# #Hynne2001_Glycolysis pow(x,y)=x^y root(x,y)=y^(1/x) @delay=50 # Compartment: id = extracellular, name = extracellular, constant par extracell=1.0 # Compartment: id = cytosol, name = cytosol, constant par cytosol=1.0 # Reaction: id = vinGlc, name = Glucose Mixed flow to extracellular medium # Local Parameter: # Parameter: id = k0, name = k0, constant par k0=0.048 vinGlc=extracell * k0 * (GlcX0 - GlcX) # Reaction: id = vGlcTrans, name = Glucose uptake # Local Parameter: # Parameter: id = V2f, name = V2f, constant par V2f=1014.96 # Local Parameter: # Parameter: id = Yvol, name = Yvol, constant par Yvol=59.0 # Local Parameter: # Parameter: id = K2Glc, name = K2Glc, constant par K2Glc=1.7 # Local Parameter: # Parameter: id = P2, name = P2, constant par P2=1.0 # Local Parameter: # Parameter: id = K2IG6P, name = K2IG6P, constant par K2IG6P=1.2 # Local Parameter: # Parameter: id = K2IIG6P, name = K2IIG6P, constant par K2IIG6P=7.2 # Local Parameter: # Parameter: id = V2r, name = V2r, constant par V2r=1014.96 vGlcTrans=extracell * V2f / Yvol * (GlcX / K2Glc / (1 + GlcX / K2Glc + (P2 * (GlcX / K2Glc) + 1) / (P2 * (Glc / K2Glc) + 1) * (1 + Glc / K2Glc + G6P / K2IG6P + Glc * G6P / (K2Glc * K2IIG6P)))) - cytosol * V2r / Yvol * (Glc / K2Glc / (1 + Glc / K2Glc + (P2 * (Glc / K2Glc) + 1) / (P2 * (GlcX / K2Glc) + 1) * (1 + GlcX / K2Glc) + G6P / K2IG6P + Glc * G6P / (K2Glc * K2IIG6P))) # Reaction: id = vHK, name = Hexokinase # Local Parameter: # Parameter: id = V3m, name = V3m, constant par V3m=51.7547 # Local Parameter: # Parameter: id = K3DGlc, name = K3DGlc, constant par K3DGlc=0.37 # Local Parameter: # Parameter: id = K3ATP, name = K3ATP, constant par K3ATP=0.1 # Local Parameter: # Parameter: id = K3Glc, name = K3Glc, constant par K3Glc=0.0 vHK=cytosol * V3m * ATP * Glc / (K3DGlc * K3ATP + K3Glc * ATP + K3ATP * Glc + Glc * ATP) # Reaction: id = vPGI, name = Phosphoglucoisomerase # Local Parameter: # Parameter: id = V4f, name = V4f, constant par V4f=496.042 # Local Parameter: # Parameter: id = K4G6P, name = K4G6P, constant par K4G6P=0.8 # Local Parameter: # Parameter: id = K4F6P, name = K4F6P, constant par K4F6P=0.15 # Local Parameter: # Parameter: id = V4r, name = V4r, constant par V4r=496.042 # Local Parameter: # Parameter: id = K4eq, name = K4eq, constant par K4eq=0.13 vPGI=cytosol * (V4f * G6P / (K4G6P + G6P + K4G6P / K4F6P * F6P) - V4r * (F6P / K4eq) / (K4G6P + G6P + K4G6P / K4F6P * F6P)) # Reaction: id = vPFK, name = Phosphofructokinase # Local Parameter: # Parameter: id = V5m, name = V5m, constant par V5m=45.4327 # Local Parameter: # Parameter: id = K5, name = K5, constant par K5=0.021 # Local Parameter: # Parameter: id = kappa5, name = kappa5, constant par kappa5=0.15 vPFK=cytosol * (V5m * pow(F6P, 2) / (K5 * (1 + kappa5 * (ATP / AMP) * (ATP / AMP)) + pow(F6P, 2))) # Reaction: id = vALD, name = Aldolase # Local Parameter: # Parameter: id = V6f, name = V6f, constant par V6f=2207.82 # Local Parameter: # Parameter: id = K6FBP, name = K6FBP, constant par K6FBP=0.3 # Local Parameter: # Parameter: id = K6DHAP, name = K6DHAP, constant par K6DHAP=2.0 # Local Parameter: # Parameter: id = K6eq, name = K6eq, constant par K6eq=0.081 # Local Parameter: # Parameter: id = ratio6, name = ratio6, constant par ratio6=5.0 # Local Parameter: # Parameter: id = K6GAP, name = K6GAP, constant