Discretization of the induced-charge boundary integral equation.

Journal Article · Wed Jul 01 04:00:00 EDT 2009 · Phys. Rev. E

DOI:https://doi.org/10.1103/PhysRevE.80.011906· OSTI ID:962878

Bardhan, J P; Eisenberg, R S; Gillespie, D

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 et al. [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.

• Research Organization: Argonne National Laboratory (ANL)
• Sponsoring Organization: SC; NIH; Wilkinson Fellowship
• DOE Contract Number: AC02-06CH11357
• OSTI ID: 962878
• Report Number(s): ANL/BIO/JA-63359
• Journal Information: Phys. Rev. E, Journal Name: Phys. Rev. E Journal Issue: Jul. 2009 Vol. 80; ISSN PLEEE8; ISSN 1063-651X
• Country of Publication: United States
• Language: ENGLISH

Related Subjects

36 MATERIALS SCIENCE
ACCURACY
AQUEOUS SOLUTIONS
BOUNDARY ELEMENT METHOD
DIELECTRIC MATERIALS
IMPLEMENTATION
INTEGRAL EQUATIONS
MATRIX ELEMENTS
POLARIZATION
PROTEINS