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Reaction Systems and Synchronous Digital Circuits

by 1,2,†, 2,†, 3,4 and 1,*
School of Electrical Engineering, Southwest Jiaotong University, Chengdu 611756, Sichuan, China
Laboratoire d’Algorithmique, Complexité et Logique, Université Paris Est Créteil, 94010 Créteil, France
Department of Mathematics and Statistics, University of Turku, FI-20014 Turku, Finland
National Institute for Research and Development in Biological Sciences, 060031 Bucharest, Romania
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editors: Quan Zou, Xiangxiang Zeng and Alfonso Rodríguez-Patón
Molecules 2019, 24(10), 1961;
Received: 25 March 2019 / Revised: 26 April 2019 / Accepted: 28 April 2019 / Published: 21 May 2019
(This article belongs to the Special Issue Molecular Computing and Bioinformatics II)
A reaction system is a modeling framework for investigating the functioning of the living cell, focused on capturing cause–effect relationships in biochemical environments. Biochemical processes in this framework are seen to interact with each other by producing the ingredients enabling and/or inhibiting other reactions. They can also be influenced by the environment seen as a systematic driver of the processes through the ingredients brought into the cellular environment. In this paper, the first attempt is made to implement reaction systems in the hardware. We first show a tight relation between reaction systems and synchronous digital circuits, generally used for digital electronics design. We describe the algorithms allowing us to translate one model to the other one, while keeping the same behavior and similar size. We also develop a compiler translating a reaction systems description into hardware circuit description using field-programming gate arrays (FPGA) technology, leading to high performance, hardware-based simulations of reaction systems. This work also opens a novel interesting perspective of analyzing the behavior of biological systems using established industrial tools from electronic circuits design. View Full-Text
Keywords: reaction systems; synchronous digital circuits; field-programming gate arrays reaction systems; synchronous digital circuits; field-programming gate arrays
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MDPI and ACS Style

Shang, Z.; Verlan, S.; Petre, I.; Zhang, G. Reaction Systems and Synchronous Digital Circuits. Molecules 2019, 24, 1961.

AMA Style

Shang Z, Verlan S, Petre I, Zhang G. Reaction Systems and Synchronous Digital Circuits. Molecules. 2019; 24(10):1961.

Chicago/Turabian Style

Shang, Zeyi, Sergey Verlan, Ion Petre, and Gexiang Zhang. 2019. "Reaction Systems and Synchronous Digital Circuits" Molecules 24, no. 10: 1961.

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