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An implicit boundary integral method for computing electric potential of macromolecules in solvent
KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. University of Texas, United States.ORCID iD: 0000-0001-8441-3678
2018 (English)In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 359, p. 199-215Article in journal (Refereed) Published
Abstract [en]

A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equation that arises in mathematical models for the electrostatics of molecules in solvent. The proposed method uses an implicit boundary integral formulation to derive a linear system defined on Cartesian nodes in a narrowband surrounding the closed surface that separates the molecule and the solvent. The needed implicit surface is constructed from the given atomic description of the molecules, by a sequence of standard level set algorithms. A fast multipole method is applied to accelerate the solution of the linear system. A few numerical studies involving some standard test cases are presented and compared to other existing results.

Place, publisher, year, edition, pages
Academic Press, 2018. Vol. 359, p. 199-215
Keyword [en]
Poisson-Boltzmann equation, Implicit boundary integral method, Level set method, Fast multipole method, Electrostatics, Implicit solvent model
National Category
Computational Mathematics
Identifiers
URN: urn:nbn:se:kth:diva-225168DOI: 10.1016/j.jcp.2018.01.021ISI: 000427396200010Scopus ID: 2-s2.0-85041659256OAI: oai:DiVA.org:kth-225168DiVA, id: diva2:1194954
Note

QC 20180404

Available from: 2018-04-04 Created: 2018-04-04 Last updated: 2018-04-11Bibliographically approved

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Tsai, Yen-Hsi Richard

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