Kauffman Model with spatially separated ligation and cleavage reactions

Schneider, Johannes Josef, Hotz, Peter Eggenberger, Jamieson, William David ORCID: https://orcid.org/0000-0001-8260-5211, Faggian, Alessia, Li, Jin ORCID: https://orcid.org/0000-0002-4672-6806, Matuttis, Hans-Georg, Caliari, Adriano, Weyland, Mathias Sebastian, Flumini, Dandolo, Diaz, Aitor Patino, Holler, Silvia, Casiraghi, Federica, Sanahuja, Lorena Cebolla, Hanczyc, Martin Michael, Barrow, David ORCID: https://orcid.org/0000-0003-2096-7262, Dimitriou, Pantelitsa, Castell, Oliver ORCID: https://orcid.org/0000-0002-6059-8062 and Fuchslin, Rudolf Marcel 2024. Kauffman Model with spatially separated ligation and cleavage reactions. Presented at: Italian Workshop on Artificial Life and Evolutionary Computation, Venice, 6-8 September 2023. Published in: Villani, M., Cagnoni, S. and Serra, R. eds. Artificial Life and Evolutionary Computation. WIVACE 2023. Communications in Computer and Information Science , vol.1977 Cham, Switzerland: Springer, pp. 141-160. 10.1007/978-3-031-57430-6_12

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Abstract

One of the open questions regarding the origin of life is the problem how macromolecules could be created. One possible answer is the existence of autocatalytic sets in which some macromolecules mutually catalyze each other’s formation. This mechanism is theoretically described in the Kauffman model. We introduce and simulate an extension of the Kauffman model, in which ligation and cleavage reactions are spatially separated in different containers connected by diffusion, and provide computational results for instances with and without autocatalytic sets, focusing on the time evolution of the densities of the various molecules. Furthermore, we study the rich behavior of a randomly generated instance containing an autocatalytic metabolism, in which molecules are created by ligation processes and destroyed by cleavage processes and vice versa or generated and destroyed both by ligation processes.

Item Type:	Conference or Workshop Item (Paper)
Date Type:	Published Online
Status:	Published
Schools:	Engineering Pharmacy
Publisher:	Springer
ISBN:	978-3-031-57429-0
Date of First Compliant Deposit:	29 March 2024
Date of Acceptance:	30 March 2024
Last Modified:	08 Apr 2024 13:38
URI:	https://orca.cardiff.ac.uk/id/eprint/167628

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