Reaction Systems and Synchronous Digital Circuits

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 inhib...

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Vydáno v:Molecules (Basel, Switzerland) Ročník 24; číslo 10; s. 1961
Hlavní autoři: Shang, Zeyi, Verlan, Sergey, Petre, Ion, Zhang, Gexiang
Médium: Journal Article
Jazyk:angličtina
Vydáno: Switzerland MDPI AG 21.05.2019
MDPI
Témata:
Algebra
Algorithms
Biochemical Phenomena
Boolean
Circuits
Computer Science
Computers
Electronics
field-programming gate arrays
Formal Languages and Automata Theory
Investigations
reaction systems
Simulation
synchronous digital circuits
synchronous digital circuits
field-programming gate arrays
reaction systems
ISSN:1420-3049, 1420-3049
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Shrnutí: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.
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PMCID: PMC6571626
These authors contributed equally to this work.
ISSN:1420-3049
1420-3049
DOI:10.3390/molecules24101961