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Dynamical Modularity in Automata Models of Biochemical Networks
Given the large size and complexity of most biochemical regulation and signaling networks, there is a non-trivial relationship between the micro-level logic of component interactions and the observed macro-dynamics. Here we address this issue by formalizing the concept of pathway modules developed b...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cornell University
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10081338/ https://www.ncbi.nlm.nih.gov/pubmed/37033454 |
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author | Parmer, Thomas Rocha, Luis M. |
author_facet | Parmer, Thomas Rocha, Luis M. |
author_sort | Parmer, Thomas |
collection | PubMed |
description | Given the large size and complexity of most biochemical regulation and signaling networks, there is a non-trivial relationship between the micro-level logic of component interactions and the observed macro-dynamics. Here we address this issue by formalizing the concept of pathway modules developed by Marques-Pita and Rocha [1], which are sequences of state updates that are guaranteed to occur (barring outside interference) in the causal dynamics of automata networks after the perturbation of a subset of driver nodes. We present a novel algorithm to automatically extract pathway modules from networks and characterize the interactions that may take place between the modules. This methodology uses only the causal logic of individual node variables (micro-dynamics) without the need to compute the dynamical landscape of the networks (macro-dynamics). Specifically, we identify complex modules, which maximize pathway length and require synergy between their components. This allows us to propose a new take on dynamical modularity that partitions complex networks into causal pathways of variables that are guaranteed to transition to specific dynamical states given a perturbation to a set of driver nodes. Thus, the same node variable can take part in distinct modules depending on the state it takes. Our measure of dynamical modularity of a network is then inversely proportional to the overlap among complex modules and maximal when complex modules are completely decouplable from one another in the network dynamics. We estimate dynamical modularity for several genetic regulatory networks, including the full Drosophila melanogaster segment-polarity network. We discuss how identifying complex modules and the dynamical modularity portrait of networks explains the macro-dynamics of biological networks, such as uncovering the (more or less) decouplable building blocks of emergent computation (or collective behavior) in biochemical regulation and signaling. |
format | Online Article Text |
id | pubmed-10081338 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Cornell University |
record_format | MEDLINE/PubMed |
spelling | pubmed-100813382023-04-08 Dynamical Modularity in Automata Models of Biochemical Networks Parmer, Thomas Rocha, Luis M. ArXiv Article Given the large size and complexity of most biochemical regulation and signaling networks, there is a non-trivial relationship between the micro-level logic of component interactions and the observed macro-dynamics. Here we address this issue by formalizing the concept of pathway modules developed by Marques-Pita and Rocha [1], which are sequences of state updates that are guaranteed to occur (barring outside interference) in the causal dynamics of automata networks after the perturbation of a subset of driver nodes. We present a novel algorithm to automatically extract pathway modules from networks and characterize the interactions that may take place between the modules. This methodology uses only the causal logic of individual node variables (micro-dynamics) without the need to compute the dynamical landscape of the networks (macro-dynamics). Specifically, we identify complex modules, which maximize pathway length and require synergy between their components. This allows us to propose a new take on dynamical modularity that partitions complex networks into causal pathways of variables that are guaranteed to transition to specific dynamical states given a perturbation to a set of driver nodes. Thus, the same node variable can take part in distinct modules depending on the state it takes. Our measure of dynamical modularity of a network is then inversely proportional to the overlap among complex modules and maximal when complex modules are completely decouplable from one another in the network dynamics. We estimate dynamical modularity for several genetic regulatory networks, including the full Drosophila melanogaster segment-polarity network. We discuss how identifying complex modules and the dynamical modularity portrait of networks explains the macro-dynamics of biological networks, such as uncovering the (more or less) decouplable building blocks of emergent computation (or collective behavior) in biochemical regulation and signaling. Cornell University 2023-04-17 /pmc/articles/PMC10081338/ /pubmed/37033454 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use. |
spellingShingle | Article Parmer, Thomas Rocha, Luis M. Dynamical Modularity in Automata Models of Biochemical Networks |
title | Dynamical Modularity in Automata Models of Biochemical Networks |
title_full | Dynamical Modularity in Automata Models of Biochemical Networks |
title_fullStr | Dynamical Modularity in Automata Models of Biochemical Networks |
title_full_unstemmed | Dynamical Modularity in Automata Models of Biochemical Networks |
title_short | Dynamical Modularity in Automata Models of Biochemical Networks |
title_sort | dynamical modularity in automata models of biochemical networks |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10081338/ https://www.ncbi.nlm.nih.gov/pubmed/37033454 |
work_keys_str_mv | AT parmerthomas dynamicalmodularityinautomatamodelsofbiochemicalnetworks AT rochaluism dynamicalmodularityinautomatamodelsofbiochemicalnetworks |