XPP model

This model was converted from XPP ode format to SBML using sbmlutils-0.1.5a6.

# Markov model for cardiac Na(+) channel implemented by Dr. Jiun-Shian Wu, Dr. Sheng-Nan Wu, 
# and Dr. Ruey J. Sung, Han-Dong Chang.
# Clancy CE and Rudy Y. Na(+) channel mutation that causes both Brugada and long-QT 
# syndrome phenotypes: a simulation study of mechanism. Circulation 2002;105:1208-13.
# This simulation makes traces similar to fig 3A of the paper by Makita et al (2002).
# Makita N et al. Drug-induced long-QT syndrome associated with a subclinical SCN5A mutation. 
# Circulation 2002;106:1269-74.

# Constant:
Rk=8314
Fara=96485
Temp=310

# Initial values
init C3=1, C2=0, C1=0
init IC3=0, IC2=0, iif=0, IM1=0, IM2=0
init O=0

# Values of the model parameters
par ko=4.5, ki=136.89149
par nao=140, nai=15
par vhold=-80, vtest_1=30, vtest_2=-50
par cai=7.9e-5
par scale=1000

# voltage-clamp protocols
par ton=5, toff=20, toff_r=5000
v=vhold+heav(t-ton)*heav(toff-t)*(vtest_1-vhold)+heav(t-toff)*heav(toff_r-t)*(vtest_2-vhold)
Ena=((Rk*temp)/Fara)*ln(nao/nai)

# Expressions:
a11 = 3.802/(0.1027*exp(-v/17.0)+0.20*exp(-v/150))
a12 = 3.802/(0.1027*exp(-v/15.0)+0.23*exp(-v/150))
a13 = 3.802/(0.1027*exp(-v/12.0)+0.25*exp(-v/150))

b11 = 0.1917*exp(-v/20.3)
b12 = 0.20*exp(-(v-5)/20.3)
b13 = 0.22*exp(-(v-10)/20.3)

a2 = (9.178*exp(v/29.68))
b2 = (a13*a2*a3)/( b13*b3)

a3 = (3.7933*0.00000001)*exp(-v/7.7)
b3 = (0.0084+0.00002*v)

a4 = a2/100
b4 = a3

a5 = a2/(9.5*10000)
b5 = a3/50

# Gating functions
C1' = C2*a12-C1*b12+O*b13-C1*a13+iif*a3-C1*b3
C2' = C3*a11-C2*b11-C2*a12+C1*b12+IC2*a3-C2*b3
C3' = C2*b11-C3*a11+IC3*a3-C3*b3
O'  = C1*a13-O*b13+iif*b2-O*a2 

IC3' = C3*b3-IC3*a3+IC2*b11-IC3*a11
IC2' = IC3*a11-IC2*b11+iif*b12-IC2*a12+C2*b3-IC2*a3
iif' = IC2*a12-iif*b12+IM1*b4-iif*a4+C1*b3-iif*a3+O*a2-iif*b2
IM1'= IM2*b5-IM1*a5+iif*a4-IM1*b4
IM2'= IM1*a5-IM2*b5

Gna=23.5
aux ina=Gna*(O/(IC3+IC2+iif+IM1+IM2+C3+C2+C1+O))*(v-Ena)/scale

@ meth=Euler, dt=.005, total=20
@ yp=ina, yhi=0.1, ylo=-0.5, xlo=0, xhi=20

done
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Terms of use

Copyright © 2017 Matthias Koenig

Redistribution and use of any part of this model, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. Redistributions in a different form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


Model :

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Access SBML model  L3V1

FunctionDefinitions [4] name math sbo cvterm
max minimum x y x x y y
min maximum x y x x y y
heav heavyside x 0 x 0 0.5 x 0 1 x 0 0
mod modulo x y x y x y x 0 y 0 x y x y

Parameters [43] name constant value unit derived unit sbo cvterm
c3 c3 = 1 1.0 None
c2 c2 = 0 0.0 None
c1 c1 = 0 0.0 None
ic3 ic3 = 0 0.0 None
ic2 ic2 = 0 0.0 None
iif iif = 0 0.0 None
im1 im1 = 0 0.0 None
im2 im2 = 0 0.0 None
o o = 0 0.0 None
ko ko = 4.5 4.5 None
ki ki = 136.89149 136.89149 None
nao nao = 140 140.0 None
nai nai = 15 15.0 None
vhold vhold = -80 -80.0 None
vtest_1 vtest_1 = 30 30.0 None
vtest_2 vtest_2 = -50 -50.0 None
cai cai = 7.9e-5 7.9e-05 None
scale scale = 1000 1000.0 None
ton ton = 5 5.0 None
toff toff = 20 20.0 None
toff_r toff_r = 5000 5000.0 None
rk 0.0 dimensionless None
fara 0.0 dimensionless None
temp 0.0 dimensionless None
v 0.0 dimensionless None
ena 0.0 dimensionless None
a11 0.0 dimensionless None
a12 0.0 dimensionless None
a13 0.0 dimensionless None
b11 0.0 dimensionless None
b12 0.0 dimensionless None
b13 0.0 dimensionless None
a2 0.0 dimensionless None
b2 0.0 dimensionless None
a3 0.0 dimensionless None
b3 0.0 dimensionless None
a4 0.0 dimensionless None
b4 0.0 dimensionless None
a5 0.0 dimensionless None
b5 0.0 dimensionless None
gna 0.0 dimensionless None
ina 0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [31]   assignment name derived units sbo cvterm
d c1/dt = c2 a12 c1 b12 o b13 c1 a13 iif a3 c1 b3 None
d c2/dt = c3 a11 c2 b11 c2 a12 c1 b12 ic2 a3 c2 b3 None
d c3/dt = c2 b11 c3 a11 ic3 a3 c3 b3 None
d o/dt = c1 a13 o b13 iif b2 o a2 None
d ic3/dt = c3 b3 ic3 a3 ic2 b11 ic3 a11 None
d ic2/dt = ic3 a11 ic2 b11 iif b12 ic2 a12 c2 b3 ic2 a3 None
d iif/dt = ic2 a12 iif b12 im1 b4 iif a4 c1 b3 iif a3 o a2 iif b2 None
d im1/dt = im2 b5 im1 a5 iif a4 im1 b4 None
d im2/dt = im1 a5 im2 b5 None
rk = 8314 None
fara = 96485 None
temp = 310 None
v = vhold heav t ton heav toff t vtest_1 vhold heav t toff heav toff_r t vtest_2 vhold None
ena = rk temp fara nao nai None
a11 = 3.802 0.1027 v 17 0.2 v 150 None
a12 = 3.802 0.1027 v 15 0.23 v 150 None
a13 = 3.802 0.1027 v 12 0.25 v 150 None
b11 = 0.1917 v 20.3 None
b12 = 0.2 v 5 20.3 None
b13 = 0.22 v 10 20.3 None
a2 = 9.178 v 29.68 None
b2 = a13 a2 a3 b13 b3 None
a3 = 3.7933 1 -8 v 7.7 None
b3 = 0.0084 2 -5 v None
a4 = a2 100 None
b4 = a3 None
a5 = a2 9.5 10000 None
b5 = a3 50 None
gna = 23.5 None
ina = gna o ic3 ic2 iif im1 im2 c3 c2 c1 o v ena scale None
t = time None