par K6GAP=4.0 # Local Parameter: # Parameter: id = K6IGAP, name = K6IGAP, constant par K6IGAP=10.0 vALD=cytosol * (V6f * FBP / (K6FBP + FBP + GAP * K6DHAP * V6f / (K6eq * V6f * ratio6) + DHAP * K6GAP * V6f / (K6eq * V6f * ratio6) + FBP * GAP / K6IGAP + GAP * DHAP * V6f / (K6eq * V6f * ratio6)) - V6f * GAP * DHAP / K6eq / (K6FBP + FBP + GAP * K6DHAP * V6f / (K6eq * V6f * ratio6) + DHAP * K6GAP * V6f / (K6eq * V6f * ratio6) + FBP * GAP / K6IGAP + GAP * DHAP * V6f / (K6eq * V6f * ratio6))) # Reaction: id = vTIM, name = Triosephosphate isomerase # Local Parameter: # Parameter: id = V7f, name = V7f, constant par V7f=116.365 # Local Parameter: # Parameter: id = K7DHAP, name = K7DHAP, constant par K7DHAP=1.23 # Local Parameter: # Parameter: id = K7GAP, name = K7GAP, constant par K7GAP=1.27 # Local Parameter: # Parameter: id = V7r, name = V7r, constant par V7r=116.365 # Local Parameter: # Parameter: id = K7eq, name = K7eq, constant par K7eq=0.055 vTIM=cytosol * (V7f * DHAP / (K7DHAP + DHAP + K7DHAP / K7GAP * GAP) - V7r * (GAP / K7eq) / (K7DHAP + DHAP + K7DHAP / K7GAP * GAP)) # Reaction: id = vGAPDH, name = Glyceraldehyde 3-phosphate dehydrogenase # Local Parameter: # Parameter: id = V8f, name = V8f, constant par V8f=833.858 # Local Parameter: # Parameter: id = K8GAP, name = K8GAP, constant par K8GAP=0.6 # Local Parameter: # Parameter: id = K8NAD, name = K8NAD, constant par K8NAD=0.1 # Local Parameter: # Parameter: id = K8BPG, name = K8BPG, constant par K8BPG=0.01 # Local Parameter: # Parameter: id = K8NADH, name = K8NADH, constant par K8NADH=0.06 # Local Parameter: # Parameter: id = V8r, name = V8r, constant par V8r=833.858 # Local Parameter: # Parameter: id = K8eq, name = K8eq, constant par K8eq=0.0055 vGAPDH=cytosol * (V8f * GAP * NAD / K8GAP / K8NAD / ((1 + GAP / K8GAP + BPG / K8BPG) * (1 + NAD / K8NAD + NADH / K8NADH)) - V8r * BPG * NADH / K8eq / K8GAP / K8NAD / ((1 + GAP / K8GAP + BPG / K8BPG) * (1 + NAD / K8NAD + NADH / K8NADH))) # Reaction: id = vlpPEP, name = Phosphoenolpyruvate synthesis # Local Parameter: # Parameter: id = k9f, name = k9f, constant par k9f=443866.0 # Local Parameter: # Parameter: id = k9r, name = k9r, constant par k9r=1528.62 vlpPEP=cytosol * (k9f * BPG * ADP - k9r * PEP * ATP) # Reaction: id = vPK, name = Pyruvate kinase # Local Parameter: # Parameter: id = V10m, name = V10m, constant par V10m=343.096 # Local Parameter: # Parameter: id = K10PEP, name = K10PEP, constant par K10PEP=0.2 # Local Parameter: # Parameter: id = K10ADP, name = K10ADP, constant par K10ADP=0.17 vPK=cytosol * (V10m * ADP * PEP / ((K10PEP + PEP) * (K10ADP + ADP))) # Reaction: id = vPDC, name = Pyruvate decarboxylase # Local Parameter: # Parameter: id = V11m, name = V11m, constant par V11m=53.1328 # Local Parameter: # Parameter: id = K11, name = K11, constant par K11=0.3 vPDC=cytosol * (V11m * Pyr / (K11 + Pyr)) # Reaction: id = vADH, name = Alcohol dehydrogenase # Local Parameter: # Parameter: id = V12m, name = V12m, constant par V12m=89.8023 # Local Parameter: # Parameter: id = K12NADH, name = K12NADH, constant par K12NADH=0.1 # Local Parameter: # Parameter: id = K12ACA, name = K12ACA, constant par K12ACA=0.71 vADH=cytosol * (V12m * ACA * NADH / ((K12NADH + NADH) * (K12ACA + ACA))) # Reaction: id = vdifEtOH, name = Ethanol out # Local Parameter: # Parameter: id = k13, name = k13, constant par k13=16.72 # Local Parameter: # Parameter: id = Yvol, name = Yvol, constant par Yvol_1=59.0 vdifEtOH=k13 / Yvol_1 * (cytosol * EtOH - extracell * EtOHX) # Reaction: id = voutEtOH, name = Ethanol flow # Local Parameter: # Parameter: id = k0, name = k0, constant par k0_1=0.048 voutEtOH=extracell * k0_1 * EtOHX # Reaction: id = vlpGlyc, name = Glycerol synthesis # Local Parameter: # Parameter: id = V15m, name = V15m, constant par V15m=81.4797 # Local Parameter: # Parameter: id = K15DHAP, name = K15DHAP, constant par K15DHAP=25.0 # Local Parameter: # Parameter: id = K15INADH, name = K15INADH, constant par K15INADH=0.034 # Local Parameter: # Parameter: id = K15INAD, name = K15INAD, constant par K15INAD=0.13 # Local Parameter: # Parameter: id = K15NADH, name = K15NADH, constant par K15NADH=0.13 vlpGlyc=cytosol * (V15m * DHAP / (K15DHAP * (1 + K15INADH / NADH * (1 + NAD / K15INAD)) + DHAP * (1 + K15NADH / NADH * (1 + NAD / K15INAD)))) # Reaction: id = vdifGlyc, name = Glycerol out # Local Parameter: # Parameter: id = k16, name = k16, constant par k16=1.9 # Local Parameter: # Parameter: id = Yvol, name = Yvol, constant par Yvol_1_2=59.0 vdifGlyc=k16 / Yvol_1_2 * (cytosol * Glyc - extracell * GlycX) # Reaction: id = voutGlyc, name = Glycerol flow # Local Parameter: # Parameter: id = k0, name = k0, constant par k0_1_2=0.048 voutGlyc=extracell * k0_1_2 * GlycX # Reaction: id = vdifACA, name = Acetaldehyde out # Local Parameter: # Parameter: id = k18, name = k18, constant par k18=24.7 # Local Parameter: # Parameter: id = Yvol, name = Yvol, constant par Yvol_1__3=59.0 vdifACA=k18 / Yvol_1__3 * (cytosol * ACA - extracell * ACAX) # Reaction: id = voutACA, name = Acetaldehyde flow # Local Parameter: # Parameter: id = k0, name = k0, constant par k0_1_2_3=0.048 voutACA=extracell * k0_1_2_3 * ACAX # Reaction: id = vlacto, name = Cyanide-Acetaldehyde flow # Local Parameter: # Parameter: id = k20, name = k20, constant par k20=0.00283828 vlacto=extracell * k20 * ACAX * CNX # Reaction: id = vinCN, name = Cyanide flow # Local Parameter: # Parameter: id = k0, name = k0, constant par k0_1_2__4=0.048 vinCN=extracell * k0_1_2__4 * (CNX0 - CNX) # Reaction: id = vstorage, name = Storage # Local Parameter: # Parameter: id = k22, name = k22, constant par k22=2.25932 vstorage=cytosol * k22 * ATP * G6P # Reaction: id = vconsum, name = ATP consumption # Local Parameter: # Parameter: id = k23, name = k23, constant par k23=3.2076 vconsum=cytosol * k23 * ATP # Reaction: id = vAK, name = Adenylate kinase # Local Parameter: # Parameter: id = k24f, name = k24f, constant par k24f=432.9 # Local Parameter: # Parameter: id = k24r, name = k24r, constant par k24r=133.333 vAK=cytosol * (k24f * AMP * ATP - k24r * pow(ADP, 2)) # Species: id = GlcX, name = Extracellular glucose, affected by kineticLaw init GlcX=6.7 dGlcX/dt=(1/(extracell))*(( 1 * vinGlc) + (-1 * vGlcTrans)) # Species: id = Glc, name = Cytosolic glucose, affected by kineticLaw init Glc=0.573074 dGlc/dt=(1/(cytosol))*(( 59.0 * vGlcTrans) + (-1 * vHK)) # Species: id = ATP, name = ATP, affected by kineticLaw init ATP=2.1 dATP/dt=(1/(cytosol))*((-1 * vHK) + (-1 * vPFK) + ( 1 * vlpPEP) + ( 1 * vPK) + (-1 * vstorage) + (-1 * vconsum) + (-1 * vAK)) # Species: id = G6P, name = Glucose-6-Phosphate, affected by kineticLaw init G6P=4.2 