\documentclass[gaussianfits]{article}

\usepackage[english]{babel}
\usepackage[utf8x]{inputenc}
\usepackage{amsmath}
\usepackage{graphicx}
\usepackage{indentfirst}
\date{}

\title{SUPPLEMENTAL MATERIAL\\Influence of Model Resolution on Geometric Simulations of Antibody Aggregation}
\author{Kasra Manavi, Bruna Jacobson, Brittany Hoard and Lydia Tapia}

\begin{document}

\maketitle

\section{BioNetGen Files for Rule-Based Model}

Below are the files which describe the rule-based model in .bngl format. These specific files simulate the 0\% resolution model, to simulate other resolutions only the rate constants listed near the top of the files need to be changed.

\subsection{Strand I BNGL File}
{\scriptsize
\begin{verbatim}
begin model
# comments are written after hashtags

#Tr = tropomyosin
#IgE = Receptor

begin parameters
	TrTot	100 #molecules
	IgEtot	1000

#Backward rate:
	kr 0.01 #1/seconds
#Forward rate:
	kf1 = 1.00 #1/s*mol
	kf2 = 0.07
	kf3 = 1.00
	kf4 = 0.00
#Zero forward rate:
	kf_zero = 0.00

end parameters


begin molecule types
	Tr(a,b,c,d,f,g)
	IgE(s,s)
end molecule types

begin seed species
	Tr(a,b,c,d,f,g)	TrTot
	IgE(s,s)        IgEtot
end seed species

begin observables

#Binding of 1 IgE to 1 site on Tr:

	Molecules TIa Tr(a!1,b,c,d,f,g).IgE(s!1,s)
	Molecules TIb Tr(a,b!1,c,d,f,g).IgE(s!1,s)
	Molecules TIc Tr(a,b,c!1,d,f,g).IgE(s!1,s)
	Molecules TId Tr(a,b,c,d!1,f,g).IgE(s!1,s)
	Molecules TIf Tr(a,b,c,d,f!1,g).IgE(s!1,s)
	Molecules TIg Tr(a,b,c,d,f,g!1).IgE(s!1,s)

#Binding of 2 IgE to Tr:

#One site each:
	Molecules TIaIb Tr(a!1,b!2,c,d,f,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIaIc Tr(a!1,b,c!2,d,f,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIaId Tr(a!1,b,c,d!2,f,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIaIf Tr(a!1,b,c,d,f!2,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIaIg Tr(a!1,b,c,d,f,g!2).IgE(s!1,s).IgE(s!2,s)

	Molecules TIbIc Tr(a,b!1,c!2,d,f,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIbId Tr(a,b!1,c,d!2,f,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIbIf Tr(a,b!1,c,d,f!2,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIbIg Tr(a,b!1,c,d,f,g!2).IgE(s!1,s).IgE(s!2,s)

	Molecules TIcId Tr(a,b,c!1,d!2,f,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIcIf Tr(a,b,c!1,d,f!2,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIcIg Tr(a,b,c!1,d,f,g!2).IgE(s!1,s).IgE(s!2,s)

	Molecules TIdIf Tr(a,b,c,d!1,f!2,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIdIg Tr(a,b,c,d!1,f,g!2).IgE(s!1,s).IgE(s!2,s)

	Molecules TIfIg Tr(a,b,c,d,f!1,g!2).IgE(s!1,s).IgE(s!2,s)

# 3 IgEs bind to Tr

# each of the 3 IgEs binds to a different site:

	Molecules TIaIbIc Tr(a!1,b!2,c!3,d,f,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIaIbId Tr(a!1,b!2,c,d!3,f,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIaIbIf Tr(a!1,b!2,c,d,f!3,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIaIbIg Tr(a!1,b!2,c,d,f,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIaIcId Tr(a!1,b,c!2,d!3,f,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIaIcIf Tr(a!1,b,c!2,d,f!3,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIaIcIg Tr(a!1,b,c!2,d,f,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIaIdIf Tr(a!1,b,c,d!2,f!3,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIaIdIg Tr(a!1,b,c,d!2,f,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIaIfIg Tr(a!1,b,c,d,f!2,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIbIcId Tr(a,b!1,c!2,d!3,f,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIbIcIf Tr(a,b!1,c!2,d,f!3,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIbIcIg Tr(a,b!1,c!2,d,f,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIbIdIf Tr(a,b!1,c,d!2,f!3,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIbIdIg Tr(a,b!1,c,d!2,f,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIbIfIg Tr(a,b!1,c,d,f!2,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIcIdIf Tr(a,b,c!1,d!2,f!3,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIcIdIg Tr(a,b,c!1,d!2,f,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIcIfIg Tr(a,b,c!1,d,f!2,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIdIfIg Tr(a,b,c,d!1,f!2,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

