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Reaction Systems and Synchronous Digital Circuits

Zeyi Shang, Sergey Verlan, Ion Petre, Gexiang Zhang, Reaction Systems and Synchronous Digital Circuits. Molecules , 1–13, 2019.

http://dx.doi.org/10.3390/molecules24101961

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.

BibTeX entry:

@ARTICLE{jShVePeZh19a,
  title = {Reaction Systems and Synchronous Digital Circuits},
  author = {Shang, Zeyi and Verlan, Sergey and Petre, Ion and Zhang, Gexiang},
  journal = {Molecules},
  pages = {1–13},
  year = {2019},
  keywords = {reaction systems; synchronous digital circuits; field-programming gate arrays},
  ISSN = {1420-3049},
}

Belongs to TUCS Research Unit(s): Computational Biomodeling Laboratory (Combio Lab)

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