(*Mitochondrial deoxynucleotide metabolism and DNA replication*)
(*Vishal V Gandhi and David C Samuels*)
(*The model simulates transport of deoxynucleosides and dexoynucleotides into and out of a mitochondrion,*)(*their subsequent phosphorylation and dephosphorylation and uptake into mtDNA*)

ClearAll["Global`*"]; (*clear any previous variables in memory*)
Off[General::spell1]; (*Turn off spelling checker*)
            Off[General::spell];

(* directory where this file and constants file is located *)
SetDirectory["C:\\Documents and Settings\\gandhiv\\My Documents\\pro\\data\\mathematicaexpbase\\transport_experiments"]; 

 celltype=1;

(*Choose the number of separate mitochondrial DNA replication events*)
(*Partially overlapping mtDNA replication events are not supported in this version of the code*)
numDNAmols=1;
replication=1; (*0 = Off, 1 = On, starts immediately with the simulation*)
                                       
(*Set the length of the total simulation in minutes*)
(*Replication time is determined by initial and spot dNTP levels*)

simtime=120;(*Total simulation time (min)*)

replengths = {};
repdurations = {};
parameters = {};

Do[
<<modelconstants.txt;(*Load constants file*)

parameters = Append[parameters,{dT0,dC0,dA0,dG0,dTMP0,dTDP0,dTTP0,dCMP0,dCDP0,dCTP0,dAMP0,dADP0,dATP0,dGMP0,dGDP0,dGTP0}];

count = 0;
Do[
count++;

(*Michaelis Menten equations of deoxythymidine metabolism*)

dTnucleosidetransport= mm10[transportervmax,transporterkm,dTcyto,dCcyto,transporterkm,dAcyto,transporterkm,dGcyto,transporterkm,dUcyto,transporterkm,rUcyto,transporterkm,rCcyto,transporterkm,rAcyto,transporterkm,rGcyto,transporterkm,dIcyto,transporterkm,rIcyto,transporterkm]-mm10[transportervmax,transporterkm,dT[t],dC[t],transporterkm,dA[t],transporterkm,dG[t],transporterkm,dU,transporterkm,rU,transporterkm,rC,transporterkm,rA,transporterkm,rG,transporterkm,dI,transporterkm,rI,transporterkm]; 
(*nucleoside transport in and out*)
dTnucleosidekinase= hill5[Vmax1PfdT,km1PfdT,dT[t],dTTP[t],kidttptk2,dC[t],kidctk2,dCTP[t],kidctptk2,dU,kidutk2,dUTP,kidutptk2,tk2hill];(*nucleoside kinase*)
dTnucleotidase=mm2[Vmax1PrdT,km1PrdT,dTMP[t],dUMP,km1PrdU,rUMP,km1PrrU]+mm12[Vmax1PrdTen,km1PrdTen,dTMP[t],dCMP[t],km1PrdC,dAMP[t],km1PrdA,dGMP[t],km1PrdG,dUMP,km1PrdUen,rUMP,km1PrrUen,rCMP,km1PrrC,rAMP,km1PrrA,rGMP,km1PrrG,dIMP,km1PrdI,rIMP,km1PrrI,rADP,kiadpen,rATP,kiatpen];(*nucleotidase modeled through both dnt2 and ectonucleotidase*)
dTmpkforward= mm5[Vmax2PfdT,km2PfdT,dTMP[t],dTDP[t],km2PrdT,dUMP,km2PfdUtmpk2,dUDP,km2PrdUtmpk2,dTTP[t],kidttptmpk2,dT[t],kidttmpk2]; (*nucleoside monophosphate kinase forward*)
dTmpkreverse=mm5[Vmax2PrdT,km2PrdT,dTDP[t], dTMP[t], km2PfdT, dUMP, km2PfdUtmpk2,dUDP,km2PrdUtmpk2,dTTP[t],kidttptmpk2,dT[t],kidttmpk2];(*nucleoside monophosphate kinase reverse*)
dTdpkforward= mm21[Vmax3PfdT,km3PfdT,dTDP[t],dCDP[t],km3PfdC,dADP[t],km3PfdA,dGDP[t],km3PfdG,dTTP[t], km3PrdT, dCTP[t],km3PrdC, dATP[t],km3PrdA,dGTP[t],km3PrdG,dUDP,km3PfdU,dUTP,km3PrdU,rUDP,km3PfrU,rUTP,km3PrrU,rCDP,km3PfrC,rCTP,km3PrrC,rADP,km3PfrA,rATP,km3PrrA,rGDP,km3PfrG,rGTP,km3PrrG,rIDP,km3PfrI,rITP,km3PrrI,dIDP,km3PfdI,dITP,km3PrdI];(*nucleoside diphosphate kinase forward*)
dTdpkreverse=mm21[Vmax3PrdT,km3PrdT,dTTP[t],dTDP[t],km3PfdT,dCDP[t],km3PfdC,dADP[t],km3PfdA,dGDP[t],km3PfdG,dCTP[t],km3PrdC, dATP[t],km3PrdA,dGTP[t],km3PrdG,dUDP,km3PfdU,dUTP,km3PrdU,rUDP,km3PfrU,rUTP,km3PrrU,rCDP,km3PfrC,rCTP,km3PrrC,rADP,km3PfrA,rATP,km3PrrA,rGDP,km3PfrG,rGTP,km3PrrG,rIDP,km3PfrI,rITP,km3PrrI,dIDP,km3PfdI,dITP,km3PrdI];(*nucleoside diphosphate kinase reverse*)
 
