Discretization of the induced-charge boundary integral equation.
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.
Bardhan
Jaydeep P
JP
Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA. jbardhan@alum.mit.edu
Eisenberg
Robert S
RS
Gillespie
Dirk
D
D017097:Electric Impedance; D008956:Models, Chemical; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D055672:Static Electricity; D014867:Water / Q000737:chemistry
D011506:Proteins; D014867:Water