title: Comparison of three-dimensional poisson solution methods for particle-based simulation and inhomogeneous dielectrics.
abstract: Particle-based simulation represents a powerful approach to modeling physical systems in electronics, molecular biology, and chemical physics. Accounting for the interactions occurring among charged particles requires an accurate and efficient solution of Poisson's equation. For a system of discrete charges with inhomogeneous dielectrics, i.e., a system with discontinuities in the permittivity, the boundary element method (BEM) is frequently adopted. It provides the solution of Poisson's equation, accounting for polarization effects due to the discontinuity in the permittivity by computing the induced charges at the dielectric boundaries. In this framework, the total electrostatic potential is then found by superimposing the elemental contributions from both source and induced charges. In this paper, we present a comparison between two BEMs to solve a boundary-integral formulation of Poisson's equation, with emphasis on the BEMs' suitability for particle-based simulations in terms of solution accuracy and computation speed. The two approaches are the collocation and qualocation methods. Collocation is implemented following the induced-charge computation method of D. Boda et al. [J. Chem. Phys. 125, 034901 (2006)]. The qualocation method is described by J. Tausch et al. [IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 20, 1398 (2001)]. These approaches are studied using both flat and curved surface elements to discretize the dielectric boundary, using two challenging test cases: a dielectric sphere embedded in a different dielectric medium and a toy model of an ion channel. Earlier comparisons of the two BEM approaches did not address curved surface elements or semiatomistic models of ion channels. Our results support the earlier findings that for flat-element calculations, qualocation is always significantly more accurate than collocation. On the other hand, when the dielectric boundary is discretized with curved surface elements, the two methods are essentially equivalent; i.e., they have comparable accuracies for the same number of elements. We find that ions in water--charges embedded in a high-dielectric medium--are harder to compute accurately than charges in a low-dielectric medium.
authors.affiliation: ARCES, University of Bologna and IUNET, Via Venezia 260, I-47521 Cesena, Italy. cberti@arces.unibo.it
authors.forename: Claudio
authors.initials: C
authors.lastname: Berti
authors.forename: Dirk
authors.initials: D
authors.lastname: Gillespie
authors.forename: Jaydeep P
authors.initials: JP
authors.lastname: Bardhan
authors.forename: Robert S
authors.initials: RS
authors.lastname: Eisenberg
authors.forename: Claudio
authors.initials: C
authors.lastname: Fiegna
mesh_terms: D000818:Animals; D001704:Biopolymers / Q000737:chemistry* / Q000378:metabolism*; D003198:Computer Simulation; D006801:Humans; D008954:Models, Biological; D008956:Models, Chemical; D010316:Particle Size; D016012:Poisson Distribution
chemical_list: D001704:Biopolymers