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ORIGINAL RESEARCH article

Front. Cell Dev. Biol.
Sec. Cellular Biochemistry
Volume 12 - 2024 | doi: 10.3389/fcell.2024.1351974

Application of a Novel Numerical Simulation to Biochemical Reaction Systems

Provisionally accepted
Takashi Sato Takashi Sato *
  • Zeon Corporation, Chiyoda-ku, Tokyo, Japan

The final, formatted version of the article will be published soon.

    Recent advancements in omics and single-cell analysis highlight the necessity of numerical methods for managing the complexity of biological data. This paper introduces a simulation program for biochemical reaction systems based on the natural number simulation (NNS) method. This novel approach ensures the equitable treatment of all molecular entities, such as DNA, proteins, H2O, and hydrogen ions (H + ), in biological systems. Central to NNS is its use of stoichiometric formulas, simplifying the modeling process and facilitating efficient and accurate simulations of diverse biochemical reactions. The advantage of this method is its ability to manage all molecules uniformly, ensuring a balanced representation in simulations. Detailed in Python, NNS is adept at simulating various reactions, ranging from water ionization to Michaelis-Menten kinetics and complex genebased systems, making it an effective tool for scientific and engineering research.

    Keywords: Biochemical reaction system, numerical simulation, algorithm, Feedback, feedforward, Michaelis-Menten, allosteric, entropy

    Received: 07 Dec 2023; Accepted: 09 Aug 2024.

    Copyright: © 2024 Sato. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Takashi Sato, Zeon Corporation, Chiyoda-ku, Tokyo, Japan

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.