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prototype2
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prototype2
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/* exmpales followed:
/S7_surfaces/signal.txt
/S7_surfaces/unbounded_diffusion/emitter1.txt
/S99_more/neuron/neuron.txt
units: um us
*/
#Q: uniform distribution in a compartment?
#how to code geometry of the nanodomain
#multiple sources of ca (more than one channels)
#get rid of the black edged box
#how to make the graphics interactive?
#how to make difc of ca2+ depends on compartment?
#how to view radial diffusion of ca2+?
#how to create multiple nanodomains?
#depending on the size of nanodomain (cluster), ca2+ will choose to spread horizontally or radially
#-------------General parameters-------
graphics opengl_good
graphic_iter 1
frame_thickness 0
frame_color 1 1 1
#grid_thickness 1
dim 3
accuracy 10
boxsize 0.2
boundaries 0 -6 6 #-5000 5000
boundaries 1 -6 6 #-5000 5000
boundaries 2 -6 6 #-5000 5000
time_start 0
time_stop 1000
time_step 0.001
#-------------Molecules----------------
species ca
species cam
species cam-ca
display_size ca 0.02
display_size cam 0.02
display_size cam-ca 0.02
color ca red
color cam black
color cam-ca cyan
difc ca 60/1000000 #nm^2 us^(-1)
difc cam 50/1000000
difc cam-ca 50/1000000 #assumption
#------------surfaces------------------
start_surface cell
action both all reflect
color both black 0
polygon both edge
#cell membrane
read_file cell
end_surface
start_surface shell
action both all t #t
color both grey 0.5
polygon both edge
read_file shell
end_surface
start_compartment nano
surface shell
surface cell
point 0 0 4.99
point 0 4.99 0
point 4.99 0 0
point 0 0 -4.99
point 0 -4.99 0
point -4.99 0 0
end_compartment
start_compartment cytol
surface shell
point 0 0 0
end_compartment
#-----------reactions------------------
reaction n_bound ca + cam -> cam-ca 1.309/1000000 #nm^3 us^(-1)
reaction n_unbound cam-ca -> ca + cam 0.16 #us^(-1)
#------------molecules in compartment--
mol 1000 ca 0 0 4.99
mol 1000 ca 0 4.99 0
mol 1000 ca 4.99 0 0
mol 1000 ca 0 0 -4.99
mol 1000 ca 0 -4.99 0
mol 1000 ca -4.99 0 0
compartment_mol 25 cam nano
compartment_mol 0 cam-ca nano
#------------commands------------------
#cmd e pointsource ca 5 0 0 4.99
#cmd e pointsource ca 5 0 4.99 0
#cmd e pointsource ca 5 4.99 0 0
text_display ca
text_display cam
text_display cam-ca
cmd b pause
#tiff_name prototype
end_file