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fceri.mdlr
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fceri.mdlr
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ITERATIONS = 3000
TIME_STEP = 5e-06
VACANCY_SEARCH_DISTANCE = 100
INCLUDE_FILE = "icogeometry.mdl"
DEFINE_SURFACE_CLASSES
{
reflect {
REFLECTIVE = ALL_MOLECULES
}
}
MODIFY_SURFACE_REGIONS
{
EC[wall]
{
SURFACE_CLASS = reflect
}
EC[obj_wall]
{
SURFACE_CLASS = reflect
}
CP[PM]
{
SURFACE_CLASS = reflect
}
CP[obj_wall]
{
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 = 0.88/rxn_layer_t /*Surface area*/
vol_EC = 39
vol_PM = 0.01/rxn_layer_t /*Surface area*/
vol_CP = 1
Lig_tot = 6.0e3
Rec_tot = 4.0e2
Lyn_tot = 2.8e2
Syk_tot = 4e2
kp1 = 0.000166057788110262*Nav
km1 = 0.00
kp2 = 1.66057788110262e-06/rxn_layer_t
km2 = 0.00
kpL = 0.0166057788110262/rxn_layer_t
kmL = 20
kpLs = 0.0166057788110262/rxn_layer_t
kmLs = 0.12
kpS = 0.0166057788110262*Nav
kmS = 0.13
pLb = 30
pLbs = 100
pLg = 1
pLgs = 3
pLS = 30
pLSs = 100
pSS = 100
pSSs = 200
dm = 0.1
dc = 0.1
/* 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 = 5
}
Lyn(U,SH2)
{
DIFFUSION_CONSTANT_2D = 10
}
Syk(tSH2,l~Y~pY,a~Y~pY)
{
DIFFUSION_CONSTANT_3D = 5
}
Rec(a,b~Y~pY,g~Y~pY)
{
DIFFUSION_CONSTANT_2D = "Einstein_Stokes(T=3, mu=2)"
}
}
#DEFINE_REACTIONS
{
/* Ligand-receptor binding */
Rec(a) + Lig(l,l) <-> Rec(a!1).Lig(l!1,l) [kp1, km1]
/* Receptor-aggregation*/
Rec(a) + Lig(l,l!+) <-> Rec(a!2).Lig(l!2,l!+) [kp2, km2]
/* Constitutive Lyn-receptor binding */
Rec(b~Y) + Lyn(U,SH2) <-> Rec(b~Y!1).Lyn(U!1,SH2) [kpL, kmL]
/* Transphosphorylation of beta by constitutive Lyn */
Lig(l!1,l!2).Lyn(U!3,SH2).Rec(a!2,b~Y!3).Rec(a!1,b~Y) -> Lig(l!1,l!2).Lyn(U!3,SH2).Rec(a!2,b~Y!3).Rec(a!1,b~pY) [pLb]
/* Transphosphorylation of gamma by constitutive Lyn */
Lig(l!1,l!2).Lyn(U!3,SH2).Rec(a!2,b~Y!3).Rec(a!1,g~Y) -> Lig(l!1,l!2).Lyn(U!3,SH2).Rec(a!2,b~Y!3).Rec(a!1,g~pY) [pLg]
/* Lyn-receptor binding through SH2 domain */
Rec(b~pY) + Lyn(U,SH2) <-> Rec(b~pY!1).Lyn(U,SH2!1) [kpLs, kmLs]
/* Transphosphorylation of beta by SH2-bound Lyn */
Lig(l!1,l!2).Lyn(U,SH2!3).Rec(a!2,b~pY!3).Rec(a!1,b~Y) -> Lig(l!1,l!2).Lyn(U,SH2!3).Rec(a!2,b~pY!3).Rec(a!1,b~pY) [pLbs]
/* Transphosphorylation of gamma by SH2-bound Lyn */
Lig(l!1,l!2).Lyn(U,SH2!3).Rec(a!2,b~pY!3).Rec(a!1,g~Y) -> Lig(l!1,l!2).Lyn(U,SH2!3).Rec(a!2,b~pY!3).Rec(a!1,g~pY) [pLgs]
/* Syk-receptor binding through tSH2 domain */
Rec(g~pY) + Syk(tSH2) <-> Rec(g~pY!1).Syk(tSH2!1) [kpS, kmS]
/* Transphosphorylation of Syk by constitutive Lyn */
Lig(l!1,l!2).Lyn(U!3,SH2).Rec(a!2,b~Y!3).Rec(a!1,g~pY!4).Syk(tSH2!4,l~Y) -> Lig(l!1,l!2).Lyn(U!3,SH2).Rec(a!2,b~Y!3).Rec(a!1,g~pY!4).Syk(tSH2!4,l~pY) [pLS]