# 4 IgEs bind to Tr

# One IgE per site:

	Molecules TIaIbIcId Tr(a!1,b!2,c!3,d!4,f,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIbIcIf Tr(a!1,b!2,c!3,d,f!4,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIbIcIg Tr(a!1,b!2,c!3,d,f,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIbIdIf Tr(a!1,b!2,c,d!3,f!4,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIbIdIg Tr(a!1,b!2,c,d!3,f,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIbIfIg Tr(a!1,b!2,c,d,f!3,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIcIdIf Tr(a!1,b,c!2,d!3,f!4,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIcIdIg Tr(a!1,b,c!2,d!3,f,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIcIfIg Tr(a!1,b,c!2,d,f!3,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIdIfIg Tr(a!1,b,c,d!2,f!3,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)

	Molecules TIbIcIdIf Tr(a,b!1,c!2,d!3,f!4,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIbIcIdIg Tr(a,b!1,c!2,d!3,f,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIbIcIfIg Tr(a,b!1,c!2,d,f!3,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIbIdIfIg Tr(a,b!1,c,d!2,f!3,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)

	Molecules TIcIdIfIg Tr(a,b,c!1,d!2,f!3,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)

# 5 IgEs bind to Tr:

	Molecules TIaIbIcIdIf Tr(a!1,b!2,c!3,d!4,f!5,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s).IgE(s!5,s)
	Molecules TIaIbIcIdIg Tr(a!1,b!2,c!3,d!4,f,g!5).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s).IgE(s!5,s)
	Molecules TIaIbIcIfIg Tr(a!1,b!2,c!3,d,f!4,g!5).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s).IgE(s!5,s)
	Molecules TIaIbIdIfIg Tr(a!1,b!2,c,d!3,f!4,g!5).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s).IgE(s!5,s)
	Molecules TIaIcIdIfIg Tr(a!1,b,c!2,d!3,f!4,g!5).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s).IgE(s!5,s)
	Molecules TIbIcIdIfIg Tr(a,b!1,c!2,d!3,f!4,g!5).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s).IgE(s!5,s)

# 6 IgEs bind to Tr:

	Molecules TIaIbIcIdIfIg Tr(a!1,b!2,c!3,d!4,f!5,g!6).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s).IgE(s!5,s).IgE(s!6,s)

# Free molecules: (2)

	Molecules TrFree Tr(a,b,c,d,f,g)
	Molecules IgEfree IgE(s,s)

end observables

begin functions
	TrBound() TrTot-TrFree()
end functions

begin reaction rules

Tr(a,b) + IgE(s,s) <-> Tr(a!1,b).IgE(s!1,s) kf1,kr
Tr(a,b!2).IgE(s!2,s) + IgE(s,s) <-> Tr(a!1,b!2).IgE(s!1,s).IgE(s!2,s) kf2,kr

Tr(a,b,c,d) + IgE(s,s) <-> Tr(a,b!1,c,d).IgE(s!1,s) kf1,kr
Tr(a!2,b,c).IgE(s!2,s) + IgE(s,s) <-> Tr(a!2,b!1,c).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(a,b,c!2).IgE(s!2,s) + IgE(s,s) <-> Tr(a,b!1,c!2).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(a,b,c,d!2).IgE(s!2,s) + IgE(s,s) <-> Tr(a,b!1,c,d!2).IgE(s!1,s).IgE(s!2,s) kf3,kr
Tr(a!2,b,c!3).IgE(s!2,s).IgE(s!3,s) + IgE(s,s) <-> Tr(a!2,b!1,c!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s) kf4,kr

Tr(b,c,d,f,g) + IgE(s,s) <-> Tr(b,c!1,d,f,g).IgE(s!1,s) kf1,kr
Tr(b!2,c,d).IgE(s!2,s) + IgE(s,s) <-> Tr(b!2,c!1,d).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(b,c,d!2).IgE(s!2,s) + IgE(s,s) <-> Tr(b,c!1,d!2).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(b,c,d,f!2).IgE(s!2,s) + IgE(s,s) <-> Tr(b,c!1,d,f!2).IgE(s!1,s).IgE(s!2,s) kf3,kr
Tr(b,c,d,f,g!2).IgE(s!2,s) + IgE(s,s) <-> Tr(b,c!1,d,f,g!2).IgE(s!1,s).IgE(s!2,s) kf3,kr
Tr(b!2,c,d!3).IgE(s!2,s).IgE(s!3,s) + IgE(s,s) <-> Tr(b!2,c!1,d!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s) kf4,kr
        
