begin name
bradshaw
end name

begin reactions
vAndpkforward {1.0}dADP = {1.0}dATP
vAndpkreverse {1.0}dATP = {1.0}dADP
vAnmpkforward {1.0}dAMP = {1.0}dADP
vAnmpkreverse {1.0}dADP = {1.0}dAMP
vAntransport {1.0}$EXTERNAL = {1.0}dAn
vAnucleosidekinase {1.0}dAn = {1.0}dAMP
vAnucleotidase {1.0}dAMP = {1.0}dAn
vCndpkforward {1.0}dCDP = {1.0}dCTP
vCndpkreverse {1.0}dCTP = {1.0}dCDP
vCnmpkforward {1.0}dCMP = {1.0}dCDP
vCnmpkreverse {1.0}dCDP = {1.0}dCMP
vCntransport {1.0}$EXTERNAL = {1.0}dCn
vCnucleosidekinase {1.0}dCn = {1.0}dCMP
vCnucleotidase {1.0}dCMP = {1.0}dCn
vGndpkforward {1.0}dGDP = {1.0}dGTP
vGndpkreverse {1.0}dGTP = {1.0}dGDP
vGnmpkforward {1.0}dGMP = {1.0}dGDP
vGnmpkreverse {1.0}dGDP = {1.0}dGMP
vGntransport {1.0}$EXTERNAL = {1.0}dGn
vGnucleosidekinase {1.0}dGn = {1.0}dGMP
vGnucleotidase {1.0}dGMP = {1.0}dGn
vHPolrate {1.0}$EXTERNAL = {1.0}HPolrate
vLPolrate {1.0}$EXTERNAL = {1.0}LPolrate
vPolrateH {0.313}dGTP + {0.247}dATP + {0.131}dCTP + {0.309}dTTP = {1.0}HDNA
vPolrateL {0.131}dGTP + {0.309}dATP + {0.313}dCTP + {0.247}dTTP = {1.0}LDNA
vTndpkforward {1.0}dTDP = {1.0}dTTP
vTndpkreverse {1.0}dTTP = {1.0}dTDP
vTnmpkforward {1.0}dTMP = {1.0}dTDP
vTnmpkreverse {1.0}dTDP = {1.0}dTMP
vTntransport {1.0}$EXTERNAL = {1.0}dTn
vTnucleosidekinase {1.0}dTn = {1.0}dTMP
vTnucleotidase {1.0}dTMP = {1.0}dTn
vdADPexchangein {1.0}$EXTERNAL = {1.0}dADP
vdADPexchangeout {1.0}dADP = {1.0}$EXTERNAL
vdATPexchangein {1.0}$EXTERNAL = {1.0}dATP
vdATPexchangeout {1.0}dATP = {1.0}$EXTERNAL
vdCDPexchangein {1.0}$EXTERNAL = {1.0}dCDP
vdCDPexchangeout {1.0}dCDP = {1.0}$EXTERNAL
vdCTPexchangein {1.0}$EXTERNAL = {1.0}dCTP
vdCTPexchangeout {1.0}dCTP = {1.0}$EXTERNAL
vdGDPexchangein {1.0}$EXTERNAL = {1.0}dGDP
vdGDPexchangeout {1.0}dGDP = {1.0}$EXTERNAL
vdGTPexchangein {1.0}$EXTERNAL = {1.0}dGTP
vdGTPexchangeout {1.0}dGTP = {1.0}$EXTERNAL
vdTDPexchangein {1.0}$EXTERNAL = {1.0}dTDP
vdTDPexchangeout {1.0}dTDP = {1.0}$EXTERNAL
vdTTPexchangein {1.0}$EXTERNAL = {1.0}dTTP
vdTTPexchangeout {1.0}dTTP = {1.0}$EXTERNAL
end reactions

begin rate equations
vAndpkforward = (ndpkculespermito*ndpkMW*Vmax3PfA*dADP[t]*If[dADP[t] > 0, 1, 0])/(conversion*km3PfA + dADP[t] + conversion*km3PfA*((rADPin*If[conversion*rADPin > 0, 1, 0])/KiADPNDPK + (rATPin*If[conversion*rATPin > 0, 1, 0])/KiATPNDPK + (dATP[t]*If[dATP[t] > 0, 1, 0])/(conversion*km3PrA) + (dCDP[t]*If[dCDP[t] > 0, 1, 0])/(conversion*km3PfC) + (dCTP[t]*If[dCTP[t] > 0, 1, 0])/(conversion*km3PrC) + (dGDP[t]*If[dGDP[t] > 0, 1, 0])/(conversion*km3PfG) + (dGTP[t]*If[dGTP[t] > 0, 1, 0])/(conversion*km3PrG) + (dTDP[t]*If[dTDP[t] > 0, 1, 0])/(conversion*km3PfT) + (dTTP[t]*If[dTTP[t] > 0, 1, 0])/(conversion*km3PrT)))
