graphics opengl

dim 2
species Mem F Ri Ra Si Sa P Rear Amp Xi Xa L

# The species of the model and their diffusivities (roughly, in um^2/s) are as follows:
# These species describe the F-actin circuit
difc Mem(back) 0 # Discrete points on the membrane
difc F(back) 0.3 # F-actin barbed ends at the boundary; diffusion describes the lateral spread of the network due to Arp2/3-mediated branching
difc Ri(back) 0.01 # Inactive receptors at the boundary (e.g., unligated chemokine receptors or integrins)
difc Ra(back) 0.01 # Active receptors at the boundary (e.g., ligated chemokine receptors or adhesions)
difc Si 30 # Inactive signaling molecule in the cytosol (fast diffusion)
difc Sa 0.3 # Active signaling molecule in the cytosol (slower diffusion due to transient binding)
difc P(back) 0.01 # 'Poison' molecule at the boundary (e.g., bound to active receptors)

# These species form the rear of the cell, which opposes F-actin polymerization
difc Rear(back) 0.3 # Marker of cell rear
difc Amp(back) 0.01 # Amplifier of rear genesis
difc Xi 100 # Inactive 'messenger' for rear genesis (arbitrarily fast diffusion)
difc Xa 0.3 # Active 'messenger' for rear genesis (slower diffusion)
difc L 3 # Long-range inhibitor of the rear generated by F-actin

color F(back) green
color Ra(back) orange
color Si blue
color Sa cyan
color P(back) red
color Rear(back) brown
color L magenta

# These species may be shown if desired; otherwise set display size to zero
display_size F(back) 12
display_size Ra(back) 3
display_size Si 2
display_size Sa 4
display_size P(back) 6
display_size Rear(back) 12
display_size L 0

# These species are generally not shown; to change this, assign them a color 
display_size Mem(back) 0
display_size Ri(back) 0
display_size Amp(back) 0
display_size Xi 0
display_size Xa 0

time_start 0
time_stop 10000
time_step 0.05

# Export tiff images, one for every 10 time steps
tiff_iter 10
tiff_name Tcell/tcell
tiff_max 3000

# Export positions of actin and myosin molecules at every 10 time points
output_root Tcell/
output_files actinout.txt
cmd n 10 molpos F(back) actinout.txt
output_files myosinout.txt
cmd n 10 molpos Rear(back) myosinout.txt

boundaries 0 0 30
boundaries 1 0 30
frame_thickness 1

# The boundary is a circle of radius 10
start_surface membrane
action both all reflect
color both 0 0 0
thickness 1
panel sphere 15 15 10 100 s1
end_surface

# Populate the membrane with the species Mem and Ri
surface_mol 2000 Mem(back) membrane sphere s1
surface_mol 2000 Ri(back) membrane sphere s1

start_compartment cell
surface membrane
point 15 15
end_compartment

# Populate the cell interior with the inactive cytosolic species, Si and Xi
compartment_mol 1000 Si cell
compartment_mol 100 Xi cell # The lower number here allows for faster simulations.

# The following are the reactions of the F-actin circuit
reaction r1 Mem(back) -> Mem(back) + F(back) 0.00001 # Spontaneous formation of F-actin (rare event, required to begin 'protrusion')
reaction r2 F(back) -> 0 0.02 # Loss of F-actin barbed ends, e.g. by capping.  Set to approximately 1/min
reaction r3 F(back) + Ri(back) -> F(back) + Ra(back) 0.0000001 # Protrusion promotes receptor activation, e.g. by spreading over immobilized ligands on the surface
reaction r4 Ra(back) -> Ri(back) 1 # Inactivation or desensitization of receptors
reaction r5 Ra(back) + Si(bsoln) -> Ra(back) + Sa(bsoln) 100 # Efficient activation of the signaling molecule by active receptors
reaction r6 Sa(soln) -> Si(soln) 1 # Inactivation of the signaling molecule
reaction r7 Sa(bsoln) + F(back) -> Sa(bsoln) + F(back) + F(back) 0.3 # Autocatalytic generation of F-actin barbed ends, promoted by the active signaling molecule
reaction r8 Ra(back) -> Ra(back) + P(back)  0.3 # Active receptors also generate a poison
reaction r9 P(back) + F(back) -> P(back) 1 # The poison consumes F-actin
reaction r10 P(back) -> 0 0.2 # The poison has a finite lifetime

# The following are the reactions governing the cell rear; commenting them out removes the rear
reaction r11 Mem(back) -> Mem(back) + Rear(back) 0.00001 # Spontaneous formation of 'rear marker' (rare event)
reaction r12 Rear(back) -> 0 1 # The rear marker has a finite lifetime
reaction r13 Rear(back) + Mem(back) -> Rear(back) + Amp(back) 0.0000001 # The rear generates an amplifier molecule at the boundary
reaction r14 Amp(back) -> Mem(back) 1 # The amplifier molecule has a finite lifetime
reaction r15 Amp(back) + Xi(bsoln) -> Amp(back) + Xa(bsoln) 10 # The amplifier molecule activates the rear 'messenger'
reaction r16 Xa(soln) -> Xi(soln) 1 # Inactivation of the rear messenger
reaction r17 Xa(bsoln) + Rear(back) -> Xa(bsoln) + Rear(back) + Rear(back) 1 # The active messenger promotes autocatalytic growth of the rear
reaction r18 Rear(back) + F(back) -> Rear(back) 0.3 # The rear acts as a sink for F-actin that moves into it
reaction r19 F(back) -> F(back) + L(bsoln) 1 # F-actin produces a long-range inhibitor
reaction r20 L(soln) -> 0 1 # The long-range inhibitor has a finite lifetime
reaction r21 L(bsoln) + Rear(back) -> L(bsoln) 0.2 # The long-range inhibitor consumes the rear, effectively moving it in tandem with the wave(s) of protrusion

end_file