This bundle includes the following packages to simulate a reaction-diffusion model of the Chlamydomonas CO2-concentrating mechnism and analyze simulation data:
Engineering contains the performances and costs of each engineering state, and the general algorithms that compute simple paths from a given starting state to the target state with the best performance.
FullModel contains the equations and code to run the reaction-diffusion model and return the desired data as output.
ThylakoidStacks contains algorithms that compute the effective diffusion constant through thyklakoid stacks with realistic geometries.
For a more detailed discription of the model, see our paper here.
ThylakoidStacks and FullModel require installation of FEniCS. Instructions can be found here. A list of packages installed in the virtual environment is stored in fenics-envs.rtf. Note that meshio and pygmsh are NOT installed in fenics by default, but they are required for ThylakoidStacks.
ThylakoidStacks requires installation of Gmsh, which can be downloaded here. Note that pygmsh 6.1.1 and Gmsh 3.0.6 are recommended. Other versions may result in syntax issues.
Engineering
load variables.mat Type "gen_distance(BarCode)" to create the distance matrix Type "engineering(dist, NcffList, ATPperCO2fixed, start)" where "start" is the desired starting state to generate engineering paths.
FullModel
Type "python ccm_main.py" to run the model for one set of parameters Type "python ccm_scan.py" to run the model for a range of parameters and save the specified output
ThylakoidStacks
Type "python -u EffectiveDiffusion_v2.py" to run the algorithm
See the text files in each folder and the comments in the code files for more details.
If you encounter any issues please contact:
Chenyi Fei (cfei@princeton.edu)
Alexandra Wilson (aw29@princeton.edu)