Pseudoknots in a homopolymer

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

Volumn 70, Issue 1 1, 2004, Pages

  Kabakcioglu A ^a   Stella, A L ^a  

^a UNIVERSITY OF PADOVA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION THEORY; DNA; ENTROPY; HAMILTONIANS; MATHEMATICAL MODELS; MATHEMATICAL PROGRAMMING; PROTEINS; SUPERCONDUCTING TRANSITION TEMPERATURE; TEMPERATURE DISTRIBUTION; THERMODYNAMICS; TOPOLOGY;

DENATURATION; FIRST ORDER TRANSITION; HOMOPOLYMER; PSEUDOKNOTS;

POLYMERS;

EID: 45849155550     PISSN: 15393755     EISSN: None     Source Type: Journal    
DOI: 10.1103/PhysRevE.70.011802     Document Type: Article

References (43)

1. E. B. ten Dam, C. W. A. Pleij, and D. Draper, Biochemistry 31, 11665 (1992); C. W. A. Pleij, Curr. Opin. Struct. Biol. 4, 337 (1994).
2. E. B. ten Dam, C. W. A. Pleij, and D. Draper, Biochemistry 31, 11665 (1992); C. W. A. Pleij, Curr. Opin. Struct. Biol. 4, 337 (1994).
3. A. Xayaphoummine, T. Bucher, F. Thalmann, and H. Isambert, Proc. Natl. Acad. Sci. U.S.A. 100, 15310 (2003).
4. D. S. McPheeters, G. D. Stormo, and L. Gold, J. Mol. Biol. 201, 517 (1990).
5. Z. Du, J. A. Holland, M. R. Hansen, D. P. Giedroc, and D. W. Hoffman, J. Mol. Biol. 271, 463 (1997).
6. N. M. Wills, R. F. Gesteland, and J. F. Atkins, Proc. Natl. Acad. Sci. U.S.A. 88, 6991 (1991).
7. P. J. Farabaugh, Cell 74, 591 (1993).
8. R. Nussinov and A. B. Jacobson, Proc. Natl. Acad. Sci. U.S.A. 77, 6309 (1980).
9. M. Zuker and P. Stiegler, Nucleic Acids Res. 9, 133 (1981).
10. R. Bundschuh and T. Hwa, Phys. Rev. Lett. 83, 1479 (1999).
11. E. Rivas and S. Eddy, J. Mol. Biol. 285, 2053 (1999).
12. Y. Uemura, A. Hasegawa, S. Kobayashi, and T. Yokomori, Theor. Comput. Sci. 210, 277 (1999).
13. M. Pilsbury, J. A. Taylor, H. Orland, and A. Zee, e-print cond-mat/0310505.
14. M. Baiesi, E. Orlandini, and A. L. Stella, Phys. Rev. Lett. 87, 070602 (2003).
15. A. Lucas and K. A. Dill, J. Chem. Phys. 119, 2414 (2003).
16. P. Leoni and C. Vanderzande, Phys. Rev. E 68, 051904 (2003).
17. +2 concentration in the solution. See, e.g., V. P. Misra and D. E. Draper, Biopolymers 48, 113 (1999).
18. I. Tinoco Jr. and C. Bustamante, J. Mol. Biol. 293, 271 (1999).
19. M. Vendruscolo, B. Subramanian, I. Kanter, E. Domany, and J. Lebowitz, Phys. Rev. E 59, 977 (1999).
20. M. R. Garey and D. S. Johnson, Computers and Intractability: A Guide to the Theory of NP-Completeness (W. H. Freeman & Co., San Francisco, 1979).
21. M. Weigt and A. K. Hartmann, Phys. Rev. E 63, 056127 (2001).
22. R. B. Lyngso and C. N. S. Pedersen, J. Comput. Biol. 7, 409 (2000).
23. G. Chartrand and O. Oellermann, Applied and Algorithmic Graph Theory (McGraw-Hill, New York, 1992).
24. N. Madras and G. Slade, The Self-Avoiding Walk, (Birkhäuser Press, Boston, 1996).
25. H.-P. Hsu, V. Mehra, W. Nadler, and P. Grassberger, J. Chem. Phys. 118, 444 (2003).
26. E. Orlandini, F. Seno, and A. L. Stella, Phys. Rev. Lett. 84, 294 (2000).
27. M. Aizenman, B. Duplantier, and A. Aharony, Phys. Rev. Lett. 83, 1359 (1999).
28. B. Duplantier J. Stat. Phys. 54, 581 (1988).
29. The connection between the crossover exponent and the sub-dominant factor in the free energy was recently emphasized to explain certain numerical results. See A. L. Owczarek and T. Prellberg, Phys. Rev. E 67, 032801 (2003).
30. M. Baiesi, E. Carlon, E. Orlandini, and A. L. Stella, Phys. Rev. E 63, 041801 (2001).
31. B. Drossel and M. Kardar, Phys. Rev. E 53, 5861 (1996).
32. A naive argument based on a mapping of the low-temperature AB contacts to high-temperature SAW suggests an exponent φ=2/3.
33. C. Vanderzande, Lattice Models of Polymers (Cambridge University Press, Cambridge, England, 1996).
34. V. Privman, P. C. Hohenberg, and A. Aharony, in Phase Transitions and Critical Phenomena, edited by C. Domb and J. L. Lebowitz (Academic Press, New York, 1991), Vol. 14, p. 1.
35. S. Leibler, R. R. P. Singh, and M. E. Fisher, Phys. Rev. Lett. 59, 1989 (1987).
36. E. Orlandini, F. Seno, A. L. Stella, and M. C. Tesi, Phys. Rev. Lett. 68, 488 (1992).
37. R. Dekeyser, E. Orlandini, A. L. Stella, and M. C. Tesi, Phys. Rev. E 52, 5214 (1995).
38. A. L. Stella, Phys. Rev. E 50, 3259 (1994).
39. F. Seno and C. Vanderzande, J. Phys. A 27, 5813 (1994).
40. N. Madras and E. J. Janse van Rensburg, J. Stat. Phys. 86, 1 (1997).
41. D. K. Treiber, M. S. Rook, P. P. Zarrinkar, and J. R. Williamson, Science 279, 1943 (1998).
42. J. Pan and S. A. Woodson, J. Mol. Biol. 280, 597 (1998).
43. H. Qui, K. Kaluarachchi, Z. Du, D. W. Hoffman, and D. P. Giedroc, Biochemistry 35, 4176 (1996).