#nazaret1

FIX: H H2O He O2 iP

#reactions
v1:
 $pool = {1.0}Pyr
  mitochondrion * k1
v2:
 {1.0}Pyr + {1.0}NAD = {1.0}AcCoA
  mitochondrion * k2 * Pyr * NAD
v3:
 {1.0}OAA + {1.0}AcCoA = {1.0}Cit
  mitochondrion * k3 * OAA * AcCoA
v4:
 {1.0}Cit + {1.0}NAD = {1.0}KG
  mitochondrion * k4 * Cit * NAD
v5:
 {1.0}KG + {2.0}NAD = {1.0}OAA + {1.0}ATP
  mitochondrion * k5 * KG * NAD * (At - ATP)
v6:
 {1.0}OAA = {1.0}KG
  mitochondrion * k6 * (OAA - KG / Keq)
v7:
 {1.0}Pyr + {1.0}ATP = {1.0}OAA
  mitochondrion * k7 * Pyr * ATP
v8:
 {1.0}OAA = $pool
  mitochondrion * k8 * OAA
vANT:
 {1.0}ATP = $pool
  mitochondrion * JANT
vATP:
 {1.0}iP + {3.0}He = {1.0}ATP + {1.0}H2O + {3.0}H
  mitochondrion * JATP
vleak:
 {1.0}He = {1.0}H
  mitochondrion * Jleak
vresp:
 {0.5}O2 + {11.0}H = {1.0}NAD + {1.0}H2O + {10.0}He
  mitochondrion * Jresp


#parameters
At = 4.16
C = 6.75e-06
DeltaPsim = 150.0
F = 96485.0
K = 2.0
Kapp = 4.4e-09
Nt = 1.07
R = 8314.0
T = 298.0
a = 0.1
b = 0.004
kANT = 0.05387
kATP = 131.9
kleak = 0.000426
kresp = 2.5
H = 1.0
H2O = 1.0
He = 1.0
O2 = 1.0
iP = 2.44
v1_k1 = 0.038
v2_k2 = 0.152
v3_k3 = 57.142
v4_k4 = 0.053
v5_k5 = 0.082361
v6_k6 = 0.0032
v6_Keq = 0.3975
v7_k7 = 0.04
v8_k8 = 3.6
cytoplasm = 1.0
mitochondrion = 1.0


#initial values
ATP = 3.536
AcCoA = 0.063
Cit = 0.44
KG = 0.225
NAD = 0.856
OAA = 0.005
Pyr = 0.154
DeltaPsi = 150


#assignment rules
!F NADH = Nt - NAD
!F ADP = At - ATP
!F DeltaGtransport = 1.2 * F * DeltaPsi
!F ATPcrit = At / (1.0 + exp(-3.0 * DeltaGtransport / (R * T)) / (Kapp * iP))
!F JATP = kATP * (2.0 / (1.0 + exp(b * (ATP - ATPcrit))) - 1.0)
!F Jresp = kresp * ((Nt - NAD) / (K + Nt - NAD)) / (1.0 + exp(a * (DeltaPsi - DeltaPsim)))
!F Jleak = kleak * DeltaPsi
!F JANT = kANT * ATP