Application of a novel numerical simulation to biochemical reaction systems

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 ensu...

Full description

Saved in:
Bibliographic Details
Published inFrontiers in cell and developmental biology Vol. 12; p. 1351974
Main Author Sato, Takashi
Format Journal Article
LanguageEnglish
Published Switzerland Frontiers Media S.A 2024
Subjects
algorithm
biochemical reaction system
feedback
feedforward
Michaelis-Menten
numerical simulation
feedback
biochemical reaction system
allosteric
entropy
feedforward
Michaelis-Menten
numerical simulation
algorithm
Online AccessGet full text

Cover

More Information
Summary: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, H 2 O, 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 gene-based systems, making it an effective tool for scientific and engineering research.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:2296-634X
2296-634X
DOI:10.3389/fcell.2024.1351974