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Analog Computation by DNA Strand Displacement Circuits.

Publication ,  Journal Article
Song, T; Garg, S; Mokhtar, R; Bui, H; Reif, J
Published in: ACS synthetic biology
August 2016

DNA circuits have been widely used to develop biological computing devices because of their high programmability and versatility. Here, we propose an architecture for the systematic construction of DNA circuits for analog computation based on DNA strand displacement. The elementary gates in our architecture include addition, subtraction, and multiplication gates. The input and output of these gates are analog, which means that they are directly represented by the concentrations of the input and output DNA strands, respectively, without requiring a threshold for converting to Boolean signals. We provide detailed domain designs and kinetic simulations of the gates to demonstrate their expected performance. On the basis of these gates, we describe how DNA circuits to compute polynomial functions of inputs can be built. Using Taylor Series and Newton Iteration methods, functions beyond the scope of polynomials can also be computed by DNA circuits built upon our architecture.

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Published In

ACS synthetic biology

DOI

EISSN

2161-5063

ISSN

2161-5063

Publication Date

August 2016

Volume

5

Issue

8

Start / End Page

898 / 912

Related Subject Headings

  • Kinetics
  • DNA
  • Computers, Molecular
  • Algorithms
  • 3102 Bioinformatics and computational biology
  • 3101 Biochemistry and cell biology
  • 0903 Biomedical Engineering
  • 0601 Biochemistry and Cell Biology
  • 0304 Medicinal and Biomolecular Chemistry
 

Citation

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Song, T., Garg, S., Mokhtar, R., Bui, H., & Reif, J. (2016). Analog Computation by DNA Strand Displacement Circuits. ACS Synthetic Biology, 5(8), 898–912. https://doi.org/10.1021/acssynbio.6b00144
Song, Tianqi, Sudhanshu Garg, Reem Mokhtar, Hieu Bui, and John Reif. “Analog Computation by DNA Strand Displacement Circuits.ACS Synthetic Biology 5, no. 8 (August 2016): 898–912. https://doi.org/10.1021/acssynbio.6b00144.
Song T, Garg S, Mokhtar R, Bui H, Reif J. Analog Computation by DNA Strand Displacement Circuits. ACS synthetic biology. 2016 Aug;5(8):898–912.
Song, Tianqi, et al. “Analog Computation by DNA Strand Displacement Circuits.ACS Synthetic Biology, vol. 5, no. 8, Aug. 2016, pp. 898–912. Epmc, doi:10.1021/acssynbio.6b00144.
Song T, Garg S, Mokhtar R, Bui H, Reif J. Analog Computation by DNA Strand Displacement Circuits. ACS synthetic biology. 2016 Aug;5(8):898–912.
Journal cover image

Published In

ACS synthetic biology

DOI

EISSN

2161-5063

ISSN

2161-5063

Publication Date

August 2016

Volume

5

Issue

8

Start / End Page

898 / 912

Related Subject Headings

  • Kinetics
  • DNA
  • Computers, Molecular
  • Algorithms
  • 3102 Bioinformatics and computational biology
  • 3101 Biochemistry and cell biology
  • 0903 Biomedical Engineering
  • 0601 Biochemistry and Cell Biology
  • 0304 Medicinal and Biomolecular Chemistry