Qualitative Dynamics of Chemical Reaction Networks: An Investigation Using Partial Tropical Equilibrations

Aurélien Desoeuvres; Peter Szmolyan; Ovidiu Radulescu

doi:10.1007/978-3-031-15034-0_4

Qualitative Dynamics of Chemical Reaction Networks: An Investigation Using Partial Tropical Equilibrations

Aurélien Desoeuvres, Peter Szmolyan, Ovidiu Radulescu^*

^*Corresponding author for this work

Research output: Contribution to book/anthology/report/conference proceeding › Article in proceeding › Research › peer-review

5 Citations (Scopus)

Abstract

We discuss a method to describe the qualitative dynamics of chemical reaction networks in terms of symbolic dynamics. The method, that can be applied to mass-action reaction networks with separated timescales, uses solutions of the partial tropical equilibration problem as proxies for symbolic states. The partial tropical equilibration solutions are found algorithmically. These solutions also provide the scaling needed for slow-fast decomposition and model reduction. Any trace of the model can thus be represented as a sequence of local approximations of the full model. We illustrate the method using as case study a biochemical model of the cell cycle.

Original language	English
Title of host publication	Computational Methods in Systems Biology - 20th International Conference, CMSB 2022, Proceedings
Editors	Ion Petre, Andrei Păun
Number of pages	25
Publisher	Springer
Publication date	2022
Pages	61-85
ISBN (Print)	9783031150333
DOIs	https://doi.org/10.1007/978-3-031-15034-0_4
Publication status	Published - 2022
Externally published	Yes
Event	20th International Conference on Computational Methods in Systems Biology, CMSB 2022 - Bucharest, Romania Duration: 14 Sept 2022 → 16 Sept 2022

Conference

Conference	20th International Conference on Computational Methods in Systems Biology, CMSB 2022
Country/Territory	Romania
City	Bucharest
Period	14/09/2022 → 16/09/2022

Series	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	13447 LNBI
ISSN	0302-9743

Bibliographical note

Publisher Copyright:
© 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Access to Document

10.1007/978-3-031-15034-0_4

https://arxiv.org/pdf/2205.07360.pdf

AUB Link

Search for the material in Aalborg University Library's search engine

Cite this

Desoeuvres, Aurélien ; Szmolyan, Peter ; Radulescu, Ovidiu. / Qualitative Dynamics of Chemical Reaction Networks : An Investigation Using Partial Tropical Equilibrations. Computational Methods in Systems Biology - 20th International Conference, CMSB 2022, Proceedings. editor / Ion Petre ; Andrei Păun. Springer, 2022. pp. 61-85 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 13447 LNBI).

@inproceedings{146380dac1244f6581dac1563e650aa5,

title = "Qualitative Dynamics of Chemical Reaction Networks: An Investigation Using Partial Tropical Equilibrations",

abstract = "We discuss a method to describe the qualitative dynamics of chemical reaction networks in terms of symbolic dynamics. The method, that can be applied to mass-action reaction networks with separated timescales, uses solutions of the partial tropical equilibration problem as proxies for symbolic states. The partial tropical equilibration solutions are found algorithmically. These solutions also provide the scaling needed for slow-fast decomposition and model reduction. Any trace of the model can thus be represented as a sequence of local approximations of the full model. We illustrate the method using as case study a biochemical model of the cell cycle.",

author = "Aur{\'e}lien Desoeuvres and Peter Szmolyan and Ovidiu Radulescu",

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.; 20th International Conference on Computational Methods in Systems Biology, CMSB 2022 ; Conference date: 14-09-2022 Through 16-09-2022",

year = "2022",

doi = "10.1007/978-3-031-15034-0_4",

language = "English",

isbn = "9783031150333",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

publisher = "Springer",

pages = "61--85",

editor = "Ion Petre and Andrei P{\u a}un",

booktitle = "Computational Methods in Systems Biology - 20th International Conference, CMSB 2022, Proceedings",

address = "Germany",

}

Desoeuvres, A, Szmolyan, P & Radulescu, O 2022, Qualitative Dynamics of Chemical Reaction Networks: An Investigation Using Partial Tropical Equilibrations. in I Petre & A Păun (eds), Computational Methods in Systems Biology - 20th International Conference, CMSB 2022, Proceedings. Springer, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 13447 LNBI, pp. 61-85, 20th International Conference on Computational Methods in Systems Biology, CMSB 2022, Bucharest, Romania, 14/09/2022. https://doi.org/10.1007/978-3-031-15034-0_4

Qualitative Dynamics of Chemical Reaction Networks: An Investigation Using Partial Tropical Equilibrations. / Desoeuvres, Aurélien; Szmolyan, Peter; Radulescu, Ovidiu.
Computational Methods in Systems Biology - 20th International Conference, CMSB 2022, Proceedings. ed. / Ion Petre; Andrei Păun. Springer, 2022. p. 61-85 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 13447 LNBI).

Research output: Contribution to book/anthology/report/conference proceeding › Article in proceeding › Research › peer-review

TY - GEN

T1 - Qualitative Dynamics of Chemical Reaction Networks

T2 - 20th International Conference on Computational Methods in Systems Biology, CMSB 2022

AU - Desoeuvres, Aurélien

AU - Szmolyan, Peter

AU - Radulescu, Ovidiu

PY - 2022

Y1 - 2022

N2 - We discuss a method to describe the qualitative dynamics of chemical reaction networks in terms of symbolic dynamics. The method, that can be applied to mass-action reaction networks with separated timescales, uses solutions of the partial tropical equilibration problem as proxies for symbolic states. The partial tropical equilibration solutions are found algorithmically. These solutions also provide the scaling needed for slow-fast decomposition and model reduction. Any trace of the model can thus be represented as a sequence of local approximations of the full model. We illustrate the method using as case study a biochemical model of the cell cycle.

AB - We discuss a method to describe the qualitative dynamics of chemical reaction networks in terms of symbolic dynamics. The method, that can be applied to mass-action reaction networks with separated timescales, uses solutions of the partial tropical equilibration problem as proxies for symbolic states. The partial tropical equilibration solutions are found algorithmically. These solutions also provide the scaling needed for slow-fast decomposition and model reduction. Any trace of the model can thus be represented as a sequence of local approximations of the full model. We illustrate the method using as case study a biochemical model of the cell cycle.

UR - http://www.scopus.com/inward/record.url?scp=85136925526&partnerID=8YFLogxK

U2 - 10.1007/978-3-031-15034-0_4

DO - 10.1007/978-3-031-15034-0_4

M3 - Article in proceeding

AN - SCOPUS:85136925526

SN - 9783031150333

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 61

EP - 85

BT - Computational Methods in Systems Biology - 20th International Conference, CMSB 2022, Proceedings

A2 - Petre, Ion

A2 - Păun, Andrei

PB - Springer

Y2 - 14 September 2022 through 16 September 2022

ER -

Desoeuvres A, Szmolyan P, Radulescu O. Qualitative Dynamics of Chemical Reaction Networks: An Investigation Using Partial Tropical Equilibrations. In Petre I, Păun A, editors, Computational Methods in Systems Biology - 20th International Conference, CMSB 2022, Proceedings. Springer. 2022. p. 61-85. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 13447 LNBI). doi: 10.1007/978-3-031-15034-0_4