Reaction Systems and Synchronous Digital Circuits

Author:

Shang ZeyiORCID,Verlan SergeyORCID,Petre IonORCID,Zhang GexiangORCID

Abstract

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.

Funder

National Natural Science Foundation of China

Publisher

MDPI AG

Subject

Chemistry (miscellaneous),Analytical Chemistry,Organic Chemistry,Physical and Theoretical Chemistry,Molecular Medicine,Drug Discovery,Pharmaceutical Science

Cited by 5 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

1. Solving subset sum and SAT problems by reaction systems;Natural Computing;2024-04-06

2. Quantitative extensions of reaction systems based on SOS semantics;Neural Computing and Applications;2023-01-24

3. Verification of Reaction Systems Processes;Intelligent Systems Reference Library;2023

4. A logical and graphical framework for reaction systems;Theoretical Computer Science;2021-07

5. Simulation of reaction systems by the strictly minimal ones;Journal of Membrane Computing;2020-07-20

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