Welcome to AppCoM’s documentation!

The Apposed-Cortex Model library provides an interface to implement a biomechanical model of an epithelial tissue. In this model, each cell cortex is represented as an active, continuum morphoelastic rod with resistance to bending and extension. Adhesions are modelled as agents explicitly coupling neighbouring cell cortices.

Note

Take a look at the theoretical development of the model here: TBA.

Quickstart demo

Load a tissue with 14 cells:

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with open('pickled_tissues/14_cells', 'rb') as new_tissue:
    eptm = dill.load(new_tissue)

Update the adhesions (passing the connectivity data to the cells) and apply some active contractility (a prestretch) on the bicellular junction shared by cells A and B:

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eptm.update_adhesion_points_between_all_cortices()
prestrech_magnitude = 1 - 0.01
eptm.apply_prestretch_to_cell_identity_pairs(prestrech_magnitude, [['A','B']])

Perform 10 simulation timesteps (update restlengths and relax to equilibrium) and save the result:

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num_timesteps = 10
for time_step in range(num_timesteps):
    eptm.run_simulation_timestep()
eptm.pickle_self(name='my_test_file')

Have a look at the result, colouring the cortex with tension and bulk with cell pressure:

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import matplotlib.pyplot as plt
fig, ax = plt.subplots(figsize=(11, 9))
eptm.plot_xy_on_trijunction(ax=ax, plot_stress=True, plot_tension=True)
plt.show()

More coming soon!

Indices and tables