Numerical solution of boundary-integral equations for molecular electrostatics

Journal of Chemical Physics

Volumn 130, Issue 9, 2009, Pages

  Bardhan, Jaydeep P ^a,b  

^a RUSH UNIVERSITY   (United States)

^b Department of Molecular Biophysics and Physiology ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOPHYSICS; CONTINUUM MECHANICS; DISSOCIATION; ELECTROSTATICS; INTEGRAL EQUATIONS; NUMERICAL METHODS; SAILING VESSELS; SOLVATION;

ALTERNATIVE APPROACHES; BOUNDARY-INTEGRAL EQUATIONS; CONTINUUM MODELS; DISCRETE POINTS; DISCRETIZATION; ELECTROSTATIC CONTRIBUTIONS; ELEMENT METHODS; EQUATION FORMULATIONS; ION PERMEATIONS; MOLECULAR PROCESS; NUMERICAL EXAMPLES; NUMERICAL IMPLEMENTATIONS; NUMERICAL SOLUTIONS; POINT COLLOCATIONS; QUALOCATION METHODS; SIMULATION TIME; SOLVATION FREE ENERGIES; THEORETICAL INVESTIGATIONS; THROUGH CHANNELS;

BOUNDARY ELEMENT METHOD;

SOLVENT;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; SOLUBILITY; STATIC ELECTRICITY;

MODELS, CHEMICAL; SOLUBILITY; SOLVENTS; STATIC ELECTRICITY;

EID: 62249173004     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3080769     Document Type: Article

References (96)