vAndpkreverse = (ndpkculespermito*ndpkMW*rADPin*Vmax3PfA*dATP[t]*If[dATP[t] > 0, 1, 0])/(rATPin*(conversion*km3PrA + dATP[t] + conversion*km3PrA*((rADPin*If[conversion*rADPin > 0, 1, 0])/KiADPNDPK + (rATPin*If[conversion*rATPin > 0, 1, 0])/KiATPNDPK + (dADP[t]*If[dADP[t] > 0, 1, 0])/(conversion*km3PfA) + (dCDP[t]*If[dCDP[t] > 0, 1, 0])/(conversion*km3PfC) + (dCTP[t]*If[dCTP[t] > 0, 1, 0])/(conversion*km3PrC) + (dGDP[t]*If[dGDP[t] > 0, 1, 0])/(conversion*km3PfG) + (dGTP[t]*If[dGTP[t] > 0, 1, 0])/(conversion*km3PrG) + (dTDP[t]*If[dTDP[t] > 0, 1, 0])/(conversion*km3PfT) + (dTTP[t]*If[dTTP[t] > 0, 1, 0])/(conversion*km3PrT))))
vAnmpkforward = (akMW*culesAK*Vmax2PfA*dAMP[t]*If[dAMP[t] > 0, 1, 0])/(conversion*km2PfA + dAMP[t] + conversion*km2PfA*((rADPin*If[conversion*rADPin > 0, 1, 0])/km2PrA + (rAMPin*If[conversion*rAMPin > 0, 1, 0])/km2PfA + (dADP[t]*If[dADP[t] > 0, 1, 0])/(conversion*km2PrA)))
vAnmpkreverse = (akMW*culesAK*Vmax2PfA*dADP[t]*If[dADP[t] > 0, 1, 0])/(2*(conversion*km2PrA + dADP[t] + conversion*km2PrA*((rADPin*If[conversion*rADPin > 0, 1, 0])/km2PrA + (rAMPin*If[conversion*rAMPin > 0, 1, 0])/km2PfA + (dAMP[t]*If[dAMP[t] > 0, 1, 0])/(conversion*km2PfA))))
vAntransport = (conversion*dnucsidecytoA*dnuctransvmax*If[conversion*dnucsidecytoA > 0, 1, 0])/(conversion*dnucsidecytoA + conversion*dnuctranskm + conversion*dnuctranskm*((dnucsidecytoC*If[conversion*dnucsidecytoC > 0, 1, 0])/dnuctranskm + (dnucsidecytoT*If[conversion*dnucsidecytoT > 0, 1, 0])/dnuctranskm)) - (dnuctransvmax*dAn[t]*If[dAn[t] > 0, 1, 0])/(conversion*dnuctranskm + dAn[t] + conversion*dnuctranskm*((dCn[t]*If[dCn[t] > 0, 1, 0])/(conversion*dnuctranskm) + (dTn[t]*If[dTn[t] > 0, 1, 0])/(conversion*dnuctranskm)))
vAnucleosidekinase = (dgkculespermito*nuckinMW*Vmax1PfA*dAn[t])/(conversion*km1PfA + dAn[t] + conversion*km1PfA*(dAMP[t]/(conversion*KiAmpdgk) + dATP[t]/(conversion*KiAtpdgk) + dGMP[t]/(conversion*KiGmpdgk) + dGn[t]/(conversion*KiGdgk) + dGTP[t]/(conversion*KiGtpdgk)))
vAnucleotidase = (Vmax1PrA*dAMP[t]*If[dAMP[t] > 0, 1, 0])/(conversion*km1PrA + dAMP[t] + conversion*km1PrA*((rADPin*If[conversion*rADPin > 0, 1, 0])/KiADPtidase + (rAMPin*If[conversion*rAMPin > 0, 1, 0])/KiAMPtidase + (rATPin*If[conversion*rATPin > 0, 1, 0])/KiATPtidase))
vCndpkforward = (ndpkculespermito*ndpkMW*Vmax3PfC*dCDP[t]*If[dCDP[t] > 0, 1, 0])/(conversion*km3PfC + dCDP[t] + conversion*km3PfC*((rADPin*If[conversion*rADPin > 0, 1, 0])/KiADPNDPK + (rATPin*If[conversion*rATPin > 0, 1, 0])/KiATPNDPK + (dADP[t]*If[dADP[t] > 0, 1, 0])/(conversion*km3PfA) + (dATP[t]*If[dATP[t] > 0, 1, 0])/(conversion*km3PrA) + (dCTP[t]*If[dCTP[t] > 0, 1, 0])/(conversion*km3PrC) + (dGDP[t]*If[dGDP[t] > 0, 1, 0])/(conversion*km3PfG) + (dGTP[t]*If[dGTP[t] > 0, 1, 0])/(conversion*km3PrG) + (dTDP[t]*If[dTDP[t] > 0, 1, 0])/(conversion*km3PfT) + (dTTP[t]*If[dTTP[t] > 0, 1, 0])/(conversion*km3PrT)))
