 981 (1994).
18. R. A. Neher and U. Gerland, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.73.030902 73, 030902 (2006).
19. Y. Kafri, D. Mukamel, and L. Peliti, Eur. Phys. J. B 27, 135 (2002).
20. E. Carlon, E. Orlandini, and A. L. Stella, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.88.198101 88, 198101 (2002).
21. R. Blake, Bioinformatics BOINFP 1367-4803 10.1093/bioinformatics/15.5.370 15 (5), 370 (1999). (Pubitemid 29312625)
22. J. Rudnick and R. Bruinsma, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.65.030902 65, 030902 (R) (2002). (Pubitemid 40619070)
23. T. Garel, H. Orland, and E. Yeramian, e-print arXiv: q-bio/0407036.
24. A. Kabakçoǧlu, E. Orlandini, and D. Mukamel, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.80.010903 80, 010903 (R) (2009).
25. A. Kabakçoǧlu, E. Orlandini, and D. Mukamel, Physica A PHYADX 0378-4371 10.1016/j.physa.2009.12.063 389, 3002 (2010).
26. M. Sayar, B. Avşaroǧlu, and A. Kabakçoǧlu, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.81.041916 81, 041916 (2010).
27. L. Yan and H. Iwasaki, Jpn. J. Appl. Phys. JAPLD8 0021-4922 10.1143/JJAP.41.7556 41, 7556 (2002).
28. B. Duplantier, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.57. 941 57, 941 (1986).
29. L. Lewin, Polylogarithms and Associated Functions (North-Holland Publishing Co., New York, 1981).
30. M. Abramowitz and I. Stegun, Handbook of Mathematical Functions, 5th ed. (Dover, New York, 1964).
31. M. Evans and T. Hanney, J. Phys. A JPHAC5 0305-4470 10.1088/0305-4470/38/ 19/R01 38, R195 (2005). (Pubitemid 40900388)
32. M. R. Evans, S. N. Majumdar, and R. K. P. Zia, J. Stat. Phys. JSTPBS 0022-4715 10.1007/s10955-006-9046-6 123, 357 (2006). (Pubitemid 43707530)
33. B. Coluzzi and E. Yeramian, Eur. Phys. J. B EPJBFY 1434-6028 10.1140/epjb/e2007-00140-5 56, 349 (2007). (Pubitemid 46828795)