TABI-PB 2.0: An Improved Version of the Treecode-Accelerated Boundary Integral Poisson-Boltzmann Solver

Leighton Wilson, Weihua Geng, Robert Krasny

2022The Journal of Physical Chemistry B21 citationsDOI

Abstract

This work describes TABI-PB 2.0, an improved version of the treecode-accelerated boundary integral Poisson-Boltzmann solver. The code computes the electrostatic potential on the molecular surface of a solvated biomolecule, and further processing yields the electrostatic solvation energy. The new implementation utilizes the NanoShaper surface triangulation code, node-patch boundary integral discretization, a block preconditioner, and a fast multipole method based on barycentric Lagrange interpolation and dual tree traversal. Performance-critical portions of the code were implemented on a GPU. Numerical results for protein 1A63 and two viral capsids (Zika, H1N1) demonstrate the code's accuracy and efficiency.

Topics & Concepts

SolverBarycentric coordinate systemComputational scienceBoundary (topology)Computer scienceCode (set theory)Interpolation (computer graphics)DiscretizationPoisson–Boltzmann equationBlock (permutation group theory)AlgorithmParallel computingPhysicsMathematicsMathematical optimizationGeometryMathematical analysisAnimationComputer graphics (images)Set (abstract data type)Quantum mechanicsIonProgramming languageRNA Interference and Gene DeliveryProtein Structure and DynamicsNanopore and Nanochannel Transport Studies