Transitions and Thermodynamics on Species Graphs of Chemical Reaction Networks
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arXiv
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| Auteurs principaux: | , , |
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| Format: | Preprint |
| Publié: |
2024
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| _version_ | 1866910418278023168 |
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| author | Sugie, Keisuke Loutchko, Dimitri Kobayashi, Tetsuya J. |
| author_facet | Sugie, Keisuke Loutchko, Dimitri Kobayashi, Tetsuya J. |
| contents | Chemical reaction networks (CRNs) exhibit complex dynamics governed by their underlying network structure. In this paper, we propose a novel approach to study the dynamics of CRNs by representing them on species graphs (S-graphs). By scaling concentrations by conservation laws, we obtain a graph representation of transitions compatible with the S-graph, which allows us to treat the dynamics in CRNs as transitions between chemicals. We also define thermodynamic-like quantities on the S-graph from the introduced transitions and investigate their properties, including the relationship between specieswise forces, activities, and conventional thermodynamic quantities. Remarkably, we demonstrate that this formulation can be developed for a class of irreversible CRNs, while for reversible CRNs, it is related to conventional thermodynamic quantities associated with reactions. The behavior of these specieswise quantities is numerically validated using an oscillating system (Brusselator). Our work provides a novel methodology for studying dynamics on S-graphs, paving the way for a deeper understanding of the intricate interplay between the structure and dynamics of chemical reaction networks. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2404_14336 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Transitions and Thermodynamics on Species Graphs of Chemical Reaction Networks Sugie, Keisuke Loutchko, Dimitri Kobayashi, Tetsuya J. Molecular Networks Biological Physics Chemical Physics Chemical reaction networks (CRNs) exhibit complex dynamics governed by their underlying network structure. In this paper, we propose a novel approach to study the dynamics of CRNs by representing them on species graphs (S-graphs). By scaling concentrations by conservation laws, we obtain a graph representation of transitions compatible with the S-graph, which allows us to treat the dynamics in CRNs as transitions between chemicals. We also define thermodynamic-like quantities on the S-graph from the introduced transitions and investigate their properties, including the relationship between specieswise forces, activities, and conventional thermodynamic quantities. Remarkably, we demonstrate that this formulation can be developed for a class of irreversible CRNs, while for reversible CRNs, it is related to conventional thermodynamic quantities associated with reactions. The behavior of these specieswise quantities is numerically validated using an oscillating system (Brusselator). Our work provides a novel methodology for studying dynamics on S-graphs, paving the way for a deeper understanding of the intricate interplay between the structure and dynamics of chemical reaction networks. |
| title | Transitions and Thermodynamics on Species Graphs of Chemical Reaction Networks |
| topic | Molecular Networks Biological Physics Chemical Physics |
| url | https://arxiv.org/abs/2404.14336 |