Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.
| Name | Definition | |
|---|---|---|
| — | 1e-09 mole | |
| — | 3600.0 second |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| Cell | cytoplasm | 3.0 | 1.0 | |
| compartment_0000002 | nucleus | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| CC | Cytosolic PER-TIM Complex | 0.0 | Cell (cytoplasm) | ✘ | |
| Cn | Nuclear PER-TIM Complex | 0.0 | compartment_0000002 (nucleus) | ✘ |
|
| Mp | PER mRNA | 0.0 | Cell (cytoplasm) | ✘ |
|
| Mt | TIM mRNA | 0.0 | Cell (cytoplasm) | ✘ |
|
| P0 | PER Protein (unphosphorylated) | 0.0 | Cell (cytoplasm) | ✘ |
|
| P1 | PER Protein (mono-phosphorylated) | 0.0 | Cell (cytoplasm) | ✘ |
|
| P2 | PER Protein (bi-phosphorylated) | 0.0 | Cell (cytoplasm) | ✘ |
|
| T0 | TIM Protein (unphosphorylated) | 0.0 | Cell (cytoplasm) | ✘ |
|
| T1 | TIM Protein (mono-phosphorylated) | 0.0 | Cell (cytoplasm) | ✘ |
|
| T2 | TIM Protein (bi-phosphorylated) | 0.0 | Cell (cytoplasm) | ✘ |
|
Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.
| Definition |
|---|
| Id | Name | Objective coefficient | Reaction Equation and Kinetic Law | Flux bounds | |
|---|---|---|---|---|---|
| Mp_degradation | PER mRNA degradation | Mp > ∅ Cell * k_d * Mp + Cell * V_mP * Mp / (K_mP + Mp) |
|
||
| Mp_production | PER mRNA production | ∅ > Mp Cell * v_sP * pow(K_IP, n) / (pow(K_IP, n) + pow(Cn, n)) |
|
||
| Mt_degradation | TIM mRNA degradation | Mt > ∅ Cell * k_d * Mt + Cell * V_mT * Mt / (K_mT + Mt) |
|
||
| Mt_production | TIM mRNA production | ∅ > Mt Cell * V_sT * pow(K_IT, n) / (pow(K_IT, n) + pow(Cn, n)) |
|
||
| P0_degradation | PER degradation | P0 > ∅ Cell * k_d * P0 |
|
||
| P0_production | PER production | ∅ > P0 Cell * k_sP * Mp |
|
||
| P0_to_P1 | First Phosphorylation of PER | P0 > P1 Cell * V_1P * P0 / (K1_P + P0) |
|
||
| P1_degradation | PER-1 degradation | P1 > ∅ Cell * k_d * P1 |
|
||
| P1_to_P0 | Dephosphorylation of PER (1st P) | P1 > P0 Cell * V_2P * P1 / (K_2P + P1) |
|
||
| P1_to_P2 | Second Phosphorylation of PER | P1 > P2 Cell * V_3P * P1 / (K_3P + P1) |
|
||
| P2_degradation | PER-2 degradation | P2 > ∅ Cell * k_d * P2 + Cell * V_dP * P2 / (K_dP + P2) |
|
||
| P2_to_P1 | Dephosphorylation of PER (2nd P) | P2 > P1 Cell * V_4P * P2 / (K_4P + P2) |
|
||
| PT_complex_degradation | PER-TIM complex degradation (cytosol) | CC > ∅ Cell * k_dC * CC |
|
||
| PT_complex_formation | PER-TIM complex formation | P2 + T2 = CC Cell * k3 * P2 * T2 - Cell * k4 * CC |
|
||
| PT_complex_nucleation | PER-TIM complex nucleation | CC = Cn Cell * k1 * CC - compartment_0000002 * k2 * Cn |
|
||
| PTnucl_complex_degradation | PER-TIM complex degradation (nuclear) | Cn > ∅ compartment_0000002 * k_dN * Cn |
|
||
| T0_degradation | TIM degradation | T0 > ∅ Cell * k_d * T0 |
|
||
| T0_production | TIM production | ∅ > T0 Cell * k_sT * Mt |
|
||
| T0_to_T1 | First Phosphorylation of TIM | T0 > T1 Cell * V_1T * T0 / (K_1T + T0) |
|
||
| T1_degradation | TIM-1 degradation | T1 > ∅ Cell * k_d * T1 |
|
||
| T1_to_T0 | Dephosphorylation of TIM (1st P) | T1 > T0 Cell * V_2T * T1 / (K_2T + T1) |
|
||
| T1_to_T2 | Second Phosphorylation of TIM | T1 > T2 Cell * V_3T * T1 / (K_3T + T1) |
