example.mdlr

ITERATIONS = 3000
TIME_STEP = 5e-06
VACANCY_SEARCH_DISTANCE = 100
 
INCLUDE_FILE = "icogeometry.mdl"
 
DEFINE_SURFACE_CLASSES
{
   reflect {
    REFLECTIVE = ALL_MOLECULES
   }
}
 
MODIFY_SURFACE_REGIONS
{

   CP[ALL]
   {
      SURFACE_CLASS = reflect
   }
} 

 
/* Model Parameters */
   Nav = 6.022e8               /* Avogadro number based on a volume size of 1 cubic um */
   rxn_layer_t = 0.01
   vol_wall = 56.5695045056029  /*Surface area*/
   vol_EC = 39
   vol_PM = 4.836624601  /*Surface area*/
   vol_CP = 1
   NaV = 602200000
   Lig_tot = 50
   Rec_tot = 50
   kp1 = 5e10
   km1 = 10
 
/* Diffusion bloc */
   T = 298.15      /* Temperature, K */
   h = rxn_layer_t      /* Thickness of 2D compartment, um */
   Rs = 0.002564      /* Radius of a (spherical) molecule in 3D compartment, um */
   Rc = 0.0015      /* Radius of a (cylindrical) molecule in 2D compartment, um */
   gamma = 0.5722      /* Euler's constant */
   KB = 1.3806488e-19     /* Boltzmann constant, cm^2.kg/K.s^2 */
   mu_wall = 1e-9      /* Viscosity in compartment wall, kg/um.s */
   mu_EC = 1e-9      /* Viscosity in compartment EC, kg/um.s */
   mu_PM = 1e-9      /* Viscosity in compartment PM, kg/um.s */
   mu_CP = 1e-9      /* Viscosity in compartment CP, kg/um.s */
 



#DEFINE_MOLECULES
{
  Lig(l,l)
  {
      DIFFUSION_CONSTANT_3D = Einstein_Stokes(T, mu_EC, Lig_radius)
 
  }
  Rec(a){
      DIFFUSION_CONSTANT_3D = Einstein_Stokes(T, mu_EC, Lig_radius)
  }
}


 
 
#DEFINE_REACTIONS
{
    /* Ligand-receptor binding      */
   Rec(a) + Lig(l,l!+) <-> Rec(a!1).Lig(l!1,l!+)  [kp1, km1]
}
 
 
#INSTANTIATE Scene OBJECT
{
  EC OBJECT EC {}
  CP OBJECT CP {
    PARENT = EC
    MEMBRANE = PM OBJECT CP[ALL]
  }

   ligand_rel RELEASE_SITE
   {
    SHAPE = Scene.EC[ALL] - Scene.CP[ALL]
    MOLECULE = @EC::Lig(l!1,l).Rec(a!1)
    NUMBER_TO_RELEASE = Lig_tot
    RELEASE_PROBABILITY = 1
   }
      receptor_rel RELEASE_SITE
   {
    SHAPE = Scene.EC[ALL] - Scene.CP[ALL]
    MOLECULE = Rec(a)@EC
    NUMBER_TO_RELEASE = Lig_tot
    RELEASE_PROBABILITY = 1

   }
}
 

 
/* Observables bloc */
#REACTION_DATA_OUTPUT
{
   STEP = 1e-6
 
   /*RecFree*/
   { COUNT[Rec(a), WORLD] }=> "./react_data/RecFree.dat"

   /*Ligfree*/
   { COUNT[Lig(l,l), WORLD] }=> "./react_data/LigFree.dat"
 
   /*RecBound*/
   { COUNT[Lig(l!+), WORLD]}=> "./react_data/RecBound.dat"
 
}