Overview of the whole cell translation model.

Schematic visualization of the simulated elements at the cell level (A), at the mRNA level (B) and a simplified view of the state machines at the codon level (C), for initiation and elongation (the detailed state machines appear in F-G Figs in S1 File). At the cell level, a transcriptome of mRNA molecules with a finite pool of ribosomes and tRNAs is simulated, leading to a competition for these resources. At the mRNA level, we utilized a novel generalized deterministic TASEP model that incorporates both accurate dynamics at the codon level and dependence on cellular resources, which influences these dynamics. On the codon level, for each codon the dynamics are dictated by a state machine, an object that holds the state (e.g. “this codon is anticipating a tRNA”) and the rules of state transition order and conditions (see sub-section Generalized deterministic TASEP and state machines).