 (*Michaelis Menten equations of deoxycytidine metabolism*)

dCnucleosidetransport =mm10[transportervmax,transporterkm,dCcyto,dTcyto,transporterkm,dAcyto,transporterkm,dGcyto,transporterkm,dUcyto,transporterkm,rUcyto,transporterkm,rCcyto,transporterkm,rAcyto,transporterkm,rGcyto,transporterkm,dIcyto,transporterkm,rIcyto,transporterkm]-mm10[transportervmax,transporterkm,dC[t],dT[t],transporterkm,dA[t],transporterkm,dG[t],transporterkm,dU,transporterkm,rU,transporterkm,rC,transporterkm,rA,transporterkm,rG,transporterkm,dI,transporterkm,rI,transporterkm];
(*nucleoside transport in and out*)
dCnucleosidekinase = mm5[Vmax1PfdC,km1PfdC,dC[t],dTTP[t],kidttptk2,dT[t],kidttk2,dCTP[t],kidctptk2,dU,kidutk2,dUTP,kidutptk2]+mm9[Vmax1PfdCdgk,km1PfdCdgk,dC[t],dATP[t],kidatpdgk,dGTP[t],kidgtpdgk,dGMP[t],kidgmpdgk,dAMP[t],kidampdgk,dG[t],km1PfdG,dA[t],km1PfdA,dI,kididgk,dIMP,kidimpdgk,dITP,kiditpdgk];
(*nucleoside kinase, dC transformation modeled through both tk2 and dgk routes*)
dCnucleotidase=mm12[Vmax1PrdC,km1PrdC,dCMP[t],dTMP[t],km1PrdTen,dAMP[t],km1PrdA,dGMP[t],km1PrdG,dUMP,km1PrdUen,rUMP,km1PrrUen,rCMP,km1PrrC,rAMP,km1PrrA,rGMP,km1PrrG,dIMP,km1PrdI,rIMP,km1PrrI,rADP,kiadpen,rATP,kiatpen];
dCmpkforward =mm11[Vmax2PfdC,km2PfdC,dCMP[t],dCDP[t],km2PrdC,rCMP,km2PfrC,rCDP,km2PrrC,dUMP,km2PfdUcmpk2,dUDP,km2PrdUcmpk2,rUMP,km2PfrU,rUDP,km2PrrU,rAMP,km2PfrAcmpk2,rADP,km2PrrAcmpk2,dAMP[t],km2PfdAcmpk2,dADP[t],km2PrdAcmpk2];(*nucleoside monophosphate kinase forward*)
dCmpkreverse =mm11[Vmax2PrdC,km2PrdC,dCDP[t],dCMP[t],km2PfdC,rCMP,km2PfrC,rCDP,km2PrrC,dUMP,km2PfdUcmpk2,dUDP,km2PrdUcmpk2,rUMP,km2PfrU,rUDP,km2PrrU ,rAMP,km2PfrAcmpk2,rADP,km2PrrAcmpk2,dAMP[t],km2PfdAcmpk2,dADP[t],km2PrdAcmpk2]; (*nucleoside monophosphate kinase reverse*)
dCdpkforward = mm21[Vmax3PfdC,km3PfdC,dCDP[t],dTDP[t],km3PfdT,dADP[t],km3PfdA,dGDP[t],km3PfdG,dTTP[t], km3PrdT, dCTP[t],km3PrdC, dATP[t],km3PrdA,dGTP[t],km3PrdG,dUDP,km3PfdU,dUTP,km3PrdU,rUDP,km3PfrU,rUTP,km3PrrU,rCDP,km3PfrC,rCTP,km3PrrC,rADP,km3PfrA,rATP,km3PrrA,rGDP,km3PfrG,rGTP,km3PrrG,rIDP,km3PfrI,rITP,km3PrrI,dIDP,km3PfdI,dITP,km3PrdI];(*nucleoside diphosphate kinase forward*)
dCdpkreverse = mm21[Vmax3PrdC,km3PrdC,dCTP[t],dCDP[t],km3PfdC,dTDP[t],km3PfdT,dADP[t],km3PfdA,dGDP[t],km3PfdG,dTTP[t], km3PrdT,dATP[t],km3PrdA,dGTP[t],km3PrdG,dUDP,km3PfdU,dUTP,km3PrdU,rUDP,km3PfrU,rUTP,km3PrrU,rCDP,km3PfrC,rCTP,km3PrrC,rADP,km3PfrA,rATP,km3PrrA,rGDP,km3PfrG,rGTP,km3PrrG,rIDP,km3PfrI,rITP,km3PrrI,dIDP,km3PfdI,dITP,km3PrdI];(*nucleoside diphosphate kinase reverse*)
 
(*Michaelis Menten equations of deoxyadenosine metabolism*)

dAnucleosidetransport=mm10[transportervmax,transporterkm,dAcyto,dCcyto,transporterkm,dTcyto,transporterkm,dGcyto,transporterkm,dUcyto,transporterkm,rUcyto,transporterkm,rCcyto,transporterkm,rAcyto,transporterkm,rGcyto,transporterkm,dIcyto,transporterkm,rIcyto,transporterkm]-mm10[transportervmax,transporterkm,dA[t],dC[t],transporterkm,dT[t],transporterkm,dG[t],transporterkm,dU,transporterkm,rU,transporterkm,rC,transporterkm,rA,transporterkm,rG,transporterkm,dI,transporterkm,rI,transporterkm];
(*nucleoside transport in and out*)
dAnucleosidekinase= mm8[Vmax1PfdA,km1PfdA,dA[t],dG[t],km1PfdG,dATP[t],kidatpdgk,dGTP[t],kidgtpdgk,dGMP[t],kidgmpdgk,dAMP[t],kidampdgk,dI,kididgk,dIMP,kidimpdgk,dITP,kiditpdgk];
(*nucleoside kinase*)
dAnucleotidase=mm12[Vmax1PrdA,km1PrdA,dAMP[t],dTMP[t],km1PrdTen,dCMP[t],km1PrdC,dGMP[t],km1PrdG,dUMP,km1PrdUen,rUMP,km1PrrUen,rCMP,km1PrrC,rAMP,km1PrrA,rGMP,km1PrrG,dIMP,km1PrdI,rIMP,km1PrrI,rADP,kiadpen,rATP,kiatpen];
dAmpkforward= mm7[Vmax2PfdA,km2PfdA,dAMP[t],dADP[t],km2PrdA,rAMP,km2PfrA,rADP,km2PrrA,rCMP,km2PfrCak2,rUMP,km2PfrUak2,rCDP,km2PrrCak2,rUDP,km2PrrUak2];(*nucleoside monophosphate kinase forward*)
dAmpkreverse =mm7[Vmax2PrdA,km2PrdA,dADP[t],dAMP[t],km2PfdA,rADP,km2PrrA,rAMP,km2PfrA,rCMP,km2PfrCak2,rUMP,km2PfrUak2,rCDP,km2PrrCak2,rUDP,km2PrrUak2];(*nucleoside monophosphate kinase reverse*) 
dAdpkforward= mm21[Vmax3PfdA,km3PfdA,dADP[t],dCDP[t],km3PfdC,dTDP[t],km3PfdT,dATP[t],km3PrdA,dGDP[t],km3PfdG,dTTP[t], km3PrdT, dCTP[t],km3PrdC,dGTP[t],km3PrdG,dUDP,km3PfdU,dUTP,km3PrdU,rUDP,km3PfrU,rUTP,km3PrrU,rCDP,km3PfrC,rCTP,km3PrrC,rADP,km3PfrA,rATP,km3PrrA,rGDP,km3PfrG,rGTP,km3PrrG,rIDP,km3PfrI,rITP,km3PrrI,dIDP,km3PfdI,dITP,km3PrdI ];(*nucleoside diphosphate kinase forward*)
dAdpkreverse =mm21[Vmax3PrdA,km3PrdA,dATP[t],dCDP[t],km3PfdC,dTDP[t],km3PfdT,dADP[t],km3PfdA,dGDP[t],km3PfdG,dTTP[t], km3PrdT, dCTP[t],km3PrdC,dGTP[t],km3PrdG,dUDP,km3PfdU,dUTP,km3PrdU,rUDP,km3PfrU,rUTP,km3PrrU,rCDP,km3PfrC,rCTP,km3PrrC,rADP,km3PfrA,rATP,km3PrrA,rGDP,km3PfrG,rGTP,km3PrrG,rIDP,km3PfrI,rITP,km3PrrI,dIDP,km3PfdI,dITP,km3PrdI ];(*nucleoside diphosphate kinase reverse*)

