3.5 Component states

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# Signal transduction with receptor internalization and transcriptional reg.  #
# conception: Leonard A. Harris, Justin S. Hogg, James R. Faeder              #
# modifications by Devin Sullivan and Jose Juan Tapia
begin model
begin parameters
 
  L0              1000   # initial species counts (extensive units: quantity, not concentration)
  R0              200     
 
  kp_LR           0.1    # kinetic parameters (2nd order reaction params in vol/time units)
  km_LR           1.0
  k_R_transphos   1.0
  k_R_dephos      0.1    
end parameters


begin molecule types
  L(r,d)               # Ligand w/ receptor binding and dimerization sites.
  R(l,Y~0~P)         # Receptor with ligand and TF binding sites.
end molecule types

begin seed species
  L(r,d)            L0
  R(l,Y~0)        R0
end seed species

begin observables
  Molecules  L_Tot         L()
  Molecules  L_free        L(r)
  Molecules  L_Bound       L(r!1).R(l!1)
  Molecules  R_phospo R(Y~P)
end observables

begin reaction rules
  # receptor-ligand binding.
  L(r) + R(l)  <->  L(r!1).R(l!1)            kp_LR, km_LR
  R(l!+,Y~0) -> R(l!+,Y~P)  k_R_transphos
  R(Y~P) -> R(Y~0) k_R_dephos

end reaction rules  
       


end model

# actions #

generate_network({overwrite=>1,TextReaction=>0})
simulate({method=>"ode",t_start=>0,t_end=>5,n_steps=>1000})
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