vCndpkreverse = (ndpkculespermito*ndpkMW*rADPin*Vmax3PfC*dCTP[t]*If[dCTP[t] > 0, 1, 0])/(rATPin*(conversion*km3PrC + dCTP[t] + conversion*km3PrC*((rADPin*If[conversion*rADPin > 0, 1, 0])/KiADPNDPK + (rATPin*If[conversion*rATPin > 0, 1, 0])/KiATPNDPK + (dADP[t]*If[dADP[t] > 0, 1, 0])/(conversion*km3PfA) + (dATP[t]*If[dATP[t] > 0, 1, 0])/(conversion*km3PrA) + (dCDP[t]*If[dCDP[t] > 0, 1, 0])/(conversion*km3PfC) + (dGDP[t]*If[dGDP[t] > 0, 1, 0])/(conversion*km3PfG) + (dGTP[t]*If[dGTP[t] > 0, 1, 0])/(conversion*km3PrG) + (dTDP[t]*If[dTDP[t] > 0, 1, 0])/(conversion*km3PfT) + (dTTP[t]*If[dTTP[t] > 0, 1, 0])/(conversion*km3PrT))))
vCnmpkforward = (nmpkculespermito*nmpkMW*Vmax2PfC*dCMP[t])/(conversion*km2PfC + conversion*km2PfC*(rCDPin/KiCDP + rCMPin/KiCMP + UDPin/KiUDP + UMPin/KiUMP + dCDP[t]/(conversion*km2PrC)) + dCMP[t])
vCnmpkreverse = (0.5*nmpkculespermito*nmpkMW*Vmax2PfC*dCDP[t])/(conversion*km2PrC + dCDP[t] + conversion*km2PrC*(rCDPin/KiCDP + rCMPin/KiCMP + UDPin/KiUDP + UMPin/KiUMP + dCMP[t]/(conversion*km2PfC)))
vCntransport = (conversion*dnucsidecytoC*dnuctransvmax*If[conversion*dnucsidecytoC > 0, 1, 0])/(conversion*dnucsidecytoC + conversion*dnuctranskm + conversion*dnuctranskm*((dnucsidecytoA*If[conversion*dnucsidecytoA > 0, 1, 0])/dnuctranskm + (dnucsidecytoT*If[conversion*dnucsidecytoT > 0, 1, 0])/dnuctranskm)) - (dnuctransvmax*dCn[t]*If[dCn[t] > 0, 1, 0])/(conversion*dnuctranskm + dCn[t] + conversion*dnuctranskm*((dAn[t]*If[dAn[t] > 0, 1, 0])/(conversion*dnuctranskm) + (dTn[t]*If[dTn[t] > 0, 1, 0])/(conversion*dnuctranskm)))
vCnucleosidekinase = (nuckinMW*tk2culespermito*Vmax1PfC*dCn[t]*If[dCn[t] > 0, 1, 0])/(conversion*km1PfC + dCn[t] + conversion*km1PfC*((dCTP[t]*If[dCTP[t] > 0, 1, 0])/(conversion*KiCtptk2) + (dTn[t]*If[dTn[t] > 0, 1, 0])/(conversion*KiTtk2) + (dTTP[t]*If[dTTP[t] > 0, 1, 0])/(conversion*KiTtptk2)))
vCnucleotidase = (Vmax1PrC*dCMP[t]*If[dCMP[t] > 0, 1, 0])/(conversion*km1PrC + dCMP[t] + conversion*km1PrC*((rADPin*If[conversion*rADPin > 0, 1, 0])/KiADPtidase + (rAMPin*If[conversion*rAMPin > 0, 1, 0])/KiAMPtidase + (rATPin*If[conversion*rATPin > 0, 1, 0])/KiATPtidase))
vGndpkforward = (ndpkculespermito*ndpkMW*Vmax3PfG*dGDP[t]*If[dGDP[t] > 0, 1, 0])/(conversion*km3PfG + dGDP[t] + conversion*km3PfG*((rADPin*If[conversion*rADPin > 0, 1, 0])/KiADPNDPK + (rATPin*If[conversion*rATPin > 0, 1, 0])/KiATPNDPK + (dADP[t]*If[dADP[t] > 0, 1, 0])/(conversion*km3PfA) + (dATP[t]*If[dATP[t] > 0, 1, 0])/(conversion*km3PrA) + (dCDP[t]*If[dCDP[t] > 0, 1, 0])/(conversion*km3PfC) + (dCTP[t]*If[dCTP[t] > 0, 1, 0])/(conversion*km3PrC) + (dGTP[t]*If[dGTP[t] > 0, 1, 0])/(conversion*km3PrG) + (dTDP[t]*If[dTDP[t] > 0, 1, 0])/(conversion*km3PfT) + (dTTP[t]*If[dTTP[t] > 0, 1, 0])/(conversion*km3PrT)))
vGndpkreverse = (ndpkculespermito*ndpkMW*rADPin*Vmax3PfG*dGTP[t]*If[dGTP[t] > 0, 1, 0])/(rATPin*(conversion*km3PrG + dGTP[t] + conversion*km3PrG*((rADPin*If[conversion*rADPin > 0, 1, 0])/KiADPNDPK + (rATPin*If[conversion*rATPin > 0, 1, 0])/KiATPNDPK + (dADP[t]*If[dADP[t] > 0, 1, 0])/(conversion*km3PfA) + (dATP[t]*If[dATP[t] > 0, 1, 0])/(conversion*km3PrA) + (dCDP[t]*If[dCDP[t] > 0, 1, 0])/(conversion*km3PfC) + (dCTP[t]*If[dCTP[t] > 0, 1, 0])/(conversion*km3PrC) + (dGDP[t]*If[dGDP[t] > 0, 1, 0])/(conversion*km3PfG) + (dTDP[t]*If[dTDP[t] > 0, 1, 0])/(conversion*km3PfT) + (dTTP[t]*If[dTTP[t] > 0, 1, 0])/(conversion*km3PrT))))
