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camkii-model.txt
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camkii-model.txt
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/* exmpales followed:
/S7_surfaces/signal.txt
/S7_surfaces/unbounded_diffusion/emitter1.txt
/S99_more/neuron/neuron.txt
units: nm ms
*/
define ca_src 3
#define ca_int 0.001 #1 ca2+ per 10 usec
define ca_int 0.001
#define dfc_ca 500000
define dfc_ca 50000
define stimtime 200
#define graph_on
define cam_gradient
#-------------General parameters-------
ifdefine graph_on
graphics opengl_good
graphic_iter 1
frame_thickness 0
frame_color 1 1 1
#grid_thickness 1
else
graphics none
endif
dim 3
accuracy 10
molperbox 3
#boxsize 1
boundaries 0 -500 500
boundaries 1 -500 500
boundaries 2 -5 5100
time_start 0
time_stop stimtime
time_step 0.001 #1 usec step
#-------------Molecules----------------
species ca
#species cam
species camca1
#species camca2
species camca3
#species camca4
read_file camkii-test2_v4.txt
molecule_lists calst camlst bcamkii gcamkii
mol_list ca calst
mol_list cam* camlst
mol_list b* bcamkii
mol_list g* gcamkii
define cam1_on 4250
define cam1_off 0.05
define cam2_on 150025
define cam2_off 0.05
define cam3_on 21250
define cam3_off 1.25
define cam4_on 425000
define cam4_off 1.25
reaction cam1 ca + cam -> camca1 cam1_on
reaction cam1r camca1 -> ca + cam cam1_off
reaction cam2 ca + camca1 -> camca2 cam2_on
reaction cam2r camca2 -> ca + camca1 cam2_off
reaction cam3 ca + camca2 -> camca3 cam3_on
reaction cam3r camca3 -> ca + camca2 cam3_off
reaction cam4 ca + camca3 -> camca4 cam4_on
reaction cam4r camca4 -> ca + camca3 cam4_off
difc ca dfc_ca # nm^2 us^(-1)
difc cam 0
difc camca* 50000 #50 nm^2 us^(-1) -> 50000 nm^2 ms^(-1)
difc b* 5000
difc g* 10000
difc g5 0
difc b4 0
#------------------Surfaces------------
start_surface membrane
action both all r
color both grey 0.2
polygon both edge
#panel rect +2 -250 -250 5000 500 500 #5 micron
panel rect +2 -500 -500 5000 1000 1000 #5 micron
end_surface
start_surface sides
action both all r
color both grey 0.2
polygon both e
#panel tri -250 -250 5000 250 -250 5000 0 0 0 tri1
#panel tri 250 -250 5000 250 250 5000 0 0 0 tri2
#panel tri 250 250 5000 -250 250 5000 0 0 0 tri3
#panel tri -250 250 5000 -250 -250 5000 0 0 0 tri4
panel tri -500 -500 5000 500 -500 5000 0 0 0 tri1
panel tri 500 -500 5000 500 500 5000 0 0 0 tri2
panel tri 500 500 5000 -500 500 5000 0 0 0 tri3
panel tri -500 500 5000 -500 -500 5000 0 0 0 tri4
end_surface
start_surface n_membrane
action both ca t
action both cam* t
action both b* r
action both g* t
color both grey 0.5
polygon both edge
#panel rect +2 -125 -125 2500 250 250 #2.5 micron
panel rect +2 -250 -250 2500 500 500 #2.5 micron
end_surface
start_surface shell
action both all t
color both grey 0.5
polygon both edge
#panel rect +2 -245 -245 4900 490 490 #0.1 micron
panel rect +2 -490 -490 4900 980 980 #2.5 micron
end_surface
#-------------------------------------
#example/S7/jump3.txt
#P37 jumping panels should be parallel
#P35 all panel front sides in a surface should face the same way; coincident panels -> unintentional leaks
#the jump seems not to work properly. molecules after jumping tend to diffuse out of reflective boundaries.
#start_surface jump1
#action both all j
#color both blue 0.5
#polygon both edge
#panel tri 249 249 4999 -249 249 4999 0 125 2500 tri5
#panel tri -249 -249 4999 249 -249 4999 0 -125 2500 tri6
#jump tri5 front -> tri6 front
#jump tri6 back -> tri5 back
#end_surface
#start_surface jump2
#action both all johio
#color both blue 0.5
#polygon both edge
#panel tri -249 -249 4999 -249 249 4999 -125 0 2500 tri7
#panel tri 249 -249 4999 249 249 4999 125 0 2500 tri8
##jump tri8 back -> tri7 front
##jump tri7 back -> tri8 front
#jump tri8 front -> tri7 front
#jump tri7 back -> tri8 back
#end_surface
#--------------------------------------
start_compartment nano
surface shell
surface membrane
surface sides
#surface jumping
point 0 0 4950
end_compartment
start_compartment cytol
surface shell
surface n_membrane
#surface jumping
surface sides
surface membrane
point 0 0 4800
end_compartment
start_compartment nucleus
surface n_membrane
surface membrane
#surface jumping
surface sides
point 0 0 100
end_compartment
#------------molecules in compartment--
ifdefine cam_gradient
compartment_mol 58646 cam nano
compartment_mol 146 camca1 nano
compartment_mol 13 camca2 nano
compartment_mol 9094 cam cytol
compartment_mol 23 camca1 cytol
compartment_mol 2 camca2 cytol
else
compartment_mol 4113 cam nano
compartment_mol 1 camca1 nano
compartment_mol 48350 cam cytol
compartment_mol 12 camca1 cytol
endif
compartment_mol 588 b4 nano #10# uM
compartment_mol 6912 b4 cytol #10 uM
compartment_mol 3528 g5 nano #10 uM
compartment_mol 41472 g5 cytol #10 uM
compartment_mol 3 ca nano #0.05 uM
compartment_mol 45 ca cytol #0.05 uM
#------------commands------------------
#cmd i 0 35 ca_int pointsource ca ca_src 0 0 4999.5 #single ca channel 0.0936 /usec ~ 0.03 pA#
read_file ica_burst_10usec.txt
ifdefine graph_on
display_size all 2
color ca red
color cam* blue
color b* black
color g* purple
text_display ca
text_display camca1
text_display camca2
text_display camca3
text_display camca4
text_display b4
text_display b6
text_display g5
text_display g7
text_display time
cmd b pause
else
output_root results_burst_camgradient/
output_files nano.txt
output_files cytol.txt
output_files nucleus.txt
cmd e molcountincmpt nano nano.txt
cmd e molcountincmpt cytol cytol.txt
cmd e molcountincmpt nucleus nucleus.txt
endif
end_file