Computing with Things Small, Wet, and Random: Design Automation for

March 8, 2010
Halligan 111A


This talk will discuss techniques for synthesizing circuits and biological systems that are characterized by uncertainty in the way that they are wired or that they execute. 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. The talk will present novel circuit constructs that are analog in character but based on digital components. Also, it will present biological constructs that are digital in character in the sense that they deliver robust outcomes. We propose a bio-design automation flow in which synthesis first is performed at a conceptual level, in terms of abstract biochemical reactions -- a task analogous to technology-independent logic synthesis in circuit design. Then the results are mapped onto specific biochemical reactions, selected from libraries -- a task analogous to technology mapping in circuit design. Our method targets DNA strand displacement, developed by Erik Winfree's group at Caltech, as the experimental chassis.

Biography: 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 has held positions at Marconi Canada, CAE Electronics, Toshiba, and Fujitsu Research Labs. 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 is a recipient of the NSF CAREER Award.