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Volume 18, Issue 2
Finite Volume Element Method for Predicting Electrostatics of a Biomolecule Immersed in an Ionic Solvent

Hao Wu, Jinyong Ying & Qingsong Zou

Int. J. Numer. Anal. Mod., 18 (2021), pp. 190-202.

Published online: 2021-03

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  • Abstract

Poisson-Boltzmann equation (PBE) is a classic implicit continuum model to predict the electrostatic potentials of a solvated biomolecule. In this paper, we present a finite volume element method specific to the elliptic interface problem with a non-homogeneous flux condition for solving PBE and provide a follow-up analysis. The new PBE solver is fulfilled through both Fortran and Python, afterwards the local Poisson test model coupled with an analytical solution is adopted to well validate the program. Lastly, an application of the new solver to the prediction of solvation free energies of the proteins is made.

  • Keywords

Poisson-Boltzmann equation, electrostatic free energy, finite volume element method, solvation free energy.

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COPYRIGHT: © Global Science Press

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@Article{IJNAM-18-190, author = {Wu , HaoYing , Jinyong and Zou , Qingsong}, title = {Finite Volume Element Method for Predicting Electrostatics of a Biomolecule Immersed in an Ionic Solvent}, journal = {International Journal of Numerical Analysis and Modeling}, year = {2021}, volume = {18}, number = {2}, pages = {190--202}, abstract = {

Poisson-Boltzmann equation (PBE) is a classic implicit continuum model to predict the electrostatic potentials of a solvated biomolecule. In this paper, we present a finite volume element method specific to the elliptic interface problem with a non-homogeneous flux condition for solving PBE and provide a follow-up analysis. The new PBE solver is fulfilled through both Fortran and Python, afterwards the local Poisson test model coupled with an analytical solution is adopted to well validate the program. Lastly, an application of the new solver to the prediction of solvation free energies of the proteins is made.

}, issn = {2617-8710}, doi = {https://doi.org/}, url = {http://global-sci.org/intro/article_detail/ijnam/18714.html} }
TY - JOUR T1 - Finite Volume Element Method for Predicting Electrostatics of a Biomolecule Immersed in an Ionic Solvent AU - Wu , Hao AU - Ying , Jinyong AU - Zou , Qingsong JO - International Journal of Numerical Analysis and Modeling VL - 2 SP - 190 EP - 202 PY - 2021 DA - 2021/03 SN - 18 DO - http://doi.org/ UR - https://global-sci.org/intro/article_detail/ijnam/18714.html KW - Poisson-Boltzmann equation, electrostatic free energy, finite volume element method, solvation free energy. AB -

Poisson-Boltzmann equation (PBE) is a classic implicit continuum model to predict the electrostatic potentials of a solvated biomolecule. In this paper, we present a finite volume element method specific to the elliptic interface problem with a non-homogeneous flux condition for solving PBE and provide a follow-up analysis. The new PBE solver is fulfilled through both Fortran and Python, afterwards the local Poisson test model coupled with an analytical solution is adopted to well validate the program. Lastly, an application of the new solver to the prediction of solvation free energies of the proteins is made.

Wu , HaoYing , Jinyong and Zou , Qingsong. (2021). Finite Volume Element Method for Predicting Electrostatics of a Biomolecule Immersed in an Ionic Solvent. International Journal of Numerical Analysis and Modeling. 18 (2). 190-202. doi:
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