Application of the thin-shell formulation to the numerical modeling of Stern layer in biomolecular electrostatics

✍ Scribed by Alessandra Manzin; Oriano Bottauscio; Domenico Patrizio Ansalone

• Publisher: John Wiley and Sons
• Year: 2011
• Tongue: English
• Weight: 803 KB
• Volume: 32
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.21896

✦ Synopsis

Abstract

In this article, the thin‐shell formulation is applied to efficiently modeling the Stern layer within computational algorithms oriented toward the boundary element solution of the linearized Poisson–Boltzmann equation. The attention is focused on the calculation of the electrostatic potential in proximity to a biomolecule immersed in an electrolyte medium. Following the proposed approach, the Stern layer is made to collapse to a zero‐thickness region (two‐dimensional surface) with interface conditions linking the electrostatic potential over the molecular and the bulk ion accessible surfaces. Advantages lie in the limitation of divergent integral problems and in the halving of the unknown number, with a significant impact on computational time and memory requirements when modeling large biomolecules. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011