vGnmpkforward = (nmpkculespermito*Vmax2PfG*dGMP[t]*If[dGMP[t] > 0, 1, 0])/(conversion*km2PfG + dGMP[t] + conversion*km2PfG*((rGDPin*If[conversion*rGDPin > 0, 1, 0])/KiGDP + (rGMPin*If[conversion*rGMPin > 0, 1, 0])/KiGMP + (dGDP[t]*If[dGDP[t] > 0, 1, 0])/(conversion*km2PrG)))
vGnmpkreverse = (0.5*nmpkculespermito*Vmax2PfG*dGDP[t]*If[dGDP[t] > 0, 1, 0])/(conversion*km2PrG + dGDP[t] + conversion*km2PrG*((rGDPin*If[conversion*rGDPin > 0, 1, 0])/KiGDP + (rGMPin*If[conversion*rGMPin > 0, 1, 0])/KiGMP + (dGMP[t]*If[dGMP[t] > 0, 1, 0])/(conversion*km2PfG)))
vGntransport = (conversion*dnucsidecytoG*Gdnuctransvmax*nuctransMW*proteinspermito*If[conversion*dnucsidecytoG > 0, 1, 0])/(conversion*dnucsidecytoG + conversion*Gdnuctranskm) - (Gdnuctransvmax*nuctransMW*proteinspermito*dGn[t]*If[dGn[t] > 0, 1, 0])/(conversion*Gdnuctranskm + dGn[t])
vGnucleosidekinase = (dgkculespermito*nuckinMW*Vmax1PfG*dGn[t])/(conversion*km1PfG + dGn[t] + conversion*km1PfG*(dAMP[t]/(conversion*KiAmpdgk) + dAn[t]/(conversion*KiAdgk) + dATP[t]/(conversion*KiAtpdgk) + dGMP[t]/(conversion*KiGmpdgk) + dGTP[t]/(conversion*KiGtpdgk)))
vGnucleotidase = (Vmax1PrG*dGMP[t]*If[dGMP[t] > 0, 1, 0])/(conversion*km1PrG + dGMP[t] + conversion*km1PrG*((rADPin*If[conversion*rADPin > 0, 1, 0])/KiADPtidase + (rAMPin*If[conversion*rAMPin > 0, 1, 0])/KiAMPtidase + (rATPin*If[conversion*rATPin > 0, 1, 0])/KiATPtidase))
vHPolrate = (VmaxPolA*VmaxPolC*VmaxPolG*VmaxPolT*dATP[t]*dCTP[t]*dGTP[t]*dTTP[t]*If[dATP[t] > 0, 1, 0]*If[dCTP[t] > 0, 1, 0]*If[dGTP[t] > 0, 1, 0]*If[dTTP[t] > 0, 1, 0])/((conversion*KmPolA + dATP[t])*(conversion*KmPolC + dCTP[t])*(conversion*KmPolG + dGTP[t])*(conversion*KmPolT + dTTP[t])*(0.1 + (fTH*VmaxPolA*VmaxPolC*VmaxPolG*dATP[t]*dCTP[t]*dGTP[t]*If[dATP[t] > 0, 1, 0]*If[dCTP[t] > 0, 1, 0]*If[dGTP[t] > 0, 1, 0])/((conversion*KmPolA + dATP[t])*(conversion*KmPolC + dCTP[t])*(conversion*KmPolG + dGTP[t])) + (fGH*VmaxPolA*VmaxPolC*VmaxPolT*dATP[t]*dCTP[t]*dTTP[t]*If[dATP[t] > 0, 1, 0]*If[dCTP[t] > 0, 1, 0]*If[dTTP[t] > 0, 1, 0])/((conversion*KmPolA + dATP[t])*(conversion*KmPolC + dCTP[t])*(conversion*KmPolT + dTTP[t])) + (fCH*VmaxPolA*VmaxPolG*VmaxPolT*dATP[t]*dGTP[t]*dTTP[t]*If[dATP[t] > 0, 1, 0]*If[dGTP[t] > 0, 1, 0]*If[dTTP[t] > 0, 1, 0])/((conversion*KmPolA + dATP[t])*(conversion*KmPolG + dGTP[t])*(conversion*KmPolT + dTTP[t])) + (fAH*VmaxPolC*VmaxPolG*VmaxPolT*dCTP[t]*dGTP[t]*dTTP[t]*If[dCTP[t] > 0, 1, 0]*If[dGTP[t] > 0, 1, 0]*If[dTTP[t] > 0, 1, 0])/((conversion*KmPolC + dCTP[t])*(conversion*KmPolG + dGTP[t])*(conversion*KmPolT + dTTP[t]))))
