def makeModel():
# create container for model
num = 1 # number of compartments
model = moose.Neutral( '/model' )
compartment = moose.CylMesh( '/model/compartment' )
compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
# create molecules and reactions
s = moose.Pool( '/model/compartment/s' )
#####################################################################
# Put in endo compartment. Add molecule s
endo = moose.EndoMesh( '/model/endo' )
endo.isMembraneBound = True
endo.surround = compartment
es = moose.Pool( '/model/endo/s' )
rXfer = moose.Reac( '/model/endo/rXfer' )
#####################################################################
moose.connect( rXfer, 'sub', s, 'reac' )
moose.connect( rXfer, 'prd', es, 'reac' )
volRatio = compartment.volume / endo.volume
rXfer.Kf = 0.04 # 0.04/sec
rXfer.Kb = 0.02 # 0.02/sec
#####################################################################
fixXreacs.fixXreacs( '/model' )
#fixXreacs.restoreXreacs( '/model' )
#fixXreacs.fixXreacs( '/model' )
#####################################################################
# Make solvers
ksolve = moose.Ksolve( '/model/compartment/ksolve' )
dsolve = moose.Dsolve( '/model/dsolve' )
eksolve = moose.Ksolve( '/model/endo/ksolve' )
edsolve = moose.Dsolve( '/model/endo/dsolve' )
stoich = moose.Stoich( '/model/compartment/stoich' )
stoich.compartment = compartment
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.path = "/model/compartment/##"
assert( dsolve.numPools == 1 )
s.vec.concInit = [1]*num
estoich = moose.Stoich( '/model/endo/stoich' )
estoich.compartment = endo
estoich.ksolve = eksolve
estoich.dsolve = edsolve
estoich.path = "/model/endo/##"
assert( edsolve.numPools == 2 )
edsolve.buildMeshJunctions( dsolve )
plot1 = moose.Table2( '/model/plot1' )
plot2 = moose.Table2( '/model/plot2' )
moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
plot3 = moose.Table2( '/model/plot3' )
plot4 = moose.Table2( '/model/plot4' )
moose.connect( '/model/plot3', 'requestOut', s, 'getConc' )
moose.connect( '/model/plot4', 'requestOut', es, 'getConc' )
def makeModel():
# create container for model
num = 1 # number of compartments
model = moose.Neutral('/model')
compartment = moose.CylMesh('/model/compartment')
compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
# create molecules and reactions
prd = moose.Pool('/model/compartment/prd')
rXfer = moose.Reac('/model/compartment/rXfer')
#####################################################################
# Put in endo compartment. Add molecule s
endo = moose.EndoMesh('/model/endo')
endo.isMembraneBound = True
endo.surround = compartment
sub = moose.Pool('/model/endo/sub')
enzPool = moose.Pool('/model/endo/enzPool')
enzPool.concInit = eInit
enz = moose.MMenz('/model/endo/enzPool/enz')
#####################################################################
moose.connect(enz, 'sub', sub, 'reac')
moose.connect(enz, 'prd', prd, 'reac')
moose.connect(enzPool, 'nOut', enz, 'enzDest')
moose.connect(rXfer, 'sub', prd, 'reac')
moose.connect(rXfer, 'prd', sub, 'reac')
