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Smoldyn_2.txt
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# Heterocyst model 1
#graphics opengl_good
dim 3
species Cgas Ngas Ogas Cfix Nfix ATP
time_start 0
time_stop 100000
time_step 1
color Nfix red
color Cfix green
color Ngas pink
color Cgas orange
color Ogas blue
color ATP yellow
display_size ATP 4
display_size Nfix 5
display_size Cfix 5
display_size Cgas 2
display_size Ngas 2
boundaries x -900 1100 r
boundaries y -500 500 r
boundaries z -500 500 r
frame_thickness 0
start_surface boundary
action all both reflect
color both black 0
polygon both edge
panel rect +0 -700 -71 400 871 -800
panel rect -0 900 -71 400 871 -800
panel rect +1 -700 -71 400 1600 -800
panel rect -1 -700 800 400 1600 -800
panel rect +2 -700 -71 400 1600 871
panel rect -2 -700 -71 -400 1600 871
end_surface
start_surface filament
action all both transmit
action Nfix both reflect
action Cfix both reflect
color both darkgrey 1
polygon both edge
panel hemi -580 0 0 70 1 0 0 10 5
panel cyl -580 0 0 850 0 0 70 10 5
panel disk 850 0 0 70 1 0 0 10
end_surface
start_surface cellmembrane_1
action all both transmit
color both purple 1
polygon both edge
panel sph -580 0 0 50 20 20
end_surface
start_surface cellmembrane_2
action all both reflect
color both orange 1
polygon both edge
panel sph -475 0 0 50 20 20
panel cyl -524 0 0 -531 0 0 2 10 3
end_surface
start_surface jumpsurface_123
action both all jump
color both blue
polygon both edge
panel disk -529 0 0 6 1 0 0 10 c1b
panel disk -524 0 0 6 1 0 0 10 c2a
panel disk -426 0 0 6 1 0 0 10 c2b
panel disk -419 0 0 6 1 0 0 10 c3a
jump c1b back <-> c2a front
jump c2b back <-> c3a front
end_surface
start_surface cellmembrane_3
action all both transmit
color both purple 1
polygon both edge
panel sph -370 0 0 50 20 20
panel cyl -419 0 0 -426 0 0 2 10 3
end_surface
start_surface cellmembrane_4
action all both transmit
color both purple 1
polygon both edge
panel sph -265 0 0 50 20 20
panel cyl -314 0 0 -321 0 0 2 10 3
end_surface
start_surface jumpsurface_345
action both all jump
color both blue
polygon both edge
panel disk -321 0 0 6 1 0 0 10 c3b
panel disk -314 0 0 6 1 0 0 10 c4a
panel disk -216 0 0 6 1 0 0 10 c4b
panel disk -209 0 0 6 1 0 0 10 c5a
jump c3b back <-> c4a front
jump c4b back <-> c5a front
end_surface
start_surface cellmembrane_5
action all both transmit
color both purple 1
polygon both edge
panel sph -160 0 0 50 20 20
panel cyl -209 0 0 -216 0 0 2 10 3
end_surface
start_surface cellmembrane_6
action all both transmit
colour both purple 1
polygon both edge
panel sph -55 0 0 50 20 20
panel cyl -104 0 0 -111 0 0 2 10 3
end_surface
start_surface jumpsurface_567
action both all jump
color both blue
polygon both edge
panel disk -111 0 0 6 1 0 0 10 c5b
panel disk -104 0 0 6 1 0 0 10 c6a
panel disk -6 0 0 6 1 0 0 10 c6b
panel disk +1 0 0 6 1 0 0 10 c7a
jump c5b back <-> c6a front
jump c6b back <-> c7a front
end_surface
start_surface cellmembrane_7
action all both transmit
color both purple 1
polygon both edge
panel sph 50 0 0 50 20 20
panel cyl 1 0 0 -6 0 0 2 10 3
panel cyl 99 0 0 106 0 0 2 10 3
end_surface
start_surface cellmembrane_8
action all both transmit
color both purple 1
polygon both edge
panel sph 155 0 0 50 20 20
panel cyl 204 0 0 211 0 0 2 10 3
end_surface
start_surface jumpsurface_789
action both all jump
color both blue
polygon both edge
panel disk +99 0 0 6 1 0 0 10 c7b
panel disk +116 0 0 6 1 0 0 10 c8a
panel disk +204 0 0 6 1 0 0 10 c8b
panel disk +211 0 0 6 1 0 0 10 c9a
jump c7b back <-> c8a front
jump c8b back <-> c9a front
end_surface
start_surface cellmembrane_9
action all both transmit
color both purple 1
polygon both edge
panel sph 260 0 0 50 20 20
panel cyl 309 0 0 316 0 0 2 10 3
end_surface
start_surface cellmembrane_10
action all both reflect
color both orange 1
polygon both edge
panel sph 365 0 0 50 20 20
panel cyl 414 0 0 421 0 0 2 10 3
end_surface
start_surface jumpsurface_91011
action both all jump
color both blue
polygon both edge
panel disk +309 0 0 6 1 0 0 10 c9b
panel disk +316 0 0 6 1 0 0 10 c10a
panel disk +414 0 0 6 1 0 0 10 c10b
panel disk +421 0 0 6 1 0 0 10 c11a
jump c9b back <-> c10a front
jump c10b back <-> c11a front
end_surface
start_surface cellmembrane_11
action all both transmit
color both purple 1
polygon both edge
