Robustness analysis of DNA-based biomolecular feedback controllers to parametric and time delay uncertainties

Rucha Sawlekar; Mathias Foo; Declan G. Bates

doi:10.1109/BioCAS.2016.7833853

Robustness analysis of DNA-based biomolecular feedback controllers to parametric and time delay uncertainties

Rucha Sawlekar, Mathias Foo, Declan G. Bates

University of Warwick

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

1 Citation (Scopus)

102 Downloads (Pure)

Abstract

— Recent advances in DNA computing have greatly facilitated the design of biomolecular circuitry based on DNA strand displacement reactions. An important issue to consider in the design process for such circuits is the effect of biological and experimental uncertainties on the functionality and reliability of the overall circuit. In the case of biomolecular feedback control circuits, such uncertainties could lead to a range of adverse effects, including achieving wrong concentration levels, sluggish performance and even instability. In this paper, we analyse the robustness properties of two biomolecular feedback controllers; a classical linear proportional integral (PI) and a re-cently proposed nonlinear quasi sliding mode (QSM) controller, subject to uncertainties in the experimentally implemented rates of their underlying chemical reactions, and to variations in accumulative time delays in the process to be controlled. Our results show that the nonlinear QSM controller is significantly more robust against investigated uncertainties, highlighting its potential as a practically implementable biomolecular feedback controller for future synthetic biology applications.

Publisher Statement: © 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.

Original language	English
Title of host publication	Proceedings - 2016 IEEE Biomedical Circuits and Systems Conference, BioCAS 2016
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	548-551
Number of pages	4
ISBN (Electronic)	978-1-5090-2959-4
ISBN (Print)	978-1-5090-2960-0
DOIs	https://doi.org/10.1109/BioCAS.2016.7833853
Publication status	Published - 25 Jan 2017
Event	2016 IEEE Biomedical Circuits and Systems Conference - Shanghai, China Duration: 17 Oct 2016 → 19 Oct 2016

Publication series

Name	Proceedings - 2016 IEEE Biomedical Circuits and Systems Conference, BioCAS 2016

Conference

Conference	2016 IEEE Biomedical Circuits and Systems Conference
Abbreviated title	BioCAS
Country/Territory	China
City	Shanghai
Period	17/10/16 → 19/10/16

Bibliographical note

© 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.

Keywords

Process control
Delay effects
DNA
Robustness
Chemicals
Control systems

Access to Document

10.1109/BioCAS.2016.7833853

Post-PrintAccepted author manuscript, 1.57 MB

Cite this

Sawlekar, R., Foo, M., & Bates, D. G. (2017). Robustness analysis of DNA-based biomolecular feedback controllers to parametric and time delay uncertainties. In Proceedings - 2016 IEEE Biomedical Circuits and Systems Conference, BioCAS 2016 (pp. 548-551). (Proceedings - 2016 IEEE Biomedical Circuits and Systems Conference, BioCAS 2016). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BioCAS.2016.7833853

Robustness analysis of DNA-based biomolecular feedback controllers to parametric and time delay uncertainties. / Sawlekar, Rucha; Foo, Mathias; Bates, Declan G.
Proceedings - 2016 IEEE Biomedical Circuits and Systems Conference, BioCAS 2016. Institute of Electrical and Electronics Engineers Inc., 2017. p. 548-551 (Proceedings - 2016 IEEE Biomedical Circuits and Systems Conference, BioCAS 2016).

