#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 CcaS chromophore by action of photons 'PhotoInact' CcaS(act~Off), Photon(act) -> CcaS(act~On) @ $INF #This is the reaction of phosphrilation of CcaR by action of CcaS 'SubstActBi' CcaR(act~Off), CcaS(act~On) -> CcaR(act~Off!1), CcaS(act~On!1) @ 1.0 'SubstActPh' CcaR(act~Off!1), CcaS(act~On!1) -> CcaR(act~On!1), CcaS(act~On!1) @ 200 'SubstActUb' CcaR(act~On!1), CcaS(act~On!1) -> CcaR(act~On), CcaS(act~On) @ 1.0 #This is the spontaneous auto-dephosphorilation of CcaR 'AutoDe-Act' CcaR(act~On) -> CcaR(act~Off) @ 1.0 #This is the binding of CcaR to the site CcaSite 'CcaRBdSite' CcaR(act~On), CcaR(act~On), CcaSite(S1,S2) <-> CcaR(act~On!1), CcaR(act~On!2), CcaSite(S1!1,S2!2) @ 3.0, 0.1 #This is the unbinding and production of PopS 'CcaSitePop' CcaR(act~On!1), CcaR(act~On!2), CcaSite(S1!1,S2!2) -> CcaR(act~On), CcaR(act~On), CcaSite(S1,S2), mRNA() @ 1.0 %init: 348 * (CcaR(act~Off)) # %init: 12 * (CcaR(act~On)) # %init: 180 * (CcaS(act~Off)) # %init: 3 * (CcaSite(S1,S2)) # #%obs: 'CcaS Off' CcaS(act~Off?) #%obs: 'CcaS On' CcaS(act~On?) #%obs: 'CcaR On' CcaR(act~On?) #%obs: 'CcaR Off' CcaR(act~Off?) #%obs: 'CcaSite Unbound' CcaSite(S1, S2) #%obs: 'CcaSite Bound' CcaSite(S1!_, S2!_) %obs: 'PoPs' mRNA() #%obs: 'Light' Photon(act) ##%obs: 'CcaS On B' CcaS(act~On!_) ##%obs: 'CcaR On B' CcaR(act~On!_) ##%obs: 'CcaR Off B' CcaR(act~Off!_) ##%obs: 'CcaSite B' CcaSite(S1!_, S2!_) #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>100.0 do 'PhotRadiat':=200 %mod: $T>150.0 do 'PhotRadiat':=0 %mod: $T>150.0 do 'PhotDe-Rad':=$INF