扩展网络上的Petri网计算有限多层模型的动力学。

IF 4 3区生物学 Q1 BIOLOGY

Interface Focus Pub Date : 2025-08-22 DOI:10.1098/rsfs.2024.0059

Elizabeth Andreas, Eli Quist, Tomas Gedeon

{"title":"扩展网络上的Petri网计算有限多层模型的动力学。","authors":"Elizabeth Andreas, Eli Quist, Tomas Gedeon","doi":"10.1098/rsfs.2024.0059","DOIUrl":null,"url":null,"abstract":"We discuss connections between different types of models of gene-regulatory network dynamics that include Boolean, finite multilevel and monotone Boolean models. We recast the methodology of describing attractors of Boolean and finite multilevel dynamics using motifs of the expanded network <math><mrow><mi>e</mi> <mi>R</mi> <mi>N</mi></mrow> </math> in terms of Petri net dynamics on <math><mrow><mi>e</mi> <mi>R</mi> <mi>N</mi></mrow> </math> . We show that the Petri net can be used to recover dynamics of the finite multilevel dynamics on the state transition graph. We conclude with new insights that the expanded network viewpoint offers for the robustness of equilibria and complex attractors.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"15 3","pages":"20240059"},"PeriodicalIF":4.0000,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12371345/pdf/","citationCount":"0","resultStr":"{\"title\":\"Petri net on expanded networks computes the dynamics of finite multilevel models.\",\"authors\":\"Elizabeth Andreas, Eli Quist, Tomas Gedeon\",\"doi\":\"10.1098/rsfs.2024.0059\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"We discuss connections between different types of models of gene-regulatory network dynamics that include Boolean, finite multilevel and monotone Boolean models. We recast the methodology of describing attractors of Boolean and finite multilevel dynamics using motifs of the expanded network <math><mrow><mi>e</mi> <mi>R</mi> <mi>N</mi></mrow> </math> in terms of Petri net dynamics on <math><mrow><mi>e</mi> <mi>R</mi> <mi>N</mi></mrow> </math> . We show that the Petri net can be used to recover dynamics of the finite multilevel dynamics on the state transition graph. We conclude with new insights that the expanded network viewpoint offers for the robustness of equilibria and complex attractors.\",\"PeriodicalId\":13795,\"journal\":{\"name\":\"Interface Focus\",\"volume\":\"15 3\",\"pages\":\"20240059\"},\"PeriodicalIF\":4.0000,\"publicationDate\":\"2025-08-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12371345/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Interface Focus\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1098/rsfs.2024.0059\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Interface Focus","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1098/rsfs.2024.0059","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOLOGY","Score":null,"Total":0}

引用次数: 0

摘要

我们讨论了不同类型的基因调控网络动力学模型之间的联系，包括布尔模型、有限多层模型和单调布尔模型。我们利用扩展网络e R N的基元，根据e R N上的Petri网动力学，对描述布尔和有限多能级动力学吸引子的方法进行了改造。我们证明了Petri网可以用于恢复状态转移图上有限多层动力学的动态。我们总结了扩展网络的观点为均衡和复杂吸引子的鲁棒性提供了新的见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

Petri net on expanded networks computes the dynamics of finite multilevel models.

We discuss connections between different types of models of gene-regulatory network dynamics that include Boolean, finite multilevel and monotone Boolean models. We recast the methodology of describing attractors of Boolean and finite multilevel dynamics using motifs of the expanded network $e R N$ in terms of Petri net dynamics on $e R N$ . We show that the Petri net can be used to recover dynamics of the finite multilevel dynamics on the state transition graph. We conclude with new insights that the expanded network viewpoint offers for the robustness of equilibria and complex attractors.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Interface Focus BIOLOGY-

CiteScore

9.20

自引率

0.00%

发文量

审稿时长

6-12 weeks

期刊介绍： Each Interface Focus themed issue is devoted to a particular subject at the interface of the physical and life sciences. Formed of high-quality articles, they aim to facilitate cross-disciplinary research across this traditional divide by acting as a forum accessible to all. Topics may be newly emerging areas of research or dynamic aspects of more established fields. Organisers of each Interface Focus are strongly encouraged to contextualise the journal within their chosen subject.