EECS Joint Colloquium Distinguished Lecture Series

Wednesday, September 15, 2004
Hewlett Packard Auditorium, 306 Soda Hall
4:00-5:00 p.m.

Professor Kathy Yelick

Electrical Engineering and Computer Sciences Department
U. C. Berkeley


Towards a Digital Human:
Scalable Simulation of the Heart and Other Organs




Simulation is often called the "third pillar of science," along with theory and experimentation. Simulation of the human body would enable a virtual experimental setup that would have applications in biology and medicine. While a full simulation of the human body is far from possible today, individual models exist of many of the organs within the body. One class of problems that arise in such simulations is the modeling of fluid flow within an organ, often when that fluid contains immersed elastic structures such as muscle, membrane, or other tissue. The computational cost of modeling the fluid dynamics even within a single organ is very high, requiring the use of today's fastest parallel machines.

In this talk I will describe a scalable parallel algorithm for the immersed boundary method. The method, due to Peskin and McQueen, has been used to simulate blood flow in the heart, blood clotting, the motion of bacteria and sperm, embryo growth, and the response of the cochlea to sound waves. Our parallel implementation uses a novel programming language called Titanium, which is a high performance extension of Java. I will describe the Titanium language and compiler as well as our computational framework for the immersed boundary method, which is designed to be extensible and is publicly available along with the Titanium compiler. I will also talk about some of the remaining open problems in Computer Science and Applied Mathematics motivated by this application domain.


Kathy Yelick received her Bachelors (1985), Masters (1985), and PhD (1991) degrees in Electrical Engineering and Computer Science from the Massachusetts Institute of Technology. Her research interests include parallel computing, memory hierarchy optimizations, programming languages and compilers. A summary of some current and ongoing projects is available, along with a CV in either postscript or pdf on her webpage. Recent papers and a few talks are also available online.