begin model begin molecule types L(t) #ligand molecule T(l,Phos~U~P) #receptor complex CheY(Phos~U~P) CheZ() end molecule types begin observables Molecules phosphorylated_CheY CheY(Phos~P) Molecules phosphorylated_CheA T(Phos~P) Molecules bound_ligand L(t!1).T(l!1) end observables begin parameters NaV2 6.02e8 #Unit conversion to cellular concentration M/L -> #/um^3 L0 5e3 #number of ligand molecules T0 7000 #number of receptor complexes CheY0 20000 CheZ0 6000 k_lr_bind 8.8e6/NaV2 #ligand-receptor binding k_lr_dis 35 #ligand-receptor dissociation k_T_phos 15 #receptor complex autophosphorylation k_Y_phos 3.8e6/NaV2 #receptor complex phosphorylates Y k_Y_dephos 8.6e5/NaV2 #Z dephosphorylates Y end parameters begin reaction rules LR: L(t) + T(l) <-> L(t!1).T(l!1) k_lr_bind, k_lr_dis #Free vs. ligand-bound receptor complexes autophosphorylates at different rates FreeTP: T(l,Phos~U) -> T(l,Phos~P) k_T_phos BoundTP: L(t!1).T(l!1,Phos~U) -> L(t!1).T(l!1,Phos~P) k_T_phos*0.2 YP: T(Phos~P) + CheY(Phos~U) -> T(Phos~U) + CheY(Phos~P) k_Y_phos YDep: CheZ() + CheY(Phos~P) -> CheZ() + CheY(Phos~U) k_Y_dephos end reaction rules begin species L(t) L0 T(l,Phos~U) T0*0.8 T(l,Phos~P) T0*0.2 CheY(Phos~U) CheY0*0.5 CheY(Phos~P) CheY0*0.5 CheZ() CheZ0 end species end model generate_network({overwrite=>1}) simulate({method=>"ssa", t_end=>3, n_steps=>100})