(*Michaelis Menten equations of deoxyguanosine metabolism*)

dGnucleosidetransport= mm10[transportervmax,transporterkm,dGcyto,dCcyto,transporterkm,dTcyto,transporterkm,dAcyto,transporterkm,dUcyto,transporterkm,rUcyto,transporterkm,rCcyto,transporterkm,rAcyto,transporterkm,rGcyto,transporterkm,dIcyto,transporterkm,rIcyto,transporterkm]-mm10[transportervmax,transporterkm,dG[t],dC[t],transporterkm,dT[t],transporterkm,dA[t],transporterkm,dU,transporterkm,rU,transporterkm,rC,transporterkm,rA,transporterkm,rG,transporterkm,dI,transporterkm,rI,transporterkm];
(*nucleoside transport in and out*)
dGnucleosidekinase= mm8[Vmax1PfdG,km1PfdG,dG[t],dA[t],km1PfdA,dATP[t],kidatpdgk,dGTP[t],kidgtpdgk,dGMP[t],kidgmpdgk,dAMP[t],kidampdgk,dI,kididgk,dIMP,kidimpdgk,dITP,kiditpdgk];
(*nucleoside kinase*)
dGnucleotidase=mm12[Vmax1PrdG,km1PrdG,dGMP[t],dTMP[t],km1PrdTen,dAMP[t],km1PrdA,dCMP[t],km1PrdC,dUMP,km1PrdUen,rUMP,km1PrrUen,rCMP,km1PrrC,rAMP,km1PrrA,rGMP,km1PrrG,dIMP,km1PrdI,rIMP,km1PrrI,rADP,kiadpen,rATP,kiatpen];
dGmpkforward=mm3[Vmax2PfdG,km2PfdG,dGMP[t],dGDP[t],km2PrdG,rGMP,km2PfrG,rGDP,km2PrrG];(*nucleoside monophosphare kinase forward*)
dGmpkreverse=mm3[Vmax2PrdG,km2PrdG,dGDP[t],dGMP[t],km2PfdG,rGMP,km2PfrG,rGDP,km2PrrG];(*nucleoside monophosphate kinase reverse*) 
dGdpkforward=mm21[Vmax3PfdG,km3PfdG,dGDP[t],dCDP[t],km3PfdC,dTDP[t],km3PfdT,dADP[t],km3PfdA,dATP[t],km3PrdA,dTTP[t], km3PrdT, dCTP[t],km3PrdC,dGTP[t],km3PrdG,dUDP,km3PfdU,dUTP,km3PrdU,rUDP,km3PfrU,rUTP,km3PrrU,rCDP,km3PfrC,rCTP,km3PrrC,rADP,km3PfrA,rATP,km3PrrA,rGDP,km3PfrG,rGTP,km3PrrG ,rIDP,km3PfrI,rITP,km3PrrI,dIDP,km3PfdI,dITP,km3PrdI];(*nucleoside diphosphate kinase forward*)
dGdpkreverse =mm21[Vmax3PrdG,km3PrdG,dGTP[t],dCDP[t],km3PfdC,dTDP[t],km3PfdT,dADP[t],km3PfdA,dATP[t],km3PrdA,dTTP[t], km3PrdT,dCTP[t],km3PrdC,dGDP[t],km3PfdG,dUDP,km3PfdU,dUTP,km3PrdU,rUDP,km3PfrU,rUTP,km3PrrU,rCDP,km3PfrC,rCTP,km3PrrC,rADP,km3PfrA,rATP,km3PrrA,rGDP,km3PfrG,rGTP,km3PrrG,rIDP,km3PfrI,rITP,km3PrrI,dIDP,km3PfdI,dITP,km3PrdI ];(*nucleoside diphosphate kinase reverse*)

(*Rates of polymerization for individual dNTP species alone*)
rdT:=If[replication>0,1,0]*mm[VmaxPoldT,KmPoldT,dTTP[t]];
rdC:=If[replication>0,1,0]*mm[VmaxPoldC,KmPoldC,dCTP[t]];
rdA:=If[replication>0,1,0]*mm[VmaxPoldA,KmPoldA,dATP[t]];
rdG:=If[replication>0,1,0]*mm[VmaxPoldG,KmPoldG,dGTP[t]];

(*Heavy Strand Polymerization Start and Stop Directions*)
 PolrateH:=If[ (startPol> t)  || ((HDNA[t])>strandDNA)  ,0,1]*HPolrate[t];
(*Light Strand Polymerization Start and Stop Directions*)
 PolrateL:= If[ ((startPol> t)  || ((LDNA[t])>strandDNA)|| ((HDNA[t])< Lstrandstart)),0,1]*LPolrate[t];

(*                                                                                                          *)
(*Definition of michaelis menten and hill functions*)

(*Michaelis Menten function with no inhibitors*)
mm[vmax_,km_,s_]:= If[s>0,1,0]*vmax*s/(km+s);
               
