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Unformatted text preview: 1214 IEEE TRANSACTIONS ON VERY LARGE SCALE INTEGRATION (VLSI) SYSTEMS, VOL. 12, NO. 11, NOVEMBER 2004 The Design of DNA Self-Assembled Computing Circuitry Chris Dwyer , Member, IEEE , Leandra Vicci , Senior Member, IEEE , John Poulton , Senior Member, IEEE , Dorothy Erie, Richard Superfine, Sean Washburn, and Russell M. Taylor, II , Member, IEEE Abstract— We present a design methodology for a nanoscale self- assembling fabrication process that uses the specificity of DNA hy- bridization to guide the formation of electrical circuitry. Custom design software allows us to specify the function of a structure in a way similar to that used by VLSI circuit designers. In an analo- gous manner to generating masks for a photolithographic process, our software generates an assembly procedure including DNA se- quence allocation. We have found that the number of unique DNA sequences needed to assemble a structure scales with its surface area. Using a simple face-serial assembly order we can specify an unambiguous assembly sequence for a structure of any size with only 15 unique DNA sequences. Index Terms— Associative memories, computer architecture, DNA self-assembly, nanoelectronics, parallel processing. I. INTRODUCTION C OMPUTER system design will change dramatically as nanoscale science and technology are developed to the point where practical assembly mechanisms exist for building large-scale systems. These changes will be motivated by emerging capabilities and an interest in developing early-term computing devices that can exploit the technology’s features. The advent of massively parallel near-molecular scale elec- tronic systems will open wide problem spaces yet untouched by modern computing [1]. We focus on the realization of a new computer architecture that is enabled by the development of DNA-guided self-assem- bled systems. The enormous parallelism and scale of this kind of self-assembling process has motivated research into novel forms of computation that use the intrinsic properties of DNA hy- bridization to form solutions to a problem [2], [3]. We have con- sidered a slightly different approach to developing computing devices using DNA. Instead of depending on the computability of DNA hybridization events we investigate the structural use of DNA to create electrically active nanoscale rod-lattice struc- tures. These structures can then be used in the designs of com- puting circuits that solve particular classes of problems. Later, we discuss a class of problems and a computer architecture to which this form of self assembly is suited. Manuscript received December 9, 2002; revised August 27, 2003. C. Dwyer is with the Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708 USA (e-mail: [email protected])....
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This note was uploaded on 11/28/2011 for the course COMP 790 taught by Professor Staff during the Fall '08 term at UNC.

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