Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation

Journal of Chemical Physics

Volumn 140, Issue 17, 2014, Pages

  Kekenes Huskey, P M ^a   Gillette, A K ^b   McCammon, J A ^a,c  

^a San Diego   (United States)

^b The University of Arizona   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; ELECTROSTATICS; IONIC STRENGTH; MOLECULAR STRUCTURE; VAN DER WAALS FORCES;

CELLULAR ENVIRONMENT; HOMOGENIZATION THEORY; HYDROPHILIC ENVIRONMENTS; LONG RANGE INTERACTIONS; MACROSCOPIC DIFFUSION; PHYSIOLOGICAL IONIC STRENGTH; POTENTIAL OF MEAN FORCE; SMOLUCHOWSKI EQUATION;

DIFFUSION;

ION; PROTEIN;

BIOPHYSICS; CHEMICAL PHENOMENA; CHEMISTRY; DIFFUSION; STATIC ELECTRICITY; SURFACE PROPERTY; THERMODYNAMICS;

BIOPHYSICAL PROCESSES; DIFFUSION; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; IONS; PROTEINS; STATIC ELECTRICITY; SURFACE PROPERTIES; THERMODYNAMICS;

EID: 84900017459     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4873382     Document Type: Article

References (51)

1. H.-X. Zhou, G. Rivas, and A. P. Minton, Annu. Rev. Biophys. 37, 375 (2008). 10.1146/annurev.biophys.37.032807.125817
2. J. A. Dix and A. S. Verkman, Annu. Rev. Biophys. 37, 247 (2008). 10.1146/annurev.biophys.37.032807.125824
3. P. Setny, R. Baron, P. M. Kekenes-Huskey, J. McCammon, and J. Dzubiella, Proc. Natl. Acad. Sci. U.S.A. 110, 1197 (2013). 10.1073/pnas.1221231110
4. J. A. Morrone, J. Li, and B. J. Berne, J. Phys. Chem. B 116, 378 (2012). 10.1021/jp209568n
5. K. Takahashi, S. N. V. Arjunan, and M. Tomita, FEBS Lett. 579, 1783 (2005). 10.1016/j.febslet.2005.01.072
6. P. Goel, J. Sneyd, and A. Friedman, Multiscale Model. Simul. 5, 1045 (2006). 10.1137/060660783
7. P. Shorten and J. Sneyd, Biophys. J. 96, 4764 (2009). 10.1016/j.bpj.2009.02.060
8. A. W. el Kareh, S. L. Braunstein, and T. W. Secomb, Biophys. J. 64, 1638 (1993). 10.1016/S0006-3495(93)81532-7
9. J. L. Auriault, C. Boutin, and C. Geindreau, Homogenization of Coupled Phenomena in Heterogenous Media (Wiley-ISTE, 2010).
10. C. Moyne and M. A. Murad, Transp. Porous Media 62, 333 (2006). 10.1007/s11242-005-1290-8
11. C. Moyne and M. A. Murad, Transp. Porous Media 63, 13 (2006). 10.1007/s11242-005-1291-7
12. M. Schmuck, J. Appl. Math. Mech./Z. Angew. Math. Mech. 92, 304 (2012). 10.1002/zamm.201100003
13. M. Schmuck, " Modeling and deriving porous media Stokes-Poisson-Nernst-Planck equations by a multiple-scale approach," Commun. Math. Sci. 9, 685-710 (2011). 10.4310/CMS.2011.v9.n3.a3
14. M. Schmuck and M. Z. Bazant, Homogenization of the Poisson-Nernst-Planck Equations for Ion Transport in Charged Porous Media preprint arXiv:1202.1916 (2012).
15. K. Bourbatache, O. Millet, and A. Aït-Mokhtar, " Multi-scale periodic homogenization of ionic transfer in cementitious materials," Advances in Bifurcation and Degradation in Geomaterials, Springer Series in Geomechanics and Geoengineering Vol. 11 (Springer, 2011), p. 117.
16. Y. Cheng, C. A. Chang, Z. Yu, Y. Zhang, M. Sun, T. S. Leyh, M. J. Holst, and J. Andrew McCammon, Biophys. J. 95, 4659 (2008). 10.1529/biophysj.108.140038
17. Y. Cheng, J. K. Suen, D. Zhang, S. D. Bond, Y. Zhang, Y. Song, N. A. Baker, C. L. Bajaj, M. J. Holst, and J. A. McCammon, Biophys. J. 92, 3397 (2007). 10.1529/biophysj.106.102533
18. R. C. Wade, R. R. Gabdoulline, S. K. Lüdemann, and V. Lounnas, Proc. Natl. Acad. Sci. U.S.A. 95, 5942 (1998). 10.1073/pnas.95.11.5942
19. P. Kekenes-Huskey, A. Gillette, J. Hake, and J. McCammon, Comput. Sci. Discovery 5, 014015 (2012). 10.1088/1749-4699/5/1/014015
20. A. M. Berezhkovskii, A. Szabo, and H.-X. Zhou, J. Chem. Phys. 135, 075103 (2011). 10.1063/1.3609973
