Numerical solution of the nonlinear poisson-boltzmann equation for a macroion modeled as an array of non overlapping beads

Journal of Physical Chemistry B

Volumn 115, Issue 16, 2011, Pages 4872-4879

  Allison, Stuart A ^a  

^a GEORGIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYLINDERS (SHAPES); DIMERS; IONIC STRENGTH; NONLINEAR EQUATIONS; NUCLEIC ACIDS; POISSON EQUATION;

BASE PAIRS; BEAD SIZE; BOUNDARY ELEMENTS; CHARGE EFFECT; DUPLEX DNA; NONLINEAR POISSON-BOLTZMANN EQUATION; NUMERICAL PROCEDURES; NUMERICAL SOLUTION; TEST CASE; TETRAMERS;

BOLTZMANN EQUATION;

EID: 79955385237     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp201541g     Document Type: Article

References (39)

1. Yang, A.-S.; Gunner, M. R.; Sampogna, R.; Sharp, K.; Honig, B. Proteins 1993, 15, 252-265
2. Antosiewicz, J.; Briggs, J. M.; Elcock, A. H.; Gilson, M. K.; McCammon, J. A. J. Comput. Chem. 1996, 17, 1633-1644
3. Zhou, H.-X.; Vijayakumar, M. J. Mol. Biol. 1997, 267, 1002-1011
4. Allison, S. A.; Xin, Y. J. Colloid Interface Sci. 2006, 299, 977-988
5. Allison, S. A. J. Colloid Interface Sci. 2009, 332, 1-10
6. Nakamura, H. Q. Rev. Biophys. 1996, 29, 1-90
7. Davis, M. E.; Madura, J. D.; Sines, J.; Luty, B. A.; Allison, S. A.; McCammon, J. A. Methods Enzymol. 1991, 202, 473-498
8. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. Biophys. J. 1997, 72, 1047-1069
9. Debye, P.; Huckel, E. Phys. Z. 1923, 24, 185-206
10. Warwicker, J.; Watson, H. C. J. Mol. Biol. 1982, 157, 701-710
11. Fowler, R. H. Statistical Mechanics; Cambridge University Press: Cambridge, U.K., 1929.
12. Onsager, L. Chem. Rev. 1933, 13, 73-89
13. Fixman, M. J. Chem. Phys. 1979, 70, 4995-5005
14. LeBret, M.; Zimm, B. H. Biopolymers 1984, 23, 270-285
15. Murthy, C. S.; Bacquet, R. J.; Rossky, P. J. J. Phys. Chem. 1985, 89, 701-710
16. Jayaram, B.; Sharp, K. A.; Honig, B. Biopolymers 1989, 28, 975-993
17. Allison, S. A. J. Phys. Chem. 1994, 98, 12091-12096
18. Holst, M. J.; Saied, F. J. Comput. Chem. 1995, 16, 337-364
19. Zhou, H.-X. J. Chem. Phys. 1994, 100, 3152-3162
20. Baker, N. A.; Sept, D.; Simpson, J.; Holst, M. J.; McCammon, J. A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 10037-10041
21. Allison, S. A. Biophys. Chem. 2001, 93, 197-213
22. Pei, H.; Allison, S. A. J. Chromatogr., A 2009, 1216, 1908-1916
23. Allison, S. A.; Pei, H.; Xin, Y. Biopolymers 2007, 87, 102-114
24. Tanford, C. Physical Chemistry of Macromolecules; John Wiley and Sons: New York, 1961; Chapter 7.
25. Loeb, A. L.; Overbeek, J.; Th., G.; Wiersema, P. H. The Electrical Double Layer Around a Spherical Colloid Particle; The M.I.T. Press: Cambridge, MA, 1961.
26. Allison, S. A. Macromolecules 1996, 29, 7391-7401
27. Xin, Y.; Mitchell, H.; Cameron, H.; Allison, S. A. J. Phys. Chem. B 2006, 110, 1038-1045
28. Germann, M. W.; Turner, T.; Allison, S. A. J. Phys. Chem. A 2007, 111, 1452-1455
29. Hagerman, P.; Zimm, B. H. Biopolymers 1981, 20, 1481-1502
30. Pei, H.; Allison, S. A.; Haynes, B. M. H.; Augustin, D. J. Phys. Chem. B 2008, 113, 2564-2571
31. Schellman, J. A.; Harvey, S. C. Biophys. Chem. 1995, 59, 95-114
32. Tirado, M. M.; Martinez, C. L.; Garcia de la Torre, J. J. Phys. Chem. 1984, 81, 2047-2052
33. Eimer, W.; Williamson, J. R.; Boxer, S. G.; Pecora, R. Biochemistry 1990, 29, 799-811
34. Diaz, R.; Fujimoto, B. S.; Schurr, J. M. Biophys. J. 1997, 72, A322
35. Garcia de la Torre, J.; Bloomfield, V. A. Biopolymers 1977, 16, 1747-1763
36. Garcia de la Torre, J.; del Rio Echenique, J.; Ortega, A. J. Phys. Chem. B 2007, 111, 955-961
37. Allison, S. A.; Chen, C.; Stigter, D. Biophys. J. 2001, 81, 2558-2568
38. Lewis, R. J.; Allison, S. A.; Eden, D.; Pecora, R. J. Chem. Phys. 1988, 89, 2490-2503
39. Xin, Y.; Hess, R.; Ho, N.; Allison, S. A. J. Phys. Chem. B 2006, 110, 25033-25044