# Smoldyn configuration file for transposon dynamics
# Units are microns and seconds

define k0f	1e5
define k0r	139
define k1f	0.32
define k1r	1.2e2
define k2f	4.3e-4
define k2r	1e-10
define k3	1.4e-3
define Dp	15
define Ds	5e-4

define LEN	500^(1/3)

# Graphical output
graphics opengl
graphic_iter 100

# System space and time definitions
dim 3
boundaries x 0 LEN p
boundaries y 0 LEN p
boundaries z 0 LEN p

time_start 0
time_stop 100
time_step 0.0001

# Molecular species and their properties
species A-B T2 T2nsb

difc A-B	Ds
difc T2		Dp
color A-B	blue
color T2	red
color T2nsb	green

display_size all 2

# Reactions
reaction 	rxnT2nsb	T2 <-> T2nsb	k0f k0r	
reaction_rule	rxnABbind	A-B*|*A-B + T2 <-> T2A-B*|*A-BT2	k1f k1r
reaction_rule	rxnassemble	T2&A-B <-> AT2B	k2f k2r
reaction_rule	rxnexcise	AT2B -> A-B + T2 + X	k3

expand_rules all

# initial molecules
mol 1 A-B LEN/2 LEN/2 LEN/2
mol 10 T2 u u u

#output_files transposaseout.txt
#output_format CSV
#cmd B molcountheader transposaseout.txt
#cmd N 100 molcount transposaseout.txt

end_file