Biomolecular implementation of nonlinear system theoretic operators

Mathias Foo; Rucha Sawlekar; Jongmin Kim; Declan G. Bates; Guy Bart Stan; Vishwesh Kulkarni

doi:10.1109/ECC.2016.7810556

Biomolecular implementation of nonlinear system theoretic operators

Mathias Foo, Rucha Sawlekar, Jongmin Kim, Declan G. Bates, Guy Bart Stan, Vishwesh Kulkarni

Research output: Chapter in Book/Report/Conference proceeding › Conference proceeding › peer-review

4 Citations (Scopus)

46 Downloads (Pure)

Abstract

— Synthesis of biomolecular circuits for controlling molecular-scale processes is an important goal of synthetic biology with a wide range of in vitro and in vivo applications, including biomass maximization, nanoscale drug delivery, and many others. In this paper, we present new results on how abstract chemical reactions can be used to implement com-monly used system theoretic operators such as the polynomial functions, rational functions and Hill-type nonlinearity. We first describe how idealised versions of multi-molecular reactions, catalysis, annihilation, and degradation can be combined to implement these operators. We then show how such chemical reactions can be implemented using enzyme-free, entropy-driven DNA reactions. Our results are illustrated through three applications: (1) implementation of a Stan-Sepulchre oscillator, (2) the computation of the ratio of two signals, and (3) a PI+antiwindup controller for regulating the output of a static nonlinear plant.

Original language	English
Title of host publication	2016 European Control Conference, ECC 2016
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	1824-1831
Number of pages	8
ISBN (Electronic)	978-1-5090-2591-6, 978-1-5090-2590-9
ISBN (Print)	978-1-5090-2592-3
DOIs	https://doi.org/10.1109/ECC.2016.7810556
Publication status	Published - 6 Jan 2017
Event	2016 European Control Conference - Aalborg, Denmark Duration: 29 Jun 2016 → 1 Jul 2016

Publication series

Name	2016 European Control Conference, ECC 2016

Conference

Conference	2016 European Control Conference
Abbreviated title	ECC
Country/Territory	Denmark
City	Aalborg
Period	29/06/16 → 1/07/16

Keywords

Chemicals
DNA
Steady-state
Degradation
Synthetic biology
Oscillators

Access to Document

10.1109/ECC.2016.7810556

Post-PrintAccepted author manuscript, 749 KB

Cite this

Biomolecular implementation of nonlinear system theoretic operators. / Foo, Mathias; Sawlekar, Rucha; Kim, Jongmin et al.

2016 European Control Conference, ECC 2016. Institute of Electrical and Electronics Engineers Inc., 2017. p. 1824-1831 (2016 European Control Conference, ECC 2016).

Research output: Chapter in Book/Report/Conference proceeding › Conference proceeding › peer-review

Foo, M, Sawlekar, R, Kim, J, Bates, DG, Stan, GB & Kulkarni, V 2017, Biomolecular implementation of nonlinear system theoretic operators. in 2016 European Control Conference, ECC 2016. 2016 European Control Conference, ECC 2016, Institute of Electrical and Electronics Engineers Inc., pp. 1824-1831, 2016 European Control Conference, Aalborg, Denmark, 29/06/16. https://doi.org/10.1109/ECC.2016.7810556

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abstract = "— Synthesis of biomolecular circuits for controlling molecular-scale processes is an important goal of synthetic biology with a wide range of in vitro and in vivo applications, including biomass maximization, nanoscale drug delivery, and many others. In this paper, we present new results on how abstract chemical reactions can be used to implement com-monly used system theoretic operators such as the polynomial functions, rational functions and Hill-type nonlinearity. We first describe how idealised versions of multi-molecular reactions, catalysis, annihilation, and degradation can be combined to implement these operators. We then show how such chemical reactions can be implemented using enzyme-free, entropy-driven DNA reactions. Our results are illustrated through three applications: (1) implementation of a Stan-Sepulchre oscillator, (2) the computation of the ratio of two signals, and (3) a PI+antiwindup controller for regulating the output of a static nonlinear plant.",

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AU - Kulkarni, Vishwesh

PY - 2017/1/6

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N2 - — Synthesis of biomolecular circuits for controlling molecular-scale processes is an important goal of synthetic biology with a wide range of in vitro and in vivo applications, including biomass maximization, nanoscale drug delivery, and many others. In this paper, we present new results on how abstract chemical reactions can be used to implement com-monly used system theoretic operators such as the polynomial functions, rational functions and Hill-type nonlinearity. We first describe how idealised versions of multi-molecular reactions, catalysis, annihilation, and degradation can be combined to implement these operators. We then show how such chemical reactions can be implemented using enzyme-free, entropy-driven DNA reactions. Our results are illustrated through three applications: (1) implementation of a Stan-Sepulchre oscillator, (2) the computation of the ratio of two signals, and (3) a PI+antiwindup controller for regulating the output of a static nonlinear plant.

AB - — Synthesis of biomolecular circuits for controlling molecular-scale processes is an important goal of synthetic biology with a wide range of in vitro and in vivo applications, including biomass maximization, nanoscale drug delivery, and many others. In this paper, we present new results on how abstract chemical reactions can be used to implement com-monly used system theoretic operators such as the polynomial functions, rational functions and Hill-type nonlinearity. We first describe how idealised versions of multi-molecular reactions, catalysis, annihilation, and degradation can be combined to implement these operators. We then show how such chemical reactions can be implemented using enzyme-free, entropy-driven DNA reactions. Our results are illustrated through three applications: (1) implementation of a Stan-Sepulchre oscillator, (2) the computation of the ratio of two signals, and (3) a PI+antiwindup controller for regulating the output of a static nonlinear plant.

KW - Chemicals

KW - DNA

KW - Steady-state

KW - Degradation

KW - Synthetic biology

KW - Oscillators

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DO - 10.1109/ECC.2016.7810556

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SN - 978-1-5090-2592-3

T3 - 2016 European Control Conference, ECC 2016

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BT - 2016 European Control Conference, ECC 2016

PB - Institute of Electrical and Electronics Engineers Inc.

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ER -

Biomolecular implementation of nonlinear system theoretic operators

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Keywords

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