Tr(b,c,d,f,g) + IgE(s,s) <-> Tr(b,c,d!1,f,g).IgE(s!1,s) kf1,kr
Tr(c!2,d,f,g).IgE(s!2,s) + IgE(s,s) <-> Tr(c!2,d!1,f,g).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(c,d,f!2).IgE(s!2,s) + IgE(s,s) <-> Tr(c,d!1,f!2).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(c,d,f,g!2).IgE(s!2,s) + IgE(s,s) <-> Tr(c,d!1,f,g!2).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(b!2,c,d,f,g).IgE(s!2,s) + IgE(s,s) <-> Tr(b!2,c,d!1,f,g).IgE(s!1,s).IgE(s!2,s) kf3,kr
Tr(c!2,d,f!3).IgE(s!2,s).IgE(s!3,s) + IgE(s,s) <-> Tr(c!2,d!1,f!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s) kf4,kr
Tr(c!2,d,f,g!3).IgE(s!2,s).IgE(s!3,s) + IgE(s,s) <-> Tr(c!2,d!1,f,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s) kf4,kr
        
Tr(c,d,f,g) + IgE(s,s) <-> Tr(c,d,f!1,g).IgE(s!1,s) kf1,kr
Tr(d!2,f,g).IgE(s!2,s) + IgE(s,s) <-> Tr(d!2,f!1,g).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(c!2,d,f,g).IgE(s!2,s) + IgE(s,s) <-> Tr(c!2,d,f!1,g).IgE(s!1,s).IgE(s!2,s) kf3,kr
Tr(f,g!2).IgE(s!2,s) + IgE(s,s) <-> Tr(f!1,g!2).IgE(s!1,s).IgE(s!2,s) kf4,kr
        
Tr(c,d,f,g) + IgE(s,s) <-> Tr(c,d,f,g!1).IgE(s!1,s) kf1,kr
Tr(d!2,f,g).IgE(s!2,s) + IgE(s,s) <-> Tr(d!2,f,g!1).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(c!2,d,f,g).IgE(s!2,s) + IgE(s,s) <-> Tr(c!2,d,f,g!1).IgE(s!1,s).IgE(s!2,s) kf3,kr
Tr(f!2,g).IgE(s!2,s) + IgE(s,s) <-> Tr(f!2,g!1).IgE(s!1,s).IgE(s!2,s) kf4,kr

end reaction rules

end model

#actions go here

generate_network({overwrite=>1})

simulate({method=>"ode",n_steps=>1000,t_end=>0.01,print_functions=>1})

\end{verbatim}}

\subsection{Strand II BNGL File}
{\scriptsize
\begin{verbatim}
begin model
# comments are written after hashtags

#Tr = tropomyosin
#IgE = Receptor

begin parameters
	TrTot	100 #molecules
	IgEtot	1000

#Backward rate:
	kr 0.01 #1/seconds
#Forward rate:
	kf1 = 1.00 #1/s*mol
	kf2 = 0.07
	kf3 = 1.00
	kf4 = 0.00
#Zero forward rate:
	kf_zero = 0.00

end parameters


begin molecule types
	Tr(a,b,c,d,f,g)
	IgE(s,s)
end molecule types

begin seed species
	Tr(a,b,c,d,f,g)	TrTot
	IgE(s,s)        IgEtot
end seed species

begin observables

#Binding of 1 IgE to 1 site on Tr:

	Molecules TIa Tr(a!1,b,c,d,f,g).IgE(s!1,s)
	Molecules TIb Tr(a,b!1,c,d,f,g).IgE(s!1,s)
	Molecules TIc Tr(a,b,c!1,d,f,g).IgE(s!1,s)
	Molecules TId Tr(a,b,c,d!1,f,g).IgE(s!1,s)
	Molecules TIf Tr(a,b,c,d,f!1,g).IgE(s!1,s)
	Molecules TIg Tr(a,b,c,d,f,g!1).IgE(s!1,s)

#Binding of 2 IgE to Tr:

#One site each:
	Molecules TIaIb Tr(a!1,b!2,c,d,f,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIaIc Tr(a!1,b,c!2,d,f,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIaId Tr(a!1,b,c,d!2,f,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIaIf Tr(a!1,b,c,d,f!2,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIaIg Tr(a!1,b,c,d,f,g!2).IgE(s!1,s).IgE(s!2,s)

