Applying ICC*to DNA translocation: Effect of dielectric boundaries

Computer Physics Communications

Volumn 182, Issue 1, 2011, Pages 33-35

  Kesselheim, Stefan ^a   Sega, Marcello ^b   Holm, Christian ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

^b UNIVERSITY OF TRENTO   (Italy)

Author keywords

Dielectric boundary force; DNA translocation; Electrostatic algorithm; Molecular dynamics

Indexed keywords

ALGORITHMS; DNA; ELECTROSTATICS;

DIELECTRIC BOUNDARY; DIELECTRIC CONTRASTS; DNA TRANSLOCATION; LOW SALT CONCENTRATION; MEMBRANE MATERIAL; MOLECULAR DYNAMICS SIMULATIONS; SINGLE DNA MOLECULES; SYNTHETIC NANOPORES; TRANSLOCATION PROCESS;

MOLECULAR DYNAMICS;

EID: 84962339837     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cpc.2010.08.014     Document Type: Conference Paper

References (32)

1. J. Warwicker, and H. Watson J. Mol. Biol. 157 1982 671 679
2. D. Levitt Biophys. J. 22 1978 209 219
3. B. Honig, K. Sharp, and A. Yang J. Phys. Chem. 97 1993 1101 1109
4. S. Miertus, E. Scrocco, and J. Tomasi Chem. Phys. 55 1981 117
5. P.B. Shaw Phys. Rev. A 32 1985 2476 2487
6. D. Chipman J. Chem. Phys. 120 2004 5566
7. D. Boda, D. Gillespie, W. Nonner, D. Henderson, and B. Eisenberg Phys. Rev. E 69 2004 046702
8. R. Allen, J.P. Hansen, and S. Melchionna Phys. Chem. Chem. Phys. 3 2001 4177 4186
9. J. Tomasi, and M. Persico Chem. Rev. 94 1994 2027
10. J. Bardhan, R. Eisenberg, and D. Gillespie Phys. Rev. E 80 2009 11906
11. B. Lu, X. Cheng, J. Huang, and J.A. McCammon Proc. Natl. Acad. Sci. (USA) 103 2006 19314
12. M. Fenley, W. Olson, K. Chua, and A. Boschitsch J. Comput. Chem. 17 1996 976 991
13. R. Zauhar, and A. Varnek J. Comput. Chem. 17 1996 864 877
14. E. Purisima J. Comput. Chem. 19 1998 1494 1504
15. A. Bordner, and G. Huber J. Comput. Chem. 24 2003 353 367
16. R. Bharadwaj, A. Windemuth, S. Sridharan, B. Honig, and A. Nicholls J. Comput. Chem. 16 1995 898 913
17. S. Tyagi, M. Süzen, M. Sega, M. Barbosa, S.S. Kantorovich, and C. Holm J. Chem. Phys. 132 2010 154112
18. R.W. Hockney, and J.W. Eastwood Computer Simulations Using Particles 1981 McGraw-Hill New York
19. M. Deserno, and C. Holm J. Chem. Phys. 109 1998 7678
20. M. Deserno, and C. Holm J. Chem. Phys. 109 1998 7694
21. A. Arnold, J. de Joannis, and C. Holm J. Chem. Phys. 117 2002 2496 2502
22. A. Arnold, J. de Joannis, and C. Holm J. Chem. Phys. 117 2002 2503 2512
23. A. Arnold, and C. Holm Comput. Phys. Commun. 148 2002 327 348
24. A. Arnold, and C. Holm J. Chem. Phys. 123 2005 144103
25. A. Bródka J. Chem. Phys. 125 2006 107103
26. L.N.A. Meller, and D. Branton Phys. Rev. Lett. 86 2001 3435
27. C. Dekker Nature Nanotech. 2 2007 209 215
28. S. Howorka, and Z. Siwy Chem. Soc. Rev. 38 2009 2360 2384
29. A. Storm, C. Storm, J. Chen, H. Zandbergen, J. Joanny, and C. Dekker Nano Lett. 5 2005 1193 1197
30. D.J. Bonthuis, J. Zhang, B. Hornblower, J. Mathé, B.I. Shklovskii, and A. Meller Phys. Rev. Lett. 97 2006 128104
31. M. Fixman, and J. Skolnick Macromolecules 11 1978 863
32. Y. Rabin, and M. Tanaka Phys. Rev. Lett. 94 2005 148103