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

Implementation of an Ultrasensitive Biomolecular Controller for Enzymatic Reaction Processes With Delay Using DNA Strand Displacement

In this article, a set of abstract chemical reactions has been employed to construct a novel nonlinear biomolecular controller, i.e, the Brink controller (BC) with direct positive autoregulation (DPAR) (namely BC-DPAR controller). In comparison to dual rail representation-based controllers such as the quasi sliding mode (QSM) controller, the BC-DPAR controller directly reduces the number of CRNs required for realizing an ultrasensitive input-output response because it does not involve the subtraction module, reducing the complexity of DNA implementations. Then, the action mechanism and steady-state condition constraints of two nonlinear controllers, BC-DPAR controller and QSM controller, are investigated further. Considering the mapping relationship between CRNs and DNA implementation, a CRNs-based enzymatic reaction process with delay is constructed, and a DNA strand displacement (DSD) scheme representing time delay is proposed. The BC-DPAR controller, when compared to the QSM controller, can reduce the number of abstract chemical reactions and DSD reactions required by 33.3% and 31.8%, respectively. Finally, an enzymatic reaction scheme with BC-DPAR controller is designed using DSD reactions. According to the findings, the enzymatic reaction process's output substance can approach the target level at a quasi-steady state in both delay-free and non-zero delay conditions, but the target level can only be achieved during a finite-time period, mainly due to the fuel stand depletion.

A Theoretical Framework for Implementable Nucleic Acids Feedback Systems

Chemical reaction networks can be utilised as basic components for nucleic acid feedback control systems' design for Synthetic Biology application. DNA hybridisation and programmed strand-displacement reactions are effective primitives for implementation. However, the experimental validation and scale-up of nucleic acid control systems are still considerably falling behind their theoretical designs. To aid with the progress heading into experimental implementations, we provide here chemical reaction networks that represent two fundamental classes of linear controllers: integral and static negative state feedback. We reduced the complexity of the networks by finding designs with fewer reactions and chemical species, to take account of the limits of current experimental capabilities and mitigate issues pertaining to crosstalk and leakage, along with toehold sequence design. The supplied control circuits are quintessential candidates for the first experimental validations of nucleic acid controllers, since they have a number of parameters, species, and reactions small enough for viable experimentation with current technical capabilities, but still represent challenging feedback control systems. They are also well suited to further theoretical analysis to verify results on the stability, performance, and robustness of this important new class of control systems.

DNA strand displacement reactions to accomplish a two-degree-of-freedom PID controller and its application in subtraction gate

Synthesis control circuits can be used to effectively control biochemical molecule processes. In the controller design based on chemical reaction networks (CRNs), generally only the tracking set-point is considered. However, the influence of disturbances, which are frequently encountered in biochemical systems, is often neglected, thus weakening the control effect of the system. In this article, tracking set-point input and suppressing disturbance input are considered in the control effect. Firstly, CRNs are adopted to construct a two-degree-of-freedom PID controller by combining a one-degree-of-freedom PID controller with a feedforward controller for the first time. Then, CRN expressions of the two input functions (step function and ramp function) used as input signals are defined. Furthermore, the two-degree-of-freedom PID controller is founded by DNA strand displacement (DSD) reaction networks, because DNA is an ideal engineering material to constitute molecular devices based on CRNs. The overshoot of the two-degree-of-freedom PID control system is significantly reduced compared to the one-degree-of-freedom PID control system. Finally, a leak reaction is treated as an extraneous disturbance input to a subtraction gate. The influence of external disturbance is solved by the two-degree-of-freedom PID controller. It is worth noting that the two-degree-of-freedom subtraction gate control system better restrains the impact of a disturbance input (leak reaction).