1. J. G. Kirkwood, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1749489 2, 351 (1934).
2. C. Tanford and J. G. Kirkwood, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja01577a001 79, 5333 (1957).
3. S. Miertus, E. Scrocco, and J. Tomasi, Chem. Phys. CMPHC2 0301-0104 10.1016/0301-0104(81)85090-2 55, 117 (1981).
4. J. Warwicker and H. C. Watson, J. Mol. Biol. JMOBAK 0022-2836 10.1016/0022-2836(82)90505-8 157, 671 (1982).
5. K. A. Sharp and B. Honig, Annu. Rev. Biophys. Biophys. Chem. ARBCEY 0883-9182 10.1146/annurev.bb.19.060190.001505 19, 301 (1990).
6. B. Honig and A. Nicholls, Science SCIEAS 0036-8075 10.1126/science. 7761829 268, 1144 (1995).
7. C. J. Cramer and D. G. Truhlar, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 10.1021/cr960149m 99, 2161 (1999).
8. M. Orozco and F. J. Luque, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 10.1021/cr990052a 100, 4187 (2000).
9. V. Lounnas, B. M. Pettitt, L. Findsen, and S. Subramaniam, J. Phys. Chem. JPCHAX 0022-3654 10.1021/j100197a004 96, 7157 (1992).
10. J. A. McCammon and S. C. Harvey, Dynamics of Proteins and Nucleic Acids (Cambridge University Press, Cambridge, 1987).
11. C. L. Brooks III, M. Karplus, and B. M. Pettitt, Adv. Chem. Phys. ADCPAA 0065-2385 10.1002/9780470141205.ch1 71, 1 (1988).
12. A. Jean-Charles, A. Nicholls, K. Sharp, B. Honig, A. Tempczyk, T. F. Hendrickson, and W. C. Still, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja00004a079 113, 1454 (1991).
13. S. W. Rick and B. J. Berne, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja00088a034 116, 3949 (1994).
14. B. Roux and T. Simonson, Biophys. Chem. BICIAZ 0301-4622 10.1016/S0301-4622(98)00226-9 78, 1 (1999).
15. M. K. Gilson, A. Rashin, R. Fine, and B. Honig, J. Mol. Biol. JMOBAK 0022-2836 10.1016/0022-2836(85)90297-9 184, 503 (1985).
16. M. E. Davis and J. A. McCammon, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 10.1021/cr00101a005 90, 509 (1990).
17. B. Honig, K. Sharp, and A. S. Yang, J. Phys. Chem. JPCHAX 0022-3654 10.1021/j100108a002 97, 1101 (1993).
18. J. A. Grant, B. T. Pickup, and A. Nicholls, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.1032.abs 22, 608 (2001).
19. J. Wagoner and N. A. Baker, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.20089 25, 1623 (2004).
20. J. A. Wagoner and N. A. Baker, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0600118103 103, 8331 (2006).
21. M. K. Gilson and B. Honig, Proteins 18PLAF 0887-3585 10.1002/prot. 340040104 4, 7 (1988).
22. M. K. Gilson, K. A. Sharp, and B. H. Honig, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540090407 9, 327 (1988).
23. A. Nicholls and B. Honig, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540120405 12, 435 (1991).
24. M. Holst and F. Saied, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540140114 14, 105 (1993).
25. J. D. Madura, J. M. Briggs, R. C. Wade, M. E. Davis, B. A. Luty, A. Ilin, J. Antosiewicz, M. K. Gilson, B. Bagheri, L. Ridgway-Scott, and J. A. McCammon, Comput. Phys. Commun. CPHCBZ 0010-4655 10.1016/0010-4655(95)00043-F 91, 57 (1995).
26. M. Holst, N. Baker, and F. Wang, J. Comput. Chem. 21, 1319 (2000).
27. W. Rocchia, E. Alexov, and B. Honig, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp010454y 105, 6507 (2001).
28. N. A. Baker, D. Sept, M. J. Holst, and J. A. McCammon, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.181342398 98, 10037 (2001).
29. W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.1161 23, 128 (2002).
30. S. N. Yu, Y. C. Zhou, and G. W. Wei, J. Comput. Phys. JCTPAH 0021-9991 10.1016/j.jcp.2006.10.030 224, 729 (2007).
31. S. N. Yu, W. H. Geng, and G. W. Wei, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2743020 126, 244108 (2007).
32. T. J. You and S. C. Harvey, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540140413 14, 484 (1993).
33. C. M. Cortis and R. A. Friesner, J. Comput. Chem. 18, 1591 (1997).
34. P. B. Shaw, Phys. Rev. A PLRAAN 1050-2947 10.1103/PhysRevA.32.2476 32, 2476 (1985).
35. R. J. Zauhar and R. S. Morgan, J. Mol. Biol. JMOBAK 0022-2836 10.1016/0022-2836(85)90399-7 186, 815 (1985).
36. R. J. Zauhar and R. S. Morgan, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540090209 9, 171 (1988).
37. R. J. Zauhar and R. S. Morgan, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540110509 11, 603 (1990).
38. R. J. Zauhar, J. Comput.-Aided Mol. Des. JCADEQ 0920-654X 10.1007/BF00124405 9, 149 (1995).
39. B. J. Yoon and A. M. Lenhoff, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540110911 11, 1080 (1990).
40. A. H. Juffer, E. F. F. Botta, B. A. M. van Keulen, A. van der Ploeg, and H. J. C. Berendsen, J. Comput. Phys. JCTPAH 0021-9991 10.1016/0021-9991(91) 90043-K 97, 144 (1991).
41. H. X. Zhou, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(93)81094-4 65, 955 (1993).
42. E. O. Purisima and S. H. Nilar, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540160604 16, 681 (1995).
43. E. O. Purisima, J. Comput. Chem. 19, 1494 (1998).
44. Y. N. Vorobjev and H. A. Scheraga, J. Comput. Chem. 18, 569 (1997).
45. J. Liang and S. Subramaniam, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(97)78213-4 73, 1830 (1997).
46. E. Cances, B. Mennucci, and J. Tomasi, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.474659 107, 3032 (1997).
47. R. Bharadwaj, A. Windemuth, S. Sridharan, B. Honig, and A. Nicholls, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540160707 16, 898 (1995).
