From flux analysis to self contained cellular models
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...
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Frontiers Media S.A.
2025-08-01
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| Series: | Frontiers in Systems Biology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fsysb.2025.1546072/full |
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| author | Andreas Kremling |
| author_facet | Andreas Kremling |
| author_sort | Andreas Kremling |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-86d2ca983ee54d67bfbed4a65b884460 |
| institution | Kabale University |
| issn | 2674-0702 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Systems Biology |
| spelling | doaj-art-86d2ca983ee54d67bfbed4a65b8844602025-08-22T04:10:40ZengFrontiers Media S.A.Frontiers in Systems Biology2674-07022025-08-01510.3389/fsysb.2025.15460721546072From flux analysis to self contained cellular modelsAndreas KremlingMathematical 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.https://www.frontiersin.org/articles/10.3389/fsysb.2025.1546072/fullflux balance analysiscoarse-grained modelsthermodynamicsresource allocationenzyme kinetics |
| spellingShingle | Andreas Kremling From flux analysis to self contained cellular models Frontiers in Systems Biology flux balance analysis coarse-grained models thermodynamics resource allocation enzyme kinetics |
| title | From flux analysis to self contained cellular models |
| title_full | From flux analysis to self contained cellular models |
| title_fullStr | From flux analysis to self contained cellular models |
| title_full_unstemmed | From flux analysis to self contained cellular models |
| title_short | From flux analysis to self contained cellular models |
| title_sort | from flux analysis to self contained cellular models |
| topic | flux balance analysis coarse-grained models thermodynamics resource allocation enzyme kinetics |
| url | https://www.frontiersin.org/articles/10.3389/fsysb.2025.1546072/full |
| work_keys_str_mv | AT andreaskremling fromfluxanalysistoselfcontainedcellularmodels |