(*Michaelis Menten function with 1 inhibitor*)
mm1[vmax_,km_,s_,i_,ki_]:=If[s>0,1,0]*vmax*s/(s+km+km*(If[i>0,1,0]*(i/ki)));

   (*Michaelis Menten function with 2 inhibitors*)
mm2[vmax_,km_,s_,i1_,ki1_,i2_,ki2_]:=If[s>0,1,0]*vmax*s/(s+km+km*(If[i1>0,1,0]*(i1/ki1)+If[i2>0,1,0]*(i2/ki2)));                    
                            
(*Michaelis Menten function with 3 inhibitors*)
mm3[vmax_,km_,s_,i1_,ki1_,i2_,ki2_,i3_,ki3_]:=If[s>0,1,0]*vmax*s/(s+km+km*(If[i1>0,1,0]*(i1/ki1)+If[i2>0,1,0]*(i2/ki2)+If[i3>0,1,0]*(i3/ki3)));

(*Michaelis Menten function with 4 inhibitors*) mm4[vmax_,km_,s_,i1_,ki1_,i2_,ki2_,i3_,ki3_,i4_,ki4_]:=If[s>0,1,0]*vmax*s/(s+km+km*(If[i1>0,1,0]*(i1/ki1)+If[i2>0,1,0]*(i2/ki2)+If[i3>0,1,0]*(i3/ki3)+If[i4>0,1,0]*(i4/ki4)));
                                             
(*Michaelis Menten function with 5 inhibitors*) mm5[vmax_,km_,s_,i1_,ki1_,i2_,ki2_,i3_,ki3_,i4_,ki4_,i5_,ki5_]:=If[s>0,1,0]*vmax*s/(s+km+km*(If[i1>0,1,0]*(i1/ki1)+If[i2>0,1,0]*(i2/ki2)+If[i3>0,1,0]*(i3/ki3)+If[i4>0,1,0]*(i4/ki4)+If[i5>0,1,0]*(i5/ki5)));

(*Michaelis Menten function with 6 inhibitors*)
mm6[vmax_,km_,s_,i1_,ki1_,i2_,ki2_,i3_,ki3_,i4_,ki4_,i5_,ki5_,i6_,ki6_]:=If[s>0,1,0]*
  vmax*s/(s+km+km*(If[i1>0,1,0]*(i1/ki1)+If[i2>0,1,0]*(i2/ki2)+If[i3>0,1,0]*(i3/ki3)+If[i4>0,1,0]*(i4/ki4)+If[i5>0,1,0]*(i5/ki5)+If[i6>0,1,0]*(i6/ki6)));

(*Michaelis Menten function with 7 inhibitors*)
mm7[vmax_,km_,s_,i1_,ki1_,i2_,ki2_,i3_,ki3_,i4_,ki4_,i5_,ki5_,i6_,ki6_,i7_,ki7_]:=If[s>0,1,0]*
  vmax*s/(s+km+km*(If[i1>0,1,0]*(i1/ki1)+If[i2>0,1,0]*(i2/ki2)+If[i3>0,1,0]*(i3/ki3)+If[i4>0,1,0]*(i4/ki4)+If[i5>0,1,0]*(i5/ki5)+If[i6>0,1,0]*(i6/ki6)+If[i7>0,1,0]*(i7/ki7)));                        
                     
(*Michaelis menten function with 8 inhibitors*)
mm8[vmax_,km_,s_,i1_,ki1_,i2_,ki2_,i3_,ki3_,i4_,ki4_,i5_,ki5_,i6_,ki6_,i7_,ki7_,i8_,ki8_]:=If[s>0,1,0]*vmax*s/(s+km+km*(If[i1>0,1,0]*(i1/ki1)+If[i2>0,1,0]*(i2/ki2)+If[i3>0,1,0]*(i3/ki3)+If[i4>0,1,0]*(i4/ki4)+If[i5>0,1,0]*(i5/ki5)+If[i6>0,1,0]*(i6/ki6)+If[i7>0,1,0]*(i7/ki7)+If[i8>0,1,0]*(i8/ki8)));

(*Michaelis menten function with 9 inhibitors*)
mm9[vmax_,km_,s_,i1_,ki1_,i2_,ki2_,i3_,ki3_,i4_,ki4_,i5_,ki5_,i6_,ki6_,i7_,ki7_,i8_,ki8_,i9_,ki9_]:=If[s>0,1,0]*vmax*s/(s+km+km*(If[i1>0,1,0]*(i1/ki1)+If[i2>0,1,0]*(i2/ki2)+If[i3>0,1,0]*(i3/ki3)+If[i4>0,1,0]*(i4/ki4)+If[i5>0,1,0]*(i5/ki5)+If[i6>0,1,0]*(i6/ki6)+If[i7>0,1,0]*(i7/ki7)+If[i8>0,1,0]*(i8/ki8)+If[i9>0,1,0]*(i9/ki9)));

(*Michaelis menten function with 10 inhibitors*)
mm10[vmax_,km_,s_,i1_,ki1_,i2_,ki2_,i3_,ki3_,i4_,ki4_,i5_,ki5_,i6_,ki6_,i7_,ki7_,i8_,ki8_,i9_,ki9_,i10_,ki10_]:=If[s>0,1,0]*vmax*s/(s+km+km*(If[i1>0,1,0]*(i1/ki1)+If[i2>0,1,0]*(i2/ki2)+If[i3>0,1,0]*(i3/ki3)+If[i4>0,1,0]*(i4/ki4)+If[i5>0,1,0]*(i5/ki5)+If[i6>0,1,0]*(i6/ki6)+If[i7>0,1,0]*(i7/ki7)+If[i8>0,1,0]*(i8/ki8)+If[i9>0,1,0]*(i9/ki9)+If[i10>0,1,0]*(i10/ki10)));

(*Michaelis menten function with 11 inhibitors*)
mm11[vmax_,km_,s_,i1_,ki1_,i2_,ki2_,i3_,ki3_,i4_,ki4_,i5_,ki5_,i6_,ki6_,i7_,ki7_,i8_,ki8_,i9_,ki9_,i10_,ki10_,i11_,ki11_]:=If[s>0,1,0]*vmax*s/(s+km+km*(If[i1>0,1,0]*(i1/ki1)+If[i2>0,1,0]*(i2/ki2)+If[i3>0,1,0]*(i3/ki3)+If[i4>0,1,0]*(i4/ki4)+If[i5>0,1,0]*(i5/ki5)+If[i6>0,1,0]*(i6/ki6)+If[i7>0,1,0]*(i7/ki7)+If[i8>0,1,0]*(i8/ki8)+If[i9>0,1,0]*(i9/ki9)+If[i10>0,1,0]*(i10/ki10)+If[i11>0,1,0]*(i11/ki11)));

