## title: ABp.bngl
## description: Simple model of enzyme kinetics in which A is a kinase and B is a
##              phosphorylabe substrate.
## author: Jim Faeder
## date: 27Feb2018
## note: Units consistent with uM for concentration, um^3=fL for volume
begin model
begin parameters
    # Cell volume
    V    1 # units: um^3
    # Conversion factor from uM to 1/um^3
    NaV  602*V
    # Rate constants
    kp1  1.0/(NaV) # 1/uM 1/s -> 1/molecules 1/s
    km1  1.0e-1 # 1/s
    k2   1.0e-2 # 1/s

   # Initial concentrations
    A0   0.01*NaV # uM -> molecules/cell
    B0   1.0*NaV  # uM -> molecules/cell
end parameters
begin molecule types
    A(b)
    B(a,Y~0~p)
end molecule types
begin seed species
    A(b)      A0
    B(a,Y~0)  B0
end seed species
begin observables
    Molecules Bu B(a,Y~0)
    Molecules Bp B(a,Y~p)
    Molecules AB A(b!1).B(a!1)
end observables
begin reaction rules
    ABbind: A(b) + B(a,Y~0) <-> A(b!1).B(a!1,Y~0) kp1, km1
    ABphos: A(b!1).B(a!1,Y~0) -> A(b) + B(a,Y~p) k2
end reaction rules
end model

# simulate the expanded network use ODE's
simulate({method=>"ode", t_end=>20000,n_steps=>1000})