Computing with Things Small, Wet, and Random: Design Automation for Nanoscale Technologies and Biological Processes
September 26, 2008
Prof. Marc Riedel University of Minnesota
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).