vLPolrate = (VmaxPolA*VmaxPolC*VmaxPolG*VmaxPolT*dATP[t]*dCTP[t]*dGTP[t]*dTTP[t]*If[dATP[t] > 0, 1, 0]*If[dCTP[t] > 0, 1, 0]*If[dGTP[t] > 0, 1, 0]*If[dTTP[t] > 0, 1, 0])/((conversion*KmPolA + dATP[t])*(conversion*KmPolC + dCTP[t])*(conversion*KmPolG + dGTP[t])*(conversion*KmPolT + dTTP[t])*(0.1 + (fTL*VmaxPolA*VmaxPolC*VmaxPolG*dATP[t]*dCTP[t]*dGTP[t]*If[dATP[t] > 0, 1, 0]*If[dCTP[t] > 0, 1, 0]*If[dGTP[t] > 0, 1, 0])/((conversion*KmPolA + dATP[t])*(conversion*KmPolC + dCTP[t])*(conversion*KmPolG + dGTP[t])) + (fGL*VmaxPolA*VmaxPolC*VmaxPolT*dATP[t]*dCTP[t]*dTTP[t]*If[dATP[t] > 0, 1, 0]*If[dCTP[t] > 0, 1, 0]*If[dTTP[t] > 0, 1, 0])/((conversion*KmPolA + dATP[t])*(conversion*KmPolC + dCTP[t])*(conversion*KmPolT + dTTP[t])) + (fCL*VmaxPolA*VmaxPolG*VmaxPolT*dATP[t]*dGTP[t]*dTTP[t]*If[dATP[t] > 0, 1, 0]*If[dGTP[t] > 0, 1, 0]*If[dTTP[t] > 0, 1, 0])/((conversion*KmPolA + dATP[t])*(conversion*KmPolG + dGTP[t])*(conversion*KmPolT + dTTP[t])) + (fAL*VmaxPolC*VmaxPolG*VmaxPolT*dCTP[t]*dGTP[t]*dTTP[t]*If[dCTP[t] > 0, 1, 0]*If[dGTP[t] > 0, 1, 0]*If[dTTP[t] > 0, 1, 0])/((conversion*KmPolC + dCTP[t])*(conversion*KmPolG + dGTP[t])*(conversion*KmPolT + dTTP[t]))))
vPolrateH = HPolrate[t]*If[simtime/2 > t || HDNA[t] > DNAlength/2, 0, 1]
vPolrateL = If[simtime/2 > t || LDNA[t] > DNAlength/2 || HDNA[t] < Lstrandstart, 0, 1]*LPolrate[t]
vTndpkforward = (ndpkculespermito*ndpkMW*Vmax3PfT*dTDP[t]*If[dTDP[t] > 0, 1, 0])/(conversion*km3PfT + dTDP[t] + conversion*km3PfT*((rADPin*If[conversion*rADPin > 0, 1, 0])/KiADPNDPK + (rATPin*If[conversion*rATPin > 0, 1, 0])/KiATPNDPK + (dADP[t]*If[dADP[t] > 0, 1, 0])/(conversion*km3PfA) + (dATP[t]*If[dATP[t] > 0, 1, 0])/(conversion*km3PrA) + (dCDP[t]*If[dCDP[t] > 0, 1, 0])/(conversion*km3PfC) + (dCTP[t]*If[dCTP[t] > 0, 1, 0])/(conversion*km3PrC) + (dGDP[t]*If[dGDP[t] > 0, 1, 0])/(conversion*km3PfG) + (dGTP[t]*If[dGTP[t] > 0, 1, 0])/(conversion*km3PrG) + (dTTP[t]*If[dTTP[t] > 0, 1, 0])/(conversion*km3PrT)))
vTndpkreverse = (ndpkculespermito*ndpkMW*rADPin*Vmax3PfT*dTTP[t]*If[dTTP[t] > 0, 1, 0])/(rATPin*(conversion*km3PrT + dTTP[t] + conversion*km3PrT*((rADPin*If[conversion*rADPin > 0, 1, 0])/KiADPNDPK + (rATPin*If[conversion*rATPin > 0, 1, 0])/KiATPNDPK + (dADP[t]*If[dADP[t] > 0, 1, 0])/(conversion*km3PfA) + (dATP[t]*If[dATP[t] > 0, 1, 0])/(conversion*km3PrA) + (dCDP[t]*If[dCDP[t] > 0, 1, 0])/(conversion*km3PfC) + (dCTP[t]*If[dCTP[t] > 0, 1, 0])/(conversion*km3PrC) + (dGDP[t]*If[dGDP[t] > 0, 1, 0])/(conversion*km3PfG) + (dGTP[t]*If[dGTP[t] > 0, 1, 0])/(conversion*km3PrG) + (dTDP[t]*If[dTDP[t] > 0, 1, 0])/(conversion*km3PfT))))
vTnmpkforward = (culestmpkpermito*tmpkMW*Vmax2PfT*dTMP[t]*If[dTMP[t] > 0, 1, 0])/(conversion*km2PfT + dTMP[t] + dTDP[t]*If[dTDP[t] > 0, 1, 0])
vTnmpkreverse = (0.5*culestmpkpermito*tmpkMW*Vmax2PfT*dTDP[t]*If[dTDP[t] > 0, 1, 0])/(conversion*km2PrT + dTDP[t] + dTMP[t]*If[dTMP[t] > 0, 1, 0])
