Abstract: I will present a new version of the treecode-accelerated boundary integral Poisson-Boltzmann solver which 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. Numerical results for protein 1A63 and two viral capsids (Zika, H1N1) demonstrate the code’s accuracy and efficiency. I will also discuss an extension of this approach to the Poisson-Nernst-Planck model for ion transport through channel proteins in cell membranes. 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).

Contact: AIM Seminar Organizers