A first-order system least-squares finite element method for the poisson-boltzmann equation

Journal of Computational Chemistry

Volumn 31, Issue 8, 2010, Pages 1625-1635

  Bond, Stephen D ^a   Chaudhry, Jehanzeb Hameed ^a   Cyr, Eric C ^b   Olson, Luke N ^a  

^a University of Illinois ^*  (United States)

^b SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

Adaptive refinement; Finite elements; Implicit solvent; Least squares; Poisson boltzmann

Indexed keywords

ADAPTIVE REFINEMENT; FINITE ELEMENT; IMPLICIT SOLVENTS; LEAST SQUARE; POISSON-BOLTZMANN;

BOLTZMANN EQUATION; METHANOL; POISSON EQUATION; SOLVENTS;

FINITE ELEMENT METHOD;

FASCICULIN; METHANOL; SNAKE VENOM;

ALGORITHM; ARTICLE; CHEMISTRY; COMPUTER SIMULATION; FINITE ELEMENT ANALYSIS; POISSON DISTRIBUTION; REGRESSION ANALYSIS; STATIC ELECTRICITY;

ALGORITHMS; COMPUTER SIMULATION; ELAPID VENOMS; FINITE ELEMENT ANALYSIS; LEAST-SQUARES ANALYSIS; METHANOL; POISSON DISTRIBUTION; STATIC ELECTRICITY;

EID: 77952378191     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21446     Document Type: Article

References (61)

