Bio-Geometric Modeling
Herbert Edelsbrunner, Computer Science and Mathematics, Duke University

Abstract:
Molecules have forever been modeled geometrically, either as stick-diagrams, emphasizing the covalent bonds between atoms, or as space-filling diagrams, representing the space they occupy. This talk aims at further developing the geometric view of the molecular world. It introduces the alpha complex, which is a combinatorial object that leads to fast and robust algorithms for visualization and analysis. As an example, we will see that the alpha complex can be used to compute the volume and surface area without constructing the space-filling diagram. Similarly, it can be used to compute the weighted area derivative of the surface, which is believed to have a significant contribution to the force that drives the folding process simulated by molecular dynamics.

Host: Guy Blelloch

Short Biography

Dr. Edelsbrunner's research focuses on developing algorithms to model proteins as geometric shapes to determine how protein structure affects the function of an enzyme. In a recent research milestone, Dr. Edelsbrunner, one of the founders of computational geometry, discovered how to express and compute mathematically the area derivatives of a protein in motion. Although there are thousands of researchers who focus on the study of protein structure, Dr. Edelsbrunner is one of a handful of computer scientist devoted to this field.

In 2000, Dr. Edelsbrunner received a $7.2 million grant from the National Science Foundation to collaborate with Stanford University, the University of North Carolina at Chapel Hill, and North Carolina A&T University on research into bioinformatics, applying information technology to solve the riddles of protein structure. In 1996, he and his wife Ping Fu founded Raindrop Geomagic Inc. The start-up provides software that automatically converts data scanned from a physical object, such as a cylinder head or a molded hearing aid, to production quality 3D digital models.

Dr. Edelsbrunner received his M.S. and Ph.D. from the Graz University of Technology in Austria. He is the only computer scientist to have won the National Science Foundation Waterman Award, which honors one researcher per year in science, engineering, math, or economics.