(*Michaelis menten function with 12 inhibitors*)
mm12[vmax_,km_,s_,i1_,ki1_,i2_,ki2_,i3_,ki3_,i4_,ki4_,i5_,ki5_,i6_,ki6_,i7_,ki7_,i8_,ki8_,i9_,ki9_,i10_,ki10_,i11_,ki11_,i12_,ki12_]:=If[s>0,1,0]*vmax*s/(s+km+km*(If[i1>0,1,0]*(i1/ki1)+If[i2>0,1,0]*(i2/ki2)+If[i3>0,1,0]*(i3/ki3)+If[i4>0,1,0]*(i4/ki4)+If[i5>0,1,0]*(i5/ki5)+If[i6>0,1,0]*(i6/ki6)+If[i7>0,1,0]*(i7/ki7)+If[i8>0,1,0]*(i8/ki8)+If[i9>0,1,0]*(i9/ki9)+If[i10>0,1,0]*(i10/ki10)+If[i11>0,1,0]*(i11/ki11)+If[i12>0,1,0]*(i12/ki12)));

(*Michaelis Menten function with 17 inhibitors*) mm21[vmax_,km_,s_,i1_,ki1_,i2_,ki2_,i3_,ki3_,i4_,ki4_,i5_,ki5_,i6_,ki6_,i7_,ki7_,i8_,ki8_,i9_,ki9_,i10_,ki10_,i11_,ki11_,i12_,ki12_,i13_,ki13_,i14_,ki14_,i15_,ki15_,i16_,ki16_,i17_,ki17_,i18_,ki18_,i19_,ki19_,i20_,ki20_,i21_,ki21_]:=If[s>0,1,0]*vmax*s/(s+km+km*(If[i1>0,1,0]*(i1/ki1)+If[i2>0,1,0]*(i2/ki2)+If[i3>0,1,0]*(i3/ki3)+If[i4>0,1,0]*(i4/ki4)+If[i5>0,1,0]*(i5/ki5)+If[i6>0,1,0]*(i6/ki6)+If[i7>0,1,0]*(i7/ki7)+If[i8>0,1,0]*(i8/ki8)+ +If[i9>0,1,0]*(i9/ki9)+If[i10>0,1,0]*(i10/ki10)+If[i11>0,1,0]*(i11/ki11)+If[i12>0,1,0]*(i12/ki12)+If[i13>0,1,0]*(i13/ki13)+If[i14>0,1,0]*(i14/ki14)+If[i15>0,1,0]*(i15/ki15)+If[i16>0,1,0]*(i16/ki16)+If[i17>0,1,0]*(i17/ki17)+If[i18>0,1,0]*(i18/ki18)+If[i19>0,1,0]*(i19/ki19)+If[i20>0,1,0]*(i20/ki20)+If[i21>0,1,0]*(i21/ki21))); 

(*Hill equation function with 5 inhibitors*)
hill5[vmax_,km_,s_,i1_,ki1_,i2_,ki2_,i3_,ki3_,i4_,ki4_,i5_,ki5_,hc_]:=If[s>0,1,0]*vmax*(s^hc)/((s^hc)+(km^hc+km^hc*(If[i1>0,1,0]*(i1/ki1)+If[i2>0,1,0]*(i2/ki2)+If[i3>0,1,0]*(i3/ki3)+If[i4>0,1,0]*(i4/ki4)+If[i5>0,1,0]*(i5/ki5))));

(*                                                                                                                 *)

(*The total simulation time is broken up so that one mtDNA molecule is copied each time through a loop*)
(*the amount of time of each separate differential equation*)

DNAmolreptime=simtime/numDNAmols;

(*A Do loop that replicates one molecule of mtDNA each time through, the loop counter i counts from 1 to numDNAmols*)

Timing[Do[     
(*Hold all simulation results in an array called solution, first mtDNA molecule synthesized in solution[1],  
second mtDNA molecule replicated in solution[2], so on*)
If[i!=1, Table[solution[i-1]]];

(*Variable k holds a data table of time (min) and dNTP molecules/mitochondrion*)
If[i!=1,k=Flatten[Table[{t,dTTP[t],dCTP[t],dATP[t],dGTP[t]} /.solution[i-1],{t,start,end,1}],1]];

(*Get rid of blank lines in between each data line*)
 If[i!=1,data=ToString[TableForm[k],OutputForm]];
If[i!=1,data2=StringReplace[data,{"\n\n"-> "\n"}]];
If[i!=1,data3=ToExpression["data2"]];
(*output 5 columns, the time (min), dTTP, dCTP, dATP, dGTP (molecules) to a file called dNTPs.txt*)
If[i!=1, OutputForm[data3] >>>"dNTPs.txt"];


(*loop counter used outside of loop for last iteration*)
lin=i;
(*Start polymerization at beginning*)
startPol=DNAmolreptime*(i)-DNAmolreptime;(*start time of each differential equation loop where polymerase starts*)
start=If[i==1,0,end];(*beginning time of each differential equation loop*)
end=If[i==1,DNAmolreptime,start+DNAmolreptime];(*ending time of each differential equation loop*)

