README

Tissue Fluidity Vertex Model

as detailed in :

Tissue fluidity promotes epithelial wound healing, Nature Physics (2019)

Authors / Contributors

• Michael F Staddon (University College London)
• Shiladitya Banerjee (University College London)

created at the University College London

System Requirements

This system requires Surface Evolver 2.70 which can be downloaded at: http://facstaff.susqu.edu/brakke/evolver/evolver.html

QUICKSTART GUIDE

Create a new directory for the simulation, containing the "wound_healing.fe", "wound_creation.secmd", parameters.inp", and "dynamics.secmd" files.

The "wound_healing.fe" file is the main Surface Evolver file, containing the tissue geometry, energy definitions, and code to run the simulation.

The "parameters.inp" file contains the system parameters. These are input non-dimensional except for time, which is in seconds.

The "dynamics.secmd" file contains general simulation commands which numerically solve the dynamics of the system, and record simulation statistics.

The "wound_healing.secmd" file contains simulation commands for creating the wound.

Create folders "/output/", for simulation statistics, and "/output/images/", for simulation images, in the directory.

Run the simulation. On Windows double clicking the "wound_healing.fe" file should run it. On mac use the command line e.g.,

> evolver wound_healing.fe

During running, the simulation records statistics, such as the occurence of intercalations before and after wounding, the wound area, and cell shapes. Once the simulation has completed, the following output files will have been created, where %s is the "output_name" variable:

• "output/%s_tissue_energy.csv" is a table with the following columns: simulation step, cell id, initial wound distance, current wound distance, cell energy.

• "output/%s_unwounded_t1s.csv" and "output/%s_wounded_t1s.csv" are tables recording occurences of T1s before and after wounding. "T1 Count" indicates the number of T1s that an edge has undergone, while "Last T1" shows the time since the last T1.

• "output/%s_wound_cells.txt" contains information on cell shapes. It records the vertices of the cells that were in the first 3 rows around the wound at the time of ablation. The first four columns show: time step, cell id, initial wound distance, current wound distance. The next columns show vertex positions, alternating between x and y coordinates e.g x0, y0, x1, y1... where x0 is the x position of the vertex[0].

• "output/%_wounded_stats.csv" contains wound area and number of junctions over time.

• "output/images/%s_%06d.ps" //post script images of the simulation, recorded every "image_interval" time steps, where %06d is the current timestep.

Simulations should take between 10 - 30 minutes on an average computer.

Simulation Parameters

Simulation parameters may be changed in the "parameters.inp" file. Alternatively, values can be overwritten in the simulation file by writing them under the line "read "parameters.inp";" e.g.,

read "parameters.inp";
edge_tension := -0.06;

allowing several simulation files with different parameters in the same folder.

Variable name	Type	Default value	Units	Description
Tissue properties
kappa	float	1	-	Cell elastic modulus
A0	float	1	-	Preferred cell area
gamma	float	0.04	-	Cell contractility
pzero	float	0	-	Cell preferred shape index (unused in paper)
edge_tension	float	0.00	-	Mean cell line tension
sigma_m	float	0.025	-	Cell line tension standard deviation
tau_m	float	150	s	Line tension recovery time
Dynamic properties
dt	float	3	s	Time step
viscosity	float	30	s	System viscosity
Lmin	float	0.05	-	Length under which T1s can occur
Division properties
mean_division_rate	float	2.25	1/hr	Mean % cells dividing per hour
min_division_age	float	10000	s	Time for cell division to complete
Wound properties
wound_tension	float	0.08	-	Mean purse-string tension
wound_area_decay	float	60	s	Time scale for wound area term to decay
wound_radius	float	1.33	-	Wound radius
Other properties
random_seed	int	1	-	Random seed
output_interval	int	1	-	Timesteps between wound area recording
cell_output_interval	int	10	-	Timesteps between cell shape recording
img_output_interval	int	20	-	Timesteps between image recording

Reproduction instructions

By varying parameters and random seeds, the main results of the simulations can be reproduced using this code and analysing the output files.

Contribution guidelines

• Email: shiladitya.banerjee@ucl.ac.uk

Who do I talk to?

• Michael Staddon (michael.staddon.16@ucl.ac.uk)
• Shiladitya Banerjee (shiladitya.banerjee@ucl.ac.uk)