def run_sim():
# Set up and run the simulations once, before the tests
# analyze the results.
##################### First order irreversible #########################
global KCST_foi, N_foi, tolerance_foi
KCST_foi = 5 # The reaction constant
N_foi = 50 # Can set count or conc
NITER_foi = 1 # The number of iterations
# Tolerance for the comparison.
tolerance_foi = 1e-3/100
####################### First order reversible #########################
global KCST_f_for, KCST_b_for, COUNT_for, tolerance_for
KCST_f_for = 10.0 # The reaction constant
KCST_b_for = 2.0
COUNT_for = 100000 # Can set count or conc
NITER_for = 1 # The number of iterations
# Tolerance for the comparison. The only test where tolerance must
# be relatively high
tolerance_for = 0.5/100
####################### Second order irreversible A2 ###################
global KCST_soA2, CONCA_soA2, tolerance_soA2
KCST_soA2 = 10.0e6 # The reaction constant
CONCA_soA2 = 10.0e-6
NITER_soA2 = 1 # The number of iterations
tolerance_soA2 = 1.0e-3/100
####################### Second order irreversible AA ###################
global KCST_soAA, CONCA_soAA, CONCB_soAA, tolerance_soAA
KCST_soAA = 50.0e6 # The reaction constant
CONCA_soAA = 20.0e-6
CONCB_soAA = CONCA_soAA
NITER_soAA = 1 # The number of iterations
tolerance_soAA = 1.0e-3/100
####################### Second order irreversible AB ###################
global KCST_soAB, CONCA_soAB, CONCB_soAB, tolerance_soAB
KCST_soAB = 5.0e6 # The reaction constant
CONCA_soAB = 1.0e-6
n_soAB = 2
CONCB_soAB = CONCA_soAB/n_soAB
NITER_soAB = 1 # The number of iterations
tolerance_soAB = 1.0e-3/100
####################### Third order irreversible A3 ###################
global KCST_toA3, CONCA_toA3, tolerance_toA3
KCST_toA3 = 1.0e12 # The reaction constant
CONCA_toA3 = 100.0e-6
NITER_toA3 = 1 # The number of iterations
tolerance_toA3 = 1.0e-3/100
####################### Third order irreversible A2B ###################
global KCST_toA2B, CONCA_toA2B, CONCB_toA2B, tolerance_toA2B
KCST_toA2B = 0.1e12 # The reaction constant
CONCA_toA2B = 30.0e-6
CONCB_toA2B = 20.0e-6
NITER_toA2B = 1 # The number of iterations
tolerance_toA2B = 1.0e-3/100
####################### Second order irreversible 2D ###################
global COUNTA_so2d, COUNTB_so2d, CCST_so2d, tolerance_so2d
COUNTA_so2d = 100.0
n_so2d=2.0
COUNTB_so2d = COUNTA_so2d/n_so2d
KCST_so2d = 10.0e10 # The reaction constant
AREA_so2d = 10.0e-12
CCST_so2d = KCST_so2d/(6.02214179e23*AREA_so2d)
NITER_so2d = 1 # The number of iterations
tolerance_so2d = 1.0e-3/100
############################ Common parameters ########################
global VOL
DT = 0.1 # Sampling time-step
INT = 1.1 # Sim endtime
VOL = 9.0e-18
NITER_max = 1
########################################################################
mdl = smod.Model()
volsys = smod.Volsys('vsys',mdl)
surfsys = smod.Surfsys('ssys',mdl)
# First order irreversible
A_foi = smod.Spec('A_foi', mdl)
R1_foi = smod.Reac('R1_foi', volsys, lhs = [A_foi], rhs = [], kcst = KCST_foi)
# First order reversible
A_for = smod.Spec('A_for', mdl)
B_for = smod.Spec('B_for', mdl)
R1_for = smod.Reac('R1_for', volsys, lhs = [A_for], rhs = [B_for], kcst = KCST_f_for)
R2_for = smod.Reac('R2_for', volsys, lhs = [B_for], rhs = [A_for], kcst = KCST_b_for)
# Second order irreversible A2
A_soA2 = smod.Spec('A_soA2', mdl)
C_soA2 = smod.Spec('C_soA2', mdl)
R1_soA2 = smod.Reac('R1_soA2', volsys, lhs = [A_soA2, A_soA2], rhs = [C_soA2], kcst = KCST_soA2)
# Second order irreversible AA
A_soAA = smod.Spec('A_soAA', mdl)
B_soAA = smod.Spec('B_soAA', mdl)
C_soAA = smod.Spec('C_soAA', mdl)
R1_soAA = smod.Reac('R1_soAA', volsys, lhs = [A_soAA, B_soAA], rhs = [C_soAA], kcst = KCST_soAA)
# Second order irreversible AB
A_soAB = smod.Spec('A_soAB', mdl)
B_soAB = smod.Spec('B_soAB', mdl)
C_soAB = smod.Spec('C_soAB', mdl)
R1_soAB = smod.Reac('R1_soAB', volsys, lhs = [A_soAB, B_soAB], rhs = [C_soAB], kcst = KCST_soAB)
# Third order irreversible A3
A_toA3 = smod.Spec('A_toA3', mdl)
C_toA3 = smod.Spec('C_toA3', mdl)
R1_toA3 = smod.Reac('R1_toA3', volsys, lhs = [A_toA3, A_toA3, A_toA3], rhs = [C_toA3], kcst = KCST_toA3)
# Third order irreversible A2B
A_toA2B = smod.Spec('A_toA2B', mdl)
B_toA2B = smod.Spec('B_toA2B', mdl)
C_toA2B = smod.Spec('C_toA2B', mdl)
R1_toA3 = smod.Reac('R1_toA2B', volsys, lhs = [A_toA2B, A_toA2B, B_toA2B], rhs = [C_toA2B], kcst = KCST_toA2B)
# Second order irreversible 2D
A_so2d = smod.Spec('A_so2d', mdl)
B_so2d = smod.Spec('B_so2d', mdl)
C_so2d = smod.Spec('C_so2d', mdl)
SR1_so2d = smod.SReac('SR1_so2d', surfsys, slhs = [A_so2d, B_so2d], srhs = [C_so2d], kcst = KCST_so2d)
geom = sgeom.Geom()
