directive duration 57600.0 points 10000
directive scale 500.0
directive plot {W} (*this will plot fluorescent output only*)

(*rate constants*)
def normal = 0.0003 (* normal toehold binding rate constant /nM/s *)
def slow = 0.000015 (* slow toehold binding rate constant /nM/s *)
def unbind = 0.1126 (* normal toehold dissociation rate constant /s *)
def fastunbind = 0.95 (* fast toehold dissociation rate constant /s *)

new T @slow,fastunbind
new Z'@normal,unbind
new Q @normal,unbind

(*strands*)
(12* {Z Z'^ T^ X} (*input concentration; "10" = 2nM*)
|14* <Z'^*>[T^* X* Y T^]{Q^*} (*complex A*)
|5* <Y T^ Q^> (*complex B*)
|10* <T^*>[Y* T^*]{W} (*complex C*)
|20* {Y T^} (*complex D*)
|10* <T^*>[W*]) (*fluorescent reporter*)