# Bar1 Smoldyn simulation
# by Steve Andrews, 11/30/09
# Ref: Andrews, Addy, Brent, Arkin, "Detailed simulations of cell biology with Smoldyn 2.1", PLoS Comp. Biol. 2010
# This file is Bar29.txt, from Bar28.txt
# This is Bar1+, 1 target cell, no Bar1 adsorption
# Units: microns and seconds

define WITHBAR1

# *** output file ***
define	OUTFILE1	FILEROOTout.txt
define	OUTFILE2	FILEROOTout2.txt

# *** time ***
define TIMEEND 4500

# *** boundaries ***
define	XLO	-12
define	XHI	12
define	YLO	-12
define	YHI	12
define	ZLO	-12
define	ZHI	12

# *** model parameters ***
define	NGPCR	6622	# number of GPCR
define	K1t	250	# target alpha production rate
define	K1c	12.5	# challenger alpha production rate
define	K4	100	# Bar1 production rate in um^-2/s
define	K5	5.15	# Bar1-alpha reaction rate, diff. limit is 10.3 um^3/s
define	K6	0.008303	# alpha binding to GPCR, *** 2x
define	K7	0.02	# alpha unbinding from GPCR, *** 2x

graphics opengl
graphic_iter 10000
frame_thickness 0
accuracy 10

dim 3
species Bar1 alpha GPCR GPCRalpha
max_mol 300000
boxsize 0.5

molecule_lists list3 list4 list1 list2 list5

mol_list alpha(fsoln) list1
mol_list alpha(up) list2
mol_list GPCR(up) list3
mol_list GPCRalpha(up) list4
mol_list Bar1(fsoln) list5
mol_list Bar1(up) list2

difc Bar1(fsoln) 27
difc alpha(fsoln) 132

color Bar1(fsoln) 0 1 0
color Bar1(front) 0 1 0
color alpha(fsoln) 0 0 0
color GPCR(up) 0 0 1
color GPCRalpha(up) 1 0 0.2

display_size alpha(fsoln) 1
display_size alpha(up) 0
display_size Bar1(all) 1
display_size GPCR(up) 2
display_size GPCRalpha(up) 2

time_start 0
time_stop TIMEEND
time_step 0.02

boundaries 0 XLO XHI
boundaries 1 YLO YHI
boundaries 2 ZLO ZHI

max_surface 5

start_surface sides
polygon both none
unbounded_emitter front Bar1 K4 0 0 0
unbounded_emitter front alpha K1t 5.5 0 0
unbounded_emitter front alpha K1c 2.75 4.7632 0
unbounded_emitter front alpha K1c -2.75 4.7632 0
unbounded_emitter front alpha K1c -5.5 0 0
unbounded_emitter front alpha K1c -2.75 -4.7632 0
unbounded_emitter front alpha K1c 2.75 -4.7632 0
read_file ellipse_12_12.txt
end_surface

start_surface cell
action both all reflect
polygon both face
color both 0.8 0.8 0.8
max_panels sphere 1
panel sphere 0 0 0 2.5 20 20
end_surface

start_surface alphatarget
polygon both face
color both 0.3 0.3 0.3
max_panels sphere 6
panel sphere 5.5	0	0 2.5 20 20
end_surface

start_surface alphachallenge
polygon both face
color both 0.5 0.5 0.5
max_panels sphere 6
panel sphere 2.75	4.7632	0 2.5 20 20
panel sphere -2.75	4.7632	0 2.5 20 20
panel sphere -5.5	0	0 2.5 20 20
panel sphere -2.75	-4.7632	0 2.5 20 20
panel sphere 2.75	-4.7632	0 2.5 20 20
end_surface

surface_mol NGPCR GPCR(up) cell all all

reaction_surface alphatarget	rxn1t	0 -> alpha(fsoln)	K1t	# alpha production
reaction_surface alphachallenge	rxn1c	0 -> alpha(fsoln)	K1c	# alpha production

ifdefine WITHBAR1
  reaction_surface cell		rxn4	0 -> Bar1(fsoln)	K4	# Bar1 production
  reaction rxn5	Bar1(fsoln) + alpha(fsoln) -> Bar1(fsoln)	K5	# Bar1 protease on alpha
endif

reaction rxn6	GPCR(up) + alpha(fsoln) -> GPCRalpha(up)	K6	# GPCR-alpha binding
reaction rxn7	GPCRalpha(up) -> GPCR(up) + alpha(fsoln)	K7	# GPCR-alpha unbinding
product_placement rxn7 pgemmax 0.2

cmd @ 0 set reaction_rate rxn1t 15.625
cmd @ 500 set reaction_rate rxn1t 31.25
cmd @ 1000 set reaction_rate rxn1t 62.5
cmd @ 1500 set reaction_rate rxn1t 125
cmd @ 2000 set reaction_rate rxn1t 250
cmd @ 2500 set reaction_rate rxn1t 500
cmd @ 3000 set reaction_rate rxn1t 1000
cmd @ 3500 set reaction_rate rxn1t 2000
cmd @ 4000 set reaction_rate rxn1t 4000

cmd @ 0 set reaction_rate rxn1c 0.78125
cmd @ 500 set reaction_rate rxn1c 1.5625
cmd @ 1000 set reaction_rate rxn1c 3.125
cmd @ 1500 set reaction_rate rxn1c 6.25
cmd @ 2000 set reaction_rate rxn1c 12.5
cmd @ 2500 set reaction_rate rxn1c 25
cmd @ 3000 set reaction_rate rxn1c 50.0
cmd @ 3500 set reaction_rate rxn1c 100.0
cmd @ 4000 set reaction_rate rxn1c 200.0

output_files stdout OUTFILE1 OUTFILE2

cmd B molcountheader stdout
cmd B molcountheader OUTFILE2
cmd i 0 TIMEEND 2 molcount stdout
cmd i 0 TIMEEND 2 molcount OUTFILE2
cmd i 0 TIMEEND 2 molmoments GPCRalpha(up) OUTFILE1

end_file