Simulation of steady-state diffusion: Driving force ensured by dual control volumes or local equilibrium Monte Carlo

Journal of Chemical Physics

Volumn 137, Issue 5, 2012, Pages

  Ható, Zoltán ^a   Boda, Dezsö ^a   Kristóf, Tamás ^a  

^a UNIVERSITY OF PANNONIA   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

ADJUSTABLE PARAMETERS; COMPARATIVE ANALYSIS; CONTROL-CELL; DIFFUSIVE TRANSPORT; DIRECT SIMULATION; DRIVING FORCES; DUAL CONTROL; DYNAMIC MONTE CARLO; EMPIRICAL METHOD; GRAND CANONICAL MONTE CARLO SIMULATION; LOCAL EQUILIBRIUM; MEMBRANE TRANSPORT; MOLECULAR SYSTEMS; MONTE CARLO; SIMULATION DOMAIN; SIMULATION METHODS; STEADY STATE DIFFUSION; STEADY-STATE TRANSPORT; SUBVOLUMES; TRANSPORT EQUATION;

DIFFUSION; MOLECULAR DYNAMICS; VARACTORS;

MONTE CARLO METHODS;

EID: 84864856787     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4739255     Document Type: Article

References (71)

1. J. W. Gibbs, Elementary Principles in Statistical Mechanics (Yale University, New Haven, CT, 1902).
2. R. S. Berry, S. A. Rice, and J. Ross, Physical Chemistry, 2nd ed. (Oxford University Press, New York, 2000).
3. D. A. McQuarrie, Statistical Mechanics (University Science Books, Sausalito, CA, 2000).
4. T. L. Beck, M. E. Paulaitis, and L. R. Pratt, The Potential Distribution Theorem and Models of Molecular Solutions (Cambridge University Press, Cambridge, 2006).
5. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford University Press, New York, 1987).
6. D. Frenkel and B. Smit, Understanding Molecular Simulations (Academic, San Diego, 1996).
7. R. J. Sadus, Molecular Simulation of Fluids: Theory, Algorithms, and Object-Orientation (Elsevier, Amsterdam, 1999).
8. P. Attard, Thermodynamics and Statistical Mechanics, Equilibrium by Entropy Maximisation (Academic, London, 2002).
9. P. Attard, Annu. Rep. Prog. Chem., Sect. C: Phys. Chem. 105, 63 (2009). 10.1039/b802697c
10. B. Eisenberg, Y.-K. Hyon, and C. Liu, J. Chem. Phys. 133, 104104 (2010). 10.1063/1.3476262
11. C. W. Gardiner, Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences, 2nd ed. (Springer, 1994).
12. B. Dünweg, Langevin methods., in Computer Simulations of Surfaces and Interfaces, Proceedings of the NATO Advanced Study Institute (Kluwer Academic, 2003), pp. 77-92.
13. G. S. Heffelfinger and F. van Swol, J. Chem. Phys. 100, 7548 (1994). 10.1063/1.466849
14. W. Im, S. Seefeld, and B. Roux, Biophys. J. 79, 788 (2000). 10.1016/S0006-3495(00)76336-3
15. M. Lísal, J. K. Brennan, W. R. Smith, and F. R. Siperstein, J. Chem. Phys. 121, 4901 (2004). 10.1063/1.1782031
16. P. Pohl, G. Heffelfinger, and D. Smith, Mol. Phys. 89, 1725 (1996). 10.1080/00268979609482570
17. E. Enciso, N. G. Almarza, S. Murad, and M. A. Gonzalez, Mol. Phys. 100, 2337 (2002). 10.1080/00268970210124819
18. H. E. A. Huitema and J. P. van der Eerden, J. Chem. Phys. 110, 3267 (1999). 10.1063/1.478192
19. M. G. Martin, A. P. Thompson, and T. Nenoff, J. Chem. Phys. 114, 7174 (2001). 10.1063/1.1360256
20. L. Berthier, Phys. Rev. E 76, 011507 (2007). 10.1103/PhysRevE.76.011507
21. G. Rutkai and T. Kristóf, J. Chem. Phys. 132, 124101 (2010). 10.1063/1.3359434
22. G. Rutkai, D. Boda, and T. Kristóf, J. Phys. Chem. Lett. 1, 2179 (2010). 10.1021/jz100718n
23. E. Csányi, D. Boda, D. Gillespie, and T. Kristóf, Biochim. Biophys. Acta 1818, 592 (2012). 10.1016/j.bbamem.2011.10.029
24. Y. G. Seo, G. H. Kum, and N. A. Seaton, J. Membr. Sci. 195, 65 (2002). 10.1016/S0376-7388(01)00549-X
25. D. Boda and D. Gillespie, J. Chem. Theor. Comput. 8, 824 (2012). 10.1021/ct2007988
26. I. Prigogine, Introduction to Thermodynamics of Irreversible Processes (Wiley, New York, 1961).
27. H. J. Kreuzer, Nonequilibrium Thermodynamics and its Statistical Foundations (Clarendon, Oxford, 1981).
28. S. R. de Groot and P. Mazur, Non-Equilibrium Thermodynamics (Dover, New York, 1984).
29. N. W. Tschoegl, Fundamentals of Equilibrium and Steady-State Thermodynamics (Elsevier, Amsterdam, 2000).
30. M. le Bellac, F. Mortessagne, and G. G. Batrouni, Equilibrium and Non-Equilibrium Statistical Thermodynamics (Cambridge University Press, New York, 2004).