dG6P/dt=(1/(cytosol))*(( 1 * vHK) + (-1 * vPGI) + (-1 * vstorage)) # Species: id = ADP, name = ADP, affected by kineticLaw init ADP=1.5 dADP/dt=(1/(cytosol))*(( 1 * vHK) + ( 1 * vPFK) + (-1 * vlpPEP) + (-1 * vPK) + ( 1 * vstorage) + ( 1 * vconsum) + ( 2.0 * vAK)) # Species: id = F6P, name = Fructose-6-Phosphate, affected by kineticLaw init F6P=0.49 dF6P/dt=(1/(cytosol))*(( 1 * vPGI) + (-1 * vPFK)) # Species: id = FBP, name = Fructose 1,6-bisphosphate, affected by kineticLaw init FBP=4.64 dFBP/dt=(1/(cytosol))*(( 1 * vPFK) + (-1 * vALD)) # Species: id = GAP, name = Glyceraldehyde 3-phosphate, affected by kineticLaw init GAP=0.115 dGAP/dt=(1/(cytosol))*(( 1 * vALD) + ( 1 * vTIM) + (-1 * vGAPDH)) # Species: id = DHAP, name = Dihydroxyacetone phosphate, affected by kineticLaw init DHAP=2.95 dDHAP/dt=(1/(cytosol))*(( 1 * vALD) + (-1 * vTIM) + (-1 * vlpGlyc)) # Species: id = NAD, name = NAD, affected by kineticLaw init NAD=0.65 dNAD/dt=(1/(cytosol))*((-1 * vGAPDH) + ( 1 * vADH) + ( 1 * vlpGlyc)) # Species: id = BPG, name = 1,3-Bisphosphoglycerate, affected by kineticLaw init BPG=2.7E-4 dBPG/dt=(1/(cytosol))*(( 1 * vGAPDH) + (-1 * vlpPEP)) # Species: id = NADH, name = NADH, affected by kineticLaw init NADH=0.33 dNADH/dt=(1/(cytosol))*(( 1 * vGAPDH) + (-1 * vADH) + (-1 * vlpGlyc)) # Species: id = PEP, name = Phosphoenolpyruvate, affected by kineticLaw init PEP=0.04 dPEP/dt=(1/(cytosol))*(( 1 * vlpPEP) + (-1 * vPK)) # Species: id = Pyr, name = Pyruvate, affected by kineticLaw init Pyr=8.7 dPyr/dt=(1/(cytosol))*(( 1 * vPK) + (-1 * vPDC)) # Species: id = ACA, name = Acetaldehyde, affected by kineticLaw init ACA=1.48153 dACA/dt=(1/(cytosol))*(( 1 * vPDC) + (-1 * vADH) + (-59.0 * vdifACA)) # Species: id = EtOH, name = EtOH, affected by kineticLaw init EtOH=19.2379 dEtOH/dt=(1/(cytosol))*(( 1 * vADH) + (-59.0 * vdifEtOH)) # Species: id = EtOHX, name = Extracellular ethanol, affected by kineticLaw init EtOHX=16.4514 dEtOHX/dt=(1/(extracell))*(( 1 * vdifEtOH) + (-1 * voutEtOH)) # Species: id = Glyc, name = Glycerol, affected by kineticLaw init Glyc=4.196 dGlyc/dt=(1/(cytosol))*(( 1 * vlpGlyc) + (-59.0 * vdifGlyc)) # Species: id = GlycX, name = Extracellular glycerol, affected by kineticLaw init GlycX=1.68478 dGlycX/dt=(1/(extracell))*(( 1 * vdifGlyc) + (-1 * voutGlyc)) # Species: id = ACAX, name = Extracellular acetaldehyde, affected by kineticLaw init ACAX=1.28836 dACAX/dt=(1/(extracell))*(( 1 * vdifACA) + (-1 * voutACA) + (-1 * vlacto)) # Species: id = CNX, name = Extracellular cyanide, affected by kineticLaw init CNX=5.20358 dCNX/dt=(1/(extracell))*((-1 * vlacto) + ( 1 * vinCN)) # Species: id = AMP, name = AMP, affected by kineticLaw init AMP=0.33 dAMP/dt=(1/(cytosol))*((-1 * vAK)) # Species: id = P, name = P par P=0.0 #WARNING speciesID: P, constant= false , boundaryCondition = true but is not involved in assignmentRule, rateRule or events ! # Species: id = CNX0, name = Mixed flow cyanide par CNX0=5.6 #WARNING speciesID: CNX0, constant= false , boundaryCondition = true but is not involved in assignmentRule, rateRule or events ! # Species: id = GlcX0, name = Mixed flow glucose par GlcX0=24.0 #WARNING speciesID: GlcX0, constant= false , boundaryCondition = true but is not involved in assignmentRule, rateRule or events ! @ meth=cvode, tol=1e-6, atol=1e-8 @ bound=40000, total=200 done