panel sph 470 0 0 50 20 20
panel cyl 519 0 0 526 0 0 2 10 3
end_surface
start_surface cellmembrane_12
action all both transmit
color both purple 1
polygon both edge
panel sph 575 0 0 50 20 20
end_surface
start_surface jumpsurface_1112
action both all jump
color both blue
polygon both edge
panel disk +519 0 0 6 1 0 0 10 c11b
panel disk +526 0 0 6 1 0 0 10 c12a
jump c11b back <-> c12a front
end_surface
start_compartment cytoplasm_1
surface cellmembrane_1
point -575 0 0
end_compartment
start_compartment cytoplasm_2
surface cellmembrane_2
point -470 0 0
end_compartment
start_compartment cytoplasm_3
surface cellmembrane_3
point -365 0 0
end_compartment
start_compartment cytoplasm_4
surface cellmembrane_4
point -260 0 0
end_compartment
start_compartment cytoplasm_5
surface cellmembrane_5
point -155 0 0
end_compartment
start_compartment cytoplasm_6
surface cellmembrane_6
point -50 0 0
end_compartment
start_compartment cytoplasm_7
surface cellmembrane_7
point 50 0 0
end_compartment
start_compartment cytoplasm_8
surface cellmembrane_8
point 155 0 0
end_compartment
start_compartment cytoplasm_9
surface cellmembrane_9
point 260 0 0
end_compartment
start_compartment cytoplasm_10
surface cellmembrane_10
point 365 0 0
end_compartment
start_compartment cytoplasm_11
surface cellmembrane_11
point 470 0 0
end_compartment
start_compartment cytoplasm_12
surface cellmembrane_12
point 575 0 0
end_compartment
start_compartment boundary
surface boundary
point 0 0 0
end_compartment
start_compartment filament
surface filament
point 0 0 0
end_compartment
start_compartment extracellular
surface cellmembrane_1
surface cellmembrane_2
surface cellmembrane_3
surface cellmembrane_4
surface cellmembrane_5
surface cellmembrane_6
surface cellmembrane_7
surface cellmembrane_8
surface cellmembrane_9
surface cellmembrane_10
surface cellmembrane_11
surface cellmembrane_12
surface filament
point 0 60 0
end_compartment
start_compartment intracellular
surface cellmembrane_1
surface cellmembrane_2
surface cellmembrane_3
surface cellmembrane_4
surface cellmembrane_5
surface cellmembrane_6
surface cellmembrane_7
surface cellmembrane_8
surface cellmembrane_9
surface cellmembrane_10
surface cellmembrane_11
surface cellmembrane_12
surface filament
point 50 0 0
end_compartment
start_compartment vegetative
surface cellmembrane_1
surface cellmembrane_3
surface cellmembrane_4
surface cellmembrane_5
surface cellmembrane_6
surface cellmembrane_7
surface cellmembrane_8
surface cellmembrane_9
surface cellmembrane_11
surface cellmembrane_12
point 50 0 0
end_compartment
start_compartment heterocyst
surface cellmembrane_2
surface cellmembrane_10
point 365 0 0
end_compartment
compartment_mol 1000 Ngas boundary
compartment_mol 20 Cgas boundary
compartment_mol 200 Ogas boundary
compartment_mol 50 Nfix filament
compartment_mol 50 Cfix filament
difc Nfix 5
difc Cfix 5
difc Ogas 50
difc Ngas 50
difc Cgas 50
difc ATP 10
reaction_cmpt vegetative photosynthesis Cgas -> Cfix + Ogas 2e-1
reaction_cmpt intracellular respiration Ogas + Cfix -> Cgas + ATP 2e-1
reaction_cmpt heterocyst Nfixation Ngas -> Nfix 2e-1
reaction_cmpt intracellular protein_turnover Nfix + ATP -> Ngas 2e-4
output_files cyano_out6_vegetative.txt
cmd N 5000 molcountincmpt cytoplasm_6 cyano_out6_vegetative.txt
end_file
/*
cmd i 0 199999
cmd i 200000 399999
cmd i 400000 599999
cmd i 600000 799999
cmd i 800000 1000000
*/
/*
output_files spatial_out_1.txt spatial_out_2.txt spatial_out_3.txt spatial_out_4.txt spatial_out_5.txt spatial_out_6.txt spatial_out_7.txt spatial_out_8.txt spatial_out_9.txt spatial_out_10.txt spatial_out_11.txt spatial_out_12.txt
cmd @ 100000 molcountincmpt cytoplasm_1 spatial_out_1.txt
cmd @ 100000 molcountincmpt cytoplasm_2 spatial_out_2.txt
cmd @ 100000 molcountincmpt cytoplasm_3 spatial_out_3.txt
cmd @ 100000 molcountincmpt cytoplasm_4 spatial_out_4.txt
cmd @ 100000 molcountincmpt cytoplasm_5 spatial_out_5.txt
cmd @ 100000 molcountincmpt cytoplasm_6 spatial_out_6.txt
cmd @ 100000 molcountincmpt cytoplasm_7 spatial_out_7.txt
cmd @ 100000 molcountincmpt cytoplasm_8 spatial_out_8.txt
cmd @ 100000 molcountincmpt cytoplasm_9 spatial_out_9.txt
cmd @ 100000 molcountincmpt cytoplasm_10 spatial_out_10.txt
cmd @ 100000 molcountincmpt cytoplasm_11 spatial_out_11.txt
cmd @ 100000 molcountincmpt cytoplasm_12 spatial_out_12.txt
*/
end_file