Computer simulation of biological macromolecules in generalized ensembles

International Journal of Modern Physics C

Volumn 10, Issue 8, 1999, Pages 1521-1530

  Hansmann, Ulrich H E ^a  

^a MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

Author keywords

Generalized Ensembles; Multiple Minima Problem; Numerical Simulations; Protein Folding

Indexed keywords

EID: 0033266923     PISSN: 01291831     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0129183199001303     Document Type: Article

References (35)

1. I. P. Androulakis, C. D. Maranas, and C. A. Floudas, J. Glob. Opt 11, 1 (1997).
2. S. Kirkpatrick, C. D. Gelatt Jr., and M. P. Vecchi, Science 220, 671 (1983).
3. J. N. Onuchic, Z. Luthey-Schulten, and P. G. Wolynes, Ann. Rev. Phys. Chem. 48, 545 (1997).
4. K. A. Dill and H. S. Chan, Nature Struct. Biol. 4, 10 (1997).
5. U. H. E. Hansmann and Y. Okamoto, J. Comp. Chem. 14, 1333 (1993).
6. U. H. E. Hansmann, Y. Okamoto, and F. Eisenmenger, Chem. Phys. Lett. 259, 321 (1996).
7. N. Nakajima, H. Nakamura, and A. Kidera, J. Phys. Chem. 101, 817 (1997).
8. U. H. E. Hansmann and Y. Okamoto, in Ann. Rev. Comput. Phys. VI, ed. D. Stauffer (World Scientific, Singapore, 1999), pp. 129-157.
9. G. M. Torrie and J. P. Valleau, J. Comp. Phys. 23, 187 (1977).
10. B. A. Berg and T. Neuhaus, Phys. Lett. B 267, 249 (1991).
11. B. Hesselbo and R. B. Stinchcombe, Phys. Rev. Lett. 74, 2151 (1995).
12. A. P. Lyubartsev, A. A. Martinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys. 96, 1776 (1992); E. Marinari and G. Parisi, Europhys. Lett. 19, 451 (1992).
13. A. P. Lyubartsev, A. A. Martinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys. 96, 1776 (1992); E. Marinari and G. Parisi, Europhys. Lett. 19, 451 (1992).
14. S. Kumar, P. Payne, and M. Vásquez, J. Comp. Chem. 17, 1269 (1996).
15. J. Higo, N. Nakajima, H. Shirai, A. Kidera, and H. Nakamura, J. Comp. Chem. 18, 2086 (1997).
16. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 61, 2635 (1988).
17. U. H. E. Hansmann and Y. Okamoto, Physica A 212, 415 (1994).
18. U. H. E. Hansmann, Phys. Rev. E 56, 6200 (1997).
19. U. H. E. Hansmann and Ph. de Forcrand, Int. J. Mod. Phys. C 8, 1085 (1997).
20. U. H. E. Hansmann and Y. Okamoto, Phys. Rev. E 56, 2228 (1997).
21. C. Tsallis, J. Stat. Phys. 52, 479 (1988).
22. G. J. Geyer, Stat. Sci. 7, 437 (1992); M. C. Tesi, E. J. J. van Rensburg, E. Orlandini, and S. G. Whittington, J. Stat. Phys. 82, 155 (1996); K. Hukushima and K. Nemoto, J. Phys. Soc. (Japan) 65, 1604 (1996).
23. G. J. Geyer, Stat. Sci. 7, 437 (1992); M. C. Tesi, E. J. J. van Rensburg, E. Orlandini, and S. G. Whittington, J. Stat. Phys. 82, 155 (1996); K. Hukushima and K. Nemoto, J. Phys. Soc. (Japan) 65, 1604 (1996).
24. G. J. Geyer, Stat. Sci. 7, 437 (1992); M. C. Tesi, E. J. J. van Rensburg, E. Orlandini, and S. G. Whittington, J. Stat. Phys. 82, 155 (1996); K. Hukushima and K. Nemoto, J. Phys. Soc. (Japan) 65, 1604 (1996).
25. U. H. E. Hansmann, Chem. Phys. Lett. 281, 140 (1997).
26. U. H. E. Hansmann, Y. Okamoto, and J. N. Onuchic, Proteins 34, 472 (1999).
27. J. D. Bryngelson and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 84, 524 (1987).
28. M. J. Sippl, G. Némethy, and H. A. Scheraga, J. Phys. Chem. 88, 6231 (1994); and references therein.
29. U. H. E. Hansmann, M. Masuya, and Y. Okamoto, Proc. Natl. Acad. Sci. U.S.A. 94, 10652 (1997).
30. U. H. E. Hansmann and Y. Okamoto, J. Phys. Chem. 102, 653 (1998).
31. U. H. E. Hansmann and Y. Okamoto, J. Phys. Chem. 103, 1595 (1999).
32. K. R. Shoemaker, P. S. Kim, D. N. Brems, S. Marqusee, E. J. York, I. M. Chaiken, J. M. Stewart, and R. L. Baldwin, Proc. Natl. Acad. Sci. U.S.A. 82, 2349 (1985).
33. J. J. Osterhout, R. L. Baldwin, E. J. York, J. M. Stewart, H. J. Dyson, and P. E. Wright, Biochemistry 28, 7059 (1989).
34. Y. Okamoto, Biopolymers 34, 529 (1994).
35. R. F. Tilton Jr., J. C. Dewan, and G. A. Petsko, Biochemistry 31, 2469 (1992).