Giri, Varun. “Modeling pre-biotic self-organization: The chemical dynamics of autocatalytic networks.” arXiv preprint arXiv:1304.0437 (2013).
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In this thesis we present a mathematical model describing the population dynamics of molecules in an artificial chemistry where large molecules can be produced by successive ligation of pairs of smaller molecules. The chemistry contains a large number of spontaneous reactions of which a small subset could be catalyzed by molecules produced in the chemistry with varying catalytic strengths. We show ACSs, if present in the catalytic network, can focus the resources of the system into a sparse set of molecules. ACSs can produce a bistability in the population dynamics and, in particular, steady states wherein the ACS molecules dominate the population, i.e., have higher concentrations compared to the rest of molecules in the chemistry (background). In this thesis we attempt to address two main questions: First, under what circumstances do molecules belonging to the ACSs dominate over the background, and second, starting from an initial condition that does not contain good catalysts, can a sparse set of large molecules (containing several tens or a few hundred monomers) that are good catalysts arise and be maintained in the system at concentrations significantly above the background? We show that if an ACS catalyzed by large molecules contains within it (or partially overlaps with) a smaller ACS catalyzed by smaller molecules (referred to as a `nested ACS’ structure), the catalytic strength required for the large ACS to dominate comes down significantly. We show that when the network contains a cascade of nested ACSs with the catalytic strengths of molecules increasing gradually with their size, a sparse subset of molecules including some very large molecules can come to dominate the system.