comp1 = sgeom.Comp('comp1', geom, VOL)
comp1.addVolsys('vsys')
patch1 = sgeom.Patch('patch1', geom, comp1, area = AREA_so2d)
patch1.addSurfsys('ssys')
rng = srng.create('r123', 512)
rng.initialize(1000)
sim = ssolv.Wmrk4(mdl, geom, rng)
sim.setDT(0.00001)
global tpnts, ntpnts
tpnts = numpy.arange(0.0, INT, DT)
ntpnts = tpnts.shape[0]
res_m_foi = numpy.zeros([NITER_foi, ntpnts, 1])
res_m_for = numpy.zeros([NITER_for, ntpnts, 2])
res_m_soA2 = numpy.zeros([NITER_soA2, ntpnts, 2])
res_m_soAA = numpy.zeros([NITER_soAA, ntpnts, 3])
res_m_soAB = numpy.zeros([NITER_soAB, ntpnts, 3])
res_m_toA3 = numpy.zeros([NITER_toA3, ntpnts, 2])
res_m_toA2B = numpy.zeros([NITER_toA2B, ntpnts, 3])
res_m_so2d = numpy.zeros([NITER_so2d, ntpnts, 3])
for i in range (0, NITER_max):
if i < NITER_foi:
sim.setCompCount('comp1', 'A_foi', N_foi)
if i < NITER_for:
sim.setCompCount('comp1', 'A_for', COUNT_for)
sim.setCompCount('comp1', 'B_for', 0.0)
if i < NITER_soA2:
sim.setCompConc('comp1', 'A_soA2', CONCA_soA2)
if i < NITER_soAA:
sim.setCompConc('comp1', 'A_soAA', CONCA_soAA)
sim.setCompConc('comp1', 'B_soAA', CONCB_soAA)
if i < NITER_soAB:
sim.setCompConc('comp1', 'A_soAB', CONCA_soAB)
sim.setCompConc('comp1', 'B_soAB', CONCB_soAB)
if i < NITER_toA3:
sim.setCompConc('comp1', 'A_toA3', CONCA_toA3)
if i < NITER_toA2B:
sim.setCompConc('comp1', 'A_toA2B', CONCA_toA2B)
sim.setCompConc('comp1', 'B_toA2B', CONCB_toA2B)
if i < NITER_so2d:
sim.setPatchCount('patch1', 'A_so2d', COUNTA_so2d)
sim.setPatchCount('patch1', 'B_so2d', COUNTB_so2d)
for t in range(0, ntpnts):
sim.run(tpnts[t])
if i < NITER_foi:
res_m_foi[i, t, 0] = sim.getCompCount('comp1', 'A_foi')
if i < NITER_for:
res_m_for[i, t, 0] = sim.getCompConc('comp1', 'A_for')*1e6
res_m_for[i, t, 1] = sim.getCompConc('comp1', 'B_for')*1e6
if i < NITER_soA2:
res_m_soA2[i, t, 0] = sim.getCompConc('comp1', 'A_soA2')
if i < NITER_soAA:
res_m_soAA[i, t, 0] = sim.getCompConc('comp1', 'A_soAA')
res_m_soAA[i, t, 1] = sim.getCompConc('comp1', 'B_soAA')
if i < NITER_soAB:
res_m_soAB[i, t, 0] = sim.getCompConc('comp1', 'A_soAB')
res_m_soAB[i, t, 1] = sim.getCompConc('comp1', 'B_soAB')
if i < NITER_toA3:
res_m_toA3[i, t, 0] = sim.getCompConc('comp1', 'A_toA3')
if i < NITER_toA2B:
res_m_toA2B[i, t, 0] = sim.getCompConc('comp1', 'A_toA2B')
res_m_toA2B[i, t, 1] = sim.getCompConc('comp1', 'B_toA2B')
res_m_toA2B[i, t, 2] = sim.getCompConc('comp1', 'C_toA2B')
if i < NITER_so2d:
res_m_so2d[i, t, 0] = sim.getPatchCount('patch1', 'A_so2d')
res_m_so2d[i, t, 1] = sim.getPatchCount('patch1', 'B_so2d')
global mean_res_foi
mean_res_foi = numpy.mean(res_m_foi, 0)
global mean_res_for
mean_res_for = numpy.mean(res_m_for, 0)
global mean_res_soA2
mean_res_soA2 = numpy.mean(res_m_soA2, 0)
global mean_res_soAA
mean_res_soAA = numpy.mean(res_m_soAA, 0)
global mean_res_soAB
mean_res_soAB = numpy.mean(res_m_soAB, 0)
global mean_res_toA3
mean_res_toA3 = numpy.mean(res_m_toA3, 0)
global mean_res_toA2B
mean_res_toA2B = numpy.mean(res_m_toA2B, 0)
global mean_res_so2d
mean_res_so2d = numpy.mean(res_m_so2d, 0)
global ran_sim
ran_sim = True
Pa = smodel.Spec('Pa', mdl)
Pb = smodel.Spec('Pb', mdl)
Pc = smodel.Spec('Pc', mdl)
Sa = smodel.Spec('Sa', mdl)
Sb = smodel.Spec('Sb', mdl)
#create the volume system
vsys = smodel.Volsys('vsys', mdl)
#surface system is similar to the valume system.
surfsys = smodel.Surfsys('ssys', mdl)
#the forward reaction without the forward binding reaction
A11_to_Oa_f = smodel.SReac('A11_to_Oa_f',
surfsys,
slhs=[A11],
srhs=[Oa],
kcst=1800)
Oa_to_Ob_f = smodel.SReac('Oa_to_Ob_f',
surfsys,
slhs=[Oa],
srhs=[Ob],
kcst=133)
Oc_to_Ia_f = smodel.SReac('Oc_to_Ia_f',
surfsys,
slhs=[Oc],
srhs=[Ia],
kcst=630)
A01_to_Pa_f = smodel.SReac('A01_to_Pa_f',
surfsys,
slhs=[A01],
diff_CBsf.setDcst(DCB)
diff_CBsCa = smodel.Diff('diff_CBsCa', vsys, CBsCa)
diff_CBsCa.setDcst(DCB)
diff_CBCaf = smodel.Diff('diff_CBCaf', vsys, CBCaf)
diff_CBCaf.setDcst(DCB)
diff_CBCaCa = smodel.Diff('diff_CBCaCa', vsys, CBCaCa)
diff_CBCaCa.setDcst(DCB)
diff_PV = smodel.Diff('diff_PV', vsys, PV)
diff_PV.setDcst(DPV)
diff_PVCa = smodel.Diff('diff_PVCa', vsys, PVCa)
diff_PVCa.setDcst(DPV)
diff_PVMg = smodel.Diff('diff_PVMg', vsys, PVMg)
diff_PVMg.setDcst(DPV)
#Pump
PumpD_f = smodel.SReac('PumpD_f', ssys, ilhs=[Ca], slhs=[Pump], srhs=[CaPump])
PumpD_f.setKcst(P_f_kcst)
PumpD_b = smodel.SReac('PumpD_b', ssys, slhs=[CaPump], irhs=[Ca], srhs=[Pump])
PumpD_b.setKcst(P_b_kcst)
PumpD_k = smodel.SReac('PumpD_k', ssys, slhs=[CaPump], srhs=[Pump])
PumpD_k.setKcst(P_k_kcst)
#iCBsf-fast
iCBsf1_f = smodel.Reac('iCBsf1_f',
vsys,
lhs=[Ca, iCBsf],
rhs=[iCBsCa],
kcst=iCBsf1_f_kcst)
iCBsf1_b = smodel.Reac('iCBsf1_b',
def run_sim():