31. D. J. Evans and G. Morriss, Statistical Mechanics of Nonequilibrium Liquids (Cambridge University Press, New York, 2008).
32. G. Lebon, D. Jou, and J. Casas-Vázquez, Understanding Non-equilibrium Thermodynamics: Foundations, Applications, Frontiers (Springer, Berlin, 2008).
33. D. Gillespie, L. Xu, Y. Wang, and G. Meissner, J. Phys. Chem. B 109, 15598 (2005). 10.1021/jp052471j
34. D. Gillespie, Biophys. J. 94, 1169 (2008). 10.1529/biophysj.107.116798
35. D. Boda, M. Valiskó, D. Henderson, B. Eisenberg, D. Gillespie, and W. Nonner, J. Gen. Physiol. 133, 497 (2009). 10.1085/jgp.200910211
36. J. Powles, S. Murad, and P. Ravi, Chem. Phys. Lett. 188, 21 (1992). 10.1016/0009-2614(92)85082-L
37. A. Malasics, D. Gillespie, and D. Boda, J. Chem. Phys. 128, 124102 (2008). 10.1063/1.2839302
38. A. Malasics and D. Boda, J. Chem. Phys. 132, 244103 (2010). 10.1063/1.3443558
39. D. A. Kofke and B. C. Mihalick, Fluid Phase Equilib. 194-197, 327 (2002). 10.1016/S0378-3812(01)00685-9
40. Z. Schuss, B. Nadler, and R. S. Eisenberg, Phys. Rev. E 64, 036116 (2001). 10.1103/PhysRevE.64.036116
41. G. Arya, H. C. Chang, and E. J. Maginn, J. Chem. Phys. 115, 8112 (2001). 10.1063/1.1407002
42. A. Bortz, M. Kalos, and J. Lebowitz, J. Comput. Phys. 17, 10 (1975). 10.1016/0021-9991(75)90060-1
43. D. T. Gillespie, J. Comput. Phys. 22, 403 (1976). 10.1016/0021-9991(76) 90041-3
44. D. T. Gillespie, J. Phys. Chem. 81, 2340 (1977). 10.1021/j100540a008
45. G. H. Gilmer, Science 208, 355 (1980). 10.1126/science.208.4442.355
46. A. F. Voter, Phys. Rev. B 34, 6819 (1986). 10.1103/PhysRevB.34.6819
47. K. Binder, Monte Carlo Methods in Statistical Physics (Springer, Heidelberg, 1979).
48. B. Widom, J. Chem. Phys. 39, 2808 (1963). 10.1063/1.1734110
49. B. Widom, J. Stat. Phys. 19, 563 (1978). 10.1007/BF01011768
50. J. Xu, S. Kjelstrup, and D. Bedeaux, Phys. Chem. Chem. Phys. 8, 2017 (2006). 10.1039/b516704c
51. S. Kjelstrup, D. Bedeaux, I. Inzoli, and J.-M. Simon, Energy 33, 1185 (2008). 10.1016/j.energy.2008.04.005
52. D. Chen, J. Lear, and B. Eisenberg, Biophys. J. 72, 97 (1997). 10.1016/S0006-3495(97)78650-8
53. W. Nonner and B. Eisenberg, Biophys. J. 75, 1287 (1998). 10.1016/S0006-3495(98)74048-2
54. B. Corry, S. Kuyucak, and S. H. Chung, Biophys. J. 78, 2364 (2000). 10.1016/S0006-3495(00)76781-6
55. P. Graf, M. G. Kurnikova, R. D. Coalson, and A. Nitzan, J. Phys. Chem. B 108, 2006 (2004). 10.1021/jp0355307
56. S. Y. Noskov, W. Im, and B. Roux, Biophys. J. 87, 2299 (2004). 10.1529/biophysj.104.044008
57. D. Constantin and Z. S. Siwy, Phys. Rev. E 76, 041202 (2007). 10.1103/PhysRevE.76.041202
58. Q. Zheng, D. Chen, and G.-W. Wei, J. Comput. Phys. 230, 5239 (2011). 10.1016/j.jcp.2011.03.020
59. D. Gillespie, W. Nonner, and R. S. Eisenberg, J. Phys.: Condens. Matter 14, 12129 (2002). 10.1088/0953-8984/14/46/317
60. D. Gillespie, W. Nonner, and R. S. Eisenberg, Phys. Rev. E 68, 031503 (2003). 10.1103/PhysRevE.68.031503
61. W. Almers, E. W. McCleskey, and P. T. Palade, J. Physiol. 353, 565 (1984).
62. W. Almers and E. W. McCleskey, J. Physiol. 353, 585 (1984).
63. W. A. Sather and E. W. McCleskey, Annu. Rev. Physiol. 65, 133 (2003). 10.1146/annurev.physiol.65.092101.142345
64. D. Gillespie and D. Boda, Biophys. J. 95, 2658 (2008). 10.1529/biophysj.107.127977
65. W. Nonner, D. P. Chen, and B. Eisenberg, Biophys. J. 74, 2327 (1998). 10.1016/S0006-3495(98)77942-1
66. W. Nonner, L. Catacuzzeno, and B. Eisenberg, Biophys. J. 79, 1976 (2000). 10.1016/S0006-3495(00)76446-0
67. B. Corry, T. W. Allen, S. Kuyucak, and S. H. Chung, Biophys. J. 80, 195 (2001). 10.1016/S0006-3495(01)76007-9
68. D. Boda, M. Valiskó, B. Eisenberg, W. Nonner, D. Henderson, and D. Gillespie, J. Chem. Phys. 125, 034901 (2006). 10.1063/1.2212423
69. G. Rutkai, E. Csányi, and T. Kristóf, Microporous Mesoporous Mater. 114, 455 (2008). 10.1016/j.micromeso.2008.01.044
70. D. M. Ford and E. D. Glandt, J. Membr. Sci. 107, 47 (1995). 10.1016/0376-7388(95)00101-H
71. J. Kärger, Adsorption 9, 29 (2003). 10.1023/A:1023811229823