/* Transphosphorylation of Syk by SH2-bound Lyn */
Lig(l!1,l!2).Lyn(U,SH2!3).Rec(a!2,b~pY!3).Rec(a!1,g~pY!4).Syk(tSH2!4,l~Y) -> Lig(l!1,l!2).Lyn(U,SH2!3).Rec(a!2,b~pY!3).Rec(a!1,g~pY!4).Syk(tSH2!4,l~pY) [pLSs]
/* Transphosphorylation of Syk by Syk not phosphorylated on aloop */
Lig(l!1,l!2).Syk(tSH2!3,a~Y).Rec(a!2,g~pY!3).Rec(a!1,g~pY!4).Syk(tSH2!4,a~Y) -> Lig(l!1,l!2).Syk(tSH2!3,a~Y).Rec(a!2,g~pY!3).Rec(a!1,g~pY!4).Syk(tSH2!4,a~pY) [pSS]
/* Transphosphorylation of Syk by Syk phosphorylated on aloop */
Lig(l!1,l!2).Syk(tSH2!3,a~pY).Rec(a!2,g~pY!3).Rec(a!1,g~pY!4).Syk(tSH2!4,a~Y) -> Lig(l!1,l!2).Syk(tSH2!3,a~pY).Rec(a!2,g~pY!3).Rec(a!1,g~pY!4).Syk(tSH2!4,a~pY) [pSSs]
/* Dephosphorylation of Rec beta */
Rec(b~pY) -> Rec(b~Y) [dm]
/* Dephosphorylation of Rec gamma */
Rec(g~pY) -> Rec(g~Y) [dm]
/* Dephosphorylation of Syk at membrane */
Syk(tSH2!+,l~pY) -> Syk(tSH2!+,l~Y) [dm]
Syk(tSH2!+,a~pY) -> Syk(tSH2!+,a~Y) [dm]
/* Dephosphorylation of Syk in cytosol */
Syk(tSH2,l~pY) -> Syk(tSH2,l~Y) [dc]
Syk(tSH2,a~pY) -> Syk(tSH2,a~Y) [dc]
}
#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,l)
NUMBER_TO_RELEASE = Lig_tot
RELEASE_PROBABILITY = 1
}
lyn_rel RELEASE_SITE
{
SHAPE = Scene.CP[ALL]
MOLECULE = @PM::Lyn(U,SH2)
NUMBER_TO_RELEASE = Lyn_tot
RELEASE_PROBABILITY = 1
}
syk_rel RELEASE_SITE
{
SHAPE = Scene.CP[ALL]
MOLECULE = @CP::Syk(tSH2,l~Y,a~Y)
NUMBER_TO_RELEASE = Syk_tot
RELEASE_PROBABILITY = 1
}
receptor_rel RELEASE_SITE
{
SHAPE = Scene.CP[ALL]
MOLECULE = @PM::Rec(a,b~Y,g~Y)
NUMBER_TO_RELEASE = Rec_tot
RELEASE_PROBABILITY = 1
}
}
/* Observables bloc */
#REACTION_DATA_OUTPUT
{
STEP = 5e-4
/*LynFree*/
{COUNT[Lyn(U,SH2), WORLD] } => "./react_data/LynFree.dat"
//{COUNT[Rec.Rec, WORLD] } => "./react_data/RecDim.dat"
//COUNT[Lyn(U!1).Rec(b~Y!1,a), WORLD]} => "./react_data/LynRec.dat"
//COUNT[Lyn(U!1).Rec(b~Y!1,a!2).Lig(l!2), WORLD]} => "./react_data/LynRecLig.dat"
{COUNT[Rec(b~pY!?), WORLD] } => "./react_data/RecPbeta.dat"
{COUNT[Rec(a!1).Lig(l!1,l), WORLD] + COUNT[Rec(a), WORLD]} => "./react_data/RecMon.dat"
{COUNT[Rec(a!1).Lig(l!1,l!2).Rec(a!2), WORLD]} => "./react_data/RecDim.dat"
{COUNT[Lig(l!1,l!2).Lyn(U!3,SH2).Rec(a!2,b!3).Rec(a!1,b), WORLD]} => "./react_data/RecRecLigLyn.dat"
{COUNT[Rec(g~pY),WORLD] + COUNT[Rec(g~pY!+), WORLD] } => "./react_data/RecPgamma.dat"
{COUNT[Rec(g~pY!1).Syk(tSH2!1), WORLD] } => "./react_data/RecSyk.dat"
{COUNT[Rec(g~pY!1).Syk(tSH2!1,a~pY), WORLD] } => "./react_data/RecSykPS.dat"
//{COUNT[Syk, WORLD] } => "./react_data/SykTest.dat"
//{COUNT[Lyn, WORLD] } => "./react_data/LynTest.dat"
//{COUNT[Rec, WORLD] } => "./react_data/RecTest.dat"
}