# Set up and run the simulations once, before the tests
# analyze the results.
##################### First order irreversible #########################
global KCST_foi, N_foi, tolerance_foi
KCST_foi = 5 # The reaction constant
N_foi = 50 # Can set count or conc
NITER_foi = 100000 # The number of iterations
# Tolerance for the comparison:
# In test runs, with good code, < 1% will fail with a 1.5% tolerance
tolerance_foi = 2.0 / 100
####################### First order reversible #########################
global KCST_f_for, KCST_b_for, COUNT_for, tolerance_for
KCST_f_for = 10.0 # The reaction constant
KCST_b_for = 2.0
COUNT_for = 100000 # Can set count or conc
NITER_for = 10 # The number of iterations
# In test runs, with good code, <0.1% will fail with a tolerance of 1%
tolerance_for = 1.0 / 100
####################### Second order irreversible AA ###################
global KCST_soAA, CONCA_soAA, CONCB_soAA, tolerance_soAA
KCST_soAA = 50.0e6 # The reaction constant
CONCA_soAA = 20.0e-6
CONCB_soAA = CONCA_soAA
NITER_soAA = 1000 # The number of iterations
# In test runs, with good code, <0.1% will fail with a tolerance of 1%
tolerance_soAA = 1.0 / 100
####################### Second order irreversible AB ###################
global KCST_soAB, CONCA_soAB, CONCB_soAB, tolerance_soAB
KCST_soAB = 5.0e6 # The reaction constant
CONCA_soAB = 1.0e-6
n_soAB = 2
CONCB_soAB = CONCA_soAB / n_soAB
NITER_soAB = 1000 # The number of iterations
# In test runs, with good code, <0.1% will fail with a tolerance of 1%
tolerance_soAB = 1.0 / 100
####################### Second order irreversible 2D ###################
global COUNTA_so2d, COUNTB_so2d, CCST_so2d, tolerance_so2d
COUNTA_so2d = 100.0
n_so2d = 2.0
COUNTB_so2d = COUNTA_so2d / n_so2d
KCST_so2d = 10.0e10 # The reaction constant
AREA_so2d = 10.0e-12
CCST_so2d = KCST_so2d / (6.02214179e23 * AREA_so2d)
NITER_so2d = 1000 # The number of iterations
# In tests fewer than 0.1% fail with tolerance of 2%
tolerance_so2d = 2.0 / 100
############################ Common parameters ########################
global VOL
DT = 0.1 # Sampling time-step
INT = 1.1 # Sim endtime
VOL = 9.0e-18
NITER_max = 100000
########################################################################
mdl = smod.Model()
volsys = smod.Volsys('vsys', mdl)
surfsys = smod.Surfsys('ssys', mdl)
# First order irreversible
A_foi = smod.Spec('A_foi', mdl)
R1_foi = smod.Reac('R1_foi', volsys, lhs=[A_foi], rhs=[], kcst=KCST_foi)
# First order reversible
A_for = smod.Spec('A_for', mdl)
B_for = smod.Spec('B_for', mdl)
R1_for = smod.Reac('R1_for',
volsys,
lhs=[A_for],
rhs=[B_for],
kcst=KCST_f_for)
R2_for = smod.Reac('R2_for',
volsys,
lhs=[B_for],
rhs=[A_for],
kcst=KCST_b_for)
# Second order irreversible AA
A_soAA = smod.Spec('A_soAA', mdl)
B_soAA = smod.Spec('B_soAA', mdl)
C_soAA = smod.Spec('C_soAA', mdl)
R1_soAA = smod.Reac('R1_soAA',
volsys,
lhs=[A_soAA, B_soAA],
rhs=[C_soAA],
kcst=KCST_soAA)
# Second order irreversible AB
A_soAB = smod.Spec('A_soAB', mdl)
B_soAB = smod.Spec('B_soAB', mdl)
C_soAB = smod.Spec('C_soAB', mdl)
R1_soAB = smod.Reac('R1_soAB',
volsys,
lhs=[A_soAB, B_soAB],
rhs=[C_soAB],
kcst=KCST_soAB)
# Second order irreversible 2D
A_so2d = smod.Spec('A_so2d', mdl)
B_so2d = smod.Spec('B_so2d', mdl)
C_so2d = smod.Spec('C_so2d', mdl)
SR1_so2d = smod.SReac('SR1_so2d',
surfsys,
slhs=[A_so2d, B_so2d],
srhs=[C_so2d],
kcst=KCST_so2d)
geom = sgeom.Geom()
comp1 = sgeom.Comp('comp1', geom, VOL)
comp1.addVolsys('vsys')
patch1 = sgeom.Patch('patch1', geom, comp1, area=AREA_so2d)
patch1.addSurfsys('ssys')
rng = srng.create('r123', 512)
rng.initialize(1000)
sim = ssolv.Wmdirect(mdl, geom, rng)
sim.reset()
global tpnts, ntpnts
tpnts = numpy.arange(0.0, INT, DT)
ntpnts = tpnts.shape[0]
res_m_foi = numpy.zeros([NITER_foi, ntpnts, 1])
res_std1_foi = numpy.zeros([ntpnts, 1])
res_std2_foi = numpy.zeros([ntpnts, 1])
res_m_for = numpy.zeros([NITER_for, ntpnts, 2])
res_m_soAA = numpy.zeros([NITER_soAA, ntpnts, 3])
res_m_soAB = numpy.zeros([NITER_soAB, ntpnts, 3])
res_m_so2d = numpy.zeros([NITER_so2d, ntpnts, 3])
for i in range(0, NITER_max):
sim.reset()
if i < NITER_foi:
sim.setCompCount('comp1', 'A_foi', N_foi)
if i < NITER_for:
sim.setCompCount('comp1', 'A_for', COUNT_for)
sim.setCompCount('comp1', 'B_for', 0.0)
if i < NITER_soAA:
sim.setCompConc('comp1', 'A_soAA', CONCA_soAA)
sim.setCompConc('comp1', 'B_soAA', CONCB_soAA)
if i < NITER_soAB:
sim.setCompConc('comp1', 'A_soAB', CONCA_soAB)
sim.setCompConc('comp1', 'B_soAB', CONCB_soAB)
if i < NITER_so2d:
sim.setPatchCount('patch1', 'A_so2d', COUNTA_so2d)
sim.setPatchCount('patch1', 'B_so2d', COUNTB_so2d)
for t in range(0, ntpnts):
sim.run(tpnts[t])
if i < NITER_foi:
res_m_foi[i, t, 0] = sim.getCompCount('comp1', 'A_foi')
if i < NITER_for:
res_m_for[i, t, 0] = sim.getCompConc('comp1', 'A_for') * 1e6
res_m_for[i, t, 1] = sim.getCompConc('comp1', 'B_for') * 1e6
if i < NITER_soAA:
res_m_soAA[i, t, 0] = sim.getCompConc('comp1', 'A_soAA')
res_m_soAA[i, t, 1] = sim.getCompConc('comp1', 'B_soAA')
if i < NITER_soAB:
