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Title: New Architectures for a New Biology
Speaker(s): Dr. David E. Shaw, D.E. Shaw Research and Development and Center for computational Biology and Informatics, Columbia University
Time: 4-5:30pm
Location: MIT, 32-123
Abstract: 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.

David E. Shaw serves as chairman of the D. E. Shaw group of companies, 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, a specialized investment and technology development firm with approximately $18 billion in assets whose activities center on various aspects of the intersection between technology and finance. While he continues to serve as chairman of the top-level parent companies of the D. E. Shaw group, Dr. Shaw is now spending the great majority of his time on hands-on scientific research in the field of computational biochemistry. In this capacity, he leads a small research group (currently consisting of 35 computational chemists and biologists, computer scientists and applied mathematicians, and computer architects and engineers) within an independent laboratory at D. E. Shaw Research and Development, LLC. The group is currently focusing on the development of novel physical models, computational algorithms and machine architectures for protein structure determination, computational drug design, and biomolecular simulation.

In 1994, Dr. Shaw was appointed by President Clinton to the President’s Committee of Advisors on Science and Technology, in which capacity he served as chairman of the Panel on Educational Technology. He currently serves as treasurer of the American Association for the Advancement of Science and as a member of its board of directors, as co-chairman of the steering committee of the High-Performance Computing Initiative (a DoD/DoE-sponsored program conducted under the auspices of the Council on Competitiveness), and as a member of the external advisory group of the Sloan-Kettering Institute. He also serves as chairman of the Schrödinger companies, which produce computational chemistry software used for drug discovery, and of the top-level parent company of Attenuon, LLC, a drug discovery and development firm focusing on cancer therapeutics. Dr. Shaw is the author of 78 scholarly publications, and was named a fellow of the New York Academy of Sciences in 1999.
Host: Rodney Brooks, Dertouzos Lecturer Series 2005/2006, CSAIL, MIT

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