Towards optimal boundary integral formulations of the Poisson-Boltzmann equation for molecular electrostatics

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dc.contributor.authorSearch, Stefan D.
dc.contributor.authorCooper, Christopher D.
dc.contributor.authorvan't Wout, Elwin
dc.date.accessioned2025-01-20T21:12:49Z
dc.date.available2025-01-20T21:12:49Z
dc.date.issued2022
dc.description.abstractThe Poisson-Boltzmann equation offers an efficient way to study electrostatics in molecular settings. Its numerical solution with the boundary element method is widely used, as the complicated molecular surface is accurately represented by the mesh, and the point charges are accounted for explicitly. In fact, there are several well-known boundary integral formulations available in the literature. This work presents a generalized expression of the boundary integral representation of the implicit solvent model, giving rise to new forms to compute the electrostatic potential. Moreover, it proposes a strategy to build efficient preconditioners for any of the resulting systems, improving the convergence of the linear solver. We perform systematic benchmarking of a set of formulations and preconditioners, focusing on the time to solution, matrix conditioning, and eigenvalue spectrum. We see that the eigenvalue clustering is a good indicator of the matrix conditioning, and show that they can be easily manipulated by scaling the preconditioner. Our results suggest that the optimal choice is problem-size dependent, where a simpler direct formulation is the fastest for small molecules, but more involved second-kind equations are better for larger problems. We also present a fast Calderon preconditioner for first-kind formulations, which shows promising behavior for future analysis. This work sets the basis towards choosing the most convenient boundary integral formulation of the Poisson-Boltzmann equation for a given problem.
dc.fuente.origenWOS
dc.identifier.doi10.1002/jcc.26825
dc.identifier.eissn1096-987X
dc.identifier.issn0192-8651
dc.identifier.urihttps://doi.org/10.1002/jcc.26825
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/93677
dc.identifier.wosidWOS:000760367500001
dc.issue.numero10
dc.language.isoen
dc.pagina.final691
dc.pagina.inicio674
dc.revistaJournal of computational chemistry
dc.rightsacceso restringido
dc.subjectboundary element method
dc.subjectelectrostatics
dc.subjectimplicit solvent model
dc.subjectPoisson-Boltzmann
dc.subjectpreconditioning
dc.subject.ods03 Good Health and Well-being
dc.subject.odspa03 Salud y bienestar
dc.titleTowards optimal boundary integral formulations of the Poisson-Boltzmann equation for molecular electrostatics
dc.typeartículo
dc.volumen43
sipa.indexWOS
sipa.trazabilidadWOS;2025-01-12
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