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On Nucleic Acid Feedback Controllers

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If you have a question about this talk, please contact Alberto Padoan.

Implementations of nucleic acid chemistry and DNA strand displacement reactions have demonstrated their capacity to perform analogue signal processing, to drive molecular nanomachines, and to operate “in vivo” in mammalian cells. The expanding field of DNA nanotechnology makes nucleic acids promising candidates to embed synthetic feedback control circuitry in biomolecular environments.

Theoretical frameworks are now available to represent feedback control systems as chemical reaction networks which can be readily translated into equivalent nucleic acid-based chemistry. To date, the design of feedback control systems within this framework has been restricted to simple proportional-integral controller architectures. In this seminar I describe how the framework may be expanded to realise both proportional-integral-derivative and state feedback controllers, and verify their correct implementation in nucleic acid-based chemistry using the VisualDSD simulation package.

I also show how a number of tools for the rigorous robustness analysis of feedback control systems may be applied in the context of nucleic acid-based controllers. The “dual-rail representation” with chemical reactions employed in this framework introduces additional nonlinear dynamics, even when applied to linear systems, which must be considered when analysing the stability properties of controllers to experimental uncertainty. The seminar demonstrates how the structured singular value (µ) analysis tool can be extended to evaluate the robustness of this class of systems and uncover worst-cases missed by Monte Carlo simulations.

This talk is part of the CUED Control Group Seminars series.

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