Programming dynamic nonlinear biomolecular devices using DNA strand displacement reactions

Recent advances in DNA computing have greatly facilitated the design of biomolecular circuitry based on toehold-mediated DNA strand displacement (DSD) reactions. The 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. In this thesis, new results are presented on how chemical reaction networks (CRNs) can be used as a programming language to implement commonly used linear and nonlinear system theoretic operators that can be further utilised in combination to form complex biomolecular circuits. Within the same framework, the design of an important class of nonlinear feedback controller, i.e. a quasi sliding mode (QSM) feedback controller, is proposed. The closed loop response of the nonlinear QSM controller is shown to outperform a traditional linear proportional+integrator (PI) 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. An important issue to consider in this design process for synthetic 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 thesis, the robustness properties of two biomolecular feedback controllers; PI and QSM, 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, are analysed. The simulation results show that the proposed QSM controller is significantly more robust against investigated uncertainties, highlighting its potential as a practically implementable biomolecular feedback controller for future synthetic biology applications. Finally, the thesis presents new results on the design of biomolecular feedback controllers using the set of chemical reactions underlying covalent modification cycles

Exploiting the dynamic properties of covalent modification cycle for the design of synthetic analog biomolecular circuitry

Background: Cycles of covalent modification are ubiquitous motifs in cellular signalling. Although such signalling cycles are implemented via a highly concise set of chemical reactions, they have been shown to be capable of producing multiple distinct input-output mapping behaviours – ultrasensitive, hyperbolic, signal-transducing and threshold-hyperbolic. Results: In this paper, we show how the set of chemical reactions underlying covalent modification cycles can be exploited for the design of synthetic analog biomolecular circuitry. We show that biomolecular circuits based on the dynamics of covalent modification cycles allow (a) the computation of nonlinear operators using far fewer chemical reactions than purely abstract designs based on chemical reaction network theory, and (b) the design of nonlinear feedback controllers with strong performance and robustness properties. Conclusions: Our designs provide a more efficient route for translation of complex circuits and systems from chemical reactions to DNA strand displacement-based chemistry, thus facilitating their experimental implementation in future Synthetic Biology applications

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

The use of abstract chemical reaction networks (CRNs) as a modelling and design framework for the implementation of computing and control circuits using enzyme-free, entropy driven DNA strand displacement (DSD) reactions is starting to garner widespread attention in the area of synthetic biology. Previous work in this area has demonstrated the theoretical plausibility of using this approach to design biomolecular feedback control systems based on classical proportional-integral (PI) controllers, which may be constructed from CRNs implementing gain, summation and integrator operators. Here, we propose an alternative design approach that utilises the abstract chemical reactions involved in cellular signalling cycles to implement a biomolecular controller - termed a signalling-cycle (SC) controller. We compare the performance of the PI and SC controllers in closed-loop with a nonlinear second-order chemical process. Our results show that the SC controller outperforms the PI controller in terms of both performance and robustness, and also requires fewer abstract chemical reactions to implement, highlighting its potential usefulness in the construction of biomolecular control circuits

Implementing nonlinear feedback controllers using DNA strand displacement reactions

We show how an important class of nonlinear feedback controllers can be designed using idealized abstract chemical reactions and implemented via DNA strand displacement (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 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, enthalpy/entropy driven DNA reactions using a toehold mediated strand displacement mechanism 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

Biomolecular implementation of nonlinear system theoretic operators

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, 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

Event Camera and LiDAR based Human Tracking for Adverse Lighting Conditions in Subterranean Environments

In this article, we propose a novel LiDAR and event camera fusion modality for subterranean (SubT) environments for fast and precise object and human detection in a wide variety of adverse lighting conditions, such as low or no light, high-contrast zones and in the presence of blinding light sources. In the proposed approach, information from the event camera and LiDAR are fused to localize a human or an object-of-interest in a robot's local frame. The local detection is then transformed into the inertial frame and used to set references for a Nonlinear Model Predictive Controller (NMPC) for reactive tracking of humans or objects in SubT environments. The proposed novel fusion uses intensity filtering and K-means clustering on the LiDAR point cloud and frequency filtering and connectivity clustering on the events induced in an event camera by the returning LiDAR beams. The centroids of the clusters in the event camera and LiDAR streams are then paired to localize reflective markers present on safety vests and signs in SubT environments. The efficacy of the proposed scheme has been experimentally validated in a real SubT environment (a mine) with a Pioneer 3AT mobile robot. The experimental results show real-time performance for human detection and the NMPC-based controller allows for reactive tracking of a human or object of interest, even in complete darkness.Comment: Accepted at IFAC World Congress 202

Design of an embedded inverse-feedforward biomolecular trackingcontroller for enzymatic reaction processes

Feedback control is widely used in chemical engineering to improve the performance and robustness of chemical processes. Feedback controllers require a ‘subtractor’ that is able to compute the error between the process output and the reference signal. In the case of embedded biomolecular control circuits, subtractors designed using standard chemical reaction network theory can only realise one-sided subtraction, rendering standard controller design approaches inadequate. Here, we show how a biomolecular controller that allows tracking of required changes in the outputs of enzymatic reaction processes can be designed and implemented within the framework of chemical reaction network theory. The controller architecture employs an inversion-based feedforward controller that compensates for the limitations of the one-sided subtractor that generates the error signals for a feedback controller. The proposed approach requires significantly fewer chemical reactions to implement than alternative designs, and should have wide applicability throughout the fields of synthetic biology and biological engineering

A Survey of DNA-based Computing Devices and their Applications

The research on DNA-based circuits has grown exponentially during the past few years. Having said that, the technology needed for the implementation of such circuits in living cells has been upgraded immensely as well. DNA exhibits the properties of programmable structure, self-assembly and adequate robust stability, making it an important and interesting building block to construct molecular machines. In the attempt to provide an alternative to the traditional semiconductor-based devices, extensive research has been done to construct molecular level devices with minimal components performing efficiently in living cells. In this article, we present a comprehensive survey of advancements and applications of such devices in molecular computing and nanotechnology. We cover the overview of programming languages, design and development of computational devices like logic gates and controllers, including the former approaches that originally influenced this present development. We also discuss nanorobots, such as DNA walkers and tweezers with the general objective to provide a comprehensive survey of the most state of the art approaches in the DNA based computing devices.ISBN för värdpublikationen: 978-94-6384-236-5 (print), 978-9-4638-4236-5 (electronic)</p