A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation

DelPhi is a popular scientific program which numerically solves the Poisson-Boltzmann equation (PBE) for electrostatic potentials and energies of biomolecules immersed in water via finite difference method. It is well known for its accuracy, reliability, flexibility, and efficiency. In this work, a...

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Detalles Bibliográficos
Autores principales: Li, Chuan, McGowan, Mark, Alexov, Emil, Zhao, Shan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2020
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9883664/
https://www.ncbi.nlm.nih.gov/pubmed/33378855
http://dx.doi.org/10.3934/mbe.2020331
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author Li, Chuan
McGowan, Mark
Alexov, Emil
Zhao, Shan
author_facet Li, Chuan
McGowan, Mark
Alexov, Emil
Zhao, Shan
author_sort Li, Chuan
collection PubMed
description DelPhi is a popular scientific program which numerically solves the Poisson-Boltzmann equation (PBE) for electrostatic potentials and energies of biomolecules immersed in water via finite difference method. It is well known for its accuracy, reliability, flexibility, and efficiency. In this work, a new edition of DelPhi that uses a novel Newton-like method to solve the nonlinear PBE, in addition to the already implemented Successive Over Relaxation (SOR) algorithm, is introduced. Our tests on various examples have shown that this new method is superior to the SOR method in terms of stability when solving the nonlinear PBE, being able to converge even for problems involving very strong nonlinearity.
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spelling pubmed-98836642023-01-28 A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation Li, Chuan McGowan, Mark Alexov, Emil Zhao, Shan Math Biosci Eng Article DelPhi is a popular scientific program which numerically solves the Poisson-Boltzmann equation (PBE) for electrostatic potentials and energies of biomolecules immersed in water via finite difference method. It is well known for its accuracy, reliability, flexibility, and efficiency. In this work, a new edition of DelPhi that uses a novel Newton-like method to solve the nonlinear PBE, in addition to the already implemented Successive Over Relaxation (SOR) algorithm, is introduced. Our tests on various examples have shown that this new method is superior to the SOR method in terms of stability when solving the nonlinear PBE, being able to converge even for problems involving very strong nonlinearity. 2020-09-21 /pmc/articles/PMC9883664/ /pubmed/33378855 http://dx.doi.org/10.3934/mbe.2020331 Text en https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0 (https://creativecommons.org/licenses/by/4.0/) )
spellingShingle Article
Li, Chuan
McGowan, Mark
Alexov, Emil
Zhao, Shan
A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation
title A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation
title_full A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation
title_fullStr A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation
title_full_unstemmed A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation
title_short A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation
title_sort newton-like iterative method implemented in the delphi for solving the nonlinear poisson-boltzmann equation
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9883664/
https://www.ncbi.nlm.nih.gov/pubmed/33378855
http://dx.doi.org/10.3934/mbe.2020331
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