From BioNetWiki
begin model
begin parameters
f 1 # Fraction of the cell to simulate
NA 6.02e23 # Avogadro's number (molecues/mol)
cell_dens 1e6 # Cell density in cells/ml - standard exptl. units
Vo f/(1000*cell_dens) # Effective extracelular volume of a cell
Vcyt f*3.0e-12 # Cytoplasmic volume (L)
Vmem Vcyt/chi
H 1e-2 # steric hindrance factor for cross-linking
chi 200 # enhancement factor for membrane reactions
# chi ~ (cell radius)/(3*membrane thickness)
# All concentrations are converted to number per cell
Lig_conc 1e-9 # Ligand concentration input in molar units
Lig_tot Lig_conc*NA*Vo # Copy number per cell
Rec_tot 1e5 # Copy number per cell
Lyn_tot 1e5 # Copy number per cell
Syk_tot 5e3 # Copy number per cell
# Unimolecular rate constants in 1/s
# Bimoelecular rate constants in 1/s 1/(number/cell)
# Ligand binding
kp1 2.5e6/(NA*Vo)
km1 0.01
# Receptor cross-linking
kp2 2.5e6*H/(NA*Vmem)
km2 0.01
KxRT= kp2/km2*Rec_tot
# Constitutive Lyn binding
kpL chi*1e5/(NA*Vcyt)
kmL 20
# Constitutive Lyn transphosphorylation of beta and gamma
pLb 30
pLg 1
# Syk binding to phosphorylated gamma
kpS 1e8/(NA*Vcyt)
kmS 0.13
# Lyn binding to phosphorylated beta
kpLs chi*1e5/(NA*Vcyt)
kmLs 0.12
# SH2-bound Lyn transphosphorylation of beta and gamma
pLbs 100
pLgs 3
# Syk transautophosphorylation
pSS 100
# dephosphorylation of receptor
dm 20
# dephosphorylation of Syk
dc 20
end parameters
begin molecule types
end molecule types
begin species
end species
begin reaction_rules
end reaction_rules
begin observables
end observables
end model
