Title:
Integral Equation Calculations for Electrostatics of Solvated Biomolecules
Abstract:
This talk presents a new version of the treecode-accelerated boundary integral Poisson-Boltzmann (TABI-PB) solver [1,2]. The code computes the electrostatic potential on the molecular surface of a solvated biomolecule using a well-conditioned integral equation formulation. The new version utilizes the NanoShaper surface triangulation code, node-patch boundary integral discretization, a block preconditioner, and a GPU-accelerated fast multipole method based on barycentric Lagrange interpolation and dual tree traversal [3,4]. Numerical results for protein 1A63 and two viral capsids (Zika, H1N1) demonstrate the code’s accuracy and efficiency. The talk will also discuss an extension of this approach to the Poisson-Nernst-Planck model for charge transport through transmembrane ion channels [5]. This talk reports on joint work with Zhen Chao (Western Washington University), Weihua Geng (Southern Methodist University), Svetlana Tlupova (Farmingdale State College), Nathan Vaughn (LANL), Lei Wang (U-Wisconsin, Milwaukee), and Leighton Wilson (Cerebras Systems).