res_m_soAB[i, t, 0] = sim.getCompConc('comp1', 'A_soAB')
res_m_soAB[i, t, 1] = sim.getCompConc('comp1', 'B_soAB')
if i < NITER_so2d:
res_m_so2d[i, t, 0] = sim.getPatchCount('patch1', 'A_so2d')
res_m_so2d[i, t, 1] = sim.getPatchCount('patch1', 'B_so2d')
global mean_res_foi, std_res_foi
mean_res_foi = numpy.mean(res_m_foi, 0)
std_res_foi = numpy.std(res_m_foi, 0)
global mean_res_for
mean_res_for = numpy.mean(res_m_for, 0)
global mean_res_soAA
mean_res_soAA = numpy.mean(res_m_soAA, 0)
global mean_res_soAB
mean_res_soAB = numpy.mean(res_m_soAB, 0)
global mean_res_so2d
mean_res_so2d = numpy.mean(res_m_so2d, 0)
global ran_sim
ran_sim = True
def setUp(self):
self.DCST = 0.08e-12
self.model = smodel.Model()
A = smodel.Spec('A', self.model)
X = smodel.Spec('X', self.model)
self.ssys1 = smodel.Surfsys('ssys1', self.model)
self.ssys2 = smodel.Surfsys('ssys2', self.model)
self.sreac = smodel.SReac('sreac', self.ssys1, slhs = [A], srhs = [A], kcst = 1e5)
self.diff1 = smodel.Diff('diffX1', self.ssys1, X, self.DCST)
self.diff2 = smodel.Diff('diffX2', self.ssys2, X, self.DCST)
if __name__ == "__main__":
self.mesh = meshio.loadMesh('meshes/coin_10r_1h_13861')[0]
else:
self.mesh = meshio.loadMesh('sdiff_bugfix_test/meshes/coin_10r_1h_13861')[0]
ntets = self.mesh.countTets()
self.comp = sgeom.TmComp('cyto', self.mesh, range(ntets))
alltris = self.mesh.getSurfTris()
patchA_tris = []
patchB_tris = []
patchA_bars = set()
patchB_bars = set()
for t in alltris:
vert0, vert1, vert2 = self.mesh.getTri(t)
if (self.mesh.getVertex(vert0)[2] > 0.0 \
and self.mesh.getVertex(vert1)[2] > 0.0 \
and self.mesh.getVertex(vert2)[2] > 0.0):
if self.mesh.getTriBarycenter(t)[0] > 0.0:
patchA_tris.append(t)
bar = self.mesh.getTriBars(t)
patchA_bars.add(bar[0])
patchA_bars.add(bar[1])
patchA_bars.add(bar[2])
else:
patchB_tris.append(t)
bar = self.mesh.getTriBars(t)
patchB_bars.add(bar[0])
patchB_bars.add(bar[1])
patchB_bars.add(bar[2])
self.patchA = sgeom.TmPatch('patchA', self.mesh, patchA_tris, icomp = self.comp)
self.patchA.addSurfsys('ssys1')
self.patchB = sgeom.TmPatch('patchB', self.mesh, patchB_tris, icomp = self.comp)
self.patchB.addSurfsys('ssys2')
# Find the set of bars that connect the two patches as the intersecting bars
barsDB = patchA_bars.intersection(patchB_bars)
barsDB=list(barsDB)
# Create the surface diffusion boundary
self.diffb = sgeom.SDiffBoundary('sdiffb', self.mesh, barsDB, [self.patchA, self.patchB])
ctetidx = self.mesh.findTetByPoint([0.0, 0.0, 0.5e-6])
ctet_trineighbs = self.mesh.getTetTriNeighb(ctetidx)
self.ctri_idx=-1
for t in ctet_trineighbs:
if t in patchA_tris+patchB_tris:
self.ctri_idx = t
self.rng = srng.create('r123', 512)
self.rng.initialize(1000)
self.solver = solv.Tetexact(self.model, self.mesh, self.rng)
def model(tissue):
""" initialises model using tissue array """
mdl = smodel.Model()
unique_p = []
for cell in tissue:
[unique_p.append(p) for p in cell.prtcl_names if p not in unique_p]
NP = []
NPi = []
NPR = []
# Create particles and corresponding species
for p in unique_p:
# Free NPs
NP.append(smodel.Spec('N{}'.format(p), mdl))
# internalised NPs
NPi.append(smodel.Spec('N{}i'.format(p), mdl))
# complexes state: NPs bound to a cell receptor
# NPR.append(smodel.Spec('N{}R'.format(p), mdl))
# receptor state: 'naive' state (no bound NPs)
R = smodel.Spec('R', mdl)
NPR = smodel.Spec('NPR', mdl)
d = {}
rxn_ = {}
dfsn_ = {}
# Lpop where cell and particle properties are connected to reactions
for n, cell in enumerate(tissue):
for p_idx, p in enumerate(unique_p):
tag = str(n) + p
prtcl = getattr(cell, p)
d["surfsys{}".format(tag)] = smodel.Surfsys(
"surfsys{}".format(tag), mdl)
d["volsys{}".format(tag)] = smodel.Volsys("volsys{}".format(tag),
mdl)
k_diff = prtcl['D'] / (float(cell.S) * float(cell.S))
dfsn_["frwd_{}".format(tag)] = smodel.SReac(
"frwd_{}".format(tag),
d["surfsys{}".format(tag)],
ilhs=[NP[p_idx]],
orhs=[NP[p_idx]],
kcst=k_diff)
dfsn_["bkwd_{}".format(tag)] = smodel.SReac(
"bkwd_{}".format(tag),
d["surfsys{}".format(tag)],
olhs=[NP[p_idx]],
irhs=[NP[p_idx]],
kcst=k_diff)
# binding reactions:
if 'k_a' in prtcl:
k_bind = prtcl['k_a']
k_unbind = prtcl['k_d']
k_intern = prtcl['k_i']
rxn_["bind_{}".format(tag)] = smodel.Reac(
"bind_{}".format(tag),
d["volsys{}".format(tag)],
lhs=[NP[p_idx], R],
rhs=[NPR],
kcst=k_bind)
rxn_["unbind_{}".format(tag)] = smodel.Reac(
"unbind_{}".format(tag),
d["volsys{}".format(tag)],
lhs=[NPR],
rhs=[NP[p_idx], R],
kcst=k_unbind)
rxn_["intern_{}".format(tag)] = smodel.Reac(
"intern_{}".format(tag),
d["volsys{}".format(tag)],
lhs=[NPR],
rhs=[NPi[p_idx], R],
kcst=k_intern)
# Diffusion
dfsn1 = smodel.Diff('dfsn1',
d["volsys{}".format(tag)],
NP[p_idx],
dcst=k_diff)
dfsn2 = smodel.Diff('dfsn2',
d["volsys{}".format(tag)],
NPR,
dcst=k_diff)
dfsn3 = smodel.Diff('dfsn3',
d["volsys{}".format(tag)],
R,
dcst=k_diff)
dfsn4 = smodel.Diff('dfsn4',
d["volsys{}".format(tag)],
NPi[p_idx],
dcst=k_diff)
return mdl
# receptor state: Ca bound to two inactivation sites
R2Ca = smodel.Spec('R2Ca', mdl)
# receptor state: Ca bound to three inactivation sites
R3Ca = smodel.Spec('R3Ca', mdl)
