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templateControl.txt
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templateControl.txt
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#Last edited by Sander Huisman, 26/11/2018
#Last edited by Tristan de Waard, 14/12/2018
########################### <Aan te passen!> ##############################################
define TEXTOUTPUT #Comment out to disable writing to output file "simOut_numSim.txt"
#define GRAPHICSOUTPUT #Comment out to disable graphics
define dt 10^2/(2*1710000) #tijdsstap in milliseconds
define superman 1000 #alles lekker snel reageren!
variable IED = #TAG:ied #inter enzyme distance als je scaffold simuleert
variable numSim = #TAG:i #getal achter output file, dus xxx in SimOut_xxx.txt
#random_seed #TAG:seed #als je seed hetzelfde wil houden
define makeScaffold #placeholder=vrije diffusie, makeScaffold=2Dscaffold
define K_GOx_fwd 153.51*superman
define K_GOx_bck 0.00013*superman
define K_HRP_fwd 3.91e6 #hierbij is HRP_fwd somewhat activation limited
define K_HRP_bck 0.575*superman
define K_HRP_cat 0.0115*superman
define K_GOx_cat 0.641*superman
########################### </Aan te passen!> ##############################################
define substrate_mol 4800
variable neighbour_distance = 19.375644347
variable linker_len = 7
dim 3
boundaries x 0 200
boundaries y 0 200
boundaries z 0 200
time_start 0
time_stop 40
time_step dt
ifdefine GRAPHICSOUTPUT
graphics opengl
graphic_iter 1
frame_thickness 1
frame_color black
quit_at_end yes #Quits graphics display as soon as all substrate has reacted to product, enter no if you like
background_color 0.5 0.5 0.5
endif
species Gluc GOx GOx-Gluc Perox HRP HRP-Perox ABTS-
difc Gluc 670000
difc Perox 1710000
difc ABTS- 440000
ifdefine makeScaffold
difc GOx 0
difc HRP 0
else
difc GOx 375
difc HRP 1.44
endif
color Gluc yellow
color Perox green
color ABTS- black
color GOx red
color HRP blue
color GOx-Gluc orange
color HRP-Perox brown
display_size all 4
display_size Gluc 1
display_size Perox 2
display_size ABTS- 3
ifdefine makeScaffold
start_surface scaffold
action all both reflect
color both magenta 0.8
panel rect +1 ((100-IED)/2) 100 100-1.5*neighbour_distance (100+IED) 3*neighbour_distance scaf
end_surface
endif
start_surface box
action all front jump
thickness 1
color both 0 0 0 0
panel rect +0 0 0 0 200 200 left
panel rect -0 200 0 0 200 200 right
panel rect +1 0 0 0 200 200 bottom
panel rect -1 0 200 0 200 200 top
panel rect +2 0 0 0 200 200 back
panel rect -2 0 0 200 200 200 front
jump left front <-> right front
jump bottom front <-> top front
jump back front <-> front front
end_surface
start_compartment inside_box
surface box
point 100 100 100
end_compartment
reaction GOx_fwd GOx + Gluc -> GOx-Gluc K_GOx_fwd
reaction GOx_bck GOx-Gluc -> GOx + Gluc K_GOx_bck
product_placement GOx_bck pgemmax 0.2
reaction HRP_fwd HRP + Perox -> HRP-Perox K_HRP_fwd
reaction HRP_bck HRP-Perox -> HRP + Perox K_HRP_bck
product_placement HRP_bck pgemmax 0.2
reaction HRP_cat HRP-Perox -> HRP + ABTS- K_HRP_cat
reaction GOx_cat GOx-Gluc -> GOx + Perox K_GOx_cat
compartment_mol substrate_mol Gluc inside_box
ifdefine makeScaffold
mol 1 GOx (100-(IED/2)) 100+linker_len 100-neighbour_distance
mol 1 GOx (100-(IED/2)) 100+linker_len 100
mol 1 GOx (100-(IED/2)) 100+linker_len 100+neighbour_distance
mol 1 HRP (100+(IED/2)) 100+linker_len 100-neighbour_distance
mol 1 HRP (100+(IED/2)) 100+linker_len 100
mol 1 HRP (100+(IED/2)) 100+linker_len 100+neighbour_distance
else
compartment_mol 3 GOx inside_box
compartment_mol 3 HRP inside_box
endif
text_display time Gluc Perox ABTS-
cmd N 10000 ifless Gluc 0.25*substrate_mol stop
ifdefine TEXTOUTPUT
output_files simSave.txt simOut.txt
output_file_number simOut.txt numSim
output_file_number simSave.txt numSim
cmd B savesim simSave.txt
cmd B molcountheader simOut.txt
cmd N 10000 molcount simOut.txt
endif
end_file