(*Set the nucleotide levels initially or this time through loop to the concentrations at the end of the last loop*)
dT0=If[i==1,dT0,First[dT[start]/.solution[i-1]]];
dTMP0=If[i==1,dTMP0,First[dTMP[start]/.solution[i-1]]];
dTDP0=If[i==1,dTDP0,First[dTDP[start]/.solution[i-1]]];
dTTP0=If[i==1,dTTP0,First[dTTP[start]/.solution[i-1]]];
dC0=If[i==1,dC0,First[dC[start]/.solution[i-1]]];
dCMP0=If[i==1,dCMP0,First[dCMP[start]/.solution[i-1]]];
dCDP0=If[i==1,dCDP0,First[dCDP[start]/.solution[i-1]]];
dCTP0=If[i==1,dCTP0,First[dCTP[start]/.solution[i-1]]];
dA0=If[i==1,dA0,First[dA[start]/.solution[i-1]]];
dAMP0=If[i==1,dAMP0,First[dAMP[start]/.solution[i-1]]];
dADP0=If[i==1,dADP0,First[dADP[start]/.solution[i-1]]];
dATP0=If[i==1,dATP0,First[dATP[start]/.solution[i-1]]];
dG0=If[i==1,dG0,First[dG[start]/.solution[i-1]]];
dGMP0=If[i==1,dGMP0,First[dGMP[start]/.solution[i-1]]];
dGDP0=If[i==1,dGDP0,First[dGDP[start]/.solution[i-1]]];
dGTP0=If[i==1,dGTP0,First[dGTP[start]/.solution[i-1]]];

(*                                                                                                                *)
(*differential equations*)
(*Determine individual pool levels over time by adding and subtracting kinetic equations*)

(*transport*)
ri = Range[0,1200,100]; 
(*OutputForm[ri] >>>"ri.txt";*)
 
solution[i]=NDSolve [{
dT'[t]==dTnucleosidetransport-dTnucleosidekinase+dTnucleotidase,
dTMP'[t]==dTnucleosidekinase-dTnucleotidase-dTmpkforward+dTmpkreverse,
dTDP'[t]==dTmpkforward-dTmpkreverse-dTdpkforward+dTdpkreverse,
dTTP'[t]==dTdpkforward-dTdpkreverse- PolrateL*fdTL- PolrateH*fdTH+ri[[count]],
dC'[t]==dCnucleosidetransport-dCnucleosidekinase+dCnucleotidase,
dCMP'[t]==dCnucleosidekinase-dCmpkforward+dCmpkreverse-dCnucleotidase,
dCDP'[t]==dCmpkforward-dCmpkreverse-dCdpkforward+dCdpkreverse,
dCTP'[t]==dCdpkforward-dCdpkreverse- PolrateL*fdCL-PolrateH*fdCH+ri[[count]],
dA'[t]==dAnucleosidetransport-dAnucleosidekinase+dAnucleotidase,
dAMP'[t]==dAnucleosidekinase-dAmpkforward+dAmpkreverse-dAnucleotidase,
dADP'[t]==dAmpkforward-dAmpkreverse-dAdpkforward+dAdpkreverse,
dATP'[t]==dAdpkforward-dAdpkreverse- PolrateL*fdAL-PolrateH*fdAH+ri[[count]],
dG'[t]==dGnucleosidetransport-dGnucleosidekinase+dGnucleotidase,
dGMP'[t]==dGnucleosidekinase-dGmpkforward+dGmpkreverse-dGnucleotidase,
dGDP'[t]==dGmpkforward-dGmpkreverse-dGdpkforward+dGdpkreverse,
dGTP'[t]==dGdpkforward-dGdpkreverse-  PolrateL*fdGL-  PolrateH*fdGH+ri[[count]],
LDNA'[t]==PolrateL ,
HDNA'[t]==PolrateH ,
LPolrate[t]==rdT*rdC*rdA *rdG/((fdTL*rdC*rdA*rdG)+(fdCL*rdT*rdA*rdG)+(fdAL*rdT*rdC*rdG)+ (fdGL*rdT*rdC*rdA)+0.1),
HPolrate[t]==rdT*rdC*rdA *rdG/((fdTH*rdC*rdA*rdG)+(fdCH*rdT*rdA*rdG)+(fdAH*rdT*rdC*rdG)+(fdGH*rdT*rdC*rdA)+0.1),
dT[start]==dT0,
dTMP[start]==dTMP0,
dTDP[start]==dTDP0,
dTTP[start]==dTTP0,
dC[start]==dC0,
dCMP[start]==dCMP0,
dCDP[start]==dCDP0,
dCTP[start]==dCTP0,
dA[start]==dA0,
dAMP[start]==dAMP0,
dADP[start]==dADP0,
dATP[start]==dATP0,
dG[start]==dG0,
dGMP[start]==dGMP0,
dGDP[start]==dGDP0,
dGTP[start]==dGTP0,
LDNA[start]==LDNA0,
HDNA[start]==HDNA0,
LPolrate'[start]==0,
HPolrate'[start]==0},
{dT,dTMP,dTDP,dTTP,dC,dCMP,dCDP,dCTP,dA,dAMP,dADP,dATP,dG,dGMP,dGDP,dGTP,LDNA,HDNA,LPolrate,HPolrate},
{t,start,end},MaxSteps->10000000,PrecisionGoal->4,Method->Automatic ],{i,1,numDNAmols}]];
      (*end loop*)

(*Analysis*)

k=Flatten[Table[{PolrateL+PolrateH} /.solution[lin],{t,start,end,0.1}],2];
          reptime=(10*end-Count[k,0])*0.1;(*calculate the replication time of the last mtDNA molecule replicated*)

hd=HDNA[end]/.solution[1];
ld=LDNA[end]/.solution[1];
replengths = Append[replengths,hd[[1]]+ld[[1]]];
repdurations = Append[repdurations,reptime];
reprates = replengths/repdurations;

(*OutputForm[reprates] >>>"reprates.txt"; *)

,{13}];

,{100}];
(*Analysis*)

replengths
repdurations
reprates
Max[replengths]
Min[repdurations]
TableForm[Partition[reprates,13]]
TableForm[parameters]

(*Data & Plots*)

