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arnold2

arnold2

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NADPH_prod

NADPH production

NADP > NADPH

PGA_cons

PGA consumption

PGA > RuBP

PGA_prod_Vc

PGA production - v_c

RuBP + CO2 + {2.0}NADPH > {2.0}PGA

PGA_prod_Vo

PGA production - v_o

RuBP + O2 + {2.0}NADPH > {1.5}PGA

Parameters

Global parameters

Fixed species

Initial values

Functions and Rules

Assignment rules

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)

Function definitions

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

Events

Constraints

Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.


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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.
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.