vTntransport = (conversion*dnucsidecytoT*dnuctransvmax*If[conversion*dnucsidecytoT > 0, 1, 0])/(conversion*dnucsidecytoT + conversion*dnuctranskm + conversion*dnuctranskm*((dnucsidecytoA*If[conversion*dnucsidecytoA > 0, 1, 0])/dnuctranskm + (dnucsidecytoC*If[conversion*dnucsidecytoC > 0, 1, 0])/dnuctranskm)) - (dnuctransvmax*dTn[t]*If[dTn[t] > 0, 1, 0])/(conversion*dnuctranskm + dTn[t] + conversion*dnuctranskm*((dAn[t]*If[dAn[t] > 0, 1, 0])/(conversion*dnuctranskm) + (dCn[t]*If[dCn[t] > 0, 1, 0])/(conversion*dnuctranskm)))
vTnucleosidekinase = (nuckinMW*tk2culespermito*Vmax1PfT*dTn[t]^tk2hill*If[dTn[t] > 0, 1, 0])/((conversion*km1PfT)^tk2hill + dTn[t]^tk2hill + (conversion*km1PfT)^tk2hill*((dCn[t]*If[dCn[t] > 0, 1, 0])/(conversion*KiCtk2) + (dCTP[t]*If[dCTP[t] > 0, 1, 0])/(conversion*KiCtptk2) + (dTTP[t]*If[dTTP[t] > 0, 1, 0])/(conversion*KiTtptk2)))
vTnucleotidase = (tidaseMW*tidaseTpermito*Vmax1PrT*dTMP[t]*If[dTMP[t] > 0, 1, 0])/(conversion*km1PrT + dTMP[t])
vdADPexchangein = (conversion*dADPcyto*exMW*expermito*exvmax)/(conversion*dADPcyto + conversion*exkmdA + conversion*exkmdA*(dCDPcyto/exkmdC + dGDPcyto/exkmdG + dTDPcyto/exkmdT + dATPcyto/exkmtA + dCTPcyto/exkmtC + dGTPcyto/exkmtG + dTTPcyto/exkmtT))
vdADPexchangeout = (exMW*expermito*exvmax*dADP[t])/(conversion*exkmdAin + dADP[t] + conversion*exkmdAin*(dATP[t]/(conversion*exkmtAin) + dCDP[t]/(conversion*exkmdCin) + dCTP[t]/(conversion*exkmtCin) + dGDP[t]/(conversion*exkmdGin) + dGTP[t]/(conversion*exkmtGin) + dTDP[t]/(conversion*exkmdTin) + dTTP[t]/(conversion*exkmtTin)))
vdATPexchangein = (conversion*dATPcyto*exMW*expermito*exvmax)/(conversion*dATPcyto + conversion*exkmtA + conversion*exkmtA*(dADPcyto/exkmdA + dCDPcyto/exkmdC + dGDPcyto/exkmdG + dTDPcyto/exkmdT + dCTPcyto/exkmtC + dGTPcyto/exkmtG + dTTPcyto/exkmtT))
vdATPexchangeout = (exMW*expermito*exvmax*dATP[t])/(conversion*exkmtAin + dATP[t] + conversion*exkmtAin*(dATP[t]/(conversion*exkmtAin) + dCDP[t]/(conversion*exkmdCin) + dCTP[t]/(conversion*exkmtCin) + dGDP[t]/(conversion*exkmdGin) + dGTP[t]/(conversion*exkmtGin) + dTDP[t]/(conversion*exkmdTin) + dTTP[t]/(conversion*exkmtTin)))
vdCDPexchangein = (conversion*dCDPcyto*exMW*expermito*exvmax)/(conversion*dCDPcyto + conversion*exkmdC + conversion*exkmdC*(dADPcyto/exkmdA + dGDPcyto/exkmdG + dTDPcyto/exkmdT + dATPcyto/exkmtA + dCTPcyto/exkmtC + dGTPcyto/exkmtG + dTTPcyto/exkmtT))
vdCDPexchangeout = (exMW*expermito*exvmax*dCDP[t])/(conversion*exkmdCin + dCDP[t] + conversion*exkmdCin*(dADP[t]/(conversion*exkmdAin) + dATP[t]/(conversion*exkmtAin) + dCDP[t]/(conversion*exkmdCin) + dGDP[t]/(conversion*exkmdGin) + dGTP[t]/(conversion*exkmtGin) + dTDP[t]/(conversion*exkmdTin) + dTTP[t]/(conversion*exkmtTin)))
vdCTPexchangein = (conversion*dCTPcyto*exMW*expermito*exvmax)/(conversion*dCTPcyto + conversion*exkmtC + conversion*exkmtC*(dADPcyto/exkmdA + dGDPcyto/exkmdG + dATPcyto/exkmtA + dCTPcyto/exkmtC + dGTPcyto/exkmtG + (2*dTTPcyto)/exkmtT))
vdCTPexchangeout = (exMW*expermito*exvmax*dCTP[t])/(conversion*exkmtCin + dCTP[t] + conversion*exkmtCin*(dADP[t]/(conversion*exkmdAin) + dATP[t]/(conversion*exkmtAin) + dCDP[t]/(conversion*exkmdCin) + dGDP[t]/(conversion*exkmdGin) + dGTP[t]/(conversion*exkmtGin) + dTDP[t]/(conversion*exkmdTin) + dTTP[t]/(conversion*exkmtTin)))
