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Efficient solution technique for solving the Poisson–Boltzmann equation
Author(s) -
Sayyed–Ahmad Abdallah,
Tuncay Kagan,
Ortoleva Peter J.
Publication year - 2004
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20039
Subject(s) - poisson–boltzmann equation , boltzmann equation , pentamer , poisson's equation , electrolyte , statistical physics , mathematics , physics , biological system , computer science , ion , thermodynamics , quantum mechanics , electrode , nuclear magnetic resonance , biology
The Poisson–Boltzmann (PB) equation has been extensively used to analyze the energetics and structure of proteins and other significant biomolecules immersed in electrolyte media. A new highly efficient approach for solving PB‐type equations that allows for the modeling of many‐atoms structures such as encountered in cell biology, virology, and nanotechnology is presented. We accomplish these efficiencies by reformulating the elliptic PB equation as the long‐time solution of an advection‐diffusion equation. An efficient modified, memory optimized, alternating direction implicit scheme is used to integrate the reformulated PB equation. Our approach is demonstrated on protein composites (a polio virus capsid protomer and a pentamer). The approach has great potential for the analysis of supramillion atoms immersed in a host electrolyte. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1068–1074, 2004