(*write last iteration to end of file*)
(*Variable k* holds a data table of time (min) and dN and dNXP molecules per mitochondrion*)
kn=Flatten[Table[{t, dT[t],dC[t],dA[t],dG[t]} /.solution[lin],{t,start,end,1}],1];
(*Get rid of blank lines in between each data line*)
datan=ToString[TableForm[kn],OutputForm];
data2n=StringReplace[datan,{"\n\n"-> "\n"}];
data3n=ToExpression["data2n"];
(*output 5 columns, the time (min), dT, dC, dA, dG (molecules) to a file called dNs.txt*)
OutputForm[data3n] >>>"dNs.txt"; 

kmono=Flatten[Table[{t, dTMP[t],dCMP[t],dAMP[t],dGMP[t]} /.solution[lin],{t,start,end,1}],1];
(*Get rid of blank lines in between each data line*)
datamono=ToString[TableForm[kmono],OutputForm];
data2mono=StringReplace[datamono,{"\n\n"-> "\n"}];
data3mono=ToExpression["data2mono"];
(*output 5 columns, the time (min), dTMP, dCMP, dAMP, dGMP (molecules) to a file called dNMPs.txt*)
OutputForm[data3mono] >>>"dNMPs.txt";

kdi=Flatten[Table[{t, dTDP[t],dCDP[t],dADP[t],dGDP[t]} /.solution[lin],{t,start,end,1}],1];
(*Get rid of blank lines in between each data line*)
datadi=ToString[TableForm[kdi],OutputForm];
data2di=StringReplace[datadi,{"\n\n"-> "\n"}];
data3di=ToExpression["data2di"];
(*output 5 columns, the time (min), dTDP, dCDP, dADP, dGdP (molecules) to a file called dNDPs.txt*)
OutputForm[data3di] >>>"dNDPs.txt"; 

ktri=Flatten[Table[{t, dTTP[t],dCTP[t],dATP[t],dGTP[t]} /.solution[lin],{t,start,end,1}],1];
(*Get rid of blank lines in between each data line*)
datatri=ToString[TableForm[ktri],OutputForm];
data2tri=StringReplace[datatri,{"\n\n"-> "\n"}];
data3tri=ToExpression["data2tri"];
(*output 5 columns, the time (min), dTTP, dCTP, dATP, dGTP (molecules) to a file called dNTPs.txt*)
OutputForm[data3tri] >>>"dNTPs.txt";  

kT=Flatten[Table[{t, dT[t],dTMP[t],dTDP[t],dTTP[t]} /.solution[lin],{t,start,end,1}],1];
(*Get rid of blank lines in between each data line*)
dataT=ToString[TableForm[kT],OutputForm];
data2T=StringReplace[dataT,{"\n\n"-> "\n"}];
data3T=ToExpression["data2T"];
(*output 5 columns, the time (min), dT, dTMP, dTDP, dTTP (molecules) to a file called t.txt*)
OutputForm[data3T] >>>"T.txt"; 

kC=Flatten[Table[{t, dC[t],dCMP[t],dCDP[t],dCTP[t]} /.solution[lin],{t,start,end,1}],1];
(*Get rid of blank lines in between each data line*)
dataC=ToString[TableForm[kC],OutputForm];
data2C=StringReplace[dataC,{"\n\n"-> "\n"}];
data3C=ToExpression["data2C"];
(*output 5 columns, the time (min), dC, dCMP, dCDP, dCTP (molecules) to a file called C.txt*)
OutputForm[data3C] >>>"C.txt"; 

kA=Flatten[Table[{t, dA[t],dAMP[t],dADP[t],dATP[t]} /.solution[lin],{t,start,end,1}],1];
(*Get rid of blank lines in between each data line*)
dataA=ToString[TableForm[kA],OutputForm];
data2A=StringReplace[dataA,{"\n\n"-> "\n"}];
data3A=ToExpression["data2A"];
(*output 5 columns, the time (min), dA, dAMP, dADP, dATP (molecules) to a file called A.txt*)
OutputForm[data3A] >>>"A.txt"; 

kG=Flatten[Table[{t, dG[t],dGMP[t],dGDP[t],dGTP[t]} /.solution[lin],{t,start,end,1}],1];
(*Get rid of blank lines in between each data line*)
dataG=ToString[TableForm[kG],OutputForm];
data2G=StringReplace[dataG,{"\n\n"-> "\n"}];
data3G=ToExpression["data2G"];
(*output 5 columns, the time (min), dG, dGMP, dGDP, dGTP (molecules) to a file called G.txt*)
OutputForm[data3G] >>>"G.txt"; 
(*                                                                                                                    *)
(*Plots of simulation results*)
(*Change simulation array solution[lin] to observe other mtDNA molecules besides the last*) 
(*                                                                                                                    *)

(*In the graphs of different dNTPs, T=Red, C=Green, A=Blue, G=Black*)
(*In the graphs of different phosphorylated states, dN=Red, dNMP=Green, dNDP=Blue, dNTP=Black*) 

(*Plot the levels of dNTPs for all mtDNA replications separately*)
For[i=1,i<(lin+1),i++,dNTP[i]=Plot[Evaluate[{dTTP[t]/conversion,dCTP[t]/conversion,dATP[t]/conversion,dGTP[t]/conversion} /. solution[i]],
{t,DNAmolreptime*(i-1),DNAmolreptime*i}, AxesLabel -> {"Time (min)", "concentration dNTPs (micromoles/L)"}, PlotRange-> {0,dTTPcyto},
PlotStyle->{Red,Green,Blue,Black}]

If[i==lin && i>1,Show[dNTP[i],dNTP[i-1]]]]; (*Plot dNTP levels for last two mtDNA replications together*)

(*dTXP concentration plots for the last mtDNA replication*)
Plot[Evaluate[{dT[t]/conversion,dTMP[t]/conversion,dTDP[t]/conversion,dTTP[t]/conversion} /. solution[lin]],
{t,start,end}, AxesLabel -> {"Time (min)", "Concentration T (uM)"}, PlotRange-> {0,dTTPcyto/conversion},
PlotStyle->{Red,Green,Blue,Black}]

(*dCXP concentration plots for the last mtDNA replication*)
Plot[Evaluate[{dC[t]/conversion,dCMP[t]/conversion,dCDP[t]/conversion,dCTP[t]/conversion} /. solution[lin]],
{t,start,end}, AxesLabel -> {"Time (min)", "Concentration C (uM)"}, PlotRange-> {0,dTTPcyto/conversion},
PlotStyle->{Red,Green,Blue,Black}]

(*dAXP concentration plots for the last mtDNA replication*)
Plot[Evaluate[{dA[t]/conversion,dAMP[t]/conversion,dADP[t]/conversion,dATP[t]/conversion} /. solution[lin]],
{t,start,end}, AxesLabel -> {"Time (min)", "Concentration A (uM)"}, PlotRange-> {0,dTTPcyto/conversion},
PlotStyle->{Red,Green,Blue,Black}]

(*dGXP concentration plots for the last mtDNA replication*)
Plot[Evaluate[{dG[t]/conversion,dGMP[t]/conversion,dGDP[t]/conversion,dGTP[t]/conversion} /. solution[lin]],
{t,start,end}, AxesLabel -> {"Time (min)", "Concentration G (uM)"}, PlotRange-> {0,dTTPcyto/conversion},
PlotStyle->{Red,Green,Blue,Black}]