vdGDPexchangein = (conversion*dGDPcyto*exMW*expermito*exvmax)/(conversion*dGDPcyto + conversion*exkmdG + conversion*exkmdG*(dADPcyto/exkmdA + dCDPcyto/exkmdC + dTDPcyto/exkmdT + dATPcyto/exkmtA + dCTPcyto/exkmtC + dGTPcyto/exkmtG + dTTPcyto/exkmtT))
vdGDPexchangeout = (exMW*expermito*exvmax*dGDP[t])/(conversion*exkmdGin + dGDP[t] + conversion*exkmdGin*(dADP[t]/(conversion*exkmdAin) + dATP[t]/(conversion*exkmtAin) + dCDP[t]/(conversion*exkmdCin) + dCTP[t]/(conversion*exkmtCin) + dGTP[t]/(conversion*exkmtGin) + dTDP[t]/(conversion*exkmdTin) + dTTP[t]/(conversion*exkmtTin)))
vdGTPexchangein = (conversion*dGTPcyto*exMW*expermito*exvmax)/(conversion*dGTPcyto + conversion*exkmtG + conversion*exkmtG*(dADPcyto/exkmdA + dCDPcyto/exkmdC + dGDPcyto/exkmdG + dTDPcyto/exkmdT + dATPcyto/exkmtA + dCTPcyto/exkmtC + dTTPcyto/exkmtT))
vdGTPexchangeout = (exMW*expermito*exvmax*dGTP[t])/(conversion*exkmtGin + dGTP[t] + conversion*exkmtGin*(dADP[t]/(conversion*exkmdAin) + dATP[t]/(conversion*exkmtAin) + dCDP[t]/(conversion*exkmdCin) + dCTP[t]/(conversion*exkmtCin) + dGDP[t]/(conversion*exkmdGin) + dTDP[t]/(conversion*exkmdTin) + dTTP[t]/(conversion*exkmtTin)))
vdTDPexchangein = (conversion*dTDPcyto*exMW*expermito*exvmax)/(conversion*dTDPcyto + conversion*exkmdT + conversion*exkmdT*(dADPcyto/exkmdA + dCDPcyto/exkmdC + dGDPcyto/exkmdG + dATPcyto/exkmtA + dCTPcyto/exkmtC + dGTPcyto/exkmtG + dTTPcyto/exkmtT))
vdTDPexchangeout = (exMW*expermito*exvmax*dTDP[t])/(conversion*exkmdTin + dTDP[t] + conversion*exkmdTin*(dADP[t]/(conversion*exkmdAin) + dATP[t]/(conversion*exkmtAin) + dCDP[t]/(conversion*exkmdCin) + dCTP[t]/(conversion*exkmtCin) + dGDP[t]/(conversion*exkmdGin) + dGTP[t]/(conversion*exkmtGin) + dTTP[t]/(conversion*exkmtTin)))
vdTTPexchangein = (conversion*dTTPcyto*exMW*expermito*exvmax)/(conversion*dTTPcyto + conversion*exkmtT + conversion*(dADPcyto/exkmdA + dCDPcyto/exkmdC + dGDPcyto/exkmdG + dTDPcyto/exkmdT + dATPcyto/exkmtA + dCTPcyto/exkmtC + dGTPcyto/exkmtG)*exkmtT)
vdTTPexchangeout = (exMW*expermito*exvmax*dTTP[t])/(conversion*exkmtTin + conversion*exkmtTin*(dADP[t]/(conversion*exkmdAin) + dATP[t]/(conversion*exkmtAin) + dCDP[t]/(conversion*exkmdCin) + dCTP[t]/(conversion*exkmtCin) + dGDP[t]/(conversion*exkmdGin) + dGTP[t]/(conversion*exkmtGin) + dTDP[t]/(conversion*exkmdTin)) + dTTP[t])
end rate equations

begin parameters
DNAlength = 33136.0
Gdnuctranskm = 0.64
Gdnuctransvmax = 0.00057
KiADPNDPK = 75.0
KiADPtidase = 1400.0
KiAMPtidase = 94.0
KiATPNDPK = 75.0
KiATPtidase = 660.0
KiAdgk = 467.0
KiAmpdgk = 28.0
KiAtpdgk = 41.0
KiCDP = 23.0
KiCMP = 23.0
KiCtk2 = 40.0
KiCtptk2 = 0.83
KiGDP = 17.0
KiGMP = 17.0
KiGdgk = 4.0
KiGmpdgk = 4.0
KiGtpdgk = 0.4
KiTtk2 = 4.9
KiTtptk2 = 2.3
KiUDP = 95.0
KiUMP = 95.0
KmPolA = 0.8
KmPolC = 0.9
KmPolG = 0.8
KmPolT = 0.63
