On the Existence of Synergies and the Separability of Closed Reaction Networks

Tomas Veloz; Alejandro Bassi; Pedro Maldonado; Pablo Razeto

doi:10.1007/978-3-030-19432-1_7

On the Existence of Synergies and the Separability of Closed Reaction Networks

Tomas Veloz, Alejandro Bassi, Pedro Maldonado, Pablo Razeto

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › Research

4 Citations (Scopus)

Abstract

It is well known that closure is a necessary topological property for a reaction network to be dynamically stable. In this work we combine notions of chemical organization theory with structural properties of reaction networks to distill a minimal set of closed reaction networks that encodes the non-trivial stable dynamical regimes of the network. In particular, these non-trivial closed sets are synergetic, in the sense that their dynamics cannot always be computed from the dynamics of its closed constituents. We introduce a notion of separability for reaction networks and prove that it is strictly related to the notion of synergy. In particular, we provide a characterization of the non-trivial closed reaction networks by means of their degree of internal synergy. The less trivial the dynamics of the reaction network, the less can be separated into constituents, and equivalently the more synergies the reaction network has. We also discuss the computational and analytical benefits of this new representation of the dynamical structure of a reaction network.

Original language	English
Title of host publication	Molecular Logic and Computational Synthetic Biology - 1st International Symposium, MLCSB 2018, Revised Selected Papers
Editors	Manuel A. Martins, Madalena Chaves
Publisher	Springer Verlag
Pages	105-120
Number of pages <span style="color:red"p> <font size="1.5"> ✽ </span> </font>	16
ISBN (Print)	9783030194314
DOIs	https://doi.org/10.1007/978-3-030-19432-1_7
Publication status	Published - 1 Jan 2019
Event	1st International Symposium on Molecular Logic and Computational Synthetic Biology, MLCSB 2018 - Santiago, Chile Duration: 17 Dec 2018 → 18 Dec 2018

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	11415 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	1st International Symposium on Molecular Logic and Computational Synthetic Biology, MLCSB 2018
Country/Territory	Chile
City	Santiago
Period	17/12/18 → 18/12/18

Keywords

Chemical organization theory
Closure
Reaction networks
Self-organization
Separability
Synergy

Access to Document

10.1007/978-3-030-19432-1_7

Cite this

Veloz, T., Bassi, A., Maldonado, P., & Razeto, P. (2019). On the Existence of Synergies and the Separability of Closed Reaction Networks. In M. A. Martins, & M. Chaves (Eds.), Molecular Logic and Computational Synthetic Biology - 1st International Symposium, MLCSB 2018, Revised Selected Papers (pp. 105-120). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11415 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-030-19432-1_7

Veloz, Tomas ; Bassi, Alejandro ; Maldonado, Pedro ; Razeto, Pablo. / On the Existence of Synergies and the Separability of Closed Reaction Networks. Molecular Logic and Computational Synthetic Biology - 1st International Symposium, MLCSB 2018, Revised Selected Papers. editor / Manuel A. Martins ; Madalena Chaves. Springer Verlag, 2019. pp. 105-120 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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Veloz, T, Bassi, A, Maldonado, P & Razeto, P 2019, On the Existence of Synergies and the Separability of Closed Reaction Networks. in MA Martins & M Chaves (eds), Molecular Logic and Computational Synthetic Biology - 1st International Symposium, MLCSB 2018, Revised Selected Papers. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 11415 LNCS, Springer Verlag, pp. 105-120, 1st International Symposium on Molecular Logic and Computational Synthetic Biology, MLCSB 2018, Santiago, Chile, 17/12/18. https://doi.org/10.1007/978-3-030-19432-1_7

On the Existence of Synergies and the Separability of Closed Reaction Networks. / Veloz, Tomas; Bassi, Alejandro; Maldonado, Pedro; Razeto, Pablo.

Molecular Logic and Computational Synthetic Biology - 1st International Symposium, MLCSB 2018, Revised Selected Papers. ed. / Manuel A. Martins; Madalena Chaves. Springer Verlag, 2019. p. 105-120 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11415 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › Research

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AU - Veloz, Tomas

AU - Bassi, Alejandro

AU - Maldonado, Pedro

AU - Razeto, Pablo

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N2 - It is well known that closure is a necessary topological property for a reaction network to be dynamically stable. In this work we combine notions of chemical organization theory with structural properties of reaction networks to distill a minimal set of closed reaction networks that encodes the non-trivial stable dynamical regimes of the network. In particular, these non-trivial closed sets are synergetic, in the sense that their dynamics cannot always be computed from the dynamics of its closed constituents. We introduce a notion of separability for reaction networks and prove that it is strictly related to the notion of synergy. In particular, we provide a characterization of the non-trivial closed reaction networks by means of their degree of internal synergy. The less trivial the dynamics of the reaction network, the less can be separated into constituents, and equivalently the more synergies the reaction network has. We also discuss the computational and analytical benefits of this new representation of the dynamical structure of a reaction network.

AB - It is well known that closure is a necessary topological property for a reaction network to be dynamically stable. In this work we combine notions of chemical organization theory with structural properties of reaction networks to distill a minimal set of closed reaction networks that encodes the non-trivial stable dynamical regimes of the network. In particular, these non-trivial closed sets are synergetic, in the sense that their dynamics cannot always be computed from the dynamics of its closed constituents. We introduce a notion of separability for reaction networks and prove that it is strictly related to the notion of synergy. In particular, we provide a characterization of the non-trivial closed reaction networks by means of their degree of internal synergy. The less trivial the dynamics of the reaction network, the less can be separated into constituents, and equivalently the more synergies the reaction network has. We also discuss the computational and analytical benefits of this new representation of the dynamical structure of a reaction network.

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

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Y2 - 17 December 2018 through 18 December 2018

ER -

Veloz T, Bassi A, Maldonado P, Razeto P. On the Existence of Synergies and the Separability of Closed Reaction Networks. In Martins MA, Chaves M, editors, Molecular Logic and Computational Synthetic Biology - 1st International Symposium, MLCSB 2018, Revised Selected Papers. Springer Verlag. 2019. p. 105-120. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-030-19432-1_7

On the Existence of Synergies and the Separability of Closed Reaction Networks

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1st International Symposium on Molecular Logic and Computational Synthetic Biology, MLCSB 2018

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On the Existence of Synergies and the Separability of Closed Reaction Networks

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Keywords

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1st International Symposium on Molecular Logic and Computational Synthetic Biology, MLCSB 2018

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