#vanniekerk1

FIX: glcEX glyEX lacEX pyrEX

#reactions
vPFvALD:
 {1.0}f16bpPF = {1.0}gapPF + {1.0}dhapPF
  Vpf * VPFvALD * f16bpPF / (Kf16bpPFvALD * Vpf) * (1 - dhapPF * gapPF / f16bpPF / (Vpf * KeqPFvALD)) / (1 + dhapPF / (KdhapPFvALD * Vpf) + gapPF / (KgapPFvALD * Vpf) + f16bpPF / (Kf16bpPFvALD * Vpf) + dhapPF * gapPF / (KgapPFvALD * KdhapPFvALD * Vpf * Vpf))
vPFvATPASE:
 {1.0}atpPF = {1.0}adpPF
  Vpf * VPFvATPASE * pow(atpPF / (KmPFvATPASE * Vpf), 5) / (1 + pow(atpPF / (KmPFvATPASE * Vpf), 5))
vPFvENO:
 {1.0}p2gPF = {1.0}pepPF
  Vpf * VPFvENO * p2gPF / (Kp2gPFvENO * Vpf) * (1 - pepPF / (p2gPF * KeqPFvENO)) / (1 + p2gPF / (Kp2gPFvENO * Vpf) + pepPF / (KpepPFvENO * Vpf))
vPFvG3PDH:
 {1.0}dhapPF + {1.0}nadhPF = {1.0}nadPF + {1.0}g3pPF
  Vpf * VfPFvG3PDH * dhapPF * nadhPF / (KdhapPFvG3PDH * KnadhPFvG3PDH * Vpf * Vpf) * (1 - g3pPF / Vpf * nadPF / Vpf / (KeqPFvG3PDH * dhapPF / Vpf * nadhPF / Vpf)) / ((1 + nadPF / (KnadPFvG3PDH * Vpf) + nadhPF / (KnadhPFvG3PDH * Vpf)) * (1 + g3pPF / (Kg3pPFvG3PDH * Vpf) + dhapPF / (KdhapPFvG3PDH * Vpf)))
vPFvGAPDH:
 {1.0}nadPF + {1.0}gapPF = {1.0}nadhPF + {1.0}b13pgPF
  (Vpf * VPFvGAPDH * gapPF * nadPF / (KgapPFvGAPDH * KnadPFvGAPDH * Vpf * Vpf) - Vpf * VrPFvGAPDH * nadhPF * b13pgPF / (KnadhPFvGAPDH * Kb13pgPFvGAPDH * Vpf * Vpf)) / ((1 + nadPF / (KnadPFvGAPDH * Vpf) + nadhPF / (KnadhPFvGAPDH * Vpf)) * (1 + gapPF / (KgapPFvGAPDH * Vpf) + b13pgPF / (Kb13pgPFvGAPDH * Vpf)))
vPFvGLCtr:
 {1.0}glcEX = {1.0}glcPF
  (glcEX * Vpf * VPFvGLCtr / ((1 + cytb / Ki1CytGlcTr) * KPFvGLCtr * Vex) - VPFvGLCtr * glcPF / ((1 + cytb / Ki1CytGlcTr) * KPFvGLCtr)) / (1 + glcEX * (1 + cytb / Ki2CytGlcTr) / ((1 + cytb / Ki1CytGlcTr) * KPFvGLCtr * Vex) + (1 + cytb / Ki2CytGlcTr) * glcPF / ((1 + cytb / Ki1CytGlcTr) * KPFvGLCtr * Vpf) + alphaPFvGLCtr * glcEX * glcPF / ((1 + cytb / Ki1CytGlcTr) * KPFvGLCtr**2 * Vex * Vpf))
vPFvGLYtr:
 {1.0}g3pPF = {1.0}glyEX
  Vpf * kPFvGLYtr * (g3pPF / Vpf - glyEX / Vex)
vPFvHK:
 {1.0}glcPF + {1.0}atpPF = {1.0}g6pPF + {1.0}adpPF
  Vpf * VPFvHK * glcPF / (KglcPFvHK * Vpf) * atpPF / (KatpPFvHK * Vpf) * (1 - adpPF * g6pPF / (KeqPFvHK * atpPF * glcPF)) / ((1 + atpPF / (KiatpPFvHK * Vpf)) * (1 + adpPF / (KadpPFvHK * Vpf) + atpPF / (KatpPFvHK * Vpf)) * (1 + g6pPF / (Kg6pPFvHK * Vpf) + glcPF / (KglcPFvHK * Vpf)))
vPFvLACtr:
 {1.0}lacPF = {1.0}lacEX
  Vpf * VPFvLACtr * lacPF / (KlacPFvLACtr * Vpf) * (1 - hEX * lacEX / Vex / (hPF * lacPF / Vpf)) / (1 + lacPF / (KlacPFvLACtr * Vpf) + lacEX / (KlacPFvLACtr * Vex) + pyrPF / (KipyrPFvLACtr * Vpf) + pyrEX / (KipyrPFvLACtr * Vex)) + Vpf * KdPFvLACtr * (1 - hEX * lacEX / Vex / (hPF * lacPF / Vpf)) * lacPF / Vpf