# receptor state: Ca bound to four inactivation sites
R4Ca = smodel.Spec('R4Ca', mdl)
#######################################################
# Surface system
surfsys = smodel.Surfsys('ssys', mdl)
# The 'forward' binding reactions:
R_bind_IP3_f = smodel.SReac('R_bind_IP3_f', surfsys, olhs=[IP3], slhs=[R], srhs=[RIP3])
RIP3_bind_Ca_f = smodel.SReac('RIP3_bind_Ca_f', surfsys, olhs=[Ca], slhs=[RIP3], srhs = [Ropen])
R_bind_Ca_f = smodel.SReac('R_bind_Ca_f', surfsys, olhs=[Ca], slhs=[R], srhs=[RCa])
RCa_bind_Ca_f = smodel.SReac('RCa_bind_Ca_f', surfsys, olhs=[Ca], slhs=[RCa],srhs = [R2Ca])
R2Ca_bind_Ca_f = smodel.SReac('R2Ca_bind_Ca_f', surfsys, olhs=[Ca], slhs= [R2Ca], srhs = [R3Ca])
R3Ca_bind_Ca_f = smodel.SReac('R3Ca_bind_ca_f', surfsys, olhs=[Ca], slhs=[R3Ca], srhs=[R4Ca])
# The 'backward' unbinding reactions:
R_bind_IP3_b = smodel.SReac('R_bind_IP3_b', surfsys, slhs=[RIP3], orhs=[IP3], srhs=[R])
def setUp(self):
mdl = smodel.Model()
S1 = smodel.Spec('S1', mdl)
vsys = smodel.Volsys('vsys', mdl)
ssys = smodel.Surfsys('ssys', mdl)
smodel.Reac('R01', vsys, lhs=[S1], rhs=[S1], kcst=1)
smodel.SReac('SR01', ssys, slhs=[S1], srhs=[S1], kcst=1)
vrange = [-200.0e-3, 50e-3, 1e-3]
vrate = lambda v: 2.0
Chan1 = smodel.Chan('Chan1', mdl)
chanop = smodel.ChanState('chanop', mdl, Chan1)
chancl = smodel.ChanState('chancl', mdl, Chan1)
smodel.VDepSReac('VDSR01',
ssys,
slhs=[chancl],
srhs=[chanop],
k=vrate,
vrange=vrange)
smodel.VDepSReac('VDSR02',
ssys,
srhs=[chancl],
slhs=[chanop],
k=vrate,
vrange=vrange)
Chan1_Ohm_I = smodel.OhmicCurr('Chan1_Ohm_I',
ssys,
chanstate=chanop,
g=20e-12,
erev=-77e-3)
if __name__ == "__main__":
self.mesh = meshio.importAbaqus('meshes/test.inp', 1e-7)[0]
else:
self.mesh = meshio.importAbaqus(
'missing_solver_methods_test/meshes/test.inp', 1e-7)[0]
comp1 = sgeom.TmComp('comp1', self.mesh, range(self.mesh.countTets()))
comp1.addVolsys('vsys')
patch1 = sgeom.TmPatch('patch1', self.mesh, self.mesh.getSurfTris(),
comp1)
patch1.addSurfsys('ssys')
self.c1ROIInds = range(10)
self.p1ROIInds = range(5)
self.mesh.addROI('comp1ROI', sgeom.ELEM_TET, self.c1ROIInds)
self.mesh.addROI('patch1ROI', sgeom.ELEM_TRI, self.p1ROIInds)
membrane = sgeom.Memb('membrane', self.mesh, [patch1], opt_method=1)
rng = srng.create('mt19937', 512)
rng.initialize(1234)
tet_hosts = gd.linearPartition(self.mesh, [1, 1, steps.mpi.nhosts])
tri_hosts = gd.partitionTris(self.mesh, tet_hosts,
self.mesh.getSurfTris())
self.sim = ssolver.TetOpSplit(mdl, self.mesh, rng, ssolver.EF_DEFAULT,
tet_hosts, tri_hosts)
self.sim.setEfieldDT(1e-4)
self.sim.reset()
def getModel():
# Create model container
mdl = smod.Model()
# Create chemical species
ca = smod.Spec('ca', mdl)
ip3 = smod.Spec('ip3', mdl)
plc = smod.Spec('plc', mdl)
# Create calcium buffers
GCaMP6s = smod.Spec('GCaMP6s', mdl)
ca_GCaMP6s = smod.Spec('ca_GCaMP6s', mdl)
# Create IP3R states species
unb_IP3R = smod.Spec('unb_IP3R', mdl)
ip3_IP3R = smod.Spec('ip3_IP3R', mdl)
caa_IP3R = smod.Spec('caa_IP3R', mdl)
cai_IP3R = smod.Spec('cai_IP3R', mdl)
open_IP3R = smod.Spec('open_IP3R', mdl)
cai_ip3_IP3R = smod.Spec('cai_ip3_IP3R', mdl)
ca2_IP3R = smod.Spec('ca2_IP3R', mdl)
ca2_ip3_IP3R = smod.Spec('ca2_ip3_IP3R', mdl)
# ER surface sys
ssys = smod.Surfsys('ssys', mdl)
# plasma membrane surface
mb_surf = smod.Surfsys('mb_surf', mdl)
# Create volume system
# cytosol volume system
vsys = smod.Volsys('vsys', mdl)
# ER volume system
er_vsys = smod.Volsys('er_vsys', mdl)
##################################
##### DEFINE DIFFUSION RULES #####
##################################
# Diffusion constants
# Diffusion constant of Calcium (buffered)
DCST = 0.013e-9
# Diffusion constant of IP3
DIP3 = 0.280e-9
# Diffusion constant of GCaMP6s
DGCAMP = 0.050e-9
diff_freeca = smod.Diff('diff_freeca', vsys, ca, DCST)
diff_ip3 = smod.Diff('diff_ip3', vsys, ip3, DIP3)
diff_GCaMP6s = smod.Diff('diff_GCaMP6s', vsys, GCaMP6s, DGCAMP)
diff_ca_GCaMP6s = smod.Diff('diff_ca_GCaMP6s', vsys, ca_GCaMP6s, DGCAMP)
##################################
######## DEFINE REACTIONS ########
##################################
#### Calcium in and out and Buffering Reactions ####
# Ca -> null
ca_deg = smod.Reac('ca_deg', vsys, lhs=[ca])
# Ca leak
ca_leak = smod.Reac('ca_leak', vsys, rhs=[ca])
# Calcium binding to GCaMP6s molecules
GCaMP6s_bind_ca_f = smod.Reac('GCaMP6s_bind_ca_f', vsys, \
lhs=[ca, GCaMP6s], rhs=[ca_GCaMP6s])
GCaMP6s_bind_ca_b = smod.Reac('GCaMP6s_bind_ca_b', vsys, \
lhs=[ca_GCaMP6s], rhs=[GCaMP6s, ca])
#### IP3 Influx and Buffering Reactions ######
# IP3 leak
ip3_leak = smod.Reac('ip3_leak', vsys, rhs=[ip3])
# IP3 degradation
ip3_deg = smod.Reac('ip3_deg', vsys, lhs=[ip3])
# ca activating plc_delta-dependent IP3 synthesis
plc_ip3_synthesis = smod.SReac('plc_ip3_synthesis', mb_surf, \
slhs=[plc], ilhs= [ca], srhs=[plc], irhs= [ca, ip3])
##### IP3R kinetics #####
# surface/volume reaction ca from cytosol binds activating IP3R site on unbound IP3R
unb_IP3R_bind_caa_f = smod.SReac('unb_IP3R_bind_caa_f', ssys,\
ilhs=[ca], slhs=[unb_IP3R], srhs=[caa_IP3R])