|
||
| T2_degradation | TIM-2 degradation | T2 > ∅ Cell * k_d * T2 + Cell * V_dT * T2 / (K_dT + T2) |
|
||
| T2_to_T1 | Dephosphorylation of TIM (2nd P) | T2 > T1 Cell * V_4T * T2 / (K_4T + T2) |
|
| Id | Value | |
|---|---|---|
| Pt | 0.0 |
|
| Tt | 0.0 |
|
| V_dT | 2.0 |
|
| V_mT | 0.7 |
|
| Id | Value | Reaction | |
|---|---|---|---|
| k_d | 0.01 | Mp_degradation (PER mRNA degradation) |
|
| V_mP | 0.7 | Mp_degradation (PER mRNA degradation) |
|
| K_mP | 0.2 | Mp_degradation (PER mRNA degradation) |
|
| v_sP | 1.0 | Mp_production (PER mRNA production) |
|
| K_IP | 1.0 | Mp_production (PER mRNA production) |
|
| n | 4.0 | Mp_production (PER mRNA production) |
|
| k_d | 0.01 | Mt_degradation (TIM mRNA degradation) |
|
| K_mT | 0.2 | Mt_degradation (TIM mRNA degradation) |
|
| V_sT | 1.0 | Mt_production (TIM mRNA production) |
|
| K_IT | 1.0 | Mt_production (TIM mRNA production) |
|
| n | 4.0 | Mt_production (TIM mRNA production) |
|
| k_d | 0.01 | P0_degradation (PER degradation) |
|
| k_sP | 0.9 | P0_production (PER production) |
|
| K1_P | 2.0 | P0_to_P1 (First Phosphorylation of PER) |
|
| V_1P | 8.0 | P0_to_P1 (First Phosphorylation of PER) |
|
| k_d | 0.01 | P1_degradation (PER-1 degradation) |
|
| K_2P | 2.0 | P1_to_P0 (Dephosphorylation of PER (1st P)) |
|
| V_2P | 1.0 | P1_to_P0 (Dephosphorylation of PER (1st P)) |
|
| K_3P | 2.0 | P1_to_P2 (Second Phosphorylation of PER) |
|
| V_3P | 8.0 | P1_to_P2 (Second Phosphorylation of PER) |
|
| k_d | 0.01 | P2_degradation (PER-2 degradation) |
|
| V_dP | 2.0 | P2_degradation (PER-2 degradation) |
|
| K_dP | 0.2 | P2_degradation (PER-2 degradation) |
|
| K_4P | 2.0 | P2_to_P1 (Dephosphorylation of PER (2nd P)) |
|
| V_4P | 1.0 | P2_to_P1 (Dephosphorylation of PER (2nd P)) |
|
| k_dC | 0.01 | PT_complex_degradation (PER-TIM complex degradation (cytosol)) |
|
| k3 | 1.2 | PT_complex_formation (PER-TIM complex formation) |
|
| k4 | 0.6 | PT_complex_formation (PER-TIM complex formation) |
|
| k1 | 0.6 | PT_complex_nucleation (PER-TIM complex nucleation) |
|
| k2 | 0.2 | PT_complex_nucleation (PER-TIM complex nucleation) |
|
| k_dN | 0.01 | PTnucl_complex_degradation (PER-TIM complex degradation (nuclear)) |
|
| k_d | 0.01 | T0_degradation (TIM degradation) |
|
| k_sT | 0.9 | T0_production (TIM production) |
|
| K_1T | 2.0 | T0_to_T1 (First Phosphorylation of TIM) |
|
| V_1T | 8.0 | T0_to_T1 (First Phosphorylation of TIM) |
|
| k_d | 0.01 | T1_degradation (TIM-1 degradation) |
|
| K_2T | 2.0 | T1_to_T0 (Dephosphorylation of TIM (1st P)) |
|
| V_2T | 1.0 | T1_to_T0 (Dephosphorylation of TIM (1st P)) |
|
| K_3T | 2.0 | T1_to_T2 (Second Phosphorylation of TIM) |
|
| V_3T | 8.0 | T1_to_T2 (Second Phosphorylation of TIM) |
|
| k_d | 0.01 | T2_degradation (TIM-2 degradation) |
|
| K_dT | 0.2 | T2_degradation (TIM-2 degradation) |
|
| K_4T | 2.0 | T2_to_T1 (Dephosphorylation of TIM (2nd P)) |
|
| V_4T | 1.0 | T2_to_T1 (Dephosphorylation of TIM (2nd P)) |
|
| Definition | |
|---|---|
| Tt = CC + Cn + T0 + T1 + T2 |
|
| Pt = CC + Cn + P0 + P1 + P2 |
|
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Trigger | Assignments |
|---|