Synchronous sequential computation with molecular reactions

Research output: Chapter in Book/Report/Conference proceedingConference contribution

25 Scopus citations

Abstract

Just as electronic systems implement computation in terms of voltage (energy per unit charge), molecular systems compute in terms of chemical concentrations (molecules per unit volume). Prior work has established mechanisms for implementing logical and arithmetic functions including addition, multiplication, exponentiation, and logarithms with molecular reactions. In this paper, we present a general methodology for implementing synchronous sequential computation. We generate a four-phase clock signal through robust, sustained chemical oscillations. We implement memory elements by transferring concentrations between molecular types in alternating phases of the clock. We illustrate our design methodology with examples: a binary counter as well as a four-point, two-parallel FFT. We validate our designs through ODE simulations of mass-action chemical kinetics. We are exploring DNA-based computation via strand displacement as a possible experimental chassis.

Original languageEnglish (US)
Title of host publication2011 48th ACM/EDAC/IEEE Design Automation Conference, DAC 2011
Pages836-841
Number of pages6
StatePublished - Sep 16 2011
Event2011 48th ACM/EDAC/IEEE Design Automation Conference, DAC 2011 - San Diego, CA, United States
Duration: Jun 5 2011Jun 9 2011

Publication series

NameProceedings - Design Automation Conference
ISSN (Print)0738-100X

Other

Other2011 48th ACM/EDAC/IEEE Design Automation Conference, DAC 2011
CountryUnited States
CitySan Diego, CA
Period6/5/116/9/11

Keywords

  • Computational Biology
  • Digital Design
  • Molecular Computation
  • Sequential Logic
  • Synchronous Logic
  • Synthetic Biology

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    Jiang, H., Riedel, M., & Parhi, K. (2011). Synchronous sequential computation with molecular reactions. In 2011 48th ACM/EDAC/IEEE Design Automation Conference, DAC 2011 (pp. 836-841). [5982004] (Proceedings - Design Automation Conference).