Computational Issues in Modeling Ion Transport in Biological Channels: Self-Consistent Particle-Based Simulations

Journal of Computational Electronics

Volumn 2, Issue 2-4, 2003, Pages 239-243

  Aboud, S ^a,b   Saraniti, M ^a,b   Eisenberg, R ^a  

^a RUSH MEDICAL COLLEGE   (United States)

^b Illinois Institute of Technology   (United States)

Author keywords

ion channels; KcsA; Langevin dynamics; lipid bilayer; MthK; nonequilibrium ionic transport

Indexed keywords

ELECTROLYTES; IONS; LIPID BILAYERS; PHOSPHOLIPIDS; POTASSIUM; PROTEINS;

ION CHANNEL; IONIC TRANSPORTS; KCSA; LANGEVIN DYNAMICS; MTHK;

BIOINFORMATICS;

EID: 12344316628     PISSN: 15698025     EISSN: 15728137     Source Type: Journal    
DOI: 10.1023/B:JCEL.0000011431.17843.a6     Document Type: Article

References (24)

1. B. Hille, Ionic Channels of Excitable Membranes, Sinauer, Massachusetts (1992).
2. D.A. Doyle, J.M. Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohne, B.T. Cahit, and R. MacKinnon, Science, 280, 69 (1998).
3. Y. Jiang, A. Lee, J. Chen, M. Cadene, B.T. Chait, and R. MacKinnon, Nature, 417, 515 (2002).
4. C. Millar, A. Asenov, S. Roy, and J.M. Cooper, Journal of Computational Electronics, 1, 405 (2002).
5. M. Saraniti, S.J. Wigger, Z. Schuss, and R.S. Eisenberg, in Proceedings of 2002 International Conference on Modeling and Simulation of Microsystems-MSM2002 (S. Juan, PR, April 2002).
6. R.J. Mashl, Y. Tang, J. Schnizer, and E. Jakobsson, Biophysics Journal, in press.
7. W. Im and B. Roux, Journal of Chemical Physics, 115, 4850 (2001).
8. S.-H. Chung, T.W. Allen, and S. Kuyucak, Biophysics Journal, 82, 628 (2002).
9. M.B. Partenski and P.C. Jordan, Journal of Physical Chemistry, 96, 3906 (1992).
10. C.N. Schultz and A. Warshel, Proteins, 44, 400 (2001).
11. www.gromacs.org
12. P.E. Kloeden and E. Platen, in Applications of Mathematics (Springer-Verlag, 1999).
13. R.W. Hockney and J.W. Eastwood, Computer Simulation Using Particles (Adam Hilger, Bristol, 1988).
14. C.J. Worldelman and U. Ravaioli, IEEE Transaction of Electron Devices, 47(2), 410 (2000).
15. D.A. McQuarrie, Statistical Mechanics (University Science Books, Saualito, CA, 2000).
16. V. Bacilon, D. Chen, R.S. Eisenberg, and M.A. Ratner, Journal of Chemical Physics, 98, 1193 (1993).
17. W. Hackbush, Multi-Grid Methods and Applications (Springer-Verlag, Berlin, 1985).
18. V.M.M. Lobo, Electrolyte Solutions: Literature Data on Thermodynamic and Transport Properties, (Coimbra, 1975) vol. 2.
19. J.M.G. Barthel, Physical Chemistry of Electrolyte Solutions, Topics in Physical Chemistry 5 (Springer, Steinkopf, 1998).
20. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne, The Protein Data Bank, Nucleic Acid Research, 28, 235 (2000).
21. J.D. Faraldo-Gómez, G.R. Smith, and M.S.P. Sansom, European Biophysics Journal, 31, 217 (2002).
22. D.P. Tieleman, M.S.P. Sansom, and H.J.C. Berendsen, Biophysics Journal, 76, 40 (1999).
23. J.M. Berg, J.L. Tymoczko, and L. Stryer, Biochemistry (W.H. Freeman and Company, New York, 2002).
24. M.F. Sanner, A.J. Olson, and J.C. Spehner, Biopolymers, 38, 305 (1996).