Discretization of the induced-charge boundary integral equation

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 80, Issue 1, 2009, Pages

  Bardhan, Jaydeep P ^a,b   Eisenberg, Robert S ^a,b   Gillespie, Dirk ^b  

^a ARGONNE NATIONAL LABORATORY   (United States)

^b RUSH UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BOUNDARY ELEMENT METHOD; BOUNDARY INTEGRAL EQUATIONS; BUILDING MATERIALS;

AQUEOUS SOLUTIONS; BOUNDARY ELEMENTS; COLLOCATION METHOD; COMPUTATIONAL TIME; DIELECTRIC BOUNDARY; DIELECTRIC INTERFACE; DISCRETIZATIONS; ELEMENT METHOD; FLAT TILES; INDUCED CHARGES; MATRIX; MATRIX ELEMENTS; NUMERICAL CHALLENGES; POLARIZATION CHARGES; PROTEIN FUNCTIONS; QUALOCATION METHOD;

ELECTROMAGNETIC INDUCTION;

EID: 84962460748     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.80.011906     Document Type: Article

References (100)

1. D. E. Clapham, Cell 131, 1047 (2007). 10.1016/j.cell.2007.11.028 (Pubitemid 350258556)
2. P. Graf, M. G. Kurnikova, R. D. Coalson, and A. Nitzan, J. Phys. Chem. B 108, 2006 (2004). 10.1021/jp0355307
3. D. Boda, M. Voliskó, B. Eisenberg, W. Nonner, D. Henderson, and D. Gillespie, J. Chem. Phys. 125, 034901 (2006). 10.1063/1.2212423 (Pubitemid 44107163)
4. T. Baştuǧ and S. Kuyucak, Biophys. J. 84, 2871 (2003). 10.1016/S0006-3495(03)70015-0
5. J. M. G. Barthel, H. Krienke, and W. Kunz, Physical Chemistry of Electrolyte Solutions: Modern Aspects, 1st ed. (Steinkopff-Verlag, 2002).
6. B. Svensson, B. Jonsson, C. E. Woodward, and S. Linse, Biochemistry 30, 5209 (1991). 10.1021/bi00235a014
7. W. Nonner, L. Catacuzzeno, and B. Eisenberg, Biophys. J. 79, 1976 (2000). 10.1016/S0006-3495(00)76446-0
8. V. Dahirel, M. Jardat, J.-F. Dufrêche, and P. Turq, J. Chem. Phys. 127, 095101 (2007). 10.1063/1.2767626 (Pubitemid 47381288)
9. J. Warwicker and H. C. Watson, J. Mol. Biol. 157, 671 (1982). 10.1016/0022-2836(82)90505-8
10. K. A. Sharp and B. Honig, Annu. Rev. Biophys. Biophys. Chem. 19, 301 (1990). 10.1146/annurev.bb.19.060190.001505
11. K. A. Sharp and B. Honig, J. Phys. Chem. 94, 7684 (1990). 10.1021/j100382a068
12. A. H. Juffer, E. F. F. Botta, B. A. M. van Keulen, A. van der Ploeg, and H. J. C. Berendsen, J. Comput. Phys. 97, 144 (1991). 10.1016/0021-9991(91)90043- K
13. B. Honig, K. Sharp, and A. S. Yang, J. Phys. Chem. 97, 1101 (1993). 10.1021/j100108a002
14. M. J. Holst, Ph.D. thesis, University of Illinois at Urbana-Champaign, 1993.
15. H. X. Zhou, J. Chem. Phys. 100, 3152 (1994). 10.1063/1.466406
16. N. A. Baker, D. Sept, M. J. Holst, and J. A. McCammon, Proc. Natl. Acad. Sci. U.S.A. 98, 10037 (2001). 10.1073/pnas.181342398 (Pubitemid 32802969)
17. W. Rocchia, E. Alexov, and B. Honig, J. Phys. Chem. B 105, 6507 (2001). 10.1021/jp010454y (Pubitemid 35339019)
18. N. A. Baker, Rev. Comput. Chem. 21, 349 (2005). 10.1002/0471720895.ch5
19. C. Bertonati, B. Honig, and E. Alexov, Biophys. J. 92, 1891 (2007). 10.1529/biophysj.106.092122 (Pubitemid 46495254)
