Enriched gradient recovery for interface solutions of the Poisson-Boltzmann equation
Accurate calculation of electrostatic potential and gradient on the molecular surface is highly desirable for the continuum and hybrid modeling of large scale deformation of biomolecules in solvent. In this article a new numerical method is proposed to calculate these quantities on the dielectric in...
| Publié dans: | Journal of computational physics. - 1986. - 421(2020) vom: 15. Nov. |
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| Auteur principal: | |
| Autres auteurs: | |
| Format: | Article en ligne |
| Langue: | English |
| Publié: |
2020
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| Accès à la collection: | Journal of computational physics |
| Sujets: | Journal Article Biomolecular electrostatics Gradient recovery High accuracy Interface methods Numerical solution Poisson-Boltzmann equation |
| Résumé: | Accurate calculation of electrostatic potential and gradient on the molecular surface is highly desirable for the continuum and hybrid modeling of large scale deformation of biomolecules in solvent. In this article a new numerical method is proposed to calculate these quantities on the dielectric interface from the numerical solutions of the Poisson-Boltzmann equation. Our method reconstructs a potential field locally in the least square sense on the polynomial basis enriched with Green's functions, the latter characterize the Coulomb potential induced by charges near the position of reconstruction. This enrichment resembles the decomposition of electrostatic potential into singular Coulomb component and the regular reaction field in the Generalized Born methods. Numerical experiments demonstrate that the enrichment recovery produces drastically more accurate and stable potential gradients on molecular surfaces compared to classical recovery techniques |
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| Description: | Date Revised 17.11.2021 published: Print-Electronic Citation Status PubMed-not-MEDLINE |
| ISSN: | 0021-9991 |
| DOI: | 10.1016/j.jcp.2020.109725 |