C3 photosynthesis (Farquhar, von Caemmerer, Berry) model - PLM_1, version 1

Validation Validated against original code running under GNU FORTRAN 95. Comments on numerical integration No integration needed. Comments on running the (Simile) model The variable "num errors" accumulates the number of times the ribulose bis-phosphate limited photosynthesis rate cannot be calculated. See the documentation dialogue for the Simile variable "jl_electron transport" for details.

Additional Attributes
Original Model: Language: FORTRAN 95 Author:Daniel P. Rasse File name of original code: photosynthesis.f95 Comments The model was created from the FORTRAN code for the "Arabidopsis leaf carbohydrate model (Rasse and Tocquin)" also availble on this portal. This used the C3 photosynthesis model as a submodel implemented in a subroutine stored in the file "photosynthesis.f95".
Purpose: Model of C3 photosynthesis that calculates the net rate of photosynthesis under given conditions. The model will be of interest in itself, could form a submodel of plant/crop models and be used to interpret experimental results. The model is a sequence of linked calculations with no state variables used. The "Arabidopsis leaf carbohydrate model (Rasse and Tocquin)" (also availble on this portal) provides a good example of how the model would typically be used. This leaf model needs the rate of photosynthesis and so it passes the following values to the C3 photosynthesis model: Experimental atmospheric C02 partial pressure (Pa). Total absorbed photosynthetically active radiation (PAR) per unit leaf area (micromole m-2 s-1). Leaf temperature (oC). Photosynthetic rubisco capacity per unit leaf area at 25oC (micromol C02 m-2 s-1). The photosynthesis model then calculates the rate of photosynthesis under two limiting conditions: Limited by rubisco and limited by ribulose bisphosphate (RuBP) regeneration. The net rate of leaf photosynthesis (micromol CO2 m-2 leaf s-1) returned by the model is the smaller of these two photosynthetic rates.

Related Publications
Farquhar G.D., von Caemmerer S. and Berry J.A. (1980). A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species.. Planta 149, 78-90.

Originally submitted to PLaSMo on 2010-01-27 12:41:44

SEEK ID: https://fairdomhub.org/assays/853

Modelling Analysis

BioData SynthSys

Projects: PlaSMo model repository

Investigation: Davey, Chris

Study: C3 photosynthesis (Farquhar, von Caemmerer, Berry) model - PLM_1

Assay position:

Biological problem addressed: Gene Regulatory Network

Organisms: No organisms

help Creators and Submitter
Additional credit

Chris Davey


Views: 1535

Created: 10th Jan 2019 at 16:40

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