Simulating replication with mutations under tuneable photocatalytic cofactor function

This is the mass-action chemical kinetics model used for the simulations in "Selection for Photocatalytic Function through Darwinian Evolution of Synthetic Self-Replicators". Ths model has been used to asses the possible effect of mutation rates vs. cofactor activation on the observed distribution of replicators.

The system is comprised of two types of monomeric buidling blocks (A and B), and for simplicity only considers the following trimers (food): A3, A1.5B1.5, and B3, and the following hexameric fibers (replicators): A6, A3B3, and B6. The model describes the dynamics of building blocks oxidation, and how hexameric fibers grow/elongate/replicate from the oxidized food that is bound to them. The model is based on mass-action chemical kinetics using ordinary differential equations, and simulated using MATLAB's ode15s function.

To simulate and plot Figure S123 please execute: out=FAMonomers5d(1e-1, 1e3, [2 1 1], [0.9 0.1 0; 0.2 0.6 0.2; 0 0.1 0.9], true);
Further details are given in the aforementioned manuscript, or from the author.

O.M. acknowledges support from the John Templeton Foundation (62828) and the Foundation for Science and Technology (2023.05971.CEECIND).