Extension of a biochemical model for the generalized stoichiometry of electron transport limited C<sub>3</sub> photosynthesis

Yin, Xinyou; Oijen, Marcel van; Schapendonk, A.H.C.M.

doi:10.1111/j.1365-3040.2004.01224.x

Cited by 84 publications

(127 citation statements)

References 38 publications

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“…A recent analytical development of this model integrated the alternative and cyclic pathways of electron transport (Yin et al 2004), creating a tool for the determination of these rates from the measured quantum yield of photosynthesis (Yin et al 2006).…”

Section: Introductionmentioning

confidence: 99%

C3 photosynthesis in silico

2006

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A computer model comprising light reactions, electron-proton transport, enzymatic reactions, and regulatory functions of C3 photosynthesis has been developed as a system of differential budget equations for intermediate compounds. The emphasis is on electron transport through PSII and PSI and on the modeling of Chl fluorescence and 810 nm absorptance signals. Non-photochemical quenching of PSII excitation is controlled by lumenal pH. Alternative electron transport is modeled as the Mehler type O2 reduction plus the malate-oxaloacetate shuttle based on the chloroplast malate dehydrogenase. Carbon reduction enzymes are redox-controlled by the ferredoxin-thioredoxin system, sucrose synthesis is controlled by the fructose 2,6-bisphosphate inhibition of cytosolic FBPase, and starch synthesis is controlled by ADP-glucose pyrophosphorylase. Photorespiratory glycolate pathway is included in an integrated way, sufficient to reproduce steady-state rates of photorespiration. Rate-equations are designed on principles of multisubstrate-multiproduct enzyme kinetics. The parameters of the model were adopted from literature or were estimated from fitting the photosynthetic rate and pool sizes to experimental data. The model provided good simulations for steady-state photosynthesis, Chl fluorescence, and 810 nm transmittance signals under varying light, CO2 and O2 concentrations, as well as for the transients of post-illumination CO2 uptake, Chl fluorescence induction and the 810 nm signal. The modeling shows that the present understanding of photosynthesis incorporated in the model is basically correct, but still insufficient to reproduce the dark-light induction of photosynthesis, the time kinetics of non-photochemical quenching, 'photosynthetic control' of plastoquinone oxidation, cyclic electron flow around PSI, oscillations in photosynthesis. The model may find application for predicting the results of gene transformations, the analysis of kinetic experimental data, the training of students.

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Section: Introductionmentioning

confidence: 99%

C3 photosynthesis in silico

2006

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“…It was parameterised for rice using data from the literature [17,18,19]. LEAFC3 is a generic model for the estimation of short-term steady-state fluxes of CO 2 , water vapour, and heat from leaves of C3 plant species, explicitly coupling all major processes involved in photosynthesis (biochemistry of assimilation process, stomatal conductance, leaf energy balance).…”

Section: Modelling Of Source Activitymentioning

confidence: 99%

A Rule-Based Functional-Structural Model of Rice Considering Source and Sink Functions

Henke

Jun

et al. 2009

2009 Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications

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“…An optimum response of J max to temperature is described (De Pury and Farquhar 1997, Medlyn et al 2002, Yin et al 2004: Leaf respiration rate is subtracted from photosynthetic rate to yield net C uptake. The leaf respiration rate is adjusted by temperature with a temperature coefficient: where R d25 is the respiration rate at reference temperature 25°C; R d is the respiration rate adjusted to measured ambient temperature T; Q 10 is the temperature coefficient (Q 10 = 1.78; Turnbull et al 2002), which is defined as the change of respiration rate with temperature increasing by 10°C.…”

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confidence: 99%

Application of the functional-structural tree model LIGNUM to growth simulation of short-rotation eastern cottonwood

Lu¹,

Nygren²,

Perttunen³

et al. 2011

Silva Fenn.

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The functional-structural tree growth model LIGNUM was developed as a general research tool that can be applied to several tree species. The growth simulation of short-rotation eastern cottonwood (Populus deltoides Bartr. ex Marsh.) inherits the basic LIGNUM modeling concepts including modular tree structure, L-system-based description of structural development, and carbon budget. New developments of LIGNUM model in this study were the incorporation of a biochemically-derived photosynthesis submodel; nested time steps for simulating physiological processes, structural development, and annual biomass production; incorporation of field-measured weather data for modeling the response of physiological processes to environmental variation; and application of a Monte-Carlo voxel space submodel for simulating the stochasticity of tree growth and improving computational efficiency. A specific parameter system was applied for modeling P. deltoides growth in the central Missouri, USA, environment. This adaptation of LIGNUM was applied on modeling growth of P. deltoides in a short-rotation agroforestry practice. The simulated height and biomass growth were close to field observations. Visualization of simulation results closely resembled the trees growing in an open site. The simulated response of tree growth to variations in photon flux input was reasonable. The LIGNUM model may be used as a complement to field studies on P. deltoides in short-rotation forestry and agroforestry.

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Extension of a biochemical model for the generalized stoichiometry of electron transport limited C₃ photosynthesis

Abstract: ABSTRACT

Cited by 84 publications

References 38 publications

C3 photosynthesis in silico

C3 photosynthesis in silico

A Rule-Based Functional-Structural Model of Rice Considering Source and Sink Functions

Application of the functional-structural tree model LIGNUM to growth simulation of short-rotation eastern cottonwood

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Extension of a biochemical model for the generalized stoichiometry of electron transport limited C3 photosynthesis

Abstract: ABSTRACT

Cited by 84 publications

References 38 publications

C3 photosynthesis in silico

C3 photosynthesis in silico

A Rule-Based Functional-Structural Model of Rice Considering Source and Sink Functions

Application of the functional-structural tree model LIGNUM to growth simulation of short-rotation eastern cottonwood

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Extension of a biochemical model for the generalized stoichiometry of electron transport limited C₃ photosynthesis