Adaptive Multilevel Finite Element Solution of the Poisson-Boltzmann Equation II. Refinement at Solvent-Accessible Surfaces in Biomolecular Systems

Journal of Computational Chemistry

Volumn 21, Issue 15, 2000, Pages 1343-1352

  Baker, N ^a   Holst, M ^a   Wang, F ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

A posteriori error estimation; Adaptive finite element methods; Biomolecules; Electrostatics; Poisson Boltzmann equation

Indexed keywords

EID: 0000486194     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/1096-987X(20001130)21:15<1343::AID-JCC2>3.0.CO;2-K     Document Type: Article

References (42)

1. Debye, P.; Hückel, E. Physik Z 1923, 24, 185.
2. Briggs, J. M.; McCammon, J. A. Comput Phys 1990, 6, 238.
3. Sharp, K. A.; Honig, B. Annu Rev Biophys Chem 1990, 19, 301.
4. Allison, S. A.; Sines, J. J.; Wierzbicki, A. J Phys Chem 1989, 93, 5819.
5. Gilson, M. K.; Sharp, K. A.; Honig, B. H. J Comput Chem 1988, 9, 327.
6. Jayaram, B.; Sharp, K. A.; Honig, B. Biopolymers 1989, 28, 975.
7. Luty, B. A.; Davis, M. E.; McCammon, J. A. J Comput Chem 1992, 13, 1114.
8. Nicholls, A.; Honig, B. J Comput Chem 1991, 12, 435.
9. Rashin, A. A.; Malinsky, J. J Comput Chem 1991, 12, 981.
10. Sharp, K. A.; Honig, B. J Phys Chem 1990, 94, 7684.
11. Holst, M.; Saied, F. J Comput Chem 1995, 16, 337.
12. Holst, M. Ph.D. thesis, Numerical Computing Group, University of Illinois at Urbana-Champaign, 1993; Also published as Technical Report UIUCDCS-R-03-1821.
13. Holst, M. Tech. report, Applied Mathematics and CRPC, California Institute of Technology, 1994.
14. Davis, M. E.; McCammon, J. A. J Comput Chem 1989, 10, 386.
15. Juffer, A. H.; Botta, E. F. F.; van Keulen, B. A. M.; van der Ploeg, A.; Berendsen, H. J. C. J Comput Phys 1991, 97, 144.
16. Niedermeier, C.; Schulten, K. Tech. report, Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, 1990.
17. Yoon, B. J.; Lenhoff, A. M. J Comput Chem 1990, 11, 1080.
18. Cortis, C. M.; Friesner, R. A. J Comput Chem 1997, 18, 1570.
19. Cortis, C. M.; Friesner, R. A. J Comput Chem 1997, 18, 1591.
20. Bowen, W. R.; Sharif, A. O. J Colloid Interface Sci 1997, 187, 363.
21. Holst, M.; Baker, N.; Wang, F. J Comput Chem 2000, 21, 1319.
22. Holst, M. In preparation; currently available as a technical report and User's Guide to the MC software.
23. Holst, M.; Bernstein, D. Commun Math Phys, submitted.
24. You, T.; Bashford, D. J Comput Chem 1995, 16, 743.
25. Bank, R. E.; Dupont, T. F. Math Comp 1981, 36, 35.
26. Hackbusch, W. Multi-Grid Methods and Applications; Springer-Verlag: Berlin, Germany, 1985.
27. Xu, J. SIAM Rev 1992, 34, 581.
28. Babuška, I.; Rheinboldt, W. C. Int J Numer Meth Eng 1978, 12, 1597.
29. Babuška, I.; Rheinboldt, W. C. SIAM J Numer Anal 1978, 15, 736.
30. Bank, R. E. PLTMG: A Software Package for Solving Elliptic Partial Differential Equations, Users' Guide 8.0; Software, Environments and Tools; SIAM: Philadelphia, PA, 1998, vol. 5.
31. Verfürth, R. Math Comp 1994, 62, 445.
32. Verfürth, R. A Review of A Posteriori Error Estimation and Adaptive Mesh-Refinement Techniques; John Wiley & Sons Ltd: New York, 1996.
33. Xu, J.; Zhou, A. Math Comp, to appear.
34. Rivara, M. C. Int J Num Meth Eng 1984, 20, 745.
35. Rivara, M. C. J Comput Appl Math 1991, 36, 79.
36. Isaacson, E.; Keller, H. B. Analysis of Numerical Methods; John Wiley & Sons, Inc.: New York, 1966.
37. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon Press: Oxford, 1987.
38. Hockney, R. W.; Eastwood, J. W. Computer Simulation Using Particles; McGraw-Hill: New York, 1981.
39. Quentrec, B.; Brot, C. J Comput Phys 1975, 13, 430.
40. Humphrey, W.; Dalke, A.; Schulten, K. J Mol Graph 1996, 14, 33.
41. Bourne, Y.; Taylor, P.; Bougis, P.; Marchot, P. J Biol Chem 1999, 274, 2963.
42. Marchot, P.; Bourne, Y.; Prowse, C.; Bougis, P.; Taylor, P. Toxicon 1998, 36, 1613.