Table 1 Example of dynamics
From: A stochastic model of the emergence of autocatalytic cycles
1. Initialisation | 1.1: Both the virtual and the actual ring disks are initialised according to the chosen parameters | |
|---|---|---|
1.2: In accordance with the independent reaction probability p all reactions and catalysis are instantiated | ||
2. Dynamics | 2.1: Following the Gillespie algorithm, a reaction between all the possible ones, according to the concentrations of substrates, catalysts and reaction rates, is selected and the physical time interval Δt between two successive reactions is computed and added to the overall time T | |
2.2: In accordance with the reaction selected | a) Cleavage → Two products are created and one substrate is removed. | |
b) Complex Formation → One molecular complex is created, one substrate and one catalyst are temporarily removed. | ||
c) Complex dissociation → The complex is removed, substrate and catalyst come to be available. | ||
d) Final Condensation → A complex binds the second substrate. Both the complex and the second substrate are removed, the catalyst returns available and the product is created. | ||
2.3: If new species have been created, they are evaluated. If they are completely new, they are added to the system and all the reactions and catalysis involving them are instantiated (according to p), otherwise the total number of the species is updated. | ||
2.3: Eventually, according to the time interval Δt, the influx and out flux rates, molecules are fed/removed into/from the system. | ||
2.3: Return to step 2.1 | ||