Biomolecular implementation of a quasi sliding mode feedback controller based on DNA strand displacement reactions

Sawlekar, Rucha; Montefusco, Francesco; Kulkarni, Vishwesh V.; Bates, Declan G.

doi:10.1109/embc.2015.7318520

Cited by 11 publications

(11 citation statements)

References 24 publications

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“…Without loss of generality, let (x + 2 x + e ) = (x 2 x e ) + and (x − 2 x − e ) = (x 2 x e ) − , as proposed in [25]. Then it can be verified that S N is described by the following set of ODEs:…”

Section: B Hill-type Nonlinearitymentioning

confidence: 99%

“…. , 6}) are biomolecular species (see [25] and [26]). This set of chemical reaction is better implemented through the set S N of 12 abstract chemical reactions given in Fig.…”

Section: B Hill-type Nonlinearitymentioning

confidence: 99%

“…4(C). The set S N can be represented through the following set of ordinary differential equations [25]:…”

Section: B Hill-type Nonlinearitymentioning

confidence: 99%

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Biomolecular implementation of nonlinear system theoretic operators

Foo

Sawlekar

Kim³

et al. 2016

2016 European Control Conference (ECC)

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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 commonly 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, entropydriven 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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Section: B Hill-type Nonlinearitymentioning

confidence: 99%

“…. , 6}) are biomolecular species (see [25] and [26]). This set of chemical reaction is better implemented through the set S N of 12 abstract chemical reactions given in Fig.…”

Section: B Hill-type Nonlinearitymentioning

confidence: 99%

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Biomolecular implementation of nonlinear system theoretic operators

Foo

Sawlekar

Kim³

et al. 2016

2016 European Control Conference (ECC)

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“…The indicates that SC controller's mapping of input-output signals are less sensitive to uncertainty thus yielding a much better robustness than the PI controller. Note that in [9], it was shown how alternative choices of k b1 -k b4 that produce an ultrasensitive input-output mapping allowed the design of a quasi sliding mode controller, further showcasing the versatility of this particular CRN for the purposes of control system design.…”

Section: Characteristicsmentioning

confidence: 99%

“…Sophisticated CAD tools are also now becoming available to facilitate the design of synthetic circuits using this approach [5]. Examples of complex biomolecular circuits successfully designed and implemented through this approach include predator-prey dynamics [6], oscillators [7], and both linear and nonlinear feedback controllers [3], [8], [9].…”

Section: Introductionmentioning

confidence: 99%

Biologically inspired design of feedback control systems implemented using DNA strand displacement reactions

Foo

Sawlekar

Kulkarni

et al. 2016

2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

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Role of ultrasensitivity in biomolecular circuitry for achieving homeostasis

Montefusco,

Procopio,

Bulai

et al. 2024

Nonlinear Dyn

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Living systems have developed control mechanisms for achieving homeostasis. Here, we propose a plausible biological feedback architecture that exploits ultrasensitivity and shows adaptive responses without requiring error detection mechanism (i.e., by measuring an external reference signal and deviation from this). While standard engineering control systems are usually based on error measurements, this is not the case for biological systems. We find that a two-state negative feedback control system, without explicit error measurements, is able to track a reference signal that is implicitly determined by the tunable threshold and slope characterizing the sigmoidal ultrasensitive relationship implemented by the control system. We design different ultrasensitive control functions (ultrasensitive up- or down-regulation, or both) and, by performing sensitivity analysis, show that increasing the sensitivity level of the control allows achieving robust adaptive responses to the effects of parameter variations and step disturbances. Finally, we show that the devised control system architecture without error detection is implemented within the yeast osmoregulatory response network and allows achieving adaptive responses to osmotic stress, by exploiting the ubiquitous ultrasensitive features of the involved biomolecular circuitry.

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Biomolecular implementation of a quasi sliding mode feedback controller based on DNA strand displacement reactions

Cited by 11 publications

References 24 publications

Biomolecular implementation of nonlinear system theoretic operators

Biomolecular implementation of nonlinear system theoretic operators

Biologically inspired design of feedback control systems implemented using DNA strand displacement reactions

Role of ultrasensitivity in biomolecular circuitry for achieving homeostasis

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