A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä
Reaction Systems and Synchronous Digital Circuits
Tekijät: Zeyi Shang, Sergey Verlan, Ion Petre, Gexiang Zhang
Kustantaja: MDPI
Julkaisuvuosi: 2019
Journal: Molecules
Tietokannassa oleva lehden nimi: MOLECULES
Lehden akronyymi: MOLECULES
Artikkelin numero: ARTN 961
Vuosikerta: 24
Numero: 10
Sivujen määrä: 13
ISSN: 1420-3049
eISSN: 1420-3049
DOI: https://doi.org/10.3390/molecules24101961
Rinnakkaistallenteen osoite: https://research.utu.fi/converis/portal/detail/Publication/41257012
Tiivistelmä
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.
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.
Ladattava julkaisu This is an electronic reprint of the original article. |  |
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