#This rule is for dealing with photons, see the bottom modifications for more details
'PhotRadiat'  -> Photon(act) @ 0
'PhotDe-Rad' Photon(act) -> @ 0

#This is the inactivation of the Cph8 chromophore by action of photons
'PhotoInact' Cph8(act~On), Photon(act) -> Cph8(act~Off) @ $INF

#This is the spontaneous reactivation of the enzyme
'Cph8-Tr-On' Cph8(act~Off) <-> Cph8(act~On) @ 0.01, 0.005

#This is the reaction of phosphrilation of OmpR by action of Cph8
'SubstActBi' OmpR(act~Off), Cph8(act~On) -> OmpR(act~Off!1), Cph8(act~On!1) @ 1.0
'SubstActPh' OmpR(act~Off!1), Cph8(act~On!1) -> OmpR(act~On!1), Cph8(act~On!1) @ 200
'SubstActUb' OmpR(act~On!1), Cph8(act~On!1) -> OmpR(act~On), Cph8(act~On) @ 1.0

#This is the spontaneous auto-dephosphorilation of OmpR
'AutoDe-Act' OmpR(act~On) -> OmpR(act~Off) @ 1.0

#This is the binding of OmpR to the site OmpC
'OmpRBdOmpC' OmpR(act~On), OmpR(act~On), OmpR(act~On), OmpC(S1,S2,S3) <-> OmpR(act~On!1), OmpR(act~On!2), OmpR(act~On!3), OmpC(S1!2,S2!1,S3!3) @ 3.0, 2.0

#This is the output of site OmpC, that output being protein pCI, the other rate is the degradation of said protein
'pCI-Output' OmpR(act~On!1), OmpR(act~On!2), OmpR(act~On!3), OmpC(S1!2,S2!1,S3!3) -> OmpR(act~On), OmpR(act~On), OmpR(act~On), OmpC(S1,S2,S3), pCI(act) @ 4.0
'pCI-Degrad' pCI(act?) ->  @ 0.2

#This is the binding equilibrium of protein pCI to site sCI
'pCI-Bd-sCI' pCI(act), sCI(act) <-> pCI(act!1), sCI(act!1) @ 10, 1

#This is the basal expression of site sCI
'sCIBaseExp' sCI(act) -> sCI(act), mRNA() @ 1.0


%init: 348 * (OmpR(act~Off)) #
%init: 12 * (OmpR(act~On)) #
%init: 50 * (Cph8(act~Off)) #
%init: 130 * (Cph8(act~On)) #
%init: 3 * (OmpC(S1,S2,S3), sCI(act)) #

#%obs: 'Cph8 Off' Cph8(act~Off?)
#%obs: 'Cph8 On' Cph8(act~On?)
#%obs: 'OmpR On' OmpR(act~On?)
#%obs: 'OmpR Off' OmpR(act~Off?)
#%obs: 'OmpC Unbound' OmpC(S1, S2, S3)
#%obs: 'OmpC Bound' OmpC(S1!_, S2!_, S3!_)
#%obs: 'Prot CI' pCI(act?)
#%obs: 'Prot CI bound' pCI(act!_)
%obs: 'PoPs' mRNA()
#%obs: 'Light' Photon(act)

##%obs: 'Cph8 On B' Cph8(act~On!_)
##%obs: 'OmpR On B' OmpR(act~On!_)
##%obs: 'OmpR Off B' OmpR(act~Off!_)
##%obs: 'OmpC B' OmpC(S1!_, S2!_, S3!_)


#This perturbation introduces a flux of 200 photons per second on a 10 second time period, at the end of which ALL photons disappear
%mod: $T>100 do 'PhotRadiat':=200
%mod: $T>150.0 do 'PhotRadiat':=0
%mod: $T>150.0 do 'PhotDe-Rad':=$INF