# Smoldyn configuration file to test wildcards in reactions
# This file simulates second messenger signaling with ligand (L), receptor (R),
# and messenger (M).  R is membrane-bound and can bind L and/or M.  If it binds
# both, then M gets phosphorylated to Mp.

define krl_on	20
define krl_off	0.005
define krm_on	10
define krm_off	0.1
define k_phos	1
define k_unphos	0.01

# Graphical output
graphics opengl_good

# System space and time definitions
dim 2
boundaries x 0 100
boundaries y 0 100
time_start 0
time_stop 1000
time_step 0.05

# Molecular species and their properties
species L R M Mp
difc L(all) 3
difc R(up) 0.2
difc M(all) 2
difc Mp(all) 1.5
color L(all) green
color R(all) grey
color M(all) blue
color Mp(all) red
display_size all(all) 2

# Reactions
reaction_rule rxnlr	L(fsoln) + R*(up) <-> LR*(up)	krl_on krl_off
reaction_rule rxnrm	*R(up) + M*(bsoln) <-> *RM*(up)	krm_on krm_off
reaction_rule rxnphos	LRM(up) -> LRMp(up)		k_phos
reaction_rule rxnunphos	*Mp(soln) -> *M(soln)		k_unphos

expand_rules all

# Surface parameters
start_surface membrane
action all(all) both reflect
panel rect +1 0 50 100
end_surface

start_surface outsides
action all(all) both reflect
panel rect +x 0 0 100
panel rect -x 100 0 100
panel rect +y 0 0 100
panel rect -y 0 100 100
end_surface

# initial molecules
surface_mol 20 R(up) membrane all all
mol 20 L 50 80
mol 20 M 50 20

#text_display time Mp M* LR*(all)

end_file