begin model				# Should get results after adding IPTG 1/2 hour later
begin parameters

    NA       6.022e23    # Avogadro's number (molecues/mol)
    V        1e-18       # Cell volume (L)
    IPTGbindingf	12/(6.022e7)	
 	IPTGbindingr	(6e-7)/(6.023e8)^2
 	DNA_activation	2.4
 	DNA_prot_disf	0	
 	DNA_prot_disr	960
 	mRNAsynth		0.5
 	translation		30
 	protein_degrade 1/(9*60)
 	rep_degrade		0.2
 	rna_deg 		0.462	
 	rep_mRNA		0.462
 	rep_mRNAtrans	15
 	dimerisationf	50
 	dimerisationr	1e-3
 	diffusion		0.92
 	

end parameters



begin molecule types

    DNA(prot,promoter~0~1)
    product_mRNA()
    Rep(dna,a,a)
    HBsu()
    IPTG(p)
    Rep_mRNA()
    Rep_mono()
    Rep_dimer()
    IPTG_outside(a)
    
   
    

end molecule types

begin seed species

   DNA(prot!0,promoter~0).Rep(dna!0,a,a)  1
   Rep(dna,a,a)                  		  100
   IPTG_outside(a)						15000  # 0.1mM concentration 
   
   		
   
end seed species

begin observables

 
    Molecules	repressor_tot Rep()
    Molecules	DNA_active DNA(prot,promoter~1)	
    Molecules   HBsu_xFP	HBsu() 
    Molecules	IPTG	IPTG(p)
    Molecules	mRNA	product_mRNA()
    Molecules	repmRNA	Rep_mRNA() 
       
        
end observables




begin reaction rules


    #IPTG binding repressor
	IPTG(p)  + DNA(prot!0,promoter~0).Rep(dna!0,a)  <-> IPTG(p)  + DNA(prot!0,promoter~0).Rep(dna!0,a!1).IPTG(p!1)  IPTGbindingf,IPTGbindingr
	IPTG(p!1).Rep(a!1,a!2,dna!3).IPTG(p!2).DNA(prot!3,promoter~0) -> IPTG(p!1).Rep(a!1,a!2,dna).IPTG(p!2) + DNA(prot,promoter~1)  DNA_activation
	IPTG(p) + Rep(dna,a) <-> IPTG(p!1).Rep(a!1,dna)  IPTGbindingf,IPTGbindingr
    # DNA-Protein binding/unbinding 
    DNA(prot,promoter~1) + Rep(dna,a,a) -> DNA(prot!0,promoter~0).Rep(dna!0,a,a)   DNA_prot_disf
    # mRNA synthesis 
    DNA(prot,promoter~1) -> DNA(prot,promoter~1) + product_mRNA()  mRNAsynth   
    # Protein synthesis 
    product_mRNA()  -> product_mRNA() + HBsu()  translation
    # Prot_degradtion() 
    HBsu()  -> 0 protein_degrade
    #degradation 
    product_mRNA()  -> 0 rna_deg 
    Rep_mono()  -> 0 rep_degrade
    
	# Repressor production
	0 -> Rep_mRNA()  rep_mRNA 
    Rep_mRNA() -> Rep_mono()  rep_mRNAtrans
    Rep_mono() + Rep_mono()  <-> Rep_dimer()  dimerisationf, dimerisationr
    Rep_dimer() + Rep_dimer() <-> Rep(dna,a,a)	dimerisationf,dimerisationr
    Rep_mRNA()  ->0 rna_deg  
   
   #IPTG diffusion into cell 
   IPTG_outside(a) -> IPTG(p)  diffusion
    
        
end reaction rules
end model

#actions
generate_network({overwrite=>1})
#writeSBML()

#resetConcentrations()
simulate({method=>"ssa",suffix=>"ssa",t_start=>0,t_end=>300,n_steps=>800})