Stoichiometric Modelling of String Chemistries

Uncovering the general principles that govern the architecture of metabolic networks is key to understanding the emergence and evolution of living systems. Artificial chemistries, in silico representations of chemical reaction networks arising from a defined set of mathematical rules, can help address this challenge by enabling the exploration of alternative chemical universes and the possible metabolic networks that could emerge within them. Here we focus on artificial chemistries in which strings of characters represent simplified molecules, and string concatenation and splitting represent possible chemical reactions. We study string chemistries using tools borrowed from the field of stoichiometric constraint-based modeling of organismal metabolic networks, through a novel Python package, ARtificial CHemistry NEtwork Toolbox (ARCHNET). In addition to exploring the complexity and connectivity properties of different string chemistries, we developed a network-pruning algorithm that can generate minimal metabolic networks capable of producing a specified set of biomass precursors from a given assortment of environmental molecules within the string chemistry framework. We found that the identities of the metabolites in the biomass reaction wield much more influence over the structure of the minimal metabolic networks than the identities of the nutrient metabolites -- a notion that could help us better understand the rise and evolution of biochemical organization. Our work provides a bridge between artificial chemistries and stoichiometric modeling, which can help address a broad range of open questions, from the spontaneous emergence of an organized metabolism to the structure of microbial communities.