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arxiv 2309.06862 v2 pith:WLSA5R2D submitted 2023-09-13 math.NA cs.NAmath.NT

Domain Decomposition Method for Poisson--Boltzmann Equations based on Solvent Excluded Surface

classification math.NA cs.NAmath.NT
keywords methodequationnonlineardecompositiondomainusedcoupleddefined
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In this paper, we develop a domain decomposition method for the nonlinear Poisson-Boltzmann equation based on a solvent-excluded surface widely used in computational chemistry. The model relies on a nonlinear equation defined in $\mathbb{R}^3$ with a space-dependent dielectric permittivity and an ion-exclusion function that accounts for steric effects. Potential theory arguments transform the nonlinear equation into two coupled equations defined in a bounded domain. Then, the Schwarz decomposition method is used to formulate local problems by decomposing the cavity into overlapping balls and only solving a set of coupled sub-equations in each ball. The main novelty of the proposed method is the introduction of a hybrid linear-nonlinear solver used to solve the equation. A series of numerical experiments are presented to test the method and show the importance of the nonlinear model.

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Cited by 2 Pith papers

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