Lstrandstart = 10969.0
UDPin = 200.0
UMPin = 100.0
Vmax1PfA = 0.429
Vmax1PfC = 0.789
Vmax1PfG = 0.043
Vmax1PfT = 1.288
Vmax1PrA = 3720000.0
Vmax1PrC = 3720000.0
Vmax1PrG = 3720000.0
Vmax1PrT = 74.0
Vmax2PfA = 1320.0
Vmax2PfC = 23.0
Vmax2PfG = 7860.0
Vmax2PfT = 4.0
Vmax3PfA = 325.0
Vmax3PfC = 140.0
Vmax3PfG = 325.0
Vmax3PfT = 140.0
VmaxPolA = 1350.0
VmaxPolC = 1290.0
VmaxPolG = 1110.0
VmaxPolT = 750.0
akMW = 26.0
conversion = 120.44
culesAK = 450.0
culestmpkpermito = 50.0
dADPcyto = 2.0
dATPcyto = 10.0
dCDPcyto = 2.0
dCTPcyto = 10.0
dGDPcyto = 1.0
dGTPcyto = 5.0
dTDPcyto = 4.0
dTTPcyto = 20.0
dgkculespermito = 200.0
dnucsidecytoA = 0.5
dnucsidecytoC = 0.5
dnucsidecytoG = 0.5
dnucsidecytoT = 0.5
dnuctranskm = 2.0
dnuctransvmax = 1556.19047619048
exMW = 32.0
exkmdA = 14.0
exkmdAin = 14.0
exkmdC = 99.0
exkmdCin = 99.0
exkmdG = 55.0
exkmdGin = 55.0
exkmdT = 117.0
exkmdTin = 117.0
exkmtA = 106.0
exkmtAin = 106.0
exkmtC = 423.0
exkmtCin = 423.0
exkmtG = 230.0
exkmtGin = 230.0
exkmtT = 595.0
exkmtTin = 595.0
expermito = 500.0
exvmax = 0.85
fAH = 0.247
fAL = 0.309
fCH = 0.131
fCL = 0.313
fGH = 0.313
fGL = 0.131
fTH = 0.309
fTL = 0.247
km1PfA = 4.0
km1PfC = 11.0
km1PfG = 4.0
km1PfT = 16.0
km1PrA = 1520.0
km1PrC = 1900.0
km1PrG = 560.0
km1PrT = 200.0
km2PfA = 139.0
km2PfC = 17.0
km2PfG = 17.0
km2PfT = 4.9
km2PrA = 139.0
km2PrC = 17.0
km2PrG = 17.0
km2PrT = 4.9
km3PfA = 75.0
km3PfC = 300.0
km3PfG = 75.0
km3PfT = 300.0
km3PrA = 75.0
km3PrC = 300.0
km3PrG = 75.0
km3PrT = 300.0
ndpkMW = 66.0
ndpkculespermito = 300.0
nmpkMW = 25.0
nmpkculespermito = 50.0
nuckinMW = 28.0
nuctransMW = 50.0
proteinspermito = 400000.0
rADPin = 6000.0
rAMPin = 2900.0
rATPin = 8000.0
rCDPin = 50.0
rCMPin = 50.0
rGDPin = 400.0
rGMPin = 200.0
simtime = 1200.0
tidaseMW = 25.0
tidaseTpermito = 50.0
tidasepermito = 50.0
tk2culespermito = 100.0
tk2hill = 0.5
tmpkMW = 24.0
defaultcompartment = 1.0
end parameters

begin initial conditions
HDNA[0] = HDNAi
HPolrate[0] = HPolratei
LDNA[0] = LDNAi
LPolrate[0] = LPolratei
dADP[0] = dADPi
dAMP[0] = dAMPi
dATP[0] = dATPi
dAn[0] = dAni
dCDP[0] = dCDPi
dCMP[0] = dCMPi
dCTP[0] = dCTPi
dCn[0] = dCni
dGDP[0] = dGDPi
dGMP[0] = dGMPi
dGTP[0] = dGTPi
dGn[0] = dGni
dTDP[0] = dTDPi
dTMP[0] = dTMPi
dTTP[0] = dTTPi
dTn[0] = dTni
end initial conditions

begin initial values
HDNAi = 0.0
HPolratei = 0.0
LDNAi = 0.0
LPolratei = 0.0
dADPi = 240.88
dAMPi = 120.44
dATPi = 1204.8
dAni = 60.22
dCDPi = 240.88
dCMPi = 120.44
dCTPi = 1204.4
dCni = 60.22
dGDPi = 120.44
dGMPi = 60.22
dGTPi = 602.2
dGni = 60.22
dTDPi = 481.76
dTMPi = 240.88
dTTPi = 2408.8
dTni = 60.22
end initial values

begin assignment rules
end assignment rules

begin function definitions
If[cond_,val1_,val2_] := Piecewise[{{val1, cond}}, val2]
end function definitions

begin events
end events

begin process annotations
end process annotations

begin species annotations
end species annotations

begin units
end units