graphics opengl
graphic_iter 1

# dimensionality and species

dim 3
species MinDATP MinDADP MinDmem MinE MinDE

# output of time and number of molecules per species in graphical output

text_display time MinDATP MinDADP MinDmem(front) MinE MinDE(front)

# diffusion coefficients

difc MinDATP(all) 2.5
difc MinDADP(all) 2.5
difc MinDmem(all) 0.01
difc MinE(all) 2.5
difc MinDE(all) 0.01

# information for graphical output

color MinDATP(all) 1 0 0
color MinDADP(all) 1 0 0
color MinE(all) 0 1 0
color MinDmem(all) 0 0 1
color MinDE(all) orange

display_size MinDATP(all) 0
display_size MinDADP(all) 0
display_size MinDmem(all) 3
display_size MinE(all) 0
display_size MinDE(all) 3

# run time parameters

time_start 0
time_stop 1200
time_step 0.0001

# simulation geometry

boundaries 0 0 10 r
boundaries 1 0 5 r
boundaries 2 0 0.5 r
frame_thickness 0

start_surface box
action all both reflect
color both 0.5 0.5 0.5
polygon both edge
panel rect +0 0 0 0 5 0.5
panel rect -0 10 0 0 5 0.5
panel rect +1 0 0 0 10 0.5
panel rect -1 0 5 0 10 0.5
panel rect +2 0 0 0 10 5
panel rect -2 0 0 0.5 10 5
end_surface

start_surface reactivepatches
action all both reflect
rate MinDATP fsoln front 0.025 MinDmem
color both magenta 0.1
thickness 2
polygon front face
polygon back face
panel rect +2 0 0 0 10 5
end_surface

start_compartment main
surface box
point 5. 2.5 0.25
end_compartment

# initial conditions

compartment_mol 6003 MinDADP main
compartment_mol 6003 MinDATP main
compartment_mol 3120 MinE main

# reactions

reaction_surface reactivepatches r3 MinDATP(fsoln) + MinDmem(front) -> MinDmem(front) + MinDmem(front) 0.0149
reaction_surface reactivepatches r4 MinE(fsoln) + MinDmem(front) -> MinDE(front) 0.0930
reaction_surface reactivepatches r5 MinDE(front) -> MinDADP(fsoln) + MinE(fsoln) 0.7
reaction r1 MinDADP -> MinDATP 0.5

end_file