Dimerization cBNGL

From BioNetWiki

begin model
begin parameters
NA 6.02e23 # Avogadro's number
chi 100 # Ratio of cytoplasm volume to plasma membrane volume

V_EC 1e-9 # Volume in L 
V_CP 1e-12
V_PM V_CP/chi

# Binding constants
kpL   1e10/NA  # 1/M 1/s -> L/molec 1/s
kmL  1e-2 # 1/s
kpR  1e6/NA
kmR  1e-2

# Express ligand concentration using scaled variable
# C= log (2*KL*[L])
# => L = NA*V_EC*10**(C)/(2*(kpL/kmL))  
C=0
L_tot  V_EC*10**(C)/((kpR/kmR))
R_tot 1000  # Receptor number per cell
end parameters

begin compartments
EC  3  V_EC
PM  2 V_PM  EC
CP 3 V_CP  PM
end compartments

begin molecule types
L(d,r)
R(l)
end molecule types

begin species
@EC:L(d,r)  L_tot
@PM:R(l)     R_tot
end species


begin reaction_rules
 L(d) + L(d) <-> L(d!1).L(d!1) kpL, kmL
 L(r) + R(l) <-> L(r!1).R(l!1) kpR, kmR
end reaction_rules

begin observables
 Molecules Rdim R.R
end observables
end model

generate_network({overwrite=>1});
simulate_ode({t_end=>1000,n_steps=>50});