| | Name | Initial Conc. (uM) | Volume (fL) | Buffered |
| 1 | AAs | 0 | 0.99997 | Yes |
| | |
| 2 | elRIB | 0 | 0.99997 | No |
| | Ribosome elongating protein chain. |
| 3 | ElRNAP | 0 | 0.99997 | No |
| | Polymerase elongating a given mRNA molecule. Kierzek et al assume that the RNA polymerase completes synthesis of the mRNA molecule with a rate sufficient to allow for a ribosome movement rate of 15 amino acids/sec. They do not explicitly model the elongation of mRNA. |
| 4 | nucleotides | 0 | 0.99997 | Yes |
| | |
| 5 | P | 0.0017 | 0.99997 | No |
| | The promoter region of the gene. Assume just one gene and a single promoter on it. |
| 6 | Protein | 0 | 0.99997 | No |
| | |
| 7 | P_RNAP | 0 | 0.99997 | No |
| | |
| 8 | RBS | 0 | 0.99997 | No |
| | Ribosome binding site. Kierzek et al say: Based on Yarchuk et al 1992 J Mol Biol 226:581-596 we have assumed the following interdependence between translation and mRNA decay: (i) RNase E and ribosomes compete for the RBS (ii) if RNase E binds to the RBS faster than the ribosome, it degrades mRNA in the 5prime to 3prime direction and does not interfere with the movement of the ribosomes that have been already bound; and (iii) Every ribosome that successfully binds to the RBS completes translation of the protein. |
| 9 | Ribosome | 0.5834 | 0.99997 | Yes |
| | Ribosome pool The language in the paper is a little ambiguous, but from simulation it turns out that they assume that the number of free ribosomes is held fixed at 350. In other words, buffered. |
| 10 | RibRBS | 0 | 0.99997 | No |
| | This is the ribosome binding site protected by the bound ribosome. |
| 11 | RNAP | 0.0583 | 0.99997 | Yes |
| | RNA Polymerase. Kierzek et al assume mean 35 and delta = 3.5 molecules. Turns out they assume that this is buffered. |
| 12 | TrRNAP | 0 | 0.99997 | No |
| | This is the Transcribing RNA Polymerase. |
