BLBR.bngl

## title: BLBR.bngl
#  description: Bivalent ligand - bivalent receptor (BLBR) model, which is a simple model of polymer
#               formation by receptors that can form a chain with infinite length (in the continuum limit).
#               Simulating this model using a generate and simulate approach is problematic because
#               for these parameters the required network of complexes is very large. Using network-free 
#               simulation addresses this problem.

setOption("SpeciesLabel","HNauty");
begin parameters
 kp1 1
 km1 1
 kp2 1
 km2 1
 kp3 1
 km3 1
 R0  1000
 L0  1000
end parameters

begin species
  R(r,r) R0
  L(l,l) L0
end species

begin observables
  Species R1 R==1
  Species R2 R==2
  Species R3 R==3
  Species R4 R==4
  Species R5 R==5
  Species Rbig R>20  
end observables

begin reaction rules
# Ligand addition
R(r) + L(l,l) <-> R(r!1).L(l!1,l) kp1,km1

# Chain elongation
R(r) + L(l,l!+) <-> R(r!1).L(l!1,l!+) kp2,km2

# Ring closure
#R(r).L(l) <-> R(r!1).L(l!1) kp3,km3

end reaction rules

# Do partial network expansion and simulate the ODE's corresponding to the limited network.
#generate_network({max_stoich=>{R=>5,L=>5}})
#simulate({method=>"ode",t_end=>10,n_steps=>1000})
 
simulate({method=>"nf",t_end=>10,n_steps=>1000,get_final_state=>1})