unb_IP3R_bind_caa_b = smod.SReac('unb_IP3R_bind_caa_b', ssys, \
slhs=[caa_IP3R], srhs=[unb_IP3R], irhs=[ca])
# surface/volume reaction ca from cytosol binds inactivating IP3R site on unbound IP3R
unb_IP3R_bind_cai_f = smod.SReac('unb_IP3R_bind_cai_f', ssys, \
ilhs=[ca], slhs=[unb_IP3R], srhs=[cai_IP3R])
unb_IP3R_bind_cai_b = smod.SReac('unb_IP3R_bind_cai_b', ssys, \
slhs=[cai_IP3R], srhs=[unb_IP3R], irhs=[ca])
# surface/volume reaction ca from cytosol binds activating IP3R site on caa_IP3R
caa_IP3R_bind_ca_f = smod.SReac('caa_IP3R_bind_ca_f', ssys, \
ilhs=[ca], slhs=[caa_IP3R], srhs=[ca2_IP3R])
caa_IP3R_bind_ca_b = smod.SReac('caa_IP3R_bind_ca_b', ssys, \
slhs=[ca2_IP3R], srhs=[caa_IP3R], irhs=[ca])
# surface/volume reaction ca from cytosol binds activating IP3R site on ip3_IP3R
ip3_IP3R_bind_caa_f = smod.SReac('ip3_IP3R_bind_caa_f', ssys, \
ilhs=[ca], slhs=[ip3_IP3R], srhs=[open_IP3R])
ip3_IP3R_bind_caa_b = smod.SReac('ip3_IP3R_bind_caa_b', ssys, \
slhs=[open_IP3R], srhs=[ip3_IP3R], irhs=[ca])
# surface/volume reaction ca from cytosol binds inactivating IP3R site on ip3_IP3R
ip3_IP3R_bind_cai_f = smod.SReac('ip3_IP3R_bind_cai_f', ssys, \
ilhs=[ca], slhs=[ip3_IP3R], srhs=[cai_ip3_IP3R])
ip3_IP3R_bind_cai_b = smod.SReac('ip3_IP3R_bind_cai_b', ssys, \
slhs=[cai_ip3_IP3R], srhs=[ip3_IP3R], irhs=[ca])
# surface/volume reaction ca from cytosol binds activating IP3R site on cai_IP3R
cai_IP3R_bind_ca_f = smod.SReac('cai_IP3R_bind_ca_f', ssys, \
ilhs=[ca], slhs=[cai_IP3R], srhs=[ca2_IP3R])
cai_IP3R_bind_ca_b = smod.SReac('cai_IP3R_bind_ca_b', ssys, \
slhs=[ca2_IP3R], srhs=[cai_IP3R], irhs=[ca])
# surface/volume reaction ca from cytosol binds inactivating IP3R site on open_IP3R
open_IP3R_bind_ca_f = smod.SReac('open_IP3R_bind_ca_f', ssys, \
ilhs=[ca], slhs=[open_IP3R], srhs=[ca2_ip3_IP3R])
open_IP3R_bind_ca_b = smod.SReac('open_IP3R_bind_ca_b', ssys, \
slhs=[ca2_ip3_IP3R], srhs=[open_IP3R], irhs=[ca])
# surface/volume reaction ca from cytosol binds activating IP3R site on cai_ip3_IP3R
cai_ip3_IP3R_bind_ca_f = smod.SReac('cai_ip3_IP3R_bind_ca_f', ssys, \
ilhs=[ca], slhs=[cai_ip3_IP3R], srhs=[ca2_ip3_IP3R])
cai_ip3_IP3R_bind_ca_b = smod.SReac('cai_ip3_IP3R_bind_ca_b', ssys, \
slhs=[ca2_ip3_IP3R], srhs=[cai_ip3_IP3R], irhs=[ca])
# surface/volume reaction ip3 from cytosol binds unb_IP3R
unb_IP3R_bind_ip3_f = smod.SReac('unb_IP3R_bind_ip3_f', ssys, \
ilhs=[ip3], slhs=[unb_IP3R], srhs=[ip3_IP3R])
unb_IP3R_bind_ip3_b = smod.SReac('unb_IP3R_bind_ip3_b', ssys, \
slhs=[ip3_IP3R], srhs=[unb_IP3R], irhs=[ip3])
# surface/volume reaction ip3 from cytosol binds caa_IP3R
caa_IP3R_bind_ip3_f = smod.SReac('caa_IP3R_bind_ip3_f', ssys, \
ilhs=[ip3], slhs=[caa_IP3R], srhs=[open_IP3R])
caa_IP3R_bind_ip3_b = smod.SReac('caa_IP3R_bind_ip3_b', ssys, \
slhs=[open_IP3R], srhs=[caa_IP3R], irhs=[ip3])
# surface/volume reaction ip3 from cytosol binds cai_IP3R
cai_IP3R_bind_ip3_f = smod.SReac('cai_IP3R_bind_ip3_f', ssys, \
ilhs=[ip3], slhs=[cai_IP3R], srhs=[cai_ip3_IP3R])
cai_IP3R_bind_ip3_b = smod.SReac('cai_IP3R_bind_ip3_b', ssys, \
slhs=[cai_ip3_IP3R], srhs=[cai_IP3R], irhs=[ip3])
# surface/volume reaction ip3 from cytosol binds ca2_IP3R
ca2_IP3R_bind_ip3_f = smod.SReac('ca2_IP3R_bind_ip3_f', ssys, \
ilhs=[ip3], slhs=[ca2_IP3R], srhs=[ca2_ip3_IP3R])
ca2_IP3R_bind_ip3_b = smod.SReac('ca2_IP3R_bind_ip3_b', ssys, \
slhs=[ca2_ip3_IP3R], srhs=[ca2_IP3R], irhs=[ip3])
##### Ca ions passing through open IP3R channel to cytosol #####
Ca_IP3R_flux = smod.SReac('R_Ca_channel_f', ssys, \
slhs=[open_IP3R], irhs=[ca], srhs=[open_IP3R])
##################################
#### REACTION CONSTANT VALUES ####
##################################
##### Calcium Influx and Buffering Reactions #####
# GCaMP6s mediated calcium buffering
GCaMP6s_bind_ca_f.setKcst(7.78e6)
GCaMP6s_bind_ca_b.setKcst(1.12)
############# VALUES FOR GCAMP6f #################
#### GCaMP6s_bind_ca_f.setKcst(1.05e7) ####
#### GCaMP6s_bind_ca_b.setKcst(3.93) ####
##################################################
# Ca -> null
ca_deg.setKcst(30)
# Ca leak
ca_leak.setKcst(15e-8)
##### IP3 Influx and Buffering Reactions #####
# IP3 leak does not exist in this model. IP3 synthesis only occurs through PLC activity
# IP3 -> null
ip3_deg.setKcst(1.2e-4)
# ca activating plc_delta-dependent IP3 synthesis
plc_ip3_synthesis.setKcst(1)
#### IP3R kinetics #####
caa_f = 1.2e6
cai_f = 1.6e4
ip3_f = 4.1e7
caa_b = 5e1
cai_b = 1e2
ip3_b = 4e2
unb_IP3R_bind_caa_f.setKcst(caa_f)
unb_IP3R_bind_caa_b.setKcst(caa_b)
unb_IP3R_bind_cai_f.setKcst(cai_f)
unb_IP3R_bind_cai_b.setKcst(cai_b)
caa_IP3R_bind_ca_f.setKcst(cai_f)
caa_IP3R_bind_ca_b.setKcst(cai_b)
ip3_IP3R_bind_caa_f.setKcst(caa_f)
ip3_IP3R_bind_caa_b.setKcst(caa_b)
ip3_IP3R_bind_cai_f.setKcst(cai_f)
ip3_IP3R_bind_cai_b.setKcst(cai_b)
cai_IP3R_bind_ca_f.setKcst(caa_f)
cai_IP3R_bind_ca_b.setKcst(caa_b)
open_IP3R_bind_ca_f.setKcst(cai_f)
open_IP3R_bind_ca_b.setKcst(cai_b)
unb_IP3R_bind_ip3_f.setKcst(ip3_f)
unb_IP3R_bind_ip3_b.setKcst(ip3_b)
caa_IP3R_bind_ip3_f.setKcst(ip3_f)
caa_IP3R_bind_ip3_b.setKcst(ip3_b)
