Incorporation of inhomogeneous ion diffusion coefficients into kinetic lattice grand canonical Monte Carlo simulations and application to ion current calculations in a simple model ion channel

Journal of Physical Chemistry A

Volumn 111, Issue 49, 2007, Pages 12506-12512

  Hwang, Hyonseok ^a   Schatz, George C ^b   Ratner, Mark A ^b  

^a Kangwon National University   (South Korea)

^b NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ION CURRENTS; KLGCMC CALCULATIONS; KLGCMC SIMULATION METHOD;

ALGORITHMS; DIFFUSION; MONTE CARLO METHODS; REACTION KINETICS;

IONS;

EID: 38049129674     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp075838o     Document Type: Article

References (36)

1. Graf, P.; Nitzan, A.; Kurnikova, M. G.; Coalson, R. D. J. Phys. Chem. B 2000, 104, 12324.
2. van der Straaten, T.; Kathawala, G.; Ravaioli, U. J. Comput. Electron. 2003, 2, 231.
3. Cheng, M. H.; Caseio, M.; Coalson, R. D. Biophys. J. 2005, 89, 1669.
4. Hwang, H.; Schatz, G. C.; Ratner, M. A. J. Chem Phys. 2007, 127, 024706.
5. Corry, B.; Kuyucak, S.; Chung, S. H. Biophys. J. 2000, 78, 2364.
6. Im, W.; Roux, B. J. Mol. Biol. 2002, 322, 851.
7. Burykin, A.; Schutz, G N.; Villa, J.; Warshel, A. Proteins 2002, 47, 265.
8. Marreiro, D.; Tang, Y.; Aboud, S.; Jakobsson, E.; Saraniti, M. J. Comput. Electron. 2007, 6, 377.
9. Hille, B. Ionic Channels of Excitable Membranes, 3rd ed,; Sinauer Associates, Inc.: Sunderland, MA, 2001.
10. Jakobsson, E. Methods 1998, 14, 342.
11. Roux, B. Curr. Opin. Struct. Biol. 2002, 12, 182.
12. Eisenberg, B. Biophys. Chem. 2003, 100, 507.
13. Smith, G. R.; Sansom, S. P. Biophys. J. 1998, 75, 2767.
14. Warshel, A. Acc. Chem. Res. 2002, 35, 385.
15. Allen, T. W.; Andersen, O. S.; Roux, B. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 117.
16. Hwang, H.; Schatz, G. C.; Ratner, M. A. J. Phys. Chem. B 2006, 110, 26448.
17. Chen, D.; Lear, J. D.; Eisenberg, R. S. Biophys. J. 1997, 72, 97.
18. Kurnikova, M. G.; Coalson, R. D.; Graf, P.; Nitzan, A. Biophys. J. 1999, 76, 642.
19. van der Straaten, T. A.; Tang, J.; Ravaioli, U.; Eisenberg, R. S.; Aluru, N. R. J. Comput. Electron. 2003, 2, 29.
20. Hwang, H.; Schatz, G. C.; Ratner, M. A. J. Phys. Chem. B 2006, 110, 6999.
21. Natori, A.; Godby, R. W. Phys. Rev. B 1993, 47, 15816.
22. Righi, M. C.; Pignedoli, C. A.; Felice, R. D.; Bertoni, C. M. Phys. Rev. B 2005, 71, 075303.
23. Oum, L.; Parrando, J. M. R.; Martinez, H. L. Phys. Rev. E 2003, 67, 011106.
24. Farnell, L.; Gibson, W. G. J. Comput. Phys 2005, 208, 253.
25. Gillespie, D. J. Phys. Chem. 1977, 81, 2340.
26. Fichthom, K.; Weinberg, W. H. J. Chem. Phys. 1991, 95, 1090.
27. Valleau, J. P.; Cohen, L. K. J. Chem. Phys. 1980, 72, 5935.
28. Torrie, G. M.; Valleau, J. P. J. Chem Phys. 1980, 73, 5807.
29. Torrie, G. M.; Valleau, J. P. J. Phys. Chem. 1982, 86, 3251.
30. Papadopoulou, A.; Becker, E. D.; Lupkowski, M.; van Swol, F. J. Chem. Phys. 1993, 98, 4897.
31. Hoyles, M.; Kuyucak, S.; Chung, S.-H. Phys. Rev. E 1998, 58, 3654.
32. Im, W.; Roux, B. J. Chem. Phys. 2001, 115, 4850.
33. Gillespie, D.; Nonner, W.; Eisenberg, R. S. Phys. Rev. E 2003, 68, 031503.
34. Gillespie, D.; Valisko, M.; Boda, D. J. Phys. Condens. Matter 2005, 17, 6609.
35. Jang, J.; Hong, S.; Schatz, G. C.; Ratner, M. A. J. Chem. Phys. 2001, 115, 2721.
36. Lee, N.-K.; Hong, S. J. Chem. Phys. 2006, 124, 114711.