Numerical considerations in the computation of the electrostatic free energy of interaction within the Poisson-Boltzmann theory

Journal of Computational Physics

Volumn 136, Issue 2, 1997, Pages 263-271

  Micu, Alexandru M ^a,b   Bagheri, Babak ^b   Ilin, Andrew V ^b   Scott, Ridgway L ^a,b   Pettitt, Montgomery B ^a,b  

^a University of Houston   (United States)

^b UNIVERSITY OF HOUSTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BOLTZMANN EQUATION; COMPUTATION THEORY; ELECTROSTATICS; HYDROGEN BONDS; NONLINEAR EQUATIONS; POISSON EQUATION;

BROWNIAN DYNAMICS; DYNAMIC PROGRAMS; ELECTROSTATIC FREE ENERGY; ELECTROSTATIC STRESS; FREE ENERGY OF INTERACTIONS; IONIC CONCENTRATIONS; NONLINEAR POISSON-BOLTZMANN EQUATION; ORDERS OF MAGNITUDE; POISSON-BOLTZMANN THEORY; UNIVERSITY OF HOUSTON;

FREE ENERGY;

EID: 0031572118     PISSN: 00219991     EISSN: None     Source Type: Journal    
DOI: 10.1006/jcph.1997.5707     Document Type: Article

References (38)

1. Luty B. A., Davis M. E., McCammon J. A. J. Comput. Chem. 9:1992;1114.
2. Reiner E. S., Radke C. J. J. Chem. Soc. Faraday Trans. 86:1990;3901.
3. Sharp K. A., Hönig B. J. Phys. Chem. 94:1990;7684.
4. Zhou H.-X. J. Chem. Phys. 100:1994;3152.
5. Brooks C. L. III, Karplus Martin, Pettitt B. M. Advances in Chemical Physics. 1988;Wiley, New York.
6. Davis M. E., Madura J. D., Luty B. A., McCammon J. A. Comput. Phys. Commun. 62:1991;187.
7. Madura J. D., Briggs J. M., Wade R. C., Davis M. E., Luty B. A., Ilin A., Antosciewicz J., Gilson M. K., Bagheri B., Scott L. R., McCammon J. A. Comput. Phys. Commun. 91:1995;57.
8. Gilson M. K., Davis M. E., Luty B. A., McCammon J. A. J. Phys. Chem. 97:1993;3591.
9. van Keulen H., Smit J. A. M. J. Colloid Interface Sci. 170:1995;134.
10. Feitosa E., Neto A. A., Chaimovich H. Langmuir. 9:1993;702.
11. Carnie S. L., Chan D. Y. C. J. Colloid Interface Sci. 155:1993;297.
12. Carnie S. L., Chan D. Y. C., Stankovich J. J. Colloid Interface Sci. 165:1994;116.
13. Forsten K. E., Kozack R. E., Lauffenberger D. A., Subramanian S. J. Phys. Chem. 98:1994;5586.
14. Vorobjev Y. N., Scheraga H. A. J. Phys. Chem. 97:1993;4855.
15. Schaefer M., Karplus M. J. Phys. Chem. 100:1996;1578.
16. Ewing T. J. A., Lybrand T. P. J. Phys. Chem. 98:1994;1748.
17. Vlachy V., Haymet A. D. J. J. Chem. Phys. 84:1986;5874.
18. Cheng Y.-K, Pettitt B. M. Prog. Biophys. Mol. Biol. 58:1992;225.
19. Thuong N. T., Hélène C. Angew. Chem. Int. Engl. 32:1993;666.
20. Uhlmann E., Peyman A. Chem. Rev. 90:1990;544.
21. Zimmerman S. C., Schmitt P. J. Am. Chem. Soc. 117:1995;10769.
22. Zhou B-W., Puga E., Sun J. S., Garestier T., Hélène C. J. Am. Chem. Soc. 117:1995;10425.
23. Hélène C., Toulmé J. J. Cohen J. S. Oligodeoxynucleotides: Antisense Inhibitors of Gene Expression. 1989;137 McMillan, London.
24. Pilch D. S., Brousseau R., Shafer R. H. Nucl. Ac. Res. 18:1990;5743.
25. Brenner S., Scott L. R. The Mathematical Theory of Finite Element Methods. 1994;Springer-Verlag, New York/Berlin.
26. McQuarrie D. Statistical Mechanics. 1976;Harper & Row, New York.
27. Gilson M., Sharp K. A., Hönig B. J. Comput. Chem. 9:1988;327.
28. Zacharias M., Luty B. A., Davis M. E., McCammon J. A. Biophys. J. 63:1992;1280.
29. Mohan V., Davis M. E., McCammon J. A., Pettitt B. M. J. Am. Chem. Soc. 96:1992;6428.
30. Elcock A. H., McCammon J. A. J. Am. Chem. Soc. 117:1995;10161.
31. Arnott S., Chandrasekeharan R., Birdsall D. L., Leslie A. G. W., Ratliffe R. L. Nature. 283:1980;743.
32. 1994, QUANTA, Molecular Simulations, Inc. 200 Fifth Avenue, Waltham, MA.
33. Davis M. E., McCammon J. A. J. Comput. Chem. 12:1991;909.
34. Hönig B., Nicholls A. Science. 268:1995;1144.
35. Fowler R. H. Statistical Mechanics. 1929;Cambridge Univ. Press, Cambridge.
36. Onsager L. Chem. Rev. 13:1933;73.
37. Kirkwood J. G. J. Chem. Phys. 2:1934;767.
38. Bockris J. O., Reddy A. K. N. Modern Electrochemistry. 1970;Plenum, New York.