Langevin dynamics simulations of ds-DNA translocation through synthetic nanopores

Journal of Chemical Physics

Volumn 127, Issue 1, 2007, Pages

  Forrey, Christopher ^a   Muthukumar, M ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; MOLECULAR DYNAMICS; NANOPORES; VOLTAGE CONTROL;

DS-DNA HAIRPINS; LANGEVIN DYNAMICS; TRANSLOCATION;

DNA;

DNA; NANOCOMPOSITE; NANOPARTICLE;

ARTICLE; BIOPHYSICS; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; ELECTRICITY; METHODOLOGY; MOLECULAR WEIGHT; NANOTECHNOLOGY; PHYSICAL CHEMISTRY; PROBABILITY; STATISTICAL MODEL; THEORETICAL MODEL;

BIOPHYSICS; CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; DNA; ELECTROSTATICS; MODELS, STATISTICAL; MODELS, THEORETICAL; MOLECULAR WEIGHT; NANOCOMPOSITES; NANOPARTICLES; NANOTECHNOLOGY; NUCLEIC ACID CONFORMATION; PROBABILITY;

EID: 34547889925     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2746246     Document Type: Article

References (40)

1. A. Meller, L. Nivon, E. Brandin, J. Golovchenko, and D. Branton, Proc. Natl. Acad. Sci. U.S.A. 97, 1079 (2000).
2. J. J. Kasianowicz, S. E. Henrickson, H. H. Weetall, and B. Robertson, Anal. Chem. 73, 2268 (2001).
3. A. Meller, L. Nivon, and D. Branton, Phys. Rev. Lett. 86, 3435 (2001).
4. S. Howorka, S. Cheley, and H. Bayley, Nat. Biotechnol. 19, 636 (2001).
5. D. W. Deamer and D. Branton, Acc. Chem. Res. 35, 817 (2002).
6. A. F. Sauer-Budge, J. A. Nyamwanda, D. K. Lubensky, and D. Branton, Phys. Rev. Lett. 90, 238101 (2003).
7. J. Mathe, H. Visram, V. Viasnoff, Y. Rabin, and A. Meller, Biophys. J. 87, 3205 (2004).
8. J. J. Kasianowicz, E. Brandin, D. Branton, and D. W. Deamer, Proc. Natl. Acad. Sci. U.S.A. 93, 13770 (1996).
9. M. Akeson, D. Branton, J. J. Kasianowicz, E. Brandin, and D. W. Deamer, Biophys. J. 77, 3227 (1999).
10. R. J. Murphy and M. Muthukumar, J. Chem. Phys. 126, 051101 (2007).
11. J. Li, D. Stein, C. McMullan, D. Branton, M. J. Aziz, and J. A. Golovchenko, Nature (London) 412, 166 (2001).
12. Z. Siwy and A. Fulinski, Phys. Rev. Lett. 89, 198103 (2002).
13. J. L. Li, M. Gershow, D. Stein, E. Brandin, and J. A. Golovchenko, Nat. Mater. 2, 611 (2003).
14. O. A. Saleh and L. L. Sohn, Nano Lett. 3, 37 (2003).
15. A. J. Storm, J. H. Chen, X. S. Ling, H. W. Zandbergen, and C. Dekker, Nat. Mater. 2, 537 (2003).
16. P. Chen, J. J. Gu, E. Brandin, Y. R. Kim, Q. Wang, and D. Branton, Nano Lett. 4, 2293 (2004).
17. J. B. Heng, C. Ho, T. Kim, R. Timp, A. Aksimentiev, Y. V. Grinkova, S. Sligar, K. Schulten, and G. Timp, Biophys. J. 87, 2905 (2004).
18. A. J. Storm, C. Storm, J. H. Chen, H. Zandbergen, J. F. Joanny, and C. Dekker, Nano Lett. 5, 1193 (2005).
19. W. Sung and P. J. Park, Phys. Rev. Lett. 77, 783 (1996).
20. E. A. DiMarzio and A. J. Mandell, J. Chem. Phys. 107, 5510 (1997).
21. D. K. Lubensky and D. R. Nelson, Biophys. J. 77, 1824 (1999).
22. M. Muthukumar, J. Chem. Phys. 111, 10371 (1999).
23. M. Muthukumar, Phys. Rev. Lett. 86, 3188 (2001).
24. T. Ambjornsson, S. P. Apell, Z. Konkoli, E. A. Di Marzio, and J. J. Kasianowicz, J. Chem. Phys. 117, 4063 (2002).
25. A. M. Berezhkovskii and I. V. Gopich, Biophys. J. 84, 787 (2003).
26. E. Slonkina and A. B. Kolomeisky, J. Chem. Phys. 118, 7112 (2003).
27. C. Y. Kong and M. Muthukumar, J. Chem. Phys. 120, 3460 (2004).
28. A. Aksimentiev and K. Schulten, Biophys. J. 88, 3745 (2005).
29. M. G. Fyta, S. Melchionna, E. Kaxiras, and S. Succi, Multiscale Model. Simul. 5, 1156 (2006).
30. C. Forrey and M. Muthukumar, Biophys. J. 91, 25 (2006).
31. C. T. A. M. Wong and M. Muthukumar, J. Chem. Phys. 126, 164903 (2007).
32. G. S. Manning, J. Chem. Phys. 51, 924 (1969).
33. S. Liu and M. Muthukumar, J. Chem. Phys. 116, 9975 (2002).
34. S. Liu, K. Ghosh, and M. Muthukumar, J. Chem. Phys. 119, 1813 (2003).
35. M. P. A. a. D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987).
36. J. J. Kasianowicz, in Structure and Dynamics of Confined Polymers, edited by, J. J. Kasianowicz, M. Kellermayer, and, David W. Deamer, (Springer, New York, 1999), Vol. 87.
37. A. Meller, J. Phys.: Condens. Matter 15, R581 (2003).
38. H. Wang, J. E. Dunning, A. P. H. Huang, J. A. Nyamwanda, and D. Branton, Proc. Natl. Acad. Sci. U.S.A. 101, 13472 (2004).
39. T. Z. Butler, J. H. Gundlach, and M. A. Troll, Biophys. J. 90, 190 (2006).
40. L. Z. Song, M. R. Hobaugh, C. Shustak, S. Cheley, H. Bayley, and J. E. Gouaux, Science 274, 1859 (1996).