2015/12/28 by Matthew G. Knepley, Jaydeep P. Bardhan, Knepley, Matthew G. +1
Biochemistry, Genetics and Molecular Biology · Engineering · Physics and Astronomy · #Biomolecules (q-bio.BM) #Electromagnetic Scattering and Analysis #FOS: Biological sciences #FOS: Mathematics #Microwave Engineering and Waveguides #Numerical Analysis (math.NA) #RNA Interference and Gene Delivery
paper · pdf · doi:10.48550/arxiv.1512.08406
openalex publication_date 2015/12/28 · openalex created_date 2022/10/03 · openalex updated_date 2026/08/01
The structure and function of biological molecules are strongly influenced by\nthe water and dissolved ions that surround them. This aqueous solution\n(solvent) exerts significant electrostatic forces in response to the\nbiomolecule's ubiquitous atomic charges and polar chemical groups. In this\nwork, we investigate a simple approach to numerical calculation of this model\nusing boundary-integral equation (BIE) methods and boundary-element methods\n(BEM). Traditional BEM discretizes the protein--solvent boundary into a set of\nboundary elements, or panels, and the approximate solution is defined as a\nweighted combination of basis functions with compact support. The resulting BEM\nmatrix then requires integrating singular or near singular functions, which can\nbe slow and challenging to compute. Here we investigate the accuracy and\nconvergence of a simpler representation, namely modeling the unknown surface\ncharge distribution as a set of discrete point charges on the surface. We find\nthat at low resolution, point-based BEM is more accurate than panel-based\nmethods, due to the fact that the protein surface is sampled directly, and can\nbe of significant value for numerous important calculations that require only\nmoderate accuracy, such as the preliminary stages of rational drug design and\nprotein engineering.\n