20. S. N. Yu, Y. C. Zhou, and G. W. Wei, J. Comput. Phys. 224, 729 (2007). 10.1016/j.jcp.2006.10.030
21. B. Lu, Y. C. Zhou, M. J. Holst, and J. A. McCammon, Comm. Comp. Phys. 3, 973 (2008).
22. M. D. Altman, J. P. Bardhan, J. K. White, and B. Tidor, J. Comput. Chem. 30, 132 (2009). 10.1002/jcc.21027
23. N. A. Simonov, M. Mascagni, and M. O. Fenley, J. Chem. Phys. 127, 185105 (2007). 10.1063/1.2803189 (Pubitemid 350115950)
24. S. J. de Carvalho, M. O. Fenley, and F. L. B. da Silva, J. Phys. Chem. B 112, 16766 (2008). 10.1021/jp800783x
25. N. V. Prabhu, M. Panda, Q. Yang, and K. A. Sharp, J. Comput. Chem. 29, 1113 (2008). 10.1002/jcc.20874
26. D. Boda, M. Valiskó, D. Henderson, D. Gillespie, B. Eisenberg, and M. K. Gilson, Biophys. J. 96, 1293 (2009). 10.1016/j.bpj.2008.10.059
27. C. Tanford and J. G. Kirkwood, J. Am. Chem. Soc. 79, 5333 (1957). 10.1021/ja01577a001
28. M. K. Gilson, A. Rashin, R. Fine, and B. Honig, J. Mol. Biol. 183, 503 (1985). 10.1016/0022-2836(85)90297-9 (Pubitemid 15013023)
29. I. Klapper, R. Hagstrom, R. Fine, K. Sharp, and B. Honig, Proteins 1, 47 (1986). 10.1002/prot.340010109 (Pubitemid 17073401)
30. M. Holst and F. Saied, J. Comput. Chem. 14, 105 (1993). 10.1002/jcc.540140114
31. K. E. Atkinson, The Numerical Solution of Integral Equations of the Second Kind (Cambridge University Press, Cambridge, England, 1997).
32. P. B. Shaw, Phys. Rev. A 32, 2476 (1985). 10.1103/PhysRevA.32.2476
33. D. G. Levitt, Biophys. J. 22, 209 (1978). 10.1016/S0006-3495(78)85485-X
34. P. C. Jordan, Biophys. J. 39, 157 (1982). 10.1016/S0006-3495(82)84503-7
35. P. C. Jordan, Biophys. J. 41, 189 (1983). 10.1016/S0006-3495(83)84419-1
36. M. Hoyles, S. Kuyucak, and S.-H. Chung, Biophys. J. 70, 1628 (1996). 10.1016/S0006-3495(96)79726-6
37. M. Hoyles, S. Kuyucak, and S.-H. Chung, Comput. Phys. Commun. 115, 45 (1998). 10.1016/S0010-4655(98)00090-3
38. S. Mierts̈, E. Scrocco, and J. Tomasi, Chem. Phys. 55, 117 (1981). 10.1016/0301-0104(81)85090-2
39. J. Tomasi, B. Mennucci, and R. Cammi, Chem. Rev. (Washington, D.C.) 105, 2999 (2005). 10.1021/cr9904009 (Pubitemid 41222791)
40. D. N. Chipman, Theor. Chem. Acc. 107, 80 (2002). 10.1007/s00214-001-0302- 1 (Pubitemid 40835028)
41. R. J. Zauhar and R. S. Morgan, J. Mol. Biol. 186, 815 (1985). 10.1016/0022-2836(85)90399-7
42. R. J. Zauhar and R. S. Morgan, J. Comput. Chem. 9, 171 (1988). 10.1002/jcc.540090209
43. R. J. Zauhar and R. S. Morgan, J. Comput. Chem. 11, 603 (1990). 10.1002/jcc.540110509
44. R. J. Zauhar and A. Varnek, J. Comput. Chem. 17, 864 (1996). 10.1002/(SICI)1096-987X(199605)17:7<864::AID-JCC10>3.0.CO;2-B
45. J. Liang and S. Subramaniam, Biophys. J. 73, 1830 (1997). 10.1016/S0006-3495(97)78213-4
46. L. Greengard and V. Rokhlin, J. Comput. Phys. 73, 325 (1987). 10.1016/0021-9991(87)90140-9
47. L. Greengard, The Rapid Evaluation of Potential Fields in Particle Systems (MIT Press, Cambridge, MA, 1988).
48. J. Tausch, J. Wang, and J. White, IEEE Trans. Comput.-Aided Des. 20, 1398 (2001). 10.1109/43.969433 (Pubitemid 34035688)
