Code for photosynthesis model in Johnson, Field and Berry (2021) Oecologia

Author: Jen Johnson
Email: jjohnson@carnegiescience.edu
Last revised: 2021-10-23

Citation:

Johnson, J. E., Field, C.B., Berry, J.A. 2021. The limiting factors and regulatory processes that control the environmental responses of C₃, C₃–C₄ intermediate, and C₄ photosynthesis. Oecologia, DOI: 10.1007/s00442-021-05062-y

Notes:

1. This code was written in MATLAB R2020b. It is fully compatible with GNU Octave 6.2.0 for the C₃ implementation of the model. However, the symbolic code used for the bundle sheath calculations in the C₃-C₄ and C₄ implementations is not yet compatible with Octave.

2. This directory includes three example simulations that are described below. These call functions in the subdirectory scripts and write output to the subdirectory outputs.

3. The scripts run_forward_example1.m, run_forward_example2.m, and run_forward_example3.m simulate the responses of photosynthesis to light, carbon dioxide, and temperature, respectively. Other environmental variables are held constant.

4. Each simulation can be customized by setting the pathway_opt variable to either C3, Type-I-C3-C4, or NADP-ME-C4.

5. The subdirectory inputs contains two files with the input data used in Figures 6 and 7. For the analysis in Figure 6, the forward model in scripts/model_fun_c3c4.m needs to be fit to the physiological measurements with an optimization routine. For the analysis in Figure 7, the environmental measurements can simply be substituted into the example run files to recreate the simulations.

Directory structure:

├── LICENSE
├── README.md
├── inputs
│   ├── Figure-6.csv
│   └── Figure-7.csv
├── outputs
│   ├── Example1-Light-C3
│   │   ├── Example1-Light-C3-figure.png
│   │   ├── Example1-Light-C3-modelinputs.mat
│   │   └── Example1-Light-C3-modeloutputs.mat
│   ├── Example1-Light-NADP-ME-C4
│   │   ├── Example1-Light-NADP-ME-C4-figure.png
│   │   ├── Example1-Light-NADP-ME-C4-modelinputs.mat
│   │   └── Example1-Light-NADP-ME-C4-modeloutputs.mat
│   ├── Example1-Light-Type-I-C3-C4
│   │   ├── Example1-Light-Type-I-C3-C4-figure.png
│   │   ├── Example1-Light-Type-I-C3-C4-modelinputs.mat
│   │   └── Example1-Light-Type-I-C3-C4-modeloutputs.mat
│   ├── Example2-CO2-C3
│   │   ├── Example2-CO2-C3-figure.png
│   │   ├── Example2-CO2-C3-modelinputs.mat
│   │   └── Example2-CO2-C3-modeloutputs.mat
│   ├── Example2-CO2-NADP-ME-C4
│   │   ├── Example2-CO2-NADP-ME-C4-figure.png
│   │   ├── Example2-CO2-NADP-ME-C4-modelinputs.mat
│   │   └── Example2-CO2-NADP-ME-C4-modeloutputs.mat
│   ├── Example2-CO2-Type-I-C3-C4
│   │   ├── Example2-CO2-Type-I-C3-C4-figure.png
│   │   ├── Example2-CO2-Type-I-C3-C4-modelinputs.mat
│   │   └── Example2-CO2-Type-I-C3-C4-modeloutputs.mat
│   ├── Example3-Temperature-C3
│   │   ├── Example3-Temperature-C3-figure.png
│   │   ├── Example3-Temperature-C3-modelinputs.mat
│   │   └── Example3-Temperature-C3-modeloutputs.mat
│   ├── Example3-Temperature-NADP-ME-C4
│   │   ├── Example3-Temperature-NADP-ME-C4-figure.png
│   │   ├── Example3-Temperature-NADP-ME-C4-modelinputs.mat
│   │   └── Example3-Temperature-NADP-ME-C4-modeloutputs.mat
│   └── Example3-Temperature-Type-I-C3-C4
│       ├── Example3-Temperature-Type-I-C3-C4-figure.png
│       ├── Example3-Temperature-Type-I-C3-C4-modelinputs.mat
│       └── Example3-Temperature-Type-I-C3-C4-modeloutputs.mat
├── run_forward_example1.m
├── run_forward_example2.m
├── run_forward_example3.m
└── scripts
    ├── configure_fun.m
    ├── loadvars_fun.m
    ├── model_fun_c3c4.m
    ├── plotter_forward_fun_c3c4.m
    ├── symsolver_c3c4_fun.m
    └── workspace2struct_fun.m

13 directories, 40 files