Effective Kinetics of Chemical Reaction Networks
Fuente:
arXiv
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| Natura: | Preprint |
| Pubblicazione: |
2024
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| _version_ | 1866909122221309952 |
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| author | Suda, Tomoharu |
| author_facet | Suda, Tomoharu |
| contents | Chemical reaction network theory is a powerful framework to describe and analyze chemical systems. While much about the concentration profile in an equilibrium state can be determined in terms of the graph structure, the overall reaction's time evolution depends on the network's kinetic rate function. In this article, we consider the problem of the effective kinetics of a chemical reaction network regarded as a conversion system from the feeding species to products. We define the notion of effective kinetics as a partial solution of a system of non-autonomous ordinary differential equations determined from a chemical reaction network. Examples of actual calculations include the Michaelis-Menten mechanism, for which it is confirmed that our notion of effective kinetics yields the classical formula. Further, we introduce the notion of straight-line solutions of non-autonomous ordinary differential equations to formalize the situation where a well-defined reaction rate exists and consider its relation with the quasi-stationary state approximation used in microkinetics. Our considerations here give a unified framework to formulate the reaction rate of chemical reaction networks. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2402_11762 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Effective Kinetics of Chemical Reaction Networks Suda, Tomoharu Molecular Networks Chemical reaction network theory is a powerful framework to describe and analyze chemical systems. While much about the concentration profile in an equilibrium state can be determined in terms of the graph structure, the overall reaction's time evolution depends on the network's kinetic rate function. In this article, we consider the problem of the effective kinetics of a chemical reaction network regarded as a conversion system from the feeding species to products. We define the notion of effective kinetics as a partial solution of a system of non-autonomous ordinary differential equations determined from a chemical reaction network. Examples of actual calculations include the Michaelis-Menten mechanism, for which it is confirmed that our notion of effective kinetics yields the classical formula. Further, we introduce the notion of straight-line solutions of non-autonomous ordinary differential equations to formalize the situation where a well-defined reaction rate exists and consider its relation with the quasi-stationary state approximation used in microkinetics. Our considerations here give a unified framework to formulate the reaction rate of chemical reaction networks. |
| title | Effective Kinetics of Chemical Reaction Networks |
| topic | Molecular Networks |
| url | https://arxiv.org/abs/2402.11762 |