ArticlePhysical review. E, Statistical, nonlinear, and soft matter physics2009
Discretization of the induced-charge boundary integral equation.
Article in Physical review. E, Statistical, nonlinear, and soft matter physics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Multiscale Multiphysics and Multidomain Models I: Basic Theory.Journal of theoretical & computational chemistry · 2013Article
- Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding.Molecular based mathematical biology · 2013Article
- Particle-based simulation of charge transport in discrete-charge nano-scale systems: the electrostatic problem.Nanoscale research letters · 2012Article
- Variational multiscale models for charge transport.SIAM review. Society for Industrial and Applied Mathematics · 2012Article
- A method for treating the passage of a charged hard sphere ion as it passes through a sharp dielectric boundary.The Journal of chemical physics · 2011Article
- Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids.The Journal of chemical physics · 2010Article
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Authors and funding
3 authors.
Funding
Abstract
Boundary-element methods (BEMs) for solving integral equations numerically have been used in many fields to compute the induced charges at dielectric boundaries. In this paper, we consider a more accurate implementation of BEM in the context of ions in aqueous solution near proteins, but our results are applicable more generally. The ions that modulate protein function are often within a few angstroms of the protein, which leads to the significant accumulation of polarization charge at the protein-solvent interface. Computing the induced charge accurately and quickly poses a numerical challenge in solving a popular integral equation using BEM. In particular, the accuracy of simulations can depend strongly on seemingly minor details of how the entries of the BEM matrix are calculated. We demonstrate that when the dielectric interface is discretized into flat tiles, the qualocation method of Tausch [IEEE Trans Comput.-Comput.-Aided Des. 20, 1398 (2001)] to compute the BEM matrix elements is always more accurate than the traditional centroid-collocation method. Qualocation is not more expensive to implement than collocation and can save significant computational time by reducing the number of boundary elements needed to discretize the dielectric interfaces.
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