A rapid boundary integral equation technique for protein electrostatics

Grandison, S, Penfold, R and Vanden-Broeck, J-M (2007) A rapid boundary integral equation technique for protein electrostatics. Journal of Computational Physics, 224 (2). pp. 663-680.

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Abstract

A new boundary integral formulation is proposed for the solution of electrostatic field problems involving piecewise uniform dielectric continua. Direct Coulomb contributions to the total potential are treated exactly and Green’s theorem is applied only to the residual reaction field generated by surface polarisation charge induced at dielectric boundaries. The implementation shows significantly improved numerical stability over alternative schemes involving the total field or its surface normal derivatives. Although strictly respecting the electrostatic boundary conditions, the partitioned scheme does introduce a jump artefact at the interface. Comparison against analytic results in canonical geometries, however, demonstrates that simple interpolation near the boundary is a cheap and effective way to circumvent this characteristic in typical applications. The new scheme is tested in a naive model to successfully predict the ground state orientation of biomolecular aggregates comprising the soybean storage protein, glycinin.

Item Type: Article
Faculty \ School: Faculty of Science > School of Computing Sciences
Faculty of Science > School of Mathematics
Related URLs:
Depositing User: Rhiannon Harvey
Date Deposited: 31 Jan 2012 15:26
Last Modified: 14 Aug 2018 11:31
URI: https://ueaeprints.uea.ac.uk/id/eprint/36657
DOI: 10.1016/j.jcp.2006.10.021

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