Stanford EE Computer Systems Colloquium

4:15PM, Wednesday, Oct 11, 2006
NEC Auditorium, Gates Computer Science Building B03

New Architectures for a New Biology

David E. Shaw
D. E. Shaw Research and Development
Center for Computational Biology and Bioinformatics, Columbia University
About the talk:

Some of the most important outstanding questions in the fields of biology, chemistry, and medicine remain unsolved as a result of our limited understanding of the structure, behavior and interaction of biologically significant molecules. The laws of physics that determine the form and function of these biomolecules are well understood. Current technology, however, does not allow us to simulate the effect of these laws with sufficient accuracy, and for a sufficient period of time, to answer many of the questions that biologists, biochemists, and biomedical researchers are most anxious to answer. This talk will describe the current state of the art in biomolecular simulation and explore the potential role of high-performance computing technologies in extending current capabilities. Efforts within our own lab to develop novel architectures and algorithms to accelerate molecular dynamics simulations by several orders of magnitude will be described, along with work by other researchers pursuing alternative approaches. If such efforts ultimately prove successful, one might imagine the emergence of an entirely new paradigm in which computational experiments take their place alongside those conducted in "wet" laboratories as central tools in the quest to understand living organisms at a molecular level, and to develop safe, effective, precisely targeted medicines capable of relieving suffering and saving human lives.


Download the slides for this presentation in PDF format.

About the speaker:

David E. Shaw serves as chief scientist of D. E. Shaw Research, LLC, and as a senior research fellow at the Center for Computational Biology and Bioinformatics at Columbia University.

He received his Ph.D. from Stanford University in 1980 and served on the faculty of the Computer Science Department at Columbia University before turning his attention to the emerging field of computational finance in 1986. In 1988, he founded the D. E. Shaw group, an investment and technology development firm with approximately $23 billion in assets. While he continues to serve as chairman of the firm's top-level parent companies, Dr. Shaw is now spending the great majority of his time on hands-on scientific research in the field of computational biochemistry. His research group is currently involved in the design of machine architectures and algorithms for high-speed molecular dynamics simulations, and in the use of such simulations to study biomolecular systems of interest from both a scientific and a pharmaceutical perspective. In 1994, President Clinton appointed Dr. Shaw to the President's Council of Advisors on Science and Technology, in which capacity he served as chairman of the Panel on Educational Technology. He was elected to the board of directors of the American Association for the Advancement of Science in 2000, and has testified before several Congressional committees and the National Science Board on various topics related to science and technology policy.

Contact information:

David E Shaw