Biomolecular implementation of nonlinear system theoretic operators

Foo, Mathias; Sawlekar, Rucha; Kim, Jongmin; Bates, Declan G.; Stan, Guy-Bart; Kulkarni, Vishwesh V.

doi:10.1109/ecc.2016.7810556

Cited by 6 publications

(4 citation statements)

References 30 publications

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“…Oishi and Klavins show that linear dynamical systems that are specified by linear ordinary differential equations can be realized using CRNs that are based on three classes of chemical reactions, namely catalysis, degradation and annihilation ( 11 ). This work is further extended by Foo et al to non-linear operators ( 12 ). More recently, Zechner et al show how de novo molecular circuits can be used to implement optimal filters approximately ( 13 ).…”

Section: Introductionmentioning

confidence: 78%

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Chemical reaction networks for computing logarithm

Chou

2017

Synthetic Biology

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Living cells constantly process information from their living environment. It has recently been shown that a number of cell signaling mechanisms (e.g. G protein-coupled receptor and epidermal growth factor) can be interpreted as computing the logarithm of the ligand concentration. This suggests that logarithm is a fundamental computation primitive in cells. There is also an increasing interest in the synthetic biology community to implement analog computation and computing the logarithm is one such example. The aim of this article is to study how the computation of logarithm can be realized using chemical reaction networks (CRNs). CRNs cannot compute logarithm exactly. A standard method is to use power series or rational function approximation to compute logarithm approximately. Although CRNs can realize these polynomial or rational function computations in a straightforward manner, the issue is that in order to be able to compute logarithm accurately over a large input range, it is necessary to use high-order approximation that results in CRNs with a large number of reactions. This article proposes a novel method to compute logarithm accurately in CRNs while keeping the number of reactions in CRNs low. The proposed method can create CRNs that can compute logarithm to different levels of accuracy by adjusting two design parameters. In this article, we present the chemical reactions required to realize the CRNs for computing logarithm. The key contribution of this article is a novel method to create CRNs that can compute logarithm accurately over a wide input range using only a small number of chemical reactions.

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Section: Introductionmentioning

confidence: 78%

“…To the best of our knowledge, previous work on CRNs has so far been focusing on integral powers of the input, e.g. polynomials with integral powers ( 10 ) and rational functions with integral powers ( 11 , 12 ). Therefore, a novelty of our approach is the use of non-integral exponents.…”

Section: Discussionmentioning

confidence: 99%

Chemical reaction networks for computing logarithm

Chou

2017

Synthetic Biology

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“…The SC controller design uses lesser chemical reactions and was shown to perform better than PI controller. Other research directions have also implemented a number of nonlinear system theoretic operators, such as polynomial functions, rational functions, Hill-type nonlinearities [50]. In [51], the authors discussed robustness of the DNA nonlinear circuit, based on DSD, against unintended reactions.…”

Section: B Biochemical Controllersmentioning

confidence: 99%

A Survey of DNA-based Computing Devices and their Applications

Sawlekar

Nikolakopoulos

2021

2021 European Control Conference (ECC)

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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.

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“…To get around this problem, Oishi and Klavins [3] proposed a formalism that can perform a two-sided subtraction, by letting each signal in the circuit be the difference in the concentration of two chemical species, x + and x − . In this way, a systematic framework for implementing simple linear biomolecular feedback controllers can be developed using three elementary reactions, and the same formalism has recently been extended to include more complicated mathematical operators [7] and non-linear controllers [8], [9].…”

Section: Introductionmentioning

confidence: 99%