vPFvLDH:
 {1.0}pyrPF + {1.0}nadhPF = {1.0}nadPF + {1.0}lacPF
  (Vpf * VfPFvLDH * nadhPF * pyrPF / (KnadhPFvLDH * KpyrPFvLDH * Vpf * Vpf) - Vpf * VrPFvLDH * lacPF * nadPF / (KlacPFvLDH * KnadPFvLDH * Vpf * Vpf)) / ((1 + nadPF / (KnadPFvLDH * Vpf) + nadhPF / (KnadhPFvLDH * Vpf)) * (1 + lacPF / (KlacPFvLDH * Vpf) + pyrPF / (KpyrPFvLDH * Vpf)))
vPFvPFK:
 {1.0}f6pPF + {1.0}atpPF = {1.0}f16bpPF + {1.0}adpPF
  Vpf * VPFvPFK * atpPF * f6pPF / (KatpPFvPFK * Vpf * Kf6pPFvPFK * Vpf) / ((1 + atpPF / (KatpPFvPFK * Vpf)) * (1 + adpPF / (KadpPFvPFK * Vpf) + atpPF / (KatpPFvPFK * Vpf)) * (1 + f16bpPF / (Kf16bpPFvPFK * Vpf) + f6pPF / (Kf6pPFvPFK * Vpf)))
vPFvPGI:
 {1.0}g6pPF = {1.0}f6pPF
  Vpf * VPFvPGI * g6pPF / (Kg6pPFvPGI * Vpf) * (1 - f6pPF / (g6pPF * KeqPFvPGI)) / (1 + f6pPF / (Kf6pPFvPGI * Vpf) + g6pPF / (Kg6pPFvPGI * Vpf))
vPFvPGK:
 {1.0}b13pgPF + {1.0}adpPF = {1.0}p3gPF + {1.0}atpPF
  Vpf * KadpPFvPGK * Kb13pgPFvPGK * KeqPFvPGK * VrPFvPGK / (KatpPFvPGK * Kp3gPFvPGK) * (KeqPFvPGK / (atpPF * p3gPF / (adpPF * b13pgPF)) - 1) * atpPF * p3gPF / (KatpPFvPGK * Kp3gPFvPGK * Vpf * Vpf) / ((1 + adpPF / (KadpPFvPGK * Vpf) + atpPF / (KatpPFvPGK * Vpf)) * (1 + b13pgPF / (Kb13pgPFvPGK * Vpf) + p3gPF / (Kp3gPFvPGK * Vpf)))
vPFvPGM:
 {1.0}p3gPF = {1.0}p2gPF
  Vpf * VPFvPGM * p3gPF / (Kp3gPFvPGM * Vpf) * (1 - p2gPF / (p3gPF * KeqPFvPGM)) / (1 + p2gPF / (Kp2gPFvPGM * Vpf) + p3gPF / (Kp3gPFvPGM * Vpf))
vPFvPK:
 {1.0}pepPF + {1.0}adpPF = {1.0}pyrPF + {1.0}atpPF
  Vpf * VPFvPK * adpPF / (KadpPFvPK * Vpf) * pepPF / (KpepPFvPK * Vpf) / ((1 + adpPF / (Vpf * KadpPFvPK)) * (1 + pepPF / (Vpf * KpepPFvPK)) * (1 + LPFvPK * (1 + pow(adpPF / (KiadpPFvPK * Vpf) + atpPF / (KiatpPFvPK * Vpf), h)) * (1 + pow(pepPF / (KipepPFvPK * Vpf) + pyrPF / (KipyrPFvPK * Vpf), h))))
vPFvPYRtr:
 {1.0}pyrPF = {1.0}pyrEX
  Vpf * VPFvPYRtr * pyrPF / (KpyrPFvPYRtr * Vpf) * (1 - hEX * pyrEX / Vex / (hPF * pyrPF / Vpf)) / (1 + pyrEX / (KpyrPFvPYRtr * Vex) + pyrPF / (KpyrPFvPYRtr * Vpf) + lacPF / (KilacPFvPYRtr * Vpf) + lacEX / (KilacPFvPYRtr * Vex)) + Vpf * KdPFvPYRtr * (1 - hEX * pyrEX / Vex / (hPF * pyrPF / Vpf)) * pyrPF / Vpf
vPFvTPI:
 {1.0}dhapPF = {1.0}gapPF
  Vpf * VPFvTPI * dhapPF / (KdhapPFvTPI * Vpf) * (1 - gapPF / (KeqPFvTPI * dhapPF)) / (1 + dhapPF / (KdhapPFvTPI * Vpf) + gapPF / (KgapPFvTPI * Vpf) + pepPF / (KipepPFvTPI * Vpf))


