1. Reaction Systems and Synchronous Digital Circuits
- Author
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Sergey Verlan, Shang Zeyi, Gexiang Zhang, Ion Petre, Southwest Jiaotong University (SWJTU), Laboratoire d'Algorithmique Complexité et Logique (LACL), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Åbo Akademi University [Turku], and Xihua University (XHU)
- Subjects
reaction systems ,Relation (database) ,Computer science ,Biochemical Phenomena ,Pharmaceutical Science ,0102 computer and information sciences ,02 engineering and technology ,Living cell ,computer.software_genre ,01 natural sciences ,Article ,Analytical Chemistry ,lcsh:QD241-441 ,lcsh:Organic chemistry ,[INFO.INFO-FL]Computer Science [cs]/Formal Languages and Automata Theory [cs.FL] ,Drug Discovery ,field-programming gate arrays ,Physical and Theoretical Chemistry ,Field-programmable gate array ,ComputingMilieux_MISCELLANEOUS ,Electronic circuit ,Digital electronics ,business.industry ,Computers ,Organic Chemistry ,021001 nanoscience & nanotechnology ,Computer architecture ,010201 computation theory & mathematics ,Chemistry (miscellaneous) ,Molecular Medicine ,synchronous digital circuits ,Compiler ,Reaction system ,Electronics ,0210 nano-technology ,business ,computer ,Algorithms - Abstract
A reaction system is a modeling framework for investigating the functioning of the living cell, focused on capturing cause&ndash, 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.
- Published
- 2019
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