48. A. H. Boschitsch, M. O. Fenley, and W. K. Olson, J. Comput. Phys. JCTPAH 0021-9991 10.1006/jcph.1998.6176 151, 212 (1999).
49. A. H. Boschitsch, M. O. Fenley, and H. -X. Zhou, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp013607q 106, 2741 (2002).
50. A. J. Bordner and G. A. Huber, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.10195 24, 353 (2003).
51. D. M. Chipman, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1648632 120, 5566 (2004).
52. J. Tomasi, B. Mennucci, and R. Cammi, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 10.1021/cr9904009 105, 2999 (2005).
53. P. Attard, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1580805 119, 1365 (2003).
54. B. Z. Lu, D. Q. Zhang, and J. A. McCammon, J. Chem. Phys. JCPSA6 0021-9606 214102, 122 (2005).
55. B. Z. Lu, X. L. Cheng, J. Huang, and J. A. McCammon, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0605166103 103, 19314 (2006).
56. D. Gillespie, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.107.116798 94, 1169 (2008).
57. J. P. Bardhan, M. D. Altman, J. K. White, and B. Tidor, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2743423 127, 014701 (2007).
58. D. N. Chipman, Theor. Chem. Acc. TCACFW 1432-881X 10.1007/s00214-001- 0302-1 107, 80 (2002).
59. M. Cossi, V. Barone, R. Cammi, and J. Tomasi, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/0009-2614(96)00349-1 255, 327 (1996).
60. R. Cammi and J. Tomasi, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540161202 16, 1449 (1995).
61. R. J. Zauhar and A. Varnek, J. Comput. Chem. 17, 864 (1996).
62. K. E. Atkinson, The Numerical Solution of Integral Equations of the Second Kind (Cambridge University Press, Cambridge, 1997).
63. J. Tausch, J. Wang, and J. White, IEEE Trans. Comput.-Aided Des. ITCSDI 0278-0070 10.1109/43.969433 20, 1398 2001.
64. M. D. Altman, J. P. Bardhan, J. K. White, and B. Tidor, Engineering in Medicine and Biology Conference (EMBC), 2005 (unpublished).
65. Y. Saad and M. Schultz, SIAM (Soc. Ind. Appl. Math.) J. Sci. Stat. Comput. SIJCD4 0196-5204 10.1137/0907058 7, 856 (1986).
66. L. Greengard, The Rapid Evaluation of Potential Fields in Particle Systems (MIT, Cambridge, 1988).
67. K. Nabors and J. White, IEEE Trans. Comput.-Aided Des. ITCSDI 0278-0070 10.1109/43.97624 10, 1447 (1991).
68. M. D. Altman, J. P. Bardhan, B. Tidor, and J. K. White, IEEE Trans. Comput.-Aided Des. ITCSDI 0278-0070 10.1109/TCAD.2005.855946 25, 274 (2006).
69. M. D. Altman, J. P. Bardhan, J. K. White, and B. Tidor, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.21027 30, 132 (2009).
70. D. Sitkoff, K. A. Sharp, and B. Honig, J. Phys. Chem. B 98, 1978 (1994). 1520-6106
71. M. Nina, W. Im, and B. Roux, Biophys. Chem. BICIAZ 0301-4622 10.1016/S0301-4622(98)00236-1 78, 89 (1999).
72. B. Lee and F. M. Richards, J. Mol. Biol. JMOBAK 0022-2836 10.1016/0022-2836(71)90324-X 55, 379 (1971).
73. F. M. Richards, Annu. Rev. Biophys. Bioeng. ABPBBK 0084-6589 10.1146/annurev.bb.06.060177.001055 6, 151 (1977).
74. M. L. Connolly, J. Appl. Crystallogr. JACGAR 0021-8898 10.1107/S0021889883010985 16, 548 (1983).
75. J. B. Foresman, T. A. Keith, K. B. Wiberg, J. Snoonian, and M. J. Frisch, J. Phys. Chem. JPCHAX 0022-3654 10.1021/jp960488j 100, 16098 (1996).
76. C. -G. Zhan, J. Bentley, and D. M. Chipman, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.475371 108, 177 (1998).
77. T. Simonson, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/S0959-440X(00)00197-4 11, 243 (2001).
78. C. N. Schutz and A. Warshel, Proteins 18PLAF 0887-3585 10.1002/prot.1106 44, 400 (2001).
79. J. D. Jackson, Classical Electrodynamics, 3rd ed. (Wiley, New York, 1998.
80. R. Kress, Linear Integral Equations (Springer-Verlag, Berlin, 1989).
81. J. O.'M. Bockris and A. K. N. Reddy, Modern Electrochemistry: An Introduction to an interdisciplinary area (Plenum, New York, 1973).
82. C. Pozrikidis, A Practical Guide to Boundary-Element Methods with the Software Library BEMLIB (Chapman and Hall, London / CRC, Boca Raton, FL, 2002).
83. M. H. Lean and A. Wexler, Int. J. Numer. Methods Eng. IJNMBH 0029-5981 10.1002/nme.1620210203 21, 211 (1985).
84. J. Nedelec, Comput. Methods Appl. Mech. Eng. CMMECC 0045-7825 10.1016/0045-7825(76)90053-0 8, 61 (1976).
85. B. Buchmann, Int. J. Numer. Methods Fluids 33, 125 (2000).
86. A. E. Ruehli and P. A. Brennan, IEEE Trans. Microwave Theory Tech. IETMAB 0018-9480 10.1109/TMTT.1973.1127927 21, 76 (1973).
87. A. Stroud, Approximate Calculation of Multiple Integrals (Prentice Hall, Englewoods Cliffs, NJ, 1971).
88. J. L. Hess and A. M. O. Smith, J. Ship Res. JSRHAR 0022-4502 8, 22 (1962).
89. J. N. Newman, J. Eng. Math. JLEMAU 0022-0833 10.1007/BF00042771 20, 113 (1986).
90. M. Sanner, A. J. Olson, and J. C. Spehner, Biopolymers 38, 305 (1996).
91. J. R. Phillips and J. K. White, IEEE Trans. Comput.-Aided Des. ITCSDI 0278-0070 10.1109/43.662670 16, 1059 (1997).
92. Z. Zhu, B. Song, and J. White, Proceedings of the IEEE/ACM Design Automation Conference (DAC), 2003 (unpublished).
93. S. S. Kuo, M. D. Altman, J. P. Bardhan, B. Tidor, and J. K. White, International Conference on Computer Aided Design (ICCAD), 2002 (unpublished).
94. P. Lavigne, M. P. Crump, S. M. Gagń, R. S. Hodges, C. M. Kay, and B. D. Sykes, J. Mol. Biol. 281, 165 (1998). 0022-2836
95. M. Feig, A. Onufriev, M. S. Lee, W. Im, D. A. Case, and C. L. Brooks III, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.10378 25, 265 (2004).
96. M. Feig and C. L. Brooks III, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/j.sbi.2004.03.009 14, 217 (2004).