Kauffman Model with Spatially Separated Ligation and Cleavage Reactions

• Published in: Artificial Life and Evolutionary Computation pp. 141 - 160
• Main Authors: Schneider, Johannes Josef, Eggenberger Hotz, Peter, Jamieson, William David, Faggian, Alessia, Li, Jin, Matuttis, Hans-Georg, Caliari, Adriano, Weyland, Mathias Sebastian, Flumini, Dandolo, Diaz, Aitor Patiño, Holler, Silvia, Casiraghi, Federica, Cebolla Sanahuja, Lorena, Hanczyc, Martin Michael, Barrow, David Anthony, Dimitriou, Pantelitsa, Castell, Oliver, Füchslin, Rudolf Marcel
• Format: Book Chapter
• Language: English
• Published: Cham Springer Nature Switzerland 2024
• Series: Communications in Computer and Information Science
• Subjects: autocatalytic set; chemical evolution; Fick diffusion; Kauffman model; origin of life
• ISBN: 303157429X; 9783031574290
• ISSN: 1865-0929; 1865-0937
• DOI: 10.1007/978-3-031-57430-6_12

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.