Keisuke Sugie, Dimitri Loutchko, Tetsuya J. Tobayashi
{"title":"化学反应网络物种图上的转变和热力学","authors":"Keisuke Sugie, Dimitri Loutchko, Tetsuya J. Tobayashi","doi":"arxiv-2404.14336","DOIUrl":null,"url":null,"abstract":"Chemical reaction networks (CRNs) exhibit complex dynamics governed by their\nunderlying network structure. In this paper, we propose a novel approach to\nstudy the dynamics of CRNs by representing them on species graphs (S-graphs).\nBy scaling concentrations by conservation laws, we obtain a graph\nrepresentation of transitions compatible with the S-graph, which allows us to\ntreat the dynamics in CRNs as transitions between chemicals. We also define\nthermodynamic-like quantities on the S-graph from the introduced transitions\nand investigate their properties, including the relationship between\nspecieswise forces, activities, and conventional thermodynamic quantities.\nRemarkably, we demonstrate that this formulation can be developed for a class\nof irreversible CRNs, while for reversible CRNs, it is related to conventional\nthermodynamic quantities associated with reactions. The behavior of these\nspecieswise quantities is numerically validated using an oscillating system\n(Brusselator). Our work provides a novel methodology for studying dynamics on\nS-graphs, paving the way for a deeper understanding of the intricate interplay\nbetween the structure and dynamics of chemical reaction networks.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"1 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Transitions and Thermodynamics on Species Graphs of Chemical Reaction Networks\",\"authors\":\"Keisuke Sugie, Dimitri Loutchko, Tetsuya J. Tobayashi\",\"doi\":\"arxiv-2404.14336\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Chemical reaction networks (CRNs) exhibit complex dynamics governed by their\\nunderlying network structure. In this paper, we propose a novel approach to\\nstudy the dynamics of CRNs by representing them on species graphs (S-graphs).\\nBy scaling concentrations by conservation laws, we obtain a graph\\nrepresentation of transitions compatible with the S-graph, which allows us to\\ntreat the dynamics in CRNs as transitions between chemicals. We also define\\nthermodynamic-like quantities on the S-graph from the introduced transitions\\nand investigate their properties, including the relationship between\\nspecieswise forces, activities, and conventional thermodynamic quantities.\\nRemarkably, we demonstrate that this formulation can be developed for a class\\nof irreversible CRNs, while for reversible CRNs, it is related to conventional\\nthermodynamic quantities associated with reactions. The behavior of these\\nspecieswise quantities is numerically validated using an oscillating system\\n(Brusselator). Our work provides a novel methodology for studying dynamics on\\nS-graphs, paving the way for a deeper understanding of the intricate interplay\\nbetween the structure and dynamics of chemical reaction networks.\",\"PeriodicalId\":501325,\"journal\":{\"name\":\"arXiv - QuanBio - Molecular Networks\",\"volume\":\"1 1\",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-04-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"arXiv - QuanBio - Molecular Networks\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/arxiv-2404.14336\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"arXiv - QuanBio - Molecular Networks","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/arxiv-2404.14336","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
摘要
化学反应网络(CRN)表现出复杂的动力学,受其基本网络结构的支配。在本文中,我们提出了一种研究 CRN 动力学的新方法,即在物种图(S-graph)上表示 CRN。通过守恒定律缩放浓度,我们获得了与 S-graph(物种图)兼容的转换图表示法,从而可以将 CRN 中的动力学视为化学物质之间的转换。我们还根据引入的转换定义了 S 图上的类热力学量,并研究了它们的性质,包括种力、活动和传统热力学量之间的关系。我们使用一个振荡系统(布鲁塞尔器)对这些按物种划分的量的行为进行了数值验证。我们的工作为研究 S 图上的动力学提供了一种新方法,为深入理解化学反应网络结构与动力学之间错综复杂的相互作用铺平了道路。
Transitions and Thermodynamics on Species Graphs of Chemical Reaction Networks
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.