21. G. Hummer, New J. Phys. 7, 34 (2005). 10.1088/1367-2630/7/1/034
22. R. A. R. de Graaf, A. A. van Kranenburg, and K. K. Nicolay, Biophys. J. 78, 1657 (2000). 10.1016/S0006-3495(00)76717-8
23. A. Logg, G. N. Wells, and J. Hake, " DOLFIN: A C++/Python finite element library," Automated Solution of Differential Equations by the Finite Element Method (Springer, 2012).
24. P. M. Kekenes-Huskey, T. Liao, A. K. Gillette, J. E. Hake, Y. Zhang, A. P. Michailova, A. D. Mcculloch, and J. A. McCammon, Biophys. J. 105, 2130 (2013). 10.1016/j.bpj.2013.09.020
25. Z. Hashin and S. Shtrikman, Phys. Rev. 130, 129 (1963). 10.1103/PhysRev.130.129
26. M. Vendelin and R. Birkedal, Am. J. Physiol.: Cell Physiol. 295, C1302 (2008). 10.1152/ajpcell.00313.2008
27. K. Bourbatache, O. Millet, and A. Aït-Mokhtar, Int. J. Heat Mass Transfer 55, 5979 (2012). 10.1016/j.ijheatmasstransfer.2012.06.008
28. M. Jardat, B. Hribar-Lee, V. Dahirel, and V. Vlachy, J. Chem. Phys. 137, 114507 (2012). 10.1063/1.4752111
29. R. A. Aldoroty, N. B. Garty, and E. W. April, Biophys. J. 51, 371 (1987). 10.1016/S0006-3495(87)83359-3
30. J. N. Israelachvili, Intermolecular and Surface Forces (Academic Press, 2011).
31. S. R. McGuffee and A. H. Elcock, PLoS Comput. Biol. 6, e1000694 (2010). 10.1371/journal.pcbi.1000694
32. M. Farnum and C. Zukoski, Biophys. J. 76, 2716 (1999). 10.1016/S0006-3495(99)77424-2
33. J. J. Smith and I. Zharov, Langmuir 24, 2650 (2008). 10.1021/la7013072
34. C. Eun, P. Kekenes-Huskey, and J. McCammon, J. Chem. Phys. 140, 105101 (2014). 10.1063/1.4867286
35. R. Zwanzig, Proc. Natl. Acad. Sci. 85, 2029 (1988). 10.1073/pnas.85.7. 2029
36. J. Hou, Z. Zhang, and L. A. Madsen, J. Phys. Chem. B 115, 4576 (2011). 10.1021/jp1110899
37. J. Wagner and J. Keizer, Biophys. J. 67, 447 (1994). 10.1016/S0006- 3495(94)80500-4
38. Y. Cheng, Z. Yu, M. Hoshijima, M. J. Holst, A. D. Mcculloch, J. A. McCammon, and A. P. Michailova, PLoS Comput. Biol. 6, e1000972 (2010). 10.1371/journal.pcbi.1000972
39. L. Spyracopoulos, M. X. Li, S. K. Sia, S. M. Gagné, M. Chandra, R. J. Solaro, and B. D. Sykes, Biochemistry 36, 12138 (1997). 10.1021/bi971223d
40. D. Ermak and J. McCammon, J. Chem. Phys. 69, 1352 (1978). 10.1063/1.436761
41. T. T. Ando and J. J. Skolnick, Proc. Natl. Acad. Sci. 107, 18457 (2010). 10.1073/pnas.1011354107
42. A. Kaintz, G. Baker, A. Benesi, and M. Maroncelli, J. Phys. Chem. B 117, 11697 (2013). 10.1021/jp405393d
43. J. Rotne, J. Chem. Phys. 50, 4831 (1969). 10.1063/1.1670977
44. G.-R. Liu and N.-R. Shieh, in CORD Conference Proceedings, 2010.
45. B. Li, Nonlinearity 22, 811 (2009). 10.1088/0951-7715/22/4/007
46. J. H. G. M. van Beek, Am. J. Physiol.: Cell Physiol. 293, C815 (2007). 10.1152/ajpcell.00355.2006
47. A. E. Alekseev, S. Reyes, V. A. Selivanov, P. P. Dzeja, and A. Terzic, J. Mol. Cell. Cardiol. 52, 401 (2012). 10.1016/j.yjmcc.2011.06.007
48. B. Lygren, C. R. Carlson, K. Santamaria, V. Lissandron, T. McSorley, J. Litzenberg, D. Lorenz, B. Wiesner, W. Rosenthal, M. Zaccolo, K. Tasken, and E. Klussmann, EMBO Rep. 8, 1061 (2007). 10.1038/sj.embor.7401081
49. I. M. Sokolov, R. Metzler, K. Pant, and M. C. Williams, Biophys. J. 89, 895 (2005). 10.1529/biophysj.104.057612
50. R. Alsallaq and H.-X. Zhou, J. Chem. Phys. 128, 115108 (2008). 10.1063/1.2888996
51. See supplementary material at http://dx.doi.org/10.1063/1.4873382 E-JCPSA6-140-034417 for derivation of the homogenized Smoluchowski equation, preparation of finite element meshes, definition of interaction potentials, and model validation.