#parameters
ConcAdpPF = 0.001
ConcAtpPF = 0.002
ConcB13pgPF = 0.0001
ConcDhapPF = 0.0001
ConcF16bpPF = 0.0001
ConcF6pPF = 0.0001
ConcG6pPF = 0.0001
ConcGapPF = 0.0001
ConcGlcEX = 0.005
ConcGlcPF = 0.0001
ConcGly3pPF = 0.0001
ConcGlyEX = 0.00015
ConcLacEX = 0.002
ConcLacPF = 0.0001
ConcNadPF = 0.0025
ConcNadhPF = 0.0005
ConcP2gPF = 0.0001
ConcP3gPF = 0.0001
ConcPepPF = 0.0001
ConcPyrEX = 0.0002
ConcPyrPF = 0.0001
KPFvGLCtr = 0.000213
KadpPFvHK = 0.000846735
KadpPFvPFK = 0.00074176
KadpPFvPGK = 0.00015
KadpPFvPK = 0.000317
KatpPFvHK = 0.00069647
KatpPFvPFK = 0.0007862
KatpPFvPGK = 0.00077
Kb13pgPFvGAPDH = 2.359e-05
Kb13pgPFvPGK = 1.34e-05
KdPFvLACtr = 0.005
KdPFvPYRtr = 0.0007
KdhapPFvALD = 0.00011
KdhapPFvG3PDH = 0.00034
KdhapPFvTPI = 0.001954
KeqPFvALD = 9e-05
KeqPFvENO = 4.6
KeqPFvG3PDH = 32600.0
KeqPFvHK = 1310.0
KeqPFvPGI = 0.33
KeqPFvPGK = 3200.0
KeqPFvPGM = 0.19
KeqPFvTPI = 0.04545
Kf16bpPFvALD = 6.84e-05
Kf16bpPFvPFK = 0.003626
Kf6pPFvPFK = 0.00109454
Kf6pPFvPGI = 9.6651e-05
Kg3pPFvG3PDH = 0.00398
Kg6pPFvHK = 4.3e-05
Kg6pPFvPGI = 0.00100774
KgapPFvALD = 4.6e-05
KgapPFvGAPDH = 0.000917
KgapPFvTPI = 0.000337
KglcPFvHK = 0.000168613
Ki1CytGlcTr = 8.8674635367585e-08
Ki2CytGlcTr = 2.07687280948754e-05
KiadpPFvPK = 0.002
KiatpPFvHK = 0.026
KiatpPFvPK = 0.00182
KilacPFvPYRtr = 0.000358
KipepPFvPK = 0.00292
KipepPFvTPI = 1.59e-05
KipyrPFvLACtr = 0.00163
KipyrPFvPK = 0.105
KlacPFvLACtr = 0.0038
KlacPFvLDH = 0.003611
KmPFvATPASE = 0.0045
KnadPFvG3PDH = 0.00051
KnadPFvGAPDH = 0.0005662
KnadPFvLDH = 0.000234
KnadhPFvG3PDH = 9e-05
KnadhPFvGAPDH = 2.87e-05
KnadhPFvLDH = 4.6e-05
Kp2gPFvENO = 0.000521
Kp2gPFvPGM = 0.000318
Kp3gPFvPGK = 0.000267
Kp3gPFvPGM = 0.00173
KpepPFvENO = 0.00129
KpepPFvPK = 0.000406
KpyrPFvLDH = 0.000133
KpyrPFvPYRtr = 0.0157
LPFvPK = 0.255
VPFvALD = 0.0569593147718
VPFvATPASE = 0.345
VPFvENO = 0.286295503195
VPFvGAPDH = 0.656263383259
VPFvGLCtr = 0.0469
VPFvHK = 0.083
VPFvLACtr = 0.598
VPFvPFK = 0.41
VPFvPGI = 0.800428265477
VPFvPGM = 0.186937901488
VPFvPK = 0.762
VPFvPYRtr = 0.216
VPFvTPI = 1.50599571726
VfPFvG3PDH = 0.012
VfPFvLDH = 0.542612419668
VrPFvGAPDH = 0.243199143455
VrPFvLDH = 0.290792291203
VrPFvPGK = 0.353533190557
alphaPFvGLCtr = 0.91
cytb = 0.0
h = 4.0
kPFvGLYtr = 2.0
pHConversionFactor = 1.0
phEX = 7.1
phPF = 7.2
glcEX = 0.45
glyEX = 0.013499999999999998
lacEX = 0.18
pyrEX = 0.018000000000000002
Vex = 90.0
Vpf = 28.0


#initial values
adpPF = 0.028
atpPF = 0.056
b13pgPF = 0.0028
dhapPF = 0.0028
f16bpPF = 0.0028
f6pPF = 0.0028
g3pPF = 0.0028
g6pPF = 0.0028
gapPF = 0.0028
glcPF = 0.0028
lacPF = 0.0028
nadPF = 0.07
nadhPF = 0.014
p2gPF = 0.0028
p3gPF = 0.0028
pepPF = 0.0028
pyrPF = 0.0028


#assignment rules
!F hEX = pHConversionFactor / pow(10, phEX)
!F hPF = pHConversionFactor / pow(10, phPF)