Driven polymer transport through a nanopore controlled by a rotating electric field: Off-lattice computer simulations

Journal of Chemical Physics

Volumn 126, Issue 14, 2007, Pages

  Tsai, Y S ^a   Chen, C M ^a  

^a NATIONAL TAIWAN NORMAL UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; ELECTRIC FIELD EFFECTS; MONTE CARLO METHODS; NANOPORES; REACTION KINETICS; TRANSPORT PROPERTIES;

MONTE CARLO ALGORITHMS; POLYNUCLEOTIDE CHAIN; ROTATING ELECTRIC FIELD; TRANSLOCATION KINETICS;

ORGANIC POLYMERS;

NANOMATERIAL; OLIGONUCLEOTIDE; POLYMER;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ELECTROMAGNETIC FIELD; ELECTROPORATION; METHODOLOGY; POROSITY; RADIATION DOSE; RADIATION EXPOSURE; RADIATION RESPONSE; STRUCTURE ACTIVITY RELATION; ULTRASTRUCTURE;

COMPUTER SIMULATION; DOSE-RESPONSE RELATIONSHIP, RADIATION; ELECTROMAGNETIC FIELDS; ELECTROPORATION; MODELS, CHEMICAL; MODELS, MOLECULAR; NANOSTRUCTURES; OLIGONUCLEOTIDES; POLYMERS; POROSITY; RADIATION DOSAGE; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 34247272525     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2717187     Document Type: Article

References (43)

1. F. Sanger, S. Nicklen, and A. R. Coulson, Proc. Natl. Acad. Sci. U.S.A. 74, 5463 (1977).
2. E. S. Lander, L. M. Linton, B. Birren et al., Nature (London) 409, 860 (2001).
3. J. C. Venter, M. D. Adams, E. W. Meyers et al., Science 291, 1304 (2001).
4. J. B. Hogenesch, K. A. Ching, S. Batalov, A. I. Su, J. R. Walker, Y. Y. Zhou, S. A. Kay, P. G. Schultz, and M. P. Cooke, Cell 106, 413 (2001).
5. For a review, see A. Marziali and M. Akeson, Annu. Rev. Biomed. Eng. 3, 195 (2001).
6. J. J. Kasianowicz, E. Brandin, D. Branton, and D. W. Deamer, Proc. Natl. Acad. Sci. U.S.A. 93, 13770 (1996).
7. M. Akeson, D. Branton, J. J. Kasianowicz, E. Brandin, and D. W. Deamer, Biophys. J. 77, 3227 (1999).
8. A. Meller, L. Nivon, E. Brandin, J. Golovchenko, and D. Branton, Proc. Natl. Acad. Sci. U.S.A. 97, 1079 (2000).
9. C.-M. Chen and E.-H. Peng, Appl. Phys. Lett. 82, 1308 (2003).
10. J. Li, M. Gershow, D. Stein, E. Brandin, and J. A. Golovchenko, Nat. Mater. 2, 611 (2003).
11. A. Aksimentiev, J. B. Heng, G. Timp, and K. Schulten, Biophys. J. 87, 2086 (2004).
12. P. Chen, J. Gu, E. Brandin, Y.-R. Kim, Q. Wang, and D. Branton, Nano Lett. 4, 2293 (2004).
13. D. Fologea, M. Gershow, B. Ledden, D. S. McNabb, J. A. Golovchenko, and J. Li, Nano Lett. 5, 1905 (2005).
14. J. B. Heng, A. Aksimentiev, C. Ho, P. Marks, Y. V. Grinkova, S. Sligar, K. Schulten, and G. Timp, Biophys. J. 90, 1098 (2006).
15. J. Lagerqvist, M. Zwolak, and M. D. Ventra, Nano Lett. 6, 779 (2006).
16. J. Li, D. Stein, C. Mcmullan, D. Branton, M. J. Aziz, and J. A. Golovchenko, Nature (London) 412, 166 (2001).
17. D. Stein, J. Li, and J. A. Golovchenko, Phys. Rev. Lett. 89, 276106 (2002).
18. A. J. Storm. J. H. Chen, X. S. Ling, H. W. Zandbergen, and C. Dekker, Nat. Mater. 2, 537 (2003).
19. C. C. Hartell, S. B. Lee, and C. R. Martin, Anal. Chem. 75, 6861 (2003).
20. S. G. Lemay, D. M. van den Broek, A. J. Storm, D. Krapf, R. M. M. Smeets, H. A. Heering, and C. Dekker, Anal. Chem. 77, 1911 (2005).
21. S. E. Henrickson, M. Misakian, B. Robertson, and J. J. Kasianowich, Phys. Rev. Lett. 85, 3057 (2000).
22. A. Meller, L. Nivon, and D. Branton, Phys. Rev. Lett. 86, 3435 (2001).
23. L. Movileanu and H. Bayley, Proc. Natl. Acad. Sci. U.S.A. 98, 10137 (2001).
24. S. Howorka, L. Movileanu, O. Braha, and H. Bayley, Proc. Natl. Acad. Sci. U.S.A. 98, 12996 (2001).
25. J. Li, M. Gershow, D. Stein, E. Brandin, and J. A. Golovchenko, Nat. Mater. 2, 611 (2003).
26. W. Sung and P. J. Park, Phys. Rev. Lett. 77, 783 (1996).
27. E. A. Di Marzio and A. J. Mandell, J. Chem. Phys. 107, 5510 (1997).
28. P.-G. de Gennes, Adv. Polym. Sci. 138, 91 (1999).
29. P. G. de Gennes, Proc. Natl. Acad. Sci. U.S.A. 96, 7262 (1999).
30. D. K. Lubensky and D. R. Nelson, Biophys. J. 77, 1824 (1999).
31. M. Muthukumar, Phys. Rev. Lett. 86, 3188 (2001).
32. K. L. Sebastian and A. K. R. Paul, Phys. Rev. E 62, 927 (2000).
33. T. Ambjörnsson, S. P. Apell, Z. Konkoli, E. A. Di Marzio, and J. J. Kasianowicz, J. Chem. Phys. 117, 4063 (2002).
34. S.-S. Chern, A. E. Cardenas, and R. D. Coalson, J. Chem. Phys. 115, 7772 (2001).
35. E. Slonkina and A. B. Kolomeisky, J. Chem. Phys. 118, 7112 (2003).
36. H. C. Loebl, R. Randel, S. P. Goodwin, and C. C. Matthai, Phys. Rev. E 67, 041913 (2003).
37. C.-M. Chen, Physica A 350, 95 (2005).
38. Two mpeg movies of our simulations can be found at http://-www.phy.ntnu. edu.tw/~cchen/dna/dna.html.
39. U. H. E. Hansmann, Phys. Rev. Lett. 88, 068105 (2002).
40. C.-M. Chen, Phys. Rev. E 63, 010901 (2001).
41. C.-M. Chen and Y.-A. Fwu, Phys. Rev. E 63, 011506 (2001).
42. C.-M. Chen and P. G. Higgs, J. Chem. Phys. 108, 4305 (1998).
43. J. Dzubiella and J.-P. Hansen, J. Chem. Phys. 122, 234706 (2005).