Code for photosynthesis model in Johnson and Berry (2021) Photosynthesis Research

Author: Jen Johnson ([email protected])
Last revised: 2021-05-17

Citation:

Johnson, J. E. and J. A. Berry. 2021. The role of Cytochrome b₆f in the control of steady-state photosynthesis: a conceptual and quantitative model. Photosynthesis Research, DOI: 10.1007/s11120-021-00840-4

Notes:

1. All of these scripts are compatible with MATLAB 2020b as well as GNU Octave 6.2.0.

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

3. The file run_forward_example1.m will simulate the light-response of photosynthesis, assuming that the absorption cross-sections of PS I and PS II are static.

4. The file run_forward_example2.m will simulate the light-response of photosynthesis, assuming that (a) under limiting light intensities, state transitions optimize the absorption cross-sections of PS I and PS II, and that (b) under saturating light intensities, the absorption cross-sections of PS I and PS II are fixed in the position reached by the light saturation point.

Directory structure:

├── LICENSE
├── README.md
├── outputs
│   ├── Example-1-static
│   │   ├── Example-1-static-figure1.png
│   │   ├── Example-1-static-modelinputs.mat
│   │   └── Example-1-static-modeloutputs.mat
│   └── Example-2-dynamic
│       ├── Example-2-dynamic-figure1.png
│       ├── Example-2-dynamic-modelinputs.mat
│       └── Example-2-dynamic-modeloutputs.mat
├── run_forward_example1.m
├── run_forward_example2.m
└── scripts
    ├── configure_fun.m
    ├── loadvars_fun.m
    ├── model_fun.m
    ├── plotter_forward_fun.m
    ├── symsolver_fun.m
    └── workspace2struct_fun.m

5 directories, 16 files