1. Baker, N. A.; Bashford, D.; Case, D. A. In: New Algorithms for Macromolecular Simulation, Vol.49 of Lecture Notes in Computational Science and Engineering; Leimkuhler, B.; Chipot, C.; Elber, R.; Laaksonen, A.; Mark, A.; Schlick, T.; Schutte, C.; Skeel, R. Eds.; Springer-Verlag, Berlin, 2006, pp. 263-295.
2. Bashford, D.; Case, D. A. Annu Rev Phys Chem 2000, 51, 129.
3. Chen, L.; Holst, M. J.; Xu, J. SIAM J Numer Anal 2007, 45, 2298.
4. Fogolari, F.; Zuccato, P.; Esposito, G.; Viglino, P. Biophys J 1999, 76, 1.
5. Fogolari, F.; Brigo, A.; Molinari, H. J Mol Recognit 2002, 15, 377.
6. Klapper, I.; Hagstrom, R.; Fine, R.; Sharp, K.; Honig, B. Proteins 1986, 1, 47.
7. Warwicker, J.; Watson, H. C. J Mol Biol 1982, 157, 671.
8. Gilson, M. K.; Sharp, K. A.; Honig, B. H. J Comput Chem 1987, 9, 327.
9. Davis, M. E.; McCammon, J. A. J Comput Chem 1989, 10, 386.
10. Holst, M. J.; Saied, F. J Comput Chem 1995, 16, 337.
11. Baker, N. A.; Sept, D.; Joseph, S.; Hoist, M. J.; McCammon, J. A. Proc Natl Acad Sci USA 2001, 98, 10037.
12. Luty, B. A.; Davis, M. E.; McCammon, J. A. J Comput Chem. 1992, 13, 1114.
13. Bashford, D. In Scientific Computing in Object-Oriented Parallel Environments, Vol.1343 of Lecture Notes in Computer Science; Springer, Berlin, 1997, pp. 233-240.
14. Rocchia, W.; Alexov, E.; Honig, B. J Phys Chem B 2001, 105, 6507.
15. Zhou, Y. C.; Wei, G. W. J Comput Phys 2006, 219, 228.
16. Orttung, W. H. Ann N Y Acad Sci 1977, 303, 22.
17. Cords, C. M.; Friesner, R. A. J Comput Chem 1997, 18, 1591.
18. Holst, M. J.; Baker, N. A.; Wang, F. J Comput Chem. 2000, 21, 1319.
19. Baker, N. A.; Holst, M. J.; Wang, F. J Comput Chem 2000, 21, 1343.
20. Shestakov, A. I.; Milovich, J. L.; Noy, A. J Colloid Interface Sci 2002, 247, 62.
21. Xie, D.; Zhou, S. BIT Numer Math. 2007, 47, 853.
22. Wenbin, C.; Yifan, S.; Qing, X. Appl Math Comput 2005, 164, 11.
23. Miertus, S.; Scrocco, E.; Tomasi, J. Chem Phys 1981, 55, 117.
24. Zauhar, R.; Morgan, R. J Mol Biol 1985, 186, 815.
25. Rashin, A. A. J Chem Phys 1990, 94, 1725.
26. Yoon, B. J.; Lenhoff, A. M. J Comput Chem 1990, 11, 1080.
27. Juffer, A. H.; Botta, E. F.; van Keulen, B. A.; van der Ploeg, A.; Berendsen, H. J. J Comput Phys 1991, 97, 144.
28. Vorobjev, Y. N.; Grant, J. A.; Scheraga, H. A. J Amer Chem Soc 1992, 114, 3189.
29. Zhou, H.-X. Biophys J 1993, 65, 955.
30. Bharadwaj, R.; Windemuth, A.; Sridharan, S.; Honig, B.; Nicholls, A. J Comput Chem. 1995, 16, 898.
31. Vorobjev, Y. N.; Scheraga, H. A. J Comput Chem 1997, 18, 569.
32. Liang, J.; Subramaniam, S. Biophys J 1997, 73, 1830.
33. Boschitsch, A. H.; Fenley, M. O.; Zhou, H.-X. J Phys Chem. B 2002, 106, 2741.
34. Lu, B.; Zhang, D.; McCammon, J. A. J Chem Phys 2005, 122, 214102.
35. Kuo, S. S.; Altman, M. D.; Bardhan, J. P.; Tidor, B.; White, J. K. In ICCAD '02: Proceedings of the 2002 IEEE/ACM International Conference on Computer-Aided Design; ACM Press: New York, NY, 2002; pp. 466-473.
36. Lu, B.; Cheng, X.; Huang, J.; McCammon, J. A. Proc Natl Acad Sci USA 2006, 103, 19314.
37. Cai, Z.; Lazarov, R.; Manteuffel,T. A.;McCormick, S.F. SIAMJ Numer Anal 1994, 31, 1785.
38. Cai, Z.; Manteuffel, T. A.; McCormick, S. F. SIAM J Numer Anal 1997, 34, 425.
39. Manteuffel, T. A.; McCormick, S. F.; Starke, G. In Seventh. Copper Mountain Conference on Multigrid Methods, Vol.CP 3339; Melson, N. D.; Manteuffel, T. A.; McCormick, S. F.; Douglas, C. C., Eds.; NASA: Hampton, VA, 1996; pp. 535-550.
40. Berndt, M.; Manteuffel, T. A.; McCormick, S. F.; Starke, G. SIAM J Numer Anal 2005, 43, 386.
41. Berndt, M.; Manteuffel, T. A.; McCormick, S. F. SIAM J Numer Anal 2005, 43, 409.
42. Holst, M. Adv Comput Math 2001, 15, 139.
43. Bochev, P. B.; Gunzburger, M. D. SIAM Rev 1998, 40, 789.
44. Brezzi, F.; Fortin, M. Mixed and Hybrid Finite Element Methods, Vol.15 of Springer Series in Computational Mathematics; Springer-Verlag, New York, 1991.
45. Song, Y.; Zhang, Y.; Shen, T.; Bajaj, C. L.; McCammon, J. A.; Baker, N. A. Biophys J 2001, 86, 2017.
46. Cao, Y.; Gunzburger, M. D. SIAM J Numer Anal 1998, 35, 393.
47. Girault, V.; Raviart, P.-A. Finite Element Methods for Navier-Stokes Equations, Vol.5 of Springer Series in Computational Mathematics; Springer-Verlag, Berlin, 1986.
48. Berndt, M.; Manteuffel, T. A.; McCormick, S. F. Electron Trans Numer Anal 1997, 6, 35.
49. Cyr, E. C. Numerical Methods for Computing the Free-Energy of Coarse-Grained Molecular Systems, Phd Thesis; University of Illinois at Urbana-Champaign, Illinois, 2008.
50. Cai, Z.; Westphal, C. J Non-Newtonian Fluid Mech 2009, 159, 72.
51. Yu, Z.; Holst, M.; Cheng, Y.; McCammon, J. A. J Mol Graph Model 2008, 26, 1370.
52. Holst, M. J. Multilevel Methods for the Poisson-Boltzmann Equation, Phd Thesis; University of Illinois at Urbana-Champaign, 1994.
53. Born, M. Zeitschrift für Physik 1920, 1, 45.
54. le Du, M. H.; Marchot, P.; Bougis, P. E.; Fontecilla-Camps, J. C. J Biol Chem 1992, 267, 22122.
55. Radić, Z.; .Kirchhoff, P. D.; Quinn, D. M.; McCammon, J. A.; Taylor, P. J Biol Chem 1997, 272, 23265.
56. Baker, N. A.; Helms, V.; McCammon, J. A. Proteins 1999, 36, 447.
57. Humphrey, W.; Dalke, A.; Schulten, K. J Mol Graph 1996, 14, 33.
58. Kirkwood, J. G. J Chem. Phys 1934, 2, 351.
59. Geng, W.; Yu, S.; Wei, G. J Chem Phys 2007, 127, 114106.
60. Sanner, M. F.; Olson, A. J.; Spehner, J.-C. In SCG '95: Proceedings of the Eleventh Annual Symposium on Computational Geometry; ACM, New York, NY, 1995; pp. 406-407.
61. Codd, A. L.; Manteuffel, T. A.; McCormick, S. F. SIAM J Numer Anal 2003, 41, 2197.