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spatial_compartmental.bngl
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spatial_compartmental.bngl
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begin model
begin parameters
L0 1000 # Initial number of L molecules
R0 20 # Initial number of R molecules
kp1 1 # Bimolecular rate constant for L-R binding (1/# 1/s)
km1 1 # Unimolecular rate constant for L-R unbinding (1/s)
p1 1
d1 0.1
end parameters
begin molecule types
L(r,d)
R(l,Y~0~P)
end molecule types
begin species
L(r,d) L0
R(l,Y~0) R0
end species
begin compartments
EC 3 vol_EC
PM 2 sa_PM*width EC
CP 3 vol_CP PM
EM 2 sa_EM*width CP
EN 3 vol_EN EM
end compartments
begin reaction rules
L(r) + R(l) <-> L(r!1).R(l!1) kp1, km1
R(l!+,Y~0) -> R(l!+,Y~P) p1
R(Y~P) -> R(Y~0) d1
L(d) + L(d) <-> L(d!1).L(d!1) kp_LL,km_LL
@PM:R().R() -> @EM:R().R() k_r_endo
@EM:R() -> @PM:R() k_recycle
end reaction rules
begin observables
Molecules L_tot L()
Molecules L_free L(r)
Molecules L_bound L(r!1).R(l!1)
Molecules R_phospho_unbound R(Y~P)
Molecules R_phospho R(Y~P!?)
Species R_Dimers_PM @PM:R.R
Species R_Dimers_EM @EM:R.R
end observables
end model
# generate_network({overwrite=>1})}
simulate({method=>"ode",t_end=>5,n_steps=>120})