(*Plot dNs*)
Plot[Evaluate[{dT[t],dC[t],dA[t],dG[t]} /. solution[1]],
{t,start,end}, AxesLabel -> {"Time (min)", "dNs (molecules/mitochondrion)"}, PlotRange-> {0,100},
PlotStyle->{Red,Green,Blue,Black}]

(*Plot dNMPs*)
Plot[Evaluate[{dTMP[t],dCMP[t],dAMP[t],dGMP[t]} /. solution[1]],
{t,start,end}, AxesLabel -> {"Time (min)", "dNMPs (molecules/mitochondrion)"}, PlotRange-> {0,dTTPcyto},
PlotStyle->{Red,Green,Blue,Black}]

(*Plot dNDPs*)
Plot[Evaluate[{dTDP[t],dCDP[t],dADP[t],dGDP[t]} /. solution[1]],
{t,start,end}, AxesLabel -> {"Time (min)", "dNDPs (molecules/mitochondrion)"}, PlotRange-> {0,dTTPcyto},
PlotStyle->{Red,Green,Blue,Black}]

(*Plot dNTPs*)
Plot[Evaluate[{dTTP[t],dCTP[t],dATP[t],dGTP[t]} /. solution[1]],
{t,start,end}, AxesLabel -> {"Time (min)", "dNTPs (molecules/mitochondrion)"}, PlotRange-> {0,dTTPcyto},
PlotStyle->{Red,Green,Blue,Black}]

(*Plot dNs'*)
Plot[Evaluate[{dT'[t],dC'[t],dA'[t],dG'[t]} /. solution[1]],
{t,start,end}, AxesLabel -> {"Time (min)", "dNs' (molecules per minute)"}, PlotRange-> {0,100},
PlotStyle->{Red,Green,Blue,Black}]

(*Plot dNMPs'*)
Plot[Evaluate[{dTMP'[t],dCMP'[t],dAMP'[t],dGMP'[t]} /. solution[1]],
{t,start,end}, AxesLabel -> {"Time (min)", "dNMPs' (molecules per minute)"}, PlotRange-> {0,100},
PlotStyle->{Red,Green,Blue,Black}]

(*Plot dNDPs'*)
Plot[Evaluate[{dTDP'[t],dCDP'[t],dADP'[t],dGDP'[t]} /. solution[1]],
{t,start,end}, AxesLabel -> {"Time (min)", "dNDPs' (molecules per minute)"}, PlotRange-> {0,100},
PlotStyle->{Red,Green,Blue,Black}]

(*Plot dNTPs'*)
Plot[Evaluate[{dTTP'[t],dCTP'[t],dATP'[t],dGTP'[t]} /. solution[1]],
{t,start,end}, AxesLabel -> {"Time (min)", "dNTPs' (molecules per minute)"}, PlotRange-> {0,100},
PlotStyle->{Red,Green,Blue,Black}]

Plot[Evaluate[{HDNA[t], LDNA[t], (HDNA[t]+LDNA[t])}/.solution[1]],{t,DNAmolreptime/2,end}, AxesLabel -> {"Time(min)","DNA(nucleotides)"},PlotRange -> {0,17000}, PlotStyle -> {Red,Blue, Black}]  

Plot[Evaluate[{HDNA'[t], LDNA'[t], (HDNA'[t]+LDNA'[t])}/.solution[1]],{t,DNAmolreptime/2,end}, AxesLabel -> {"Time(min)","DNA'(nucleotides per minute)"},PlotRange -> {0,500}, PlotStyle -> {Red,Blue, Black}]  

Plot[Evaluate[{dTnucleosidekinase,dCnucleosidekinase,dAnucleosidekinase,dGnucleosidekinase}/.solution[1]],{t,start,end},AxesLabel->{"Time (min)","nucleoside kinase output (molecules per minute)"},PlotRange->{0,1000},PlotStyle->{Red,Green,Blue,Black}]

Plot[Evaluate[{dTnucleotidase,dCnucleotidase,dAnucleotidase,dGnucleotidase}/.solution[1]],{t,start,end},AxesLabel->{"Time (min)","nucleotidase output (molecules per minute)"},PlotRange->{0,1000},PlotStyle->{Red,Green,Blue,Black}]

Plot[Evaluate[{dTmpkforward,dCmpkforward,dAmpkforward,dGmpkforward}/.solution[1]],{t,start,end},AxesLabel->{"Time (min)","monophosphate kinase forward output (molecules per minute)"},PlotRange->{0,1000},PlotStyle->{Red,Green,Blue,Black}]

Plot[Evaluate[{dTmpkreverse,dCmpkreverse,dAmpkreverse,dGmpkreverse}/.solution[1]],{t,start,end},AxesLabel->{"Time (min)","monophosphate kinase reverse output (molecules per minute)"},PlotRange->{0,1000},PlotStyle->{Red,Green,Blue,Black}]

Plot[Evaluate[{dTdpkforward,dCdpkforward,dAdpkforward,dGdpkforward}/.solution[1]],{t,start,end},AxesLabel->{"Time (min)","diphosphate kinase forward output (molecules per minute)"},PlotRange->{0,1000},PlotStyle->{Red,Green,Blue,Black}]

Plot[Evaluate[{dTdpkreverse,dCdpkreverse,dAdpkreverse,dGdpkreverse}/.solution[1]],{t,start,end},AxesLabel->{"Time (min)","diphosphate kinase reverse output (molecules per minute)"},PlotRange->{0,1000},PlotStyle->{Red,Green,Blue,Black}]

Plot[Evaluate[{dTnucleosidetransport,dCnucleosidetransport,dAnucleosidetransport,dGnucleosidetransport}/.solution[1]],{t,start,end},AxesLabel->{"Time (min)","nucleoside transport reaction output (molecules per minute)"},PlotRange->{-1000,1000},PlotStyle->{Red,Green,Blue,Black}]

Plot[Evaluate[{(dTnucleosidekinase-dTnucleotidase),(dCnucleosidekinase-dCnucleotidase),(dAnucleosidekinase-dAnucleotidase),(dGnucleosidekinase-dGnucleotidase)}/.solution[1]],{t,start,end},AxesