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Implementing nonlinear feedback controllers using DNA strand displacement reactions

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Sawlekar, Rucha, Montefusco, Francesco, Kulkarni, Vishwesh V. and Bates, Declan (2016) Implementing nonlinear feedback controllers using DNA strand displacement reactions. IEEE Transactions on NanoBioscience, 15 (5). pp. 443-454. doi:DOI: 10.1109/TNB.2016.2560764

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Official URL: http://ieeexplore.ieee.org/document/7463078/

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Abstract

We show how an important class of nonlinear feedback controllers can be designed using idealized abstract chemical reactions that can be implemented via DNA strand dis-placement (DSD) reactions. Exploiting chemical reaction networks (CRNs) as a programming language for the design of complex circuits and networks, we show how a set of unimolecular and bimolecular reactions can be used to realize ultrasensitive input-output dynamics that produce a nonlinear quasi sliding mode (QSM) feedback controller. The kinetics of the required chemical reactions can then be implemented as enzyme-free, entropy-driven DNA reactions using DNA strand displacement via Watson-Crick base pairing and branch migration. We demonstrate that the closed loop response of the nonlinear QSM controller outperforms a traditional linear controller by facilitating much faster tracking response dynamics without introducing overshoots in the transient response. The resulting controller is highly modular and is less affected by retroactivity effects than standard linear designs.

Item Type: Journal Article
Subjects: Q Science > QH Natural history
T Technology > TA Engineering (General). Civil engineering (General)
Divisions: Faculty of Science > Engineering
Library of Congress Subject Headings (LCSH): Synthetic biology -- Industrial applications, DNA, Substitution reactions -- Mathematical models, Biomedical engineering
Journal or Publication Title: IEEE Transactions on NanoBioscience
Publisher: IEEE
ISSN: 1536-1241
Official Date: 29 April 2016
Dates:
DateEvent
29 April 2016Published
12 February 2016Accepted
November 2016Submitted
Volume: 15
Number: 5
Page Range: pp. 443-454
DOI: DOI: 10.1109/TNB.2016.2560764
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Restricted or Subscription Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
BB/M017982/1[BBSRC] Biotechnology and Biological Sciences Research Councilhttp://dx.doi.org/10.13039/501100000268
UNSPECIFIED[EPSRC] Engineering and Physical Sciences Research Councilhttp://dx.doi.org/10.13039/501100000266
UNSPECIFIEDUniversity of Warwickhttp://dx.doi.org/10.13039/501100000741
Open Access Version:
  • https://www.ncbi.nlm.nih.gov/pubmed/2716...

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