Lisman_bifurcate.bngl

## title: Lisman_bifurcate.bngl
## description: Autophosphorylating kinase model due to Lisman.
## reference: Lisman, J E. “A Mechanism for Memory Storage Insensitive to Molecular 
#             Turnover: A Bistable Autophosphorylating Kinase.” Proceedings of the 
#             PNAS 82, no. 9 (May 1985): 3055–57.
## author: Jim Faeder
## date: 27Feb2018

begin model 
begin parameters
  S 0.01
end parameters

begin molecule types
  K1(Y~0~P)
  P(b)
end molecule types

begin seed species
  K1(Y~0) 100
  P(b)     10
end seed species

begin observables
  Molecules K1p K1(Y~P)
end observables

begin reaction rules
R1:  K1(Y~0) -> K1(Y~P) S
R2:  K1(Y~0) + K1(Y~P) -> K1(Y~P) + K1(Y~P) 0.01
R3:  K1(Y~P) + P(b) <-> K1(Y~P!1).P(b!1) 0.4, 1 
R4:  K1(Y~P!1).P(b!1) -> K1(Y~0) + P(b) 1
end reaction rules
end model 

bifurcate({method=>"ode",parameter=>"S",par_min=>1e-5,par_max=>1e-1,\
                n_scan_pts=>100,log_scale=>1,t_end=>1000,n_steps=>2})