Modular and Robust Computation with Deterministic Chemical Reaction Networks

Klinge, Titus H.

doi:10.31274/etd-180810-5369

Cited by 3 publications

(3 citation statements)

References 53 publications

(72 reference statements)

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“…A chemical reaction network is defined as a finite set of reactions involving a finite number of species [14], where these reactions occur in a wellstirred environment, aiming to realize a function or algorithm via mass action chemical reactions. Specific chemical reaction networks have already been designed for signal restoration, noise filtering, and finite automata, respectively, through a discipline known as molecular programming [15].…”

Section: B An I1-ffl-inspired Chemical Reaction Networkmentioning

confidence: 99%

A Microfluidic Feed Forward Loop Pulse Generator for Molecular Communication

Deng

Pierobon

Nallanathan

2017

GLOBECOM 2017 - 2017 IEEE Global Communications Conference

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Abstract-The design of communication systems capable of processing and exchanging information through molecules and chemical processes is a rapidly growing interdisciplinary field, which holds the promise to revolutionize how we realize computing and communication devices. While molecular communication (MC) theory has had major developments in recent years, more practical aspects in the design and prototyping of components capable of MC functionalities remain less explored. In this paper, motivated by a bulk of MC literature on information transmission via molecular pulse modulation, the design of a pulse generator is proposed as an MC component able to output a predefined pulse-shaped molecular concentration upon a triggering input. The chemical processes at the basis of this pulse generator are inspired by how cells generate pulse-shaped molecular signals in biology. At the same time, the slow-speed, unreliability, and non-scalability of these processes in cells are overcome with a microfluidic-based implementation based on standard reproducible components with well-defined design parameters. Mathematical models are presented to demonstrate the analytical tractability of each component, and are validated against a numerical finite element simulation. Finally, the complete pulse generator design is implemented and simulated in a standard engineering software framework, where the predefined nature of the output pulse shape is demonstrated together with its dependence on practical design parameters.

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Section: B An I1-ffl-inspired Chemical Reaction Networkmentioning

confidence: 99%

A Microfluidic Feed Forward Loop Pulse Generator for Molecular Communication

Deng

Pierobon

Nallanathan

2017

GLOBECOM 2017 - 2017 IEEE Global Communications Conference

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“…A chemical reaction network is defined as a finite set of reactions involving a finite number of species [21], where these reactions occur in a wellstirred environment, aiming to realize a function or algorithm via mass action chemical reactions. Specific chemical reaction networks have already been designed for signal restoration, noise filtering, and finite automata, respectively, through a discipline known as molecular programming [33].…”

Section: System Modelmentioning

confidence: 99%

Chemical Reactions-Based Microfluidic Transmitter and Receiver Design for Molecular Communication

Bi¹,

Deng²,

Pierobon³

et al. 2020

IEEE Trans. Commun.

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“…for signal restoration, noise filtering, and finite automata, respectively, through a discipline known as molecular programming [30].…”

Section: System Modelmentioning

confidence: 99%

Chemical Reactions-Based Microfluidic Transmitter and Receiver for Molecular Communication

Bi,

Deng,

Pierobon

et al. 2019

Preprint

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The design of communication systems capable of processing and exchanging information through molecules and chemical processes is a rapidly growing interdisciplinary field, which holds the promise to revolutionize how we realize computing and communication devices. While molecular communication (MC) theory has had major developments in recent years, more practical aspects in designing components capable of MC functionalities remain less explored. Motivated by this, we design a microfluidic MC system with a microfluidic MC transmitter and a microfluidic MC receiver based on chemical reactions.Considering existing MC literature on information transmission via molecular pulse modulation, the proposed microfluidic MC transmitter is capable of generating continuously predefined pulse-shaped molecular concentrations upon rectangular triggering signals using chemical reactions inspired by how cells generate pulse-shaped molecular signals in biology. We further design a microfluidic MC receiver capable of demodulating a received signal to a rectangular output signal using a thresholding reaction and an amplifying reaction. Our chemical reactions-based microfluidic molecular communication system is reproducible and well-designed, and more importantly, it overcomes the slow-speed, unreliability, and non-scalability of biological processes in cells. To reveal design insights, we also derive the theoretical signal responses for our designed microfluidic transmitter and receiver, which further facilitate the transmitter design optimization. Our theoretical results are validated via simulations performed through D. Bi and Y. Deng are with the

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Modular and Robust Computation with Deterministic Chemical Reaction Networks

Cited by 3 publications

References 53 publications

A Microfluidic Feed Forward Loop Pulse Generator for Molecular Communication

A Microfluidic Feed Forward Loop Pulse Generator for Molecular Communication

Chemical Reactions-Based Microfluidic Transmitter and Receiver Design for Molecular Communication

Chemical Reactions-Based Microfluidic Transmitter and Receiver for Molecular Communication

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