README to simulate the water and sucrose transport model as described by van den Herik et al. 2020

1. Model Implementation
Below the scripts needed for the simulations and their respective functions are given:
- potato_main includes options to change loss_mode and timestep, as well as the set of implemented differential equations
- potato_init, defines model architecture and initial conditions
- potato_parameters, defines the used parameters
- potato_transport_phloem_xylem, calculates transport in the phloem and xylem
- potato_loss_retieval, calculates loss, retrieval and removal from phloem and apoplast
Additional scripts:
- potato_plot, creates the plots as shown in figure 2 of the paper.

2. Running the baseline model
Running potato_main as supplied online simulates a 1m stem with the standard potato parameters as decribed in the manuscript.
The results from the ODE solver are stored in the t (time) and y(variables) matrices. These can be saved (save('YOURNAME.mat') or exported afterwards.
Running potato_plot with the t and y matrices in the workspace creates the plots used for figure 2 in the manuscript.

3. Loss modes and parameter variation (Figures 3 and 4)
To include efflux, retrieval or removal we included three options in potato_main:
1 = No-Leakage, 2 = loss-only, 3 = loss-Retrieval, 
by setting loss_mode to 1, 2 or 3 the mode can be changed.
To obtain results for figure 3 we performed a series of simulations while varying vmax of SWEET between 0 and 1e-8 mol/s and Km between 1 and 1000. 
Results from this parameter variation were stored in separate .mat files to be plotted using potato_plot and/or the data generated from potato_plot.
For figure 4 we changed the loss-modes and vmax of SWEETs, with a similar approach to figure 3.