Special Lecture : "A Treecode-Accelerated Boundary Integral Poisson-Boltzmann Solver for Solvated Proteins"

 

Date : November 19th (Wed.) 15:00-16:30
Place:3C Nishiura Laboratory, WPI-AIMR Main Bldg., Katahira campus, Tohoku University【MAP & Access


Speaker
Robert Krasny (Arthur F. Thurnau Professor, University of Michigan)

 

Abstract

Electrostatic effects have an important role in determining protein structure. Here we present a treecode-accelerated boundary integral (TABI) solver for electrostatics of solvated proteins described by the linear Poisson-Boltzmann equation. In this model the solvent is a continuum dielectric material with ionic screening. The treecode reduces the computational cost from $O(N^2)$ to $O(N\log N)$, where $N$ is the number of faces in the triangulated molecular surface. We compare TABI results to those obtained using the grid-based APBS code. This is joint work with Weihua Geng (Southern Methodist University).

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 Advanced Institute for Materials Research Tohoku University Mathematical Group
 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577 Japan 【Access/Contact