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. 2014 Feb 21;42(8):4813–4822. doi: 10.1093/nar/gku159

Table 1.

Parameters used in simulation

Parameter Value Descriptions
Inline graphic 8 Initiation rate (s).
Inline graphic 0.1 Termination rate (s).
Inline graphic 0.5 The weight for Inline graphic.
Inline graphic 1.0 The weight for Inline graphic.
Inline graphic 0.12/Various Dwell time at a codon caused by codon usage (s). When investigating the function of mRNA secondary structure without considering the effect of codon usage, an equal rate for all codons is used (0.12). When investigating the combined effect of mRNA secondary structure and codon usage, the value of Inline graphic depends on codon’s tAI (various).
Inline graphic Various Dwell time at a codon caused by mRNA secondary structure (s). Various means that the value depends on the PP of the codon.
Inline graphic 42 The length of the region constrained by a ribosome (nt).
Inline graphic Constant Translocation time (s). Translocation time is equal to the running time that a ribosome moves from the current codon to the next.