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arnold4

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arnold4

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000386) Biomodels notes: The steady state concentration of the metabolites involved are reproduced here. This is the reproduction of the Table S7 (referring Sharkey 2007) 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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Manuscript information

A quantitative comparison of Calvin-Benson cycle models.

  • Anne Arnold
  • Zoran Nikoloski
Trends Plant Sci. 2011; 16 (12): 676-683
Abstract
The Calvin-Benson cycle (CBC) provides the precursors for biomass synthesis necessary for plant growth. The dynamic behavior and yield of the CBC depend on the environmental conditions and regulation of the cellular state. Accurate quantitative models hold the promise of identifying the key determinants of the tightly regulated CBC function and their effects on the responses in future climates. We provide an integrative analysis of the largest compendium of existing models for photosynthetic processes. Based on the proposed ranking, our framework facilitates the discovery of best-performing models with regard to metabolomics data and of candidates for metabolic engineering.

Unit definitions 1

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

Compartments 1

Id Name Spatial dimensions Size
chloroplast chloroplast 3.0 1.0

Species 6

Id Name Initial quantity Compartment Fixed
CO2 CO2 24.5 chloroplast (chloroplast) ✔
NADP NADP 0.29 chloroplast (chloroplast) ✔
NADPH NADPH 0.21 chloroplast (chloroplast) ✘
O2 O2 21.0 chloroplast (chloroplast) ✔
PGA PGA 2.4 chloroplast (chloroplast) ✘
RuBP RuBP 2.0 chloroplast (chloroplast) ✔

Initial assignments 0

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
Reactions 4
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, Vp)
PGA_prod_Vo PGA production - v_o RuBP + O2 + {2.0}NADPH > {1.5}PGA

chloroplast * oxygenation(phi, Vc, Vj, Vp)

Parameters 0   15

Global parameters

Id Value
Gamma 3.74116898182615
J 0.0307678189755062
Kc 27.2372124161502
Ko 16.5788431231261
Nt 0.5
Rd 0.0307674936008629
Rp 3.2
TPU 0.0307585098788555
Vc 0.00892944491541968
Vcmax 0.0307602623029146
Vj 0.00593820961819415
Vp 0.110677228404984
gm 0.0307740792044142
phi 0.286292104000314
v_c 0.00593820961819415

Local parameters

Id Value Reaction

Rules 0   0   6

Assignment rules

Definition
phi = 0.21 * (gm * O2 / Ko) / ((gm * CO2 - v_c + Rd) / Kc)
v_c = (abs((abs(Vc + Vj) - abs(Vc - Vj)) / 2.0 + Vp) - abs((abs(Vc + Vj) - abs(Vc - Vj)) / 2.0 - Vp)) / 2.0
Vc = Vcmax * (CO2 - 1.0 / 2.0 * (CO2 + Kc * (1.0 + O2 / Ko) + (Vcmax - Rd) / gm - sqrt(pow(CO2 + Kc * (1.0 + O2 / Ko) + (Vcmax - Rd) / gm, 2.0) + 4.0 / gm * (Rd * (CO2 + Kc * (1.0 + O2 / Ko)) + Vcmax * (Gamma - CO2))))) / (CO2 - 1.0 / 2.0 * (CO2 + Kc * (1.0 + O2 / Ko) + (Vcmax - Rd) / gm - sqrt(pow(CO2 + Kc * (1.0 + O2 / Ko) + (Vcmax - Rd) / gm, 2.0) + 4.0 / gm * (Rd * (CO2 + Kc * (1.0 + O2 / Ko)) + Vcmax * (Gamma - CO2)))) + Kc * (1.0 + O2 / Ko))
Vp = 3.0 * TPU * ((CO2 - (3.0 * TPU - Rd) / gm) / (CO2 - (3.0 * TPU - Rd) / gm - Gamma))
NADP = Nt - NADPH
Vj = J / 4.0 * (CO2 - 1.0 / 2.0 * (CO2 + 2.0 * Gamma + (J - 4.0 * Rd) / (4.0 * gm) - sqrt(pow(CO2 + 2.0 * Gamma + (J - 4.0 * Rd) / (4.0 * gm), 2.0) + 4.0 / gm * (Rd * (CO2 + 2.0 * Gamma) + J / 4.0 * (Gamma - CO2))))) / (CO2 - 1.0 / 2.0 * (CO2 + 2.0 * Gamma + (J - 4.0 * Rd) / (4.0 * gm) - sqrt(pow(CO2 + 2.0 * Gamma + (J - 4.0 * Rd) / (4.0 * gm), 2.0) + 4.0 / gm * (Rd * (CO2 + 2.0 * Gamma) + J / 4.0 * (Gamma - CO2)))) + 2.0 * Gamma)

Rate rules

Definition

Algebraic rules

Definition

Function definitions 4

Definition
oxygenation(phi, Vc, Vj, Vp) = phi * ((Vc + Vj - abs(Vc - Vj)) / 2 + Vp - abs((Vc + Vj - abs(Vc - Vj)) / 2 - Vp)) / 2
PGA_consumption(S1, Rp, R, Nt, Vc) = S1 / Rp * (R / Nt) * Vc
NADPH_production(j, S1, Nt) = j / 2 * (S1 / Nt)
carboxylation(Vc, Vj, Vp) = ((Vc + Vj - abs(Vc - Vj)) / 2 + Vp - abs((Vc + Vj - abs(Vc - Vj)) / 2 - Vp)) / 2

Events 0

Trigger Assignments