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Current Research in Biochemical Computing

September 7, 2004

Date: Tuesday September 7, 2004
Time: 11am-12:15pm
Location: Woodward 149

Darko Stefanovic (email)
Department of Computer Science University of New Mexico

Abstract: I'll describe ongoing work in the Molecular Computing Group. In particular, I'll describe a new technology for amorphous bio-compatible computing, using deoxyribozyme-based logic gates. Oligonucleotides can act as enzymes, or ribozymes, on other oligonucleotides, yielding oligonucleotide products. Moreover, these reactions can be controlled by inputs which are also oligonucleotides. We interpret these reactions as logic gates, and the concentrations of chemical species as signals. Since these reactions are homogeneous, i.e., they use oligonucleotides for both their inputs and their outputs, we can compose them to construct complex logic circuits. I'll describe the several kinds of logic gates we have developed, as well as their initial applications in simple feed-forward circuits, including arithmetic and game-playing automata. I'll also demonstrate our open-system designs for a biomolecular realization of elementary components for a digital computer, including feedback circuits such as bistable memory elements (flip-flops) and oscillators. An eventual goal of this technology is the development of in-vivo computational devices. Thus, our system for chemical computation offers functionality similar to conventional electronic circuits with the potential for deployment inside of living cells. I'll outline some outstanding problems in the design and applications of reliable dexyribozyme logic.