	Molecules TIbIc Tr(a,b!1,c!2,d,f,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIbId Tr(a,b!1,c,d!2,f,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIbIf Tr(a,b!1,c,d,f!2,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIbIg Tr(a,b!1,c,d,f,g!2).IgE(s!1,s).IgE(s!2,s)

	Molecules TIcId Tr(a,b,c!1,d!2,f,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIcIf Tr(a,b,c!1,d,f!2,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIcIg Tr(a,b,c!1,d,f,g!2).IgE(s!1,s).IgE(s!2,s)

	Molecules TIdIf Tr(a,b,c,d!1,f!2,g).IgE(s!1,s).IgE(s!2,s)
	Molecules TIdIg Tr(a,b,c,d!1,f,g!2).IgE(s!1,s).IgE(s!2,s)

	Molecules TIfIg Tr(a,b,c,d,f!1,g!2).IgE(s!1,s).IgE(s!2,s)

# 3 IgEs bind to Tr

# each of the 3 IgEs binds to a different site:

	Molecules TIaIbIc Tr(a!1,b!2,c!3,d,f,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIaIbId Tr(a!1,b!2,c,d!3,f,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIaIbIf Tr(a!1,b!2,c,d,f!3,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIaIbIg Tr(a!1,b!2,c,d,f,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIaIcId Tr(a!1,b,c!2,d!3,f,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIaIcIf Tr(a!1,b,c!2,d,f!3,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIaIcIg Tr(a!1,b,c!2,d,f,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIaIdIf Tr(a!1,b,c,d!2,f!3,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIaIdIg Tr(a!1,b,c,d!2,f,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIaIfIg Tr(a!1,b,c,d,f!2,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIbIcId Tr(a,b!1,c!2,d!3,f,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIbIcIf Tr(a,b!1,c!2,d,f!3,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIbIcIg Tr(a,b!1,c!2,d,f,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIbIdIf Tr(a,b!1,c,d!2,f!3,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIbIdIg Tr(a,b!1,c,d!2,f,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIbIfIg Tr(a,b!1,c,d,f!2,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIcIdIf Tr(a,b,c!1,d!2,f!3,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)
	Molecules TIcIdIg Tr(a,b,c!1,d!2,f,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIcIfIg Tr(a,b,c!1,d,f!2,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

	Molecules TIdIfIg Tr(a,b,c,d!1,f!2,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s)

# 4 IgEs bind to Tr

# One IgE per site:

	Molecules TIaIbIcId Tr(a!1,b!2,c!3,d!4,f,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIbIcIf Tr(a!1,b!2,c!3,d,f!4,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIbIcIg Tr(a!1,b!2,c!3,d,f,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIbIdIf Tr(a!1,b!2,c,d!3,f!4,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIbIdIg Tr(a!1,b!2,c,d!3,f,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIbIfIg Tr(a!1,b!2,c,d,f!3,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIcIdIf Tr(a!1,b,c!2,d!3,f!4,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIcIdIg Tr(a!1,b,c!2,d!3,f,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIcIfIg Tr(a!1,b,c!2,d,f!3,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIaIdIfIg Tr(a!1,b,c,d!2,f!3,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)

	Molecules TIbIcIdIf Tr(a,b!1,c!2,d!3,f!4,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIbIcIdIg Tr(a,b!1,c!2,d!3,f,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIbIcIfIg Tr(a,b!1,c!2,d,f!3,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)
	Molecules TIbIdIfIg Tr(a,b!1,c,d!2,f!3,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)

	Molecules TIcIdIfIg Tr(a,b,c!1,d!2,f!3,g!4).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s)

# 5 IgEs bind to Tr:

	Molecules TIaIbIcIdIf Tr(a!1,b!2,c!3,d!4,f!5,g).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s).IgE(s!5,s)
	Molecules TIaIbIcIdIg Tr(a!1,b!2,c!3,d!4,f,g!5).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s).IgE(s!5,s)
	Molecules TIaIbIcIfIg Tr(a!1,b!2,c!3,d,f!4,g!5).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s).IgE(s!5,s)
	Molecules TIaIbIdIfIg Tr(a!1,b!2,c,d!3,f!4,g!5).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s).IgE(s!5,s)
	Molecules TIaIcIdIfIg Tr(a!1,b,c!2,d!3,f!4,g!5).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s).IgE(s!5,s)
	Molecules TIbIcIdIfIg Tr(a,b!1,c!2,d!3,f!4,g!5).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s).IgE(s!5,s)