rXfer.Kf = Kf # 0.04/sec
rXfer.Kb = 0.0 # 0.02/sec
enz.Km = Km
enz.kcat = kcat
# v = es.kcat/(s+Km)
# v = Kf * conc.
#####################################################################
fixXreacs.fixXreacs('/model')
fixXreacs.restoreXreacs('/model')
fixXreacs.fixXreacs('/model')
#####################################################################
# Make solvers
ksolve = moose.Ksolve('/model/compartment/ksolve')
dsolve = moose.Dsolve('/model/dsolve')
eksolve = moose.Ksolve('/model/endo/ksolve')
edsolve = moose.Dsolve('/model/endo/dsolve')
stoich = moose.Stoich('/model/compartment/stoich')
stoich.compartment = compartment
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.path = "/model/compartment/##"
assert (dsolve.numPools == 2)
sub.vec.concInit = subInit
enzPool.vec.concInit = eInit
estoich = moose.Stoich('/model/endo/stoich')
estoich.compartment = endo
estoich.ksolve = eksolve
estoich.dsolve = edsolve
estoich.path = "/model/endo/##"
assert (edsolve.numPools == 3)
edsolve.buildMeshJunctions(dsolve)
plot1 = moose.Table2('/model/plot1')
plot2 = moose.Table2('/model/plot2')
moose.connect('/model/plot1', 'requestOut', sub, 'getN')
moose.connect('/model/plot2', 'requestOut', prd, 'getN')
plot3 = moose.Table2('/model/plot3')
plot4 = moose.Table2('/model/plot4')
moose.connect('/model/plot3', 'requestOut', sub, 'getConc')
moose.connect('/model/plot4', 'requestOut', prd, 'getConc')
def makeModel():
# create container for model
num = 1 # number of compartments
model = moose.Neutral('/model')
compartment = moose.CylMesh('/model/compartment')
compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
# create molecules and reactions
s = moose.Pool('/model/compartment/s')
rXfer = moose.Reac('/model/compartment/rXfer')
#####################################################################
# Put in endo compartment. Add molecule s
endo = moose.EndoMesh('/model/endo')
# Note that the chanPool must be on the 'In' compartment.
#chanPool = moose.Pool( '/model/compartment/chanPool' )
#chan = moose.ConcChan( '/model/compartment/chanPool/chan' )
chanPool = moose.Pool('/model/endo/chanPool')
chan = moose.ConcChan('/model/endo/chanPool/chan')
endo.isMembraneBound = True
endo.surround = compartment
es = moose.Pool('/model/endo/s')
#####################################################################
moose.connect(rXfer, 'sub', s, 'reac')
moose.connect(rXfer, 'prd', es, 'reac')
moose.connect(chanPool, 'nOut', chan, 'setNumChan')
moose.connect(chan, 'out', s, 'reac')
moose.connect(chan, 'in', es, 'reac')
volRatio = compartment.volume / endo.volume
rXfer.Kf = 0.0 # 0.02/sec
rXfer.Kb = 0.0 #
s.concInit = 0.001
chanPool.nInit = 1000.0
# Flux (mM/s) = permeability * N * (conc_out - conc_in )
chan.permeability = 0.1 * chanPool.volume * 6.022e23 / chanPool.nInit
#####################################################################
fixXreacs.fixXreacs('/model')
#fixXreacs.restoreXreacs( '/model' )
#fixXreacs.fixXreacs( '/model' )
#####################################################################
# Make solvers
ksolve = moose.Ksolve('/model/compartment/ksolve')
dsolve = moose.Dsolve('/model/dsolve')
eksolve = moose.Ksolve('/model/endo/ksolve')
edsolve = moose.Dsolve('/model/endo/dsolve')
stoich = moose.Stoich('/model/compartment/stoich')
stoich.compartment = compartment
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.path = "/model/compartment/##"
assert (dsolve.numPools == 2)
estoich = moose.Stoich('/model/endo/stoich')
estoich.compartment = endo
estoich.ksolve = eksolve
estoich.dsolve = edsolve
estoich.path = "/model/endo/##"
