METHODS article
Front. Syst. Biol.
Sec. Systems Concepts, Theory and Policy in Biology and Medicine
Volume 5 - 2025 | doi: 10.3389/fsysb.2025.1546072
This article is part of the Research TopicFOSBE 2024: Building the Future; Education and Innovation in Systems and Synthetic BiologyView all articles
From flux analysis to self contained cellular models
Provisionally accepted
- Technical University of Munich, Munich, Germany
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Mathematical models for cellular systems have become more and more important for understanding the complex interplay between metabolism, signalling, and gene expression.In this manuscript, starting from the well-known flux balance analysis, tools and methods are summarised and illustrated by various examples that describe the way to models with kinetics for individual reactions steps that are finally self-contained. While flux analysis requires known (measured) input fluxes, self-contained (or self-sustained) models only get information on concentrations of environmental components. Kinetic reaction laws, feedback structures, and protein allocation then determine the temporal output of all intracellular metabolites and macromolecules. Emphasis is placed on (i) mass conservation, a crucial system property frequently overlooked in models incorporating cellular structures like macromolecular structures like proteins, RNA, and DNA, and (ii) thermodynamic constraints which further limit the solution space. Matlab Live Scripts are provided for all simulation studies shown and additional reading material is given in the appendix.
Keywords: Research Topic Systems and Synthetic Biology: What About Training, funding, and Publishing; topic: Methodology, Technology and Code, Flux balance analysis, Coarse-grained model, Resource Allocation, enzyme kinetics
Received: 16 Dec 2024; Accepted: 18 Jun 2025.
Copyright: © 2025 Kremling. 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: Andreas Kremling, Technical University of Munich, Munich, Germany
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