| | Name | Initial Conc. (uM) | Volume (fL) | Buffered |
| 1 | inactiveRas-MKKK | 0 | 0.0016667 | No |
| | This is the inactive form of Ras-MKKK. Based on the reaction scheme from Kholodenko 2000, this is equivalent to a binding of the MAPK-PP to the Ras. The amount of Ras in the model is small enough that negligible amounts of MAPK are involved in this reaction. So it is a fair approximation to the negative feedback mechanism from Kholodenko, 2000. |
| 2 | int1 | 0.001 | 0.0016667 | No |
| | This is the intermediate enzyme which catalyses the dephosphorylation of MKKK-P to MKKK. The concentration is set to 1 nM based on from Kholodenko, 2000 |
| 3 | int2 | 0.001 | 0.0016667 | No |
| | This intermediate enzyme which catalyses the dephosphorylation of MKK-PP to MKK-P. The concentration is 1nM. from Kholodenko, 2000 |
| 4 | int3 | 0.001 | 0.0016667 | No |
| | This intermediate enzyme catalyses the dephosphorylation of MKK-P to MKK. The concentration is 1nM from Kholodenko, 2000 |
| 5 | int4 | 0.001 | 0.0016667 | No |
| | This intermediate enzyme catalyses the dephosphorylation of MAPK-PP to MAPK-P. The concentration is 1nM. from Kholodenko, 2000 |
| 6 | int5 | 0.001 | 0.0016667 | No |
| | This catalyses the conversion of MAPK-P to MAPK. The concenration is 1nM. from Kholodenko, 2000 |
| 7 | MAPK | 0.3 | 0.0016667 | No |
| | The total concn. of MAPK is 300nM from Kholodenko, 2000. |
| 8 | MAPK-P | 0 | 0.0016667 | No |
| | This is the single phopshorylated form of MAPK from Kholodenko, 2000. |
| 9 | MAPK-PP | 0 | 0.0016667 | No |
| | This is the double phosphorylated and active form of MAPK. from Kholodenko, 2000. |
| 10 | MKK | 0.3 | 0.0016667 | No |
| | The total concn. of MKK is 300nM from Kholodenko,2000 |
| 11 | MKK-P | 0 | 0.0016667 | No |
| | This is the single phoshorylated form of MKK. from Kholodenko, 2000. |
| 12 | MKK-PP | 0 | 0.0016667 | No |
| | This is the double phosphorylated and active form of MKK from Kholodenko, 2000 |
| 13 | MKKK | 0.1 | 0.0016667 | No |
| | The total concn. of MKKK is 100nM from Kholodenko, 2000 |
| 14 | MKKK-P | 0 | 0.0016667 | No |
| | This is the phosphorylated form of MKKK which converts MKK to MKK-P and then to MKK-PP from Kholodenko, 2000. |
| 15 | Ras-MKKKK | 0.001 | 0.0016667 | No |
| | The concn. of Ras-MKKKK* is set to 1 nM implicitly from Kholodenko, 2000 |
