Poisson-Boltzmann equation boundary conditions for biological applications

Mathematical and Computer Modelling

Volumn 41, Issue 10, 2005, Pages 1109-1118

  Rocchia, W ^a  

^a SCUOLA NORMALE SUPERIORE   (Italy)

Author keywords

Boundary conditions, Nonlinear partial differential equations; Electrostatics in biology; Finite difference scheme; Poisson Boltzmann equation

Indexed keywords

ELECTROSTATICS; FINITE DIFFERENCE METHOD; NONLINEAR EQUATIONS; PARTIAL DIFFERENTIAL EQUATIONS; POLARIZATION; SOLVENTS;

ELECTROSTATICS IN BIOLOGY; FINITE DIFFERENCE SCHEME; NONLINEAR PARTIAL DIFFERENTIAL EQUATIONS; POISSON-BOLTZMANN EQUATION (PBE);

BOUNDARY CONDITIONS;

EID: 26844507399     PISSN: 08957177     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mcm.2005.05.006     Document Type: Article

References (16)

1. F.B. Sheinerman, R. Norel, and B. Honig Electrostatic aspects of protein interactions Current Opinion in Structural Biology 10 2000 153 159
2. Z. Radic, P. Kirchhoff, D.M. Quinn, J.A. McCammon, and P. Taylor Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase distinctions between active center ligands and fasciculin J. Biol. Chem. 272 1997 23265 23277
3. B. Honig, and A. Nicholls Classical electrostatics in biology and chemistry Science 268 1995 1144 1149
4. P. Debye, and E. Huckel Zur Theorie der Elektrolyte Physik. Zeits. 24 1923 185
5. K. Sharp, and B. Honig Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation J. Phys. Chem. 94 1990 7684 7692
6. W. Rocchia, E. Alexov, and B. Honig Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions J. Phys. Chem. B 105 28 2001 6507 6514
7. M. Holst, N. Baker, and M. Wang Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I: Algorithm and examples J. Comput. Chem. 21 2000 1319 1342
8. N. Baker, M. Holst, and M. Wang Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I: Refinement at solvent accessible surfaces in biomolecular systems J. Comput. Chem. 21 2000 1343 1352
9. W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig Rapid grid-based construction of the molecular surface for both molecules and geometric objects: Applications to the finite difference Poisson-Boltzmann method J. Comp. Chem. 23 2002 128 137
10. A. Nicholls, and B. Honig A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation J. Comput. Chem. 12 4 1991
11. B. Lee, and F.M. Richards Interpretation of protein structures J. Mol. Biol. 55 1971 379 400
12. F.M. Richards Areas, volumes, packing and protein structure Annu. Rev. Biophys. Bioeng. 6 1977 151 176
13. M.L. Connolly Solvent-accessible surfaces of proteins and nucleic acids Science 221 1983 709
14. J.O.M. Bockris and A.K. Reddy, Modern Electrochemistry, Volumes 1 and 2, Ed. Plenum Rosetta.
15. M. Grattarola, and G. Massobrio Bioelectrics Handbook 1998 McGraw Hill New York
16. M.J. Holst Multilevel methods for the Poisson-Boltzmann equation PhD Thesis 1993 Numerical Computing Group, University of Illinois at Urbana-Champaign