Efficient solution technique for solving the Poisson–Boltzmann equation

A Sayyed–Ahmad, K Tuncay… - Journal of computational …, 2004 - Wiley Online Library
Journal of computational chemistry, 2004Wiley Online Library
Abstract 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 …
Abstract
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
Wiley Online Library
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