# 6 IgEs bind to Tr:

	Molecules TIaIbIcIdIfIg Tr(a!1,b!2,c!3,d!4,f!5,g!6).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s).IgE(s!4,s).IgE(s!5,s).IgE(s!6,s)

# Free molecules: (2)

	Molecules TrFree Tr(a,b,c,d,f,g)
	Molecules IgEfree IgE(s,s)

end observables

begin functions
	TrBound() TrTot-TrFree()
end functions

begin reaction rules

Tr(a,b,c) + IgE(s,s) <-> Tr(a!1,b,c).IgE(s!1,s) kf1,kr
Tr(a,b!2).IgE(s!2,s) + IgE(s,s) <-> Tr(a!1,b!2).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(a,b,c!2).IgE(s!2,s) + IgE(s,s) <-> Tr(a!1,b,c!2).IgE(s!1,s).IgE(s!2,s) kf3,kr

Tr(a,b,c,d) + IgE(s,s) <-> Tr(a,b!1,c,d).IgE(s!1,s) kf1,kr
Tr(a!2,b,c).IgE(s!2,s) + IgE(s,s) <-> Tr(a!2,b!1,c).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(a,b,c!2).IgE(s!2,s) + IgE(s,s) <-> Tr(a,b!1,c!2).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(a,b,c,d!2).IgE(s!2,s) + IgE(s,s) <-> Tr(a,b!1,c,d!2).IgE(s!1,s).IgE(s!2,s) kf3,kr
Tr(a!2,b,c!3).IgE(s!2,s).IgE(s!3,s) + IgE(s,s) <-> Tr(a!2,b!1,c!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s) kf4,kr

Tr(a,b,c,d) + IgE(s,s) <-> Tr(a,b,c!1,d).IgE(s!1,s) kf1,kr
Tr(b!2,c,d).IgE(s!2,s) + IgE(s,s) <-> Tr(b!2,c!1,d).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(b,c,d!2).IgE(s!2,s) + IgE(s,s) <-> Tr(b,c!1,d!2).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(a!2,b,c,d).IgE(s!2,s) + IgE(s,s) <-> Tr(a!2,b,c!1,d).IgE(s!1,s).IgE(s!2,s) kf3,kr
Tr(b!2,c,d!3).IgE(s!2,s).IgE(s!3,s) + IgE(s,s) <-> Tr(b!2,c!1,d!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s) kf4,kr

Tr(b,c,d,f,g) + IgE(s,s) <-> Tr(b,c,d!1,f,g).IgE(s!1,s) kf1,kr
Tr(c!2,d,f,g).IgE(s!2,s) + IgE(s,s) <-> Tr(c!2,d!1,f,g).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(c,d,f!2).IgE(s!2,s) + IgE(s,s) <-> Tr(c,d!1,f!2).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(c,d,f,g!2).IgE(s!2,s) + IgE(s,s) <-> Tr(c,d!1,f,g!2).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(b!2,c,d,f,g).IgE(s!2,s) + IgE(s,s) <-> Tr(b!2,c,d!1,f,g).IgE(s!1,s).IgE(s!2,s) kf3,kr
Tr(c!2,d,f!3).IgE(s!2,s).IgE(s!3,s) + IgE(s,s) <-> Tr(c!2,d!1,f!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s) kf4,kr
Tr(c!2,d,f,g!3).IgE(s!2,s).IgE(s!3,s) + IgE(s,s) <-> Tr(c!2,d!1,f,g!3).IgE(s!1,s).IgE(s!2,s).IgE(s!3,s) kf4,kr

Tr(d,f,g) + IgE(s,s) <-> Tr(d,f!1,g).IgE(s!1,s) kf1,kr
Tr(d!2,f,g).IgE(s!2,s) + IgE(s,s) <-> Tr(d!2,f!1,g).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(f,g!2).IgE(s!2,s) + IgE(s,s) <-> Tr(f!1,g!2).IgE(s!1,s).IgE(s!2,s) kf4,kr

Tr(d,f,g) + IgE(s,s) <-> Tr(d,f,g!1).IgE(s!1,s) kf1,kr
Tr(d!2,f,g).IgE(s!2,s) + IgE(s,s) <-> Tr(d!2,f,g!1).IgE(s!1,s).IgE(s!2,s) kf2,kr
Tr(f!2,g).IgE(s!2,s) + IgE(s,s) <-> Tr(f!2,g!1).IgE(s!1,s).IgE(s!2,s) kf4,kr

end reaction rules

end model

#actions go here

generate_network({overwrite=>1})

simulate({method=>"ode",n_steps=>1000,t_end=>0.01,print_functions=>1})

\end{verbatim}}

\end{document}
