Optimization of Enzymatic Biochemical Logic for Noise Reduction and Scalability: How Many Biocomputing Gates Can Be Interconnected in a Circuit?

Vladimir Privman, Guinevere Strack, Dmitry Solenov, Marcos Pita and Evgeny Katz*
Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13699
J. Phys. Chem. B, 2008, 112 (37), pp 11777–11784
DOI: 10.1021/jp802673q
Publication Date (Web): August 20, 2008
Copyright © 2008 American Chemical Society
* To whom correspondence should be addressed. Tel.: +1-315-268-4421. Fax: +1-315-268-6610. E-mail: ekatz@clarkson.edu.

Abstract

We report an experimental evaluation of the “input−output surface” for a biochemical AND gate. The obtained data are modeled within the rate-equation approach, with the aim to map out the gate function and cast it in the language of logic variables appropriate for analysis of Boolean logic for scalability. In order to minimize “analog” noise, we consider a theoretical approach for determining an optimal set for the process parameters to minimize “analog” noise amplification for gate concatenation. We establish that under optimized conditions, presently studied biochemical gates can be concatenated for up to order 10 processing steps. Beyond that, new paradigms for avoiding noise buildup will have to be developed. We offer a general discussion of the ideas and possible future challenges for both experimental and theoretical research for advancing scalable biochemical computing.

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History

  • Published In Issue September 18, 2008
  • Article ASAPAugust 20, 2008
  • Received: March 27, 2008
    Revised: May 29, 2008

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