49. L. Greengard and J.-Y. Lee, J. Comput. Phys. 211, 64 (2006). 10.1016/j.jcp.2005.05.004 (Pubitemid 41363974)
50. M. D. Altman, J. P. Bardhan, J. K. White, and B. Tidor, in An Efficient and Accurate Surface Formulation for Biomolecule Electrostatics in Nonionic Solution, Engineering in Medicine and Biology Conference (EMBC), 2005 (unpublished).
51. J. P. Bardhan, J. Chem. Phys. 130, 094102 (2009). 10.1063/1.3080769
52. B. Hille, Ion Channels of Excitable Membranes, 3rd ed. (Sinauer Associates, Sunderland, MA, 2001).
53. F. M. Ashcroft, Ion Channels and Disease: Channelopathies, 1st ed. (Academic Press, New York, 2000).
54. S. M. Rao, T. K. Sarkar, and R. F. Harrington, IEEE Trans. Microwave Theory Tech. 32, 1441 (1984). 10.1109/TMTT.1984.1132869
55. E. O. Purisima, J. Comput. Chem. 19, 1494 (1998). 10.1002/(SICI)1096- 987X(199810)19:13<1494::AID-JCC6>3.0.CO;2-L
56. M. A. Jaswon and G. T. Symm, Integral Equation Methods in Potential Theory and Elastostatics (Academic Press, London, 1977).
57. R. Kress, Linear Integral Equations (Springer-Verlag, Berlin, 1989).
58. G. C. Hsiao and W. L. Wendland, in Encyclopedia of Computational Mechanics, edited by, E. Steinm, R. de Borstm and, T. J. R. Hughes, (Wiley, New York, 2004), pp. 339 - 373.
59. A. E. Ruehli and P. A. Brennan, IEEE Trans. Microwave Theory Tech. 21, 76 (1973). 10.1109/TMTT.1973.1127927
60. D. J. Griffiths, Introduction to Electrodynamics, 3rd ed. (Benjamin, New York, 1999).
61. M. Sanner, A. J. Olson, and J. C. Spehner, Biopolymers 38, 305 (1996). 10.1002/(SICI)1097-0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y
62. F. M. Richards, Annu. Rev. Biophys. Bioeng. 6, 151 (1977). 10.1146/annurev.bb.06.060177.001055
63. P. W. Bates, G. W. Wei, and S. Zhao, J. Comput. Chem. 29, 380 (2008). 10.1002/jcc.20796
64. S. N. Yu, W. H. Geng, and G. W. Wei, J. Chem. Phys. 126, 244108 (2007). 10.1063/1.2743020 (Pubitemid 47141404)
65. W. H. Geng, S. N. Yu, and G. W. Wei, J. Chem. Phys. 127, 114106 (2007). 10.1063/1.2768064 (Pubitemid 47461993)
66. Y. C. Zhou, M. Feig, and G. W. Wei, J. Comput. Chem. 29, 87 (2008). 10.1002/jcc.20769
67. J. Tausch and J. K. White, Adv. Comput. Math. 9, 217 (1998). 10.1023/A:1018973019922
68. B. Honig and A. Nicholls, Science 268, 1144 (1995). 10.1126/science. 7761829
69. J. L. Hess and A. M. O. Smith, J. Ship Res. 8, 22 (1962).
70. J. N. Newman, J. Eng. Math. 20, 113 (1986). 10.1007/BF00042771
71. B. Z. Lu, X. L. Cheng, J. Huang, and J. A. McCammon, Proc. Natl. Acad. Sci. U.S.A. 103, 19314 (2006). 10.1073/pnas.0605166103 (Pubitemid 46026029)
72. M. D. Altman, J. P. Bardhan, B. Tidor, and J. K. White, IEEE Trans. Comput.-Aided Des. 25, 274 (2006). 10.1109/TCAD.2005.855946 (Pubitemid 43146085)
73. W. Xin and A. H. Juffer, J. Comput. Phys. 223, 416 (2007). 10.1016/j.jcp.2006.09.011
74. S.-H. Chung, T. Allen, M. Hoyles, and S. Kuyucak, Biophys. J. 77, 2517 (1999). 10.1016/S0006-3495(99)77087-6
