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

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

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

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

Analysis of finite-time regulation property of biomolecular PI controller

In practical applications of dynamic DNA nanotechnology, a biomolecular controller is required for maintaining the operation of the molecular actuator at a desired condition based on the information from molecular sensors. By making use of the DNA strand displacement mechanism as a “programming language” in the controller design, a biomolecular PI controller has been proposed. However, this PI control system has been verified only at the simulation level, and a theoretical regulation analysis is still required. Accordingly, in this study, we perform a rigorous regulation analysis of the biomolecular PI control system. Specifically, we theoretically prove that the output signal approaches the target level at a quasi-steady state. To this end, we apply the concept of finite-time regulation property to the biomolecular PI control system

Finite-time regulation property of DNA feedback regulator

In dynamic DNA nanotechnology, the DNA strand displacement technique provides the cornerstone for the bottom-up design of a man-made DNA molecular system. Practically, a feedback controller for regulating the concentration of a target DNA strand to the desired level is indispensable for mediating the kinetic momentum of a molecular actuator. However, such a regulator system operates by consuming fuel strands and requires sufficient supplies of these consumables for its normal execution, indicating that, in practice, optimal controller design requires the period of time during which the regulator proceeds with normal operation to be as long as possible. The fact that the system is naturally high dimensional and nonlinear complicates the analysis of properties emerging during a finite-time period in terms of their theoretical aspects. In this paper, we first define the new concept of a “finite-time regulation property” of DNA systems in the regulation problem. Then, to theoretically analyze this regulation property, we present two-time-scale modeling based on the difference in the initial distribution of the abundance of DNA strands. Focusing on the fast mode as a subsystem with a positive quadratic structure, we propose a new method for analyzing the regulation property observed in a finite period of time

Design Of Dna Strand Displacement Based Circuits

DNA is the basic building block of any living organism. DNA is considered a popular candidate for future biological devices and circuits for solving genetic disorders and several other medical problems. With this objective in mind, this research aims at developing novel approaches for the design of DNA based circuits. There are many recent developments in the medical field such as the development of biological nanorobots, SMART drugs, and CRISPR-Cas9 technologies. There is a strong need for circuits that can work with these technologies and devices. DNA is considered a suitable candidate for designing such circuits because of the programmability of the DNA strands, small size, lightweight, known thermodynamics, higher parallelism, and exponentially reducing the cost of synthesizing techniques. The DNA strand displacement operation is useful in developing circuits with DNA strands. The circuit can be either a digital circuit, in which the logic high and logic low states of the DNA strand concentrations are considered as the signal, or it can be an analog circuit in which the concentration of the DNA strands itself will act as the signal. We developed novel approaches in this research for the design of digital, as well as analog circuits keeping in view of the number of DNA strands required for the circuit design. Towards this goal in the digital domain, we developed spatially localized DNA majority logic gates and an inverter logic gate that can be used with the existing seesaw based logic gates. The majority logic gates proposed in this research can considerably reduce the number of strands required in the design. The introduction of the logic inverter operation can translate the dual rail circuit architecture into a monorail architecture for the seesaw based logic circuits. It can also reduce the number of unique strands required for the design into approximately half. The reduction in the number of unique strands will consequently reduce the leakage reactions, circuit complexity, and cost associated with the DNA circuits. The real world biological inputs are analog in nature. If we can use those analog signals directly in the circuits, it can considerably reduce the resources required. Even though analog circuits are highly prone to noise, they are a perfect candidate for performing computations in the resource-limited environments, such as inside the cell. In the analog domain, we are developing a novel fuzzy inference engine using analog circuits such as the minimum gate, maximum gate, and fan-out gates. All the circuits discussed in this research were designed and tested in the Visual DSD software. The biological inputs are inherently fuzzy in nature, hence a fuzzy based system can play a vital role in future decision-making circuits. We hope that our research will be the first step towards realizing these larger goals. The ultimate aim of our research is to develop novel approaches for the design of circuits which can be used with the future biological devices to tackle many medical problems such as genetic disorders

High-speed atomic force microscopy for nano-visualization of dynamic biomolecular processes

金沢大学理工研究域数物科学系The atomic force microscope (AFM) has a unique capability of allowing the high-resolution imaging of biological samples on substratum surfaces in physiological solutions. Recent technological progress of AFM in biological research has resulted in remarkable improvements in both the imaging rate and the tip force acting on the sample. These improvements have enabled the direct visualization of dynamic structural changes and dynamic interactions occurring in individual biological macromolecules, which is currently not possible with other techniques. Therefore, high-speed AFM is expected to have a revolutionary impact on biological sciences. In addition, the recently achieved atomic-resolution in liquids will further expand the usefulness of AFM in biological research. In this article, we first describe the various capabilities required of AFM in biological sciences, which is followed by a detailed description of various devices and techniques developed for high-speed AFM and atomic-resolution in-liquid AFM. We then describe various imaging studies performed using our cutting-edge microscopes and their current capabilities as well as their limitations, and conclude by discussing the future prospects of AFM as an imaging tool in biological research. © 2008 Elsevier Ltd. All rights reserved

Bioinformatics

This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here