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

Sawlekar, R, Foo, M & Bates, DG 2017, Robustness analysis of DNA-based biomolecular feedback controllers to parametric and time delay uncertainties. in Proceedings - 2016 IEEE Biomedical Circuits and Systems Conference, BioCAS 2016. Proceedings - 2016 IEEE Biomedical Circuits and Systems Conference, BioCAS 2016, Institute of Electrical and Electronics Engineers Inc., pp. 548-551, 2016 IEEE Biomedical Circuits and Systems Conference, Shanghai, China, 17/10/16. https://doi.org/10.1109/BioCAS.2016.7833853

Sawlekar R, Foo M, Bates DG. Robustness analysis of DNA-based biomolecular feedback controllers to parametric and time delay uncertainties. In Proceedings - 2016 IEEE Biomedical Circuits and Systems Conference, BioCAS 2016. Institute of Electrical and Electronics Engineers Inc. 2017. p. 548-551. (Proceedings - 2016 IEEE Biomedical Circuits and Systems Conference, BioCAS 2016). doi: 10.1109/BioCAS.2016.7833853

Sawlekar, Rucha ; Foo, Mathias ; Bates, Declan G. / Robustness analysis of DNA-based biomolecular feedback controllers to parametric and time delay uncertainties. Proceedings - 2016 IEEE Biomedical Circuits and Systems Conference, BioCAS 2016. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 548-551 (Proceedings - 2016 IEEE Biomedical Circuits and Systems Conference, BioCAS 2016).

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abstract = "— Recent advances in DNA computing have greatly facilitated the design of biomolecular circuitry based on DNA strand displacement reactions. An important issue to consider in the design process for such circuits is the effect of biological and experimental uncertainties on the functionality and reliability of the overall circuit. In the case of biomolecular feedback control circuits, such uncertainties could lead to a range of adverse effects, including achieving wrong concentration levels, sluggish performance and even instability. In this paper, we analyse the robustness properties of two biomolecular feedback controllers; a classical linear proportional integral (PI) and a re-cently proposed nonlinear quasi sliding mode (QSM) controller, subject to uncertainties in the experimentally implemented rates of their underlying chemical reactions, and to variations in accumulative time delays in the process to be controlled. Our results show that the nonlinear QSM controller is significantly more robust against investigated uncertainties, highlighting its potential as a practically implementable biomolecular feedback controller for future synthetic biology applications.Publisher Statement: {\textcopyright} 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.",

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N2 - — Recent advances in DNA computing have greatly facilitated the design of biomolecular circuitry based on DNA strand displacement reactions. An important issue to consider in the design process for such circuits is the effect of biological and experimental uncertainties on the functionality and reliability of the overall circuit. In the case of biomolecular feedback control circuits, such uncertainties could lead to a range of adverse effects, including achieving wrong concentration levels, sluggish performance and even instability. In this paper, we analyse the robustness properties of two biomolecular feedback controllers; a classical linear proportional integral (PI) and a re-cently proposed nonlinear quasi sliding mode (QSM) controller, subject to uncertainties in the experimentally implemented rates of their underlying chemical reactions, and to variations in accumulative time delays in the process to be controlled. Our results show that the nonlinear QSM controller is significantly more robust against investigated uncertainties, highlighting its potential as a practically implementable biomolecular feedback controller for future synthetic biology applications.Publisher Statement: © 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.

AB - — Recent advances in DNA computing have greatly facilitated the design of biomolecular circuitry based on DNA strand displacement reactions. An important issue to consider in the design process for such circuits is the effect of biological and experimental uncertainties on the functionality and reliability of the overall circuit. In the case of biomolecular feedback control circuits, such uncertainties could lead to a range of adverse effects, including achieving wrong concentration levels, sluggish performance and even instability. In this paper, we analyse the robustness properties of two biomolecular feedback controllers; a classical linear proportional integral (PI) and a re-cently proposed nonlinear quasi sliding mode (QSM) controller, subject to uncertainties in the experimentally implemented rates of their underlying chemical reactions, and to variations in accumulative time delays in the process to be controlled. Our results show that the nonlinear QSM controller is significantly more robust against investigated uncertainties, highlighting its potential as a practically implementable biomolecular feedback controller for future synthetic biology applications.Publisher Statement: © 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.

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Robustness analysis of DNA-based biomolecular feedback controllers to parametric and time delay uncertainties

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