75. M. G. Kurnikova, R. D. Coalson, P. Graf, and A. Nitzan, Biophys. J. 76, 642 (1999). 10.1016/S0006-3495(99)77232-2
76. P. Graf, A. Nitzan, M. G. Kurnikova, and R. D. Coalson, J. Phys. Chem. B 104, 12324 (2000). 10.1021/jp001282s (Pubitemid 32087817)
77. W. Im, S. Seefeld, and B. Roux, Biophys. J. 79, 788 (2000). 10.1016/S0006-3495(00)76336-3
78. W. Im and B. Roux, J. Chem. Phys. 115, 4850 (2001). 10.1063/1.1390507 (Pubitemid 32902736)
79. D. Boda, D. Busath, B. Eisenberg, D. Henderson, and W. Nonner, Phys. Chem. Chem. Phys. 4, 5154 (2002). 10.1039/b203686j
80. A. B. Mamonov, R. D. Coalson, A. Nitzan, and M. G. Kurnikova, Biophys. J. 84, 3646 (2003). 10.1016/S0006-3495(03)75095-4
81. W. Im and B. Roux, J. Mol. Biol. 322, 851 (2002). 10.1016/S0022-2836(02) 00778-7
82. D. Boda, T. Varga, D. Henderson, D. Busath, W. Nonner, D. Gillespie, and B. Eisenberg, Mol. Simul. 30, 89 (2004). 10.1080/0892702031000152226 (Pubitemid 40026330)
83. D. Boda, W. Nonner, M. Valiskó, D. Henderson, B. Eisenberg, and D. Gillespie, Biophys. J. 93, 1960 (2007). 10.1529/biophysj.107.105478 (Pubitemid 47437580)
84. D. Boda, W. Nonner, D. Henderson, B. Eisenberg, and D. Gillespie, Biophys. J. 94, 3486 (2008). 10.1529/biophysj.107.122796
85. T. Vora, D. Bisset, and S.-H. Chung, Biophys. J. 95, 1600 (2008). 10.1529/biophysj.107.126722
86. MATLAB v.6. Mathworks, Inc.
87. J. P. Bardhan, M. D. Altman, J. K. White, and B. Tidor, J. Chem. Phys. 127, 014701 (2007). 10.1063/1.2743423 (Pubitemid 47245139)
88. J.-L. Guermond, SIAM (Soc. Ind. Appl. Math.) J. Numer. Anal. 29, 1347 (1992). 10.1137/0729078
89. C. L. Bajaj, V. Pascucci, A. Shamir, R. J. Holt, and A. N. Netravali, Discrete Appl. Math. 127, 23 (2003). 10.1016/S0166-218X(02)00283-4
90. R. J. Zauhar, J. Comput.-Aided Mol. Des. 9, 149 (1995). 10.1007/BF00124405
91. M. L. Connolly, J. Appl. Crystallogr. 16, 548 (1983). 10.1107/S0021889883010985
92. Y. N. Vorobjev and J. Hermans, Biophys. J. 73, 722 (1997). 10.1016/S0006-3495(97)78105-0
93. M. Totrov and R. Abagyan, J. Struct. Biol. 116, 138 (1996). 10.1006/jsbi.1996.0022 (Pubitemid 26093135)
94. M. Connolly, Molecular surface package, 2000, http://connolly.best.vwh. net
95. M. F. Sanner, Molecular surface computation homepage, 1996, http://www.scripps.edu/sanner/html/msms-home.html
96. Y. Saad and M. Schultz, SIAM (Soc. Ind. Appl. Math.) J. Sci. Stat. Comput. 7, 856 (1986).
97. R. Bharadwaj, A. Windemuth, S. Sridharan, B. Honig, and A. Nicholls, J. Comput. Chem. 16, 898 (1995). 10.1002/jcc.540160707
98. M. O. Fenley, W. K. Olson, K. Chua, and A. H. Boschitsch, J. Comput. Chem. 17, 976 (1996). 10.1002/(SICI)1096-987X(199606)17:8<976::AID-JCC7>3. 0.CO;2-O
99. Y. N. Vorobjev and H. A. Scheraga, J. Comput. Chem. 18, 569 (1997). 10.1002/(SICI)1096-987X(199703)18:4<569::AID-JCC10>3.0.CO;2-B
100. A. H. Boschitsch, M. O. Fenley, and H.-X. Zhou, J. Phys. Chem. B 106, 2741 (2002). 10.1021/jp013607q (Pubitemid 35275953)