cai_IP3R_bind_ip3_f.setKcst(ip3_f)
cai_IP3R_bind_ip3_b.setKcst(ip3_b)
cai_ip3_IP3R_bind_ca_f.setKcst(caa_f)
cai_ip3_IP3R_bind_ca_b.setKcst(caa_b)
ca2_IP3R_bind_ip3_f.setKcst(ip3_f)
ca2_IP3R_bind_ip3_b.setKcst(ip3_b)
# Ca ions passing through open IP3R channel
Ca_IP3R_flux.setKcst(6e3)
return mdl
RI2 = smodel.Spec('RI2', mdl)
RI3 = smodel.Spec('RI3', mdl)
P = smodel.Spec('P', mdl) #naive state 1
PI = smodel.Spec('PI', mdl)
PI2 = smodel.Spec('PI2', mdl)
PI3 = smodel.Spec('PI3', mdl)
C1 = smodel.Spec('C1', mdl)
O1 = smodel.Spec('O1', mdl) # open state 1
O2 = smodel.Spec('O2', mdl) # open state 1
# REACTIONS
#1 R <=> P
reac1_f = smodel.SReac('R_P', surfsys, slhs=[R], srhs=[P])
reac1_b = smodel.SReac('P_R', surfsys, slhs=[P], srhs=[R])
#2 R + IP3 <=> RI
reac2_f = smodel.SReac('R_RI', surfsys, olhs=[IP3], slhs=[R], srhs=[RI])
reac2_b = smodel.SReac('RI_R', surfsys, slhs=[RI], orhs=[IP3], srhs=[R])
#3 RI + IP3 <=> RI2
reac3_f = smodel.SReac('RI_RI2', surfsys, olhs=[IP3], slhs=[RI], srhs=[RI2])
reac3_b = smodel.SReac('RI2_RI', surfsys, slhs=[RI2], orhs=[IP3], srhs=[RI])
#4 RI2 + IP3 <=> RI3
reac4_f = smodel.SReac('RI2_RI3', surfsys, olhs=[IP3], slhs=[RI2], srhs=[RI3])
reac4_b = smodel.SReac('RI3_RI2', surfsys, slhs=[RI3], orhs=[IP3], srhs=[RI2])
#5 RI3 + IP3 <=> O1
# ser_x0y0 = smodel.SReac('ser_x0y0', surfsys2, slhs=[SERCA_X0Ca], srhs=[SERCA_Y0Ca] , kcst=kx0y0)
# ////////////////////////////////////////////////////////////////////////////////////////////////////////
# Ca + SERCA <-> Ca1SERCA +Ca <-> Ca2SERCA -> SERCA
DCST_MEM = 0.05e-12
SERCA = smodel.Spec('SERCA', model)
CaSERCA = smodel.Spec('CaSERCA',model)
Ca2SERCA = smodel.Spec('Ca2SERCA',model)
diff_SERCA = smodel.Diff('diff_SERCA', surfsys2, SERCA, DCST_MEM)
diff_CaSERCA = smodel.Diff('diff_CaSERCA', surfsys2, CaSERCA, DCST_MEM)
diff_Ca2SERCA = smodel.Diff('diff_Ca2SERCA', surfsys2, Ca2SERCA, DCST_MEM)
Reac9 = smodel.SReac('Reac9', surfsys2, olhs=[Ca], slhs=[SERCA], srhs=[CaSERCA], kcst=17147e6)
Reac10 = smodel.SReac('Reac10', surfsys2, slhs=[CaSERCA], orhs=[Ca], srhs=[SERCA], kcst=8426.3)
Reac11 = smodel.SReac('Reac11', surfsys2, olhs=[Ca], slhs=[CaSERCA], srhs=[Ca2SERCA], kcst=17147e6)
Reac12 = smodel.SReac('Reac12', surfsys2, slhs=[Ca2SERCA], orhs=[Ca], srhs=[CaSERCA], kcst=8426.3)
Reac13 = smodel.SReac('Reac13', surfsys2, slhs=[Ca2SERCA], srhs=[SERCA], irhs=[Ca,Ca], kcst=250)
# ////////////////////////////////////////////////////////////////////////////////////////////////////////
# PMCA species:
PMCA_P0 = smodel.Spec('PMCA_P0', model)
PMCA_P1 = smodel.Spec('PMCA_P1', model)
k1_pmca = 1.5e8
k2_pmca = 15
k3_pmca = 12
kl_pmca = 4.3
def test_soirev2d():
VOL = 1.0e-18
COUNTA = 100.0
n=2.0
COUNTB = COUNTA/n
KCST = 10.0e10 # The reaction constant
AREA = 10.0e-12
CCST = KCST/(6.02214179e23*AREA)
NITER = 1000 # The number of iterations
DT = 0.05 # Sampling time-step
INT = 1.05 # Sim endtime
# In tests fewer than 0.1% fail with tolerance of 2%
tolerance = 2.0/100
########################################################################
mdl = smod.Model()
A = smod.Spec('A', mdl)
B = smod.Spec('B', mdl)
C = smod.Spec('C', mdl)
surfsys = smod.Surfsys('ssys',mdl)
SR1 = smod.SReac('SR1', surfsys, slhs = [A, B], srhs = [C], kcst = KCST)
geom = sgeom.Geom()
comp1 = sgeom.Comp('comp1', geom, VOL)
patch1 = sgeom.Patch('patch1', geom, comp1, area = AREA)
patch1.addSurfsys('ssys')
import random
rng = srng.create('mt19937', 1000)
rng.initialize(int(random.random()*4294967295))
sim = ssolv.Wmdirect(mdl, geom, rng)
sim.reset()
tpnts = numpy.arange(0.0, INT, DT)
ntpnts = tpnts.shape[0]
res_m = numpy.zeros([NITER, ntpnts, 3])
for i in range (0, NITER):
sim.restore('./validation_cp/cp/second_order_irev_2D')
for t in range(0, ntpnts):
sim.run(tpnts[t])
res_m[i, t, 0] = sim.getPatchCount('patch1', 'A')
res_m[i, t, 1] = sim.getPatchCount('patch1', 'B')
mean_res = numpy.mean(res_m, 0)
lnBA = numpy.zeros(ntpnts)
lineAB = numpy.zeros(ntpnts)
C = COUNTA-COUNTB
passed =True
max_err = 0.0
for i in range(ntpnts):
A = mean_res[i][0]
B = mean_res[i][1]
lnBA[i] = math.log(B/A)
lineAB[i] = math.log(COUNTB/COUNTA) -C*CCST*tpnts[i]
assert(tol_funcs.tolerable(lnBA[i], lineAB[i], tolerance))
A11 = smodel.Spec('A11', mdl)
Pa = smodel.Spec('Pa', mdl)
Pb = smodel.Spec('Pb', mdl)
Pc = smodel.Spec('Pc', mdl)
Sa = smodel.Spec('Sa', mdl)
Sb = smodel.Spec('Sb', mdl)
Oa = smodel.Spec('Oa', mdl)
Ob = smodel.Spec('Ob', mdl)
Oc = smodel.Spec('Oc', mdl)
Ia = smodel.Spec('Ia', mdl)
Ib = smodel.Spec('Ib', mdl)
# REACTIONS
#1 Sa + Ca <=> Sb
reac1_f = smodel.SReac('Sa_Sb', surfsys, olhs=[Ca], slhs=[Sa], srhs=[Sb])
reac1_b = smodel.SReac('Sb_Sa', surfsys, slhs=[Sb], orhs=[Ca], srhs=[Sa])
#2 Pc <=> Sa
reac2_f = smodel.SReac('Pc_Sa', surfsys, slhs=[Pc], srhs=[Sa])
reac2_b = smodel.SReac('Sa_Pc', surfsys, slhs=[Sa], srhs=[Pc])
#3 Pb + Ca_ER <=> Pc
reac3_f = smodel.SReac('Pb_Pc', surfsys, ilhs=[Ca], slhs=[Pb], srhs=[Pc])
reac3_b = smodel.SReac('Pc_Pb', surfsys, slhs=[Pc], irhs=[Ca], srhs=[Pb])
#4 Pa <=> Pb
reac4_f = smodel.SReac('Pa_Pb', surfsys, slhs=[Pa], srhs=[Pb])
reac4_b = smodel.SReac('Pb_Pa', surfsys, slhs=[Pb], srhs=[Pa])
#5 A01 <=> Pa
# Mg
Mg = smodel.Spec('Mg', mdl_WM)
ssys_diff = smodel.Surfsys('ssys_diff', mdl_WM)
ssys_chans = smodel.Surfsys('ssys_chans', mdl_WM)
vsys_buffs = smodel.Volsys('vsys_buffs', mdl_WM)
#for EField
ssys_stoch = smodel.Surfsys('ssys_stoch', mdl_stoch)
# Diffusions
diff_Ca_inward = smodel.SReac('diff_Ca_inward',
ssys_diff,
olhs=[Ca],
irhs=[Ca],
kcst=0)
diff_Ca_outward = smodel.SReac('diff_Ca_outward',
ssys_diff,
ilhs=[Ca],
orhs=[Ca],
kcst=0)
diff_CBsf_inward = smodel.SReac('diff_CBsf_inward',
ssys_diff,
olhs=[CBsf],
irhs=[CBsf],
kcst=0)
diff_CBsf_outward = smodel.SReac('diff_CBsf_outward',
ssys_diff,
diff_CBsCa.setDcst(DCB)
diff_CBCaf = smodel.Diff('diff_CBCaf', vsys_stoch, CBCaf)
diff_CBCaf.setDcst(DCB)
diff_CBCaCa = smodel.Diff('diff_CBCaCa', vsys_stoch, CBCaCa)
diff_CBCaCa.setDcst(DCB)
diff_PV = smodel.Diff('diff_PV', vsys_stoch, PV)
diff_PV.setDcst(DPV)
diff_PVCa = smodel.Diff('diff_PVCa', vsys_stoch, PVCa)
diff_PVCa.setDcst(DPV)
diff_PVMg = smodel.Diff('diff_PVMg', vsys_stoch, PVMg)
diff_PVMg.setDcst(DPV)
#Pump
PumpD_f = smodel.SReac('PumpD_f',
ssys_det,
ilhs=[Ca_det],
slhs=[Pump],
srhs=[CaPump])
PumpD_f.setKcst(P_f_kcst)
PumpD_b = smodel.SReac('PumpD_b',
ssys_det,
slhs=[CaPump],
irhs=[Ca_det],
srhs=[Pump])
PumpD_b.setKcst(P_b_kcst)
PumpD_k = smodel.SReac('PumpD_k', ssys_det, slhs=[CaPump], srhs=[Pump])
PumpD_k.setKcst(P_k_kcst)
#iCBsf-fast
def getModel():
mdl = smodel.Model()
# Calcium
Ca = smodel.Spec('Ca', mdl)
# Pump
Pump = smodel.Spec('Pump', mdl)
# CaPump
CaPump = smodel.Spec('CaPump', mdl)
# iCBsf
iCBsf = smodel.Spec('iCBsf', mdl)
# iCBsCa
iCBsCa = smodel.Spec('iCBsCa', mdl)
# iCBCaf
iCBCaf = smodel.Spec('iCBCaf', mdl)
# iCBCaCa
iCBCaCa = smodel.Spec('iCBCaCa', mdl)
# CBsf
CBsf = smodel.Spec('CBsf', mdl)
# CBsCa
CBsCa = smodel.Spec('CBsCa', mdl)
# CBCaf
CBCaf = smodel.Spec('CBCaf', mdl)
# CBCaCa
CBCaCa = smodel.Spec('CBCaCa', mdl)
# PV
PV = smodel.Spec('PV', mdl)
# PVMg
PVMg = smodel.Spec('PVMg', mdl)
# PVCa
PVCa = smodel.Spec('PVCa', mdl)
# Mg
Mg = smodel.Spec('Mg', mdl)
# Vol/surface systems
vsys = smodel.Volsys('vsys', mdl)
ssys = smodel.Surfsys('ssys', mdl)
diff_Ca = smodel.Diff('diff_Ca', vsys, Ca)
diff_Ca.setDcst(DCST)
diff_CBsf = smodel.Diff('diff_CBsf', vsys, CBsf)
diff_CBsf.setDcst(DCB)
diff_CBsCa = smodel.Diff('diff_CBsCa', vsys, CBsCa)
diff_CBsCa.setDcst(DCB)
diff_CBCaf = smodel.Diff('diff_CBCaf', vsys, CBCaf)
diff_CBCaf.setDcst(DCB)
diff_CBCaCa = smodel.Diff('diff_CBCaCa', vsys, CBCaCa)
diff_CBCaCa.setDcst(DCB)
diff_PV = smodel.Diff('diff_PV', vsys, PV)
diff_PV.setDcst(DPV)
diff_PVCa = smodel.Diff('diff_PVCa', vsys, PVCa)
diff_PVCa.setDcst(DPV)
diff_PVMg = smodel.Diff('diff_PVMg', vsys, PVMg)
diff_PVMg.setDcst(DPV)
#Pump
PumpD_f = smodel.SReac('PumpD_f',
ssys,
ilhs=[Ca],
slhs=[Pump],
srhs=[CaPump])
PumpD_f.setKcst(P_f_kcst)
PumpD_b = smodel.SReac('PumpD_b',
ssys,
slhs=[CaPump],
irhs=[Ca],
srhs=[Pump])
PumpD_b.setKcst(P_b_kcst)
PumpD_k = smodel.SReac('PumpD_k', ssys, slhs=[CaPump], srhs=[Pump])
PumpD_k.setKcst(P_k_kcst)
#iCBsf-fast
iCBsf1_f = smodel.Reac('iCBsf1_f',
vsys,
lhs=[Ca, iCBsf],
rhs=[iCBsCa],
kcst=iCBsf1_f_kcst)
iCBsf1_b = smodel.Reac('iCBsf1_b',
vsys,
lhs=[iCBsCa],
rhs=[Ca, iCBsf],
kcst=iCBsf1_b_kcst)
#iCBsCa
iCBsCa_f = smodel.Reac('iCBsCa_f',
vsys,
lhs=[Ca, iCBsCa],
rhs=[iCBCaCa],
kcst=iCBsCa_f_kcst)
iCBsCa_b = smodel.Reac('iCBsCa_b',
vsys,
lhs=[iCBCaCa],
rhs=[Ca, iCBsCa],
kcst=iCBsCa_b_kcst)
#iCBsf_slow
iCBsf2_f = smodel.Reac('iCBsf2_f',
vsys,
lhs=[Ca, iCBsf],
rhs=[iCBCaf],
kcst=iCBsf2_f_kcst)
iCBsf2_b = smodel.Reac('iCBsf2_b',
vsys,
lhs=[iCBCaf],
rhs=[Ca, iCBsf],
kcst=iCBsf2_b_kcst)
#iCBCaf
iCBCaf_f = smodel.Reac('iCBCaf_f',
vsys,
lhs=[Ca, iCBCaf],
rhs=[iCBCaCa],
kcst=iCBCaf_f_kcst)
iCBCaf_b = smodel.Reac('iCBCaf_b',
vsys,
lhs=[iCBCaCa],
rhs=[Ca, iCBCaf],
kcst=iCBCaf_b_kcst)
#CBsf-fast
CBsf1_f = smodel.Reac('CBsf1_f',
vsys,
lhs=[Ca, CBsf],
rhs=[CBsCa],
kcst=CBsf1_f_kcst)
CBsf1_b = smodel.Reac('CBsf1_b',
vsys,
lhs=[CBsCa],
rhs=[Ca, CBsf],
kcst=CBsf1_b_kcst)
#CBsCa
CBsCa_f = smodel.Reac('CBsCa_f',
vsys,
lhs=[Ca, CBsCa],
rhs=[CBCaCa],
kcst=CBsCa_f_kcst)
CBsCa_b = smodel.Reac('CBsCa_b',
vsys,
lhs=[CBCaCa],
rhs=[Ca, CBsCa],
kcst=CBsCa_b_kcst)
#CBsf_slow
CBsf2_f = smodel.Reac('CBsf2_f',
vsys,
lhs=[Ca, CBsf],
rhs=[CBCaf],
kcst=CBsf2_f_kcst)
CBsf2_b = smodel.Reac('CBsf2_b',
vsys,
lhs=[CBCaf],
rhs=[Ca, CBsf],
kcst=CBsf2_b_kcst)
#CBCaf
CBCaf_f = smodel.Reac('CBCaf_f',
vsys,
lhs=[Ca, CBCaf],
rhs=[CBCaCa],
kcst=CBCaf_f_kcst)
CBCaf_b = smodel.Reac('CBCaf_b',
vsys,
lhs=[CBCaCa],
rhs=[Ca, CBCaf],
kcst=CBCaf_b_kcst)
#PVca
PVca_f = smodel.Reac('PVca_f',
vsys,
lhs=[Ca, PV],
rhs=[PVCa],
kcst=PVca_f_kcst)
PVca_b = smodel.Reac('PVca_b',
vsys,
lhs=[PVCa],
rhs=[Ca, PV],
kcst=PVca_b_kcst)
#PVmg
PVmg_f = smodel.Reac('PVmg_f',
vsys,
lhs=[Mg, PV],
rhs=[PVMg],
kcst=PVmg_f_kcst)
PVmg_b = smodel.Reac('PVmg_b',
vsys,
lhs=[PVMg],
rhs=[Mg, PV],
kcst=PVmg_b_kcst)
# Ca Influx converted from P Type current
CaInflux = smodel.Reac('CaInflux', vsys, lhs=[], rhs=[Ca], kcst=0.0)
return mdl