assert (edsolve.numPools == 2)
edsolve.buildMeshJunctions(dsolve)
plot1 = moose.Table2('/model/plot1')
plot2 = moose.Table2('/model/plot2')
plot3 = moose.Table2('/model/plot3')
moose.connect('/model/plot1', 'requestOut', s, 'getN')
moose.connect('/model/plot2', 'requestOut', es, 'getN')
moose.connect('/model/plot3', 'requestOut',
'/model/compartment/s_xfer_endo', 'getN')
plot4 = moose.Table2('/model/plot4')
plot5 = moose.Table2('/model/plot5')
plot6 = moose.Table2('/model/plot6')
moose.connect('/model/plot4', 'requestOut', s, 'getConc')
moose.connect('/model/plot5', 'requestOut', es, 'getConc')
moose.connect('/model/plot6', 'requestOut',
'/model/compartment/s_xfer_endo', 'getConc')
def makeModel():
# create container for model
num = 1 # number of compartments
model = moose.Neutral( '/model' )
compartment = moose.CylMesh( '/model/compartment' )
compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
# create molecules and reactions
u = moose.Pool( '/model/compartment/u' )
#####################################################################
# Put in endo compartment. Add molecule s
endo = moose.EndoMesh( '/model/endo' )
endo.isMembraneBound = True
endo.surround = compartment
rXfer = moose.Reac( '/model/endo/rXfer' )
et = moose.Pool( '/model/endo/t' )
es = moose.Pool( '/model/endo/s' )
#####################################################################
moose.connect( rXfer, 'sub', u, 'reac' )
moose.connect( rXfer, 'sub', et, 'reac' )
moose.connect( rXfer, 'prd', es, 'reac' )
u.concInit = 1.0
et.concInit = 1.0
#####################################################################
# [u0] = 1 in compt, [t0] = 1 in endo, [s0] = 0
# [u] + [s]/8 = [u0] ; [t] + [s] = [t0]; nu + ns = nu0, nt + ns = nt0
# At equil, numKf*nu*nt = numKb*ns
# Express all # in terms of ns.
# nu = nu0-ns; nt = nt0-ns Also, nu0 = 8*nt0
# So numKf*(nu0-ns)*(nt0-ns) = numKb*ns
# Target level is nt = ns = nt0/2
# So numKf*( 8nt0 - nt0/2)*nt0/2 = numKb*nt0/2
# So 7.5*nt0 = numKb/numKf
rXfer.numKb = 0.1
rXfer.numKf = 0.1/(7.5 * et.nInit)
#print( "Rates = {}, {}".format( rXfer.Kf, rXfer.Kb ))
#####################################################################
fixXreacs.fixXreacs( '/model' )
#fixXreacs.restoreXreacs( '/model' )
#fixXreacs.fixXreacs( '/model' )
#####################################################################
# Make solvers
ksolve = moose.Ksolve( '/model/compartment/ksolve' )
dsolve = moose.Dsolve( '/model/compartment/dsolve' )
eksolve = moose.Ksolve( '/model/endo/ksolve' )
edsolve = moose.Dsolve( '/model/endo/dsolve' )
stoich = moose.Stoich( '/model/compartment/stoich' )
stoich.compartment = compartment
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.path = "/model/compartment/##"
assert( dsolve.numPools == 1 )
estoich = moose.Stoich( '/model/endo/stoich' )
estoich.compartment = endo
estoich.ksolve = eksolve
estoich.dsolve = edsolve
estoich.path = "/model/endo/##"
assert( edsolve.numPools == 3 )
edsolve.buildMeshJunctions( dsolve )
plot1 = moose.Table2( '/model/plot1' )
plot2 = moose.Table2( '/model/plot2' )
plot3 = moose.Table2( '/model/plot3' )
moose.connect( '/model/plot1', 'requestOut', u, 'getN' )
moose.connect( '/model/plot2', 'requestOut', et, 'getN' )
moose.connect( '/model/plot3', 'requestOut', es, 'getN' )
plot4 = moose.Table2( '/model/plot4' )
plot5 = moose.Table2( '/model/plot5' )
plot6 = moose.Table2( '/model/plot6' )
moose.connect( '/model/plot4', 'requestOut', u, 'getConc' )
moose.connect( '/model/plot5', 'requestOut', et, 'getConc' )
moose.connect( '/model/plot6', 'requestOut', es, 'getConc' )