isca13-dna.pdf

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DNA-based Molecular Architecture with Spatially Localized Components Richard A. Muscat Karin Strauss †‡ Luis Ceze Georg Seelig University of Washington Microsoft Research ABSTRACT Performing computation inside living cells offers life-changing ap- plications, from improved medical diagnostics to better cancer ther- apy to intelligent drugs. Due to its bio-compatibility and ease of en- gineering, one promising approach for performing in-vivo compu- tation is DNA strand displacement. This paper introduces computer architects to DNA strand displacement “circuits”, discusses associ- ated architectural challenges, and proposes a new organization that provides practical composability. In particular, prior approaches rely mostly on stochastic interaction of freely diffusing compo- nents. This paper proposes practical spatial isolation of compo- nents, leading to more easily designed DNA-based circuits. DNA nanotechnology is currently at a turning point, with many proposed applications being realized [20, 9]. We believe that it is time for the computer architecture community to take notice and contribute. Categories and Subject Descriptors B. Hardware [ Emerging Technologies ] General Terms Design Keywords DNA-based In-cell Computation, Spatial Localization 1. INTRODUCTION Synthetic molecular circuits that work reliably in a complex cel- lular environment and that can sense and respond to that environ- ment offer the potential for many significant applications. For ex- ample, in-vivo computation with molecular circuits could enable novel approaches to medical diagnostics and imaging, selective drug delivery to cancer cells, and even intelligent drugs that lay latent inside cells and release automatically when a disease is first detected. DNA is an ideal physical substrate for carrying out molecular computation because its simple primitives make it amenable to ef- fective engineering. Furthermore, DNA circuitry is bio-compatible, thus well-suited for intra-cell operation. Using DNA to carry out Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. ISCA’13 Tel-Aviv, Israel Copyright 2013 ACM 978-1-4503-2079-5/13/06 ...$15.00. computation has been explored for almost two decades, starting when Adleman proposed computing Hamiltonian paths [1] with DNA. Researchers subsequently explored other basic computing primitives with DNA, from Boolean gates [33, 29, 23] to neural networks [24] to chemical reaction networks [32, 3, 4].
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