Localized Hybridization Circuits
Molecular computing executed via local interactions of spatially contiguous sets of molecules has potential advantages of (i) speed due to increased local concentration of reacting species, (ii) generally sharper switching behavior and higher precision due to single molecule interactions, (iii) parallelism since each circuit operates independently of the others and (iv) modularity and scalability due to the ability to reuse DNA sequences in spatially separated regions. We propose detailed designs for local molecular computations that involve spatially contiguous molecules arranged on addressable substrates. The circuits act via enzyme-free DNA hybridization reaction cascades. Our designs include composable OR, AND and propagation Boolean gates, and techniques to achieve higher degree fan-in and fan-out. A biophysical model of localized hybridization reactions is used to estimate the effect of locality on reaction rates. We also use the Visual DSD simulation software in conjunction with localized reaction rates to simulate a localized circuit for computing the square root of a four bit number.
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- 6.Sakamoto, K., Kiga, D., Momiya, K., Gouzu, H., Yokoyama, S., Ikeda, S., Sugiyama, H., Hagiya, M.: State Transitions by Molecules. Biosystems, 81–91 (1999)Google Scholar
- 8.Rothemund, P., Winfree, E.: The Program-Size Complexity of Self-Assembled Squares. In: Symposium on Theory of Computing, pp. 459–468 (2000)Google Scholar
- 9.Turberfield, A., Mitchell, J., Yurke, B., Mills, A., Blakey, M., Simmel, F.: DNA Fuel for Free-Running Nanomachines. Physical Review Letters 90(11) (2003)Google Scholar
- 15.Qian, L., Winfree, E.: A Simple DNA Gate Motif for Synthesizing Large-scale Circuits. DNA Computing, 70–89 (2009)Google Scholar
- 16.Cardelli, L.: Two-Domain DNA Strand Displacement. DCM, 47–61 (2010)Google Scholar
- 22.Zhang, D.: Towards Domain-Based Sequence Design for DNA Strand Displacement Reactions. DNA 16, 162–175 (2010)Google Scholar
- 28.Lakin, M., Youssef, S., Cardelli, L., Phillips, A.: Abstractions for DNA Circuit Design. Journal of The Royal Society Interface (in press, 2011)Google Scholar