Computing with Things Small, Wet, and Random: Design Automation for Nanoscale Technologies and Biological Processes

September 26, 2008
Prof. Marc Riedel University of Minnesota

Abstract:

This talk will discuss techniques for analyzing and synthesizing circuits and biological systems that are characterized by uncertainty and randomness in their components, connectivity, and execution. We adopt a novel view of computation: instead of transforming definite inputs into definite outputs, circuits and biological systems transform probability values into probability values. The computation is random at the level of bits or protein-protein reactions; nonetheless, in the aggregate, it becomes exact and robust, since the accuracy depends only on the statistical distributions of the quantities. The methodologyprovides a design strategy for coping with the noise and the glitches that occur as circuit components are scaled down in size to nanometers. In synthetic biology, it allows us to design biochemical pathways with precise and programmable functionality. The talk will present novel circuit constructs, including feedback architectures. Also, it will describe computer-aided design tools that we are developing for biology, including a biochemical "toolkit" consisting of modules for standard arithmetic operations (analogous to those performed by an arithmetic-logic unit in a microprocessor system) as well as regulatory functions (analogous to those performed by control circuitry).

Bio

Marc Riedel has been an Assistant Professor of Electrical and Computer Engineering at the University of Minnesota since 2006. He is also a member of the Graduate Faculty in Biomedical Informatics and Computational Biology. He received his Ph.D. and his M.Sc. in Electrical Engineering at Caltech and his B.Eng. in Electrical Engineering with a Minor in Mathematics at McGill University. His Ph.D. dissertation titled "Cyclic Combinational Circuits" received the Charles H. Wilts Prize for the best doctoral research in Electrical Engineering at Caltech. His paper "The Synthesis of Cyclic Combinational Circuits" received the Best Paper Award at the Design Automation Conference. He has held positions at Marconi Canada, CAE Electronics, Toshiba, and Fujitsu Research Labs.