# Simple bouncing molecules in a 2-D system

# BUG: causes seg fault due to failing wildcard parsing

graphics opengl

dim 2
species PON
species POFF
species Pol
species Xist_RNA

difc all 0 

color PON(all) green
color POFF(all) red
color Pol(all) blue
#color Pol_Tsix(all) orange
color Xist_RNA(all) yellow
display_size all(all) 5

time_start 0
time_stop 1000
time_step 0.01

boundaries 0 0 100 
boundaries 1 0 100 

start_surface DNA
panel rect +1 20 50 60 r1
end_surface

surface_drift Pol[(front)] DNA rect 2 0
surface_drift Pol[(back)] DNA rect -2 0

reaction Pactivate POFF(all) -> PON 10
reaction Pinactivate PON(all) -> POFF 20
#reaction translation Pol(front) -> Xist_RNA

surface_mol 1 PON(front) DNA rect r1 30 50
surface_mol 1 POFF(back) DNA rect r1 60 50
surface_mol 1 Pol(front) DNA rect r1 30 50
surface_mol 1 Pol(back) DNA rect r1 60 50

end_file