arnold2
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000384) Biomodels notes: The steady state concentrations of the metabolites involved are reproduced here. This is the reproduction of the Table S7 (referring Medlyn 2002) of the reference (supp. material) publication. The simulation was done using Copasi v4.7 (Build 34). JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.
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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 | |
|---|---|---|
| — | 0.001 mole |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| chloroplast | chloroplast | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| CO2 | CO2 | 245.0 | chloroplast (chloroplast) | ✔ | |
| NADP | NADP | 0.29 | chloroplast (chloroplast) | ✔ | |
| NADPH | NADPH | 0.21 | chloroplast (chloroplast) | ✘ | |
| O2 | O2 | 210.0 | chloroplast (chloroplast) | ✔ | |
| PGA | PGA | 2.4 | chloroplast (chloroplast) | ✘ | |
| RuBP | RuBP | 2.0 | chloroplast (chloroplast) | ✔ |
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 | |
|---|---|---|---|---|---|
| NADPH_prod | NADPH production | NADP > NADPH chloroplast * NADPH_production(J, NADP, Nt) | |||
| PGA_cons | PGA consumption | PGA > RuBP chloroplast * PGA_consumption(PGA, Rp, NADPH, Nt, Vcmax) | |||
| PGA_prod_Vc | PGA production - v_c | RuBP + CO2 + {2.0}NADPH > {2.0}PGA chloroplast * carboxylation(Vc, Vj) | |||
| PGA_prod_Vo | PGA production - v_o | RuBP + O2 + {2.0}NADPH > {1.5}PGA chloroplast * oxygenation(phi, Vc, Vj) |
| Id | Value | |
|---|---|---|
| Gamma | 42.8926627111176 | |
| J | 4.8582995951417 | |
| Kc | 406.066146391504 | |
| Ko | 276.900084789612 | |
| Nt | 0.5 | |
| Q | 1000.0 | |
| Rp | 3.2 | |
| Vc | 0.646926785453086 | |
| Vcmax | 2.53232284114507 | |
| Vj | 0.899589030506691 | |
| Vomax | 0.531787796640465 | |
| alpha | 0.3 | |
| phi | 0.263964911408408 | |
| teta | 0.9 |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| phi = 0.21 * (O2 / Ko) / (CO2 / Kc) | |
| Vomax = 0.21 * Vcmax | |
| NADP = Nt - NADPH | |
| Vc = Vcmax * CO2 / ((1.0 + O2 / Ko) * Kc + CO2) | |
| Vj = J / 4.0 * CO2 / (CO2 + 2.0 * Gamma) | |
| J = alpha * Q / (10.0 - 9.0 * teta) / (65.0 * 0.5) |
| Definition |
|---|
| Definition |
|---|
| Definition | |
|---|---|
| oxygenation(phi, Vc, Vj) = phi * (Vc + Vj - abs(Vc - Vj)) / 2 | |
| carboxylation(Vc, Vj) = (Vc + Vj - abs(Vc - Vj)) / 2 | |
| NADPH_production(j, S1, Nt) = j / 2 * (S1 / Nt) | |
| PGA_consumption(S1, Rp, R, Nt, Vc) = S1 / Rp * (R / Nt) * Vc |
| Trigger | Assignments |
|---|