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arnold1

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arnold1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000383) 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 230.0 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 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, Nt, kc, Epar, NADPH)
PGA_prod_Vc PGA production - v_c RuBP + CO2 + {2.0}NADPH > {2.0}PGA

chloroplast * carboxylation(kc, CO2, Kc, O2, Ko, Epar, RuBP)
PGA_prod_Vo PGA production - v_o {2.0}NADPH + RuBP + CO2 > {1.5}PGA

chloroplast * oxygenation(phi, kc, CO2, Kc, O2, Ko, Epar, RuBP)

Parameters 0   11

Global parameters

Id Value
Epar 1.33846153846
Ipar 1000.0
Kc 460.0
Ko 330.0
Nt 0.5
Rp 3.2
f 0.23
j 5.92307692308
jp 385.0
kc 2.5
phi 0.267272727273

Local parameters

Id Value Reaction

Rules 0   0   4

Assignment rules

Definition
NADP = Nt - NADPH
jp = 1.0 / 2.0 * (1.0 - f) * Ipar
phi = 0.21 * (O2 / Ko) / (CO2 / Kc)
j = (abs(jp + 467.0) - abs(jp - 467.0)) / 2.0 / 65.0

Rate rules

Definition

Algebraic rules

Definition

Function definitions 4

Definition
oxygenation(phi, kc, S2, K, R, KI, Epar, S1) = phi * (kc * S2 / (S2 + K * (1 + R / KI)) * Epar + kc * S2 / (S2 + K * (1 + R / KI)) * S1 - abs(kc * S2 / (S2 + K * (1 + R / KI)) * Epar - kc * S2 / (S2 + K * (1 + R / KI)) * S1)) / 2
PGA_consumption(S1, Rp, Nt, kc, Epar, R) = S1 / Rp * (R / Nt) * kc * Epar
carboxylation(kc, S2, K, R, KI, Epar, S1) = (kc * S2 / (S2 + K * (1 + R / KI)) * Epar + kc * S2 / (S2 + K * (1 + R / KI)) * S1 - abs(kc * S2 / (S2 + K * (1 + R / KI)) * Epar - kc * S2 / (S2 + K * (1 + R / KI)) * S1)) / 2
NADPH_production(j, S1, Nt) = j / 2 * (S1 / Nt)

Events 0

Trigger Assignments