# An attempt at a neuron simulation

# ---------- General parameters ---------

graphics opengl
graphic_iter 1000

dim 3
max_species 10
max_mol 1000
accuracy 5

boundaries 0 0 100
boundaries 1 0 100
boundaries 2 0 100

time_start 0
time_stop 10000
time_step 0.02

# ----------- Molecules -------------

species protein
species Na
species K
species protein_K
species protein_Na
species Ach
species channel
species channel_Ach

difc protein 0
difc Na 10
difc K 10
difc protein_K 0
difc protein_Na 0
difc Ach 5
difc channel 0
difc channel_Ach 0

color protein 0.8 0.8 0.8
color Na 1 0 0
color K 0 1 0
color protein_K 0.2 0.8 0.2
color protein_Na 1 0.5 0.5
color Ach 0 0 0.5
color channel 0 0 0
color channel_Ach 0 0 1

display_size protein 5
display_size Na 3
display_size K 3
display_size protein_Na 5
display_size protein_K 5
display_size Ach 3
display_size channel 5
display_size channel_Ach 5

# ------------- surfaces --------------

max_surface 2

start_surface walls
action both all reflect
color both 0 0 0
thickness 1
polygon both edge
max_panels rect 6
panel rect +0 0 0 0 100 100
panel rect -0 100 0 0 100 100
panel rect +1 0 0 0 100 100
panel rect -1 0 100 0 100 100
panel rect +2 0 0 0 100 100
panel rect -2 0 0 100 100 100
end_surface

start_surface membrane
action both protein reflect
rate K fsoln bsoln 0.02
rate K bsoln fsoln 0.02
action front Na reflect
rate Na bsoln fsoln 0.05
color both 0 0 1 0.5
thickness 1
polygon both face
max_panels rect 1
panel rect +0 20 0 0 100 100 panel1
end_surface

# -------------- reactions ---------------

reaction NaPbind    Na + protein -> protein_Na 1000
reaction NaPunbind  protein_Na -> Na + protein 0.0002
product_placement NaPunbind pgemmax 0.2

reaction KPbind     K + protein -> protein_K 1000
reaction KPunbind   protein_K -> K + protein 0.01
product_placement KPunbind pgemmax 0.2

reaction AchCbind   Ach + channel(up) -> channel_Ach(up) 500
reaction AchCunbind channel_Ach(up) -> Ach + channel(up) 0.0002
reaction Achuptake  Ach -> 0 0.002
product_placement AchCunbind pgemmax 0.2

reaction Nain       channel_Ach(up) + Na(fsoln) -> channel_Ach(up) + Na(bsoln) 100
reaction Naout      channel_Ach(up) + Na(bsoln) -> channel_Ach(up) + Na(fsoln) 100
product_placement Nain pgemmax 0.2
product_placement Naout pgemmax 0.2


# ------------- individual molecules --------------

mol 25 protein 0-20 u u
mol 75 protein_K 0-20 u u
mol 100 Na 20-100 u u
mol 10 K u u u
surface_mol 100 channel(up) membrane rect panel1

# ----------- commands --------------------

output_files neuroninside.txt neuronoutside.txt
cmd n 50 molcountinbox 0 20 0 100 0 100 neuroninside.txt
cmd n 50 molcountinbox 20 100 0 100 0 100 neuronoutside.txt
cmd @ 3000 pointsource Ach 400 99 50 50

end_file