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arXiv · 1512.08406

Work/Precision Tradeoffs in Continuum Models of Biomolecular Electrostatics

Matthew G. Knepley·Jaydeep P. Bardhan
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Abstract

The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's ubiquitous atomic charges and polar chemical groups. In this work, we investigate a simple approach to numerical calculation of this model using boundary-integral equation (BIE) methods and boundary-element methods (BEM). Traditional BEM discretizes the protein--solvent boundary into a set of boundary elements, or panels, and the approximate solution is defined as a weighted combination of basis functions with compact support. The resulting BEM matrix then requires integrating singular or near singular functions, which can be slow and challenging to compute. Here we investigate the accuracy and convergence of a simpler representation, namely modeling the unknown surface charge distribution as a set of discrete point charges on the surface. We find that at low resolution, point-based BEM is more accurate than panel-based methods, due to the fact that the protein surface is sampled directly, and can be of significant value for numerous important calculations that require only moderate accuracy, such as the preliminary stages of rational drug design and protein engineering.

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Matthew G. Knepley, Jaydeep P. Bardhan. 2015-12-28. Work/Precision Tradeoffs in Continuum Models of Biomolecular Electrostatics. https://arxiv.org/abs/1512.08406

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