Efficient solution technique for solving the Poisson-Boltzmann equation

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Date

2004-06-01

Author

Sayyed-Ahmad, A
Tuncay, Kağan
Ortoleva, PJ

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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. (C) 2004 Wiley Periodicals, Inc.

Subject Keywords

General Chemistry, Computational Mathematics

URI

https://hdl.handle.net/11511/36828

Journal

JOURNAL OF COMPUTATIONAL CHEMISTRY

DOI

https://doi.org/10.1002/jcc.20039

Collections

Department of Civil Engineering, Article

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Citation Formats

A. Sayyed-Ahmad, K. Tuncay, and P. Ortoleva, “Efficient solution technique for solving the Poisson-Boltzmann equation,” JOURNAL OF COMPUTATIONAL CHEMISTRY, pp. 1068–1074, 2004, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/36828.