Langevin dynamics simulations of the diffusion of molecular knots in tensioned polymer chains

Journal of Physical Chemistry A

Volumn 111, Issue 41, 2007, Pages 10338-10344

  Lei, Huang ^a   Makarov, Dmitrii E ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

KNOT DIFFUSION; LANGEVIN DYNAMICS; POLYMER CHAIN;

COMPUTER SIMULATION; DIFFUSION IN SOLIDS; DYNAMICS; MOLECULAR DYNAMICS; MONOMERS;

BIOPOLYMERS;

BIOPOLYMER;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; DIFFUSION; THERMODYNAMICS;

BIOPOLYMERS; COMPUTER SIMULATION; DIFFUSION; MODELS, CHEMICAL; MOLECULAR CONFORMATION; THERMODYNAMICS;

EID: 35948963619     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp071940+     Document Type: Article

References (26)

1. Kauffman, L. H. Knots and Physics; World Scientific: Singapore, New Jersey, London, Hong Kong, 2001.
2. Frank-Kamenetskii, M. D. Unraveling DNA; Perseus Books: Reading, MA, 1997.
3. Bates, A. D.; Maxwell, A. DNA Topology; Oxford University Press: Oxford, 2005.
4. Taylor, W. R. Nature 2000, 406, 916-919.
5. Saitta, A. M.; Soper, P. D.; Wasserman, E.; Klein, M. Nature 1999, 399, 46-48.
6. Saitta, A. M.; Klein, M. J. Phys. Chem. 2001, 28, 6495-6499.
7. Pieranski, P.; Przybyl, S.; Stasiak, A. Eur. Phys. J. E 2001, 6, 123-128.
8. Vologodskii, A. Biophys. J. 2006, 90, 1594-1597.
9. De Gennes, P. G. Macromolecules 1984, 77.
10. Lobovkina, T.; Dommersnes, P.; Joanny, J.-F.; Bassereau, P.; Karlson, M.; Owar, O. Proc. Natl. Acad. Sci U.S.A. 2004, 101, 7949-7953.
11. Grosberg, A. Y. Phys. Rev. Lett. 2000, 85, 003858.
12. Metzler, R.; Reisner, W.; Riehn, R.; Austin, R.; Tegenfeldt, J. O.; Sokolov, I. M. Europhys. Lett. 2006, 76, 696-702.
13. Ercolini, E.; Valle, F.; Adamcik, J.; Witz, G.; Metzler, R.; De Los Rios, P.; Roca, J.; Dietler, G. Phys. Rev. Lett. 2007, 98, 058102-1.
14. Arsuaga, J.; Vazquez, M.; Trigueros, S.; Sumners, D. W.; Roca, J. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5373-5377.
15. Metzler, R.; Hanke, A.; Dommersnes, P. G.; Kantor, Y.; Kardar, M. Phys. Rev. Lett. 2002, 88, 188101-1.
16. Kim, E.-G.; Klein, M. Macromolecules 2004, 37, 1674-1677.
17. Arai, Y.; Yasuda, R.; Akashi, K.-i.; Harada, Y.; Miyata, H.; Kinosita, K.; Itoh, H. Nature 1999, 399, 446.
18. Bao, X. R.; Lee, H. J.; Quake, S. R. Phys. Rev. Lett. 2003, 91, 265506-1.
19. Arteca, G. A. Phys. Chem. Chem. Phys. 2004, 6, 3500-3507.
20. De Gennes, P. G. Scaling Concepts in Polymer Physics; Cornell University Press: Ithaca, NY, 1979.
21. Ben-Naim, E.; Daya, Z. A.; Vorobieff, P.; Ecke, R. E. Phys. Rev. Lett. 2001, 86, 1414.
22. Gonzalez, O.; Maddocks, J. H. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 4769-4773.
23. Kirmizialtin, S.; Makarov, D. E. Phys. Rev. Lett., submitted.
24. Persson, B. N. J. Sliding Friction. Physical Principles and Applications; Springer-Vnrlag: Berlin, Heidelberg, 1998.
25. Harris, B. A.; Harvey, S. C. J. Comput. Chem. 1999, 20, 813-818.
26. Vologodskii, A. V.; Lukashin, A. V.; Frank-Kamenetskii, M. D.; Anshelevich, V. V. Sov. Phys. JETP 1974, 39, 1059.