Evaluating changes of writhe in computer simulations of supercoiled DNA

Journal of Chemical Physics

Volumn 122, Issue 6, 2005, Pages

  De Vries, Renko ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BROWNIAN MOVEMENT; COMPUTER SIMULATION; DEGREES OF FREEDOM (MECHANICS); MONTE CARLO METHODS;

BROWNIAN DYNAMICS SIMULATIONS; POLYGONAL SPACE CURVE; SUPERCOILED DNA;

DNA;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; DNA SUPERCOILING; MONTE CARLO METHOD;

ALGORITHMS; COMPUTER SIMULATION; DNA, SUPERHELICAL; MODELS, MOLECULAR; MONTE CARLO METHOD; NUCLEIC ACID CONFORMATION;

EID: 22944459180     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1846052     Document Type: Article

References (18)

1. A.D. Bates, DNA Topology (IRL, Oxford, UK, 1993).
2. K. V. Klenin, A. V. Vologodskii, V. V. Anshelevich, A. M. Dykhne, and M. D. Frank-Kamenetskii, J. Mol. Biol. 217, 413 (1991);
3. A. V. Vologodskii, S. D. Levene, K. V. Klenin, M. Frank-Kamenetskii, and N. R. Cozzarelli, 227, 1224 (1992).
4. J. A. Gebe, S. A. Allison, J. B. Clendenning, and J. M. Schurr, Biophys. J. 68, 619 (1995).
5. Yu. S. Velichko, K. Yoshikawa, and A. R. Khokhlov, J. Chem. Phys. 111, 9424 (1999);
6. Biomacromolecules 1, 459 (2000).
7. B. Mergell, M. R. Ejtehadi, and R. Everaers, Phys. Rev. E 66, 011903 (2002).
8. K. Klenin, H. Merlitz, and J. Langowski, Biophys. J. 74, 780 (1998).
9. D. A. Beard and T. Schlick, J. Chem. Phys. 112, 7323 (2000).
10. D. Sprous and S. C. Harvey, Biophys. J. 70, 1893 (1996).
11. K. Klenin and J. Langowski, Biopolymers 54, 307 (2000).
12. P. K. Agarwal, H. Edelsbrunner, and Y. Wang, Discrete Comput. Geom. 32, 37 (2004).
13. F. B. Fuller, Proc. Natl. Acad. Sci. U.S.A. 75, 3557 (1978).
14. J. Aldinger, I. Klapper, and M. Tabor, J. Knot, J. Knot Theory Ramif. 4, 343 (1995).
15. J. Cantarella, math.DG/0202236
16. SIAM J Numer. Anal. (to be published).
17. E. L. Starostin, physics/0212095.
18. A. V. Vologodskii, A. V. Lukashin, M. D. Frank-Kamenetskii, and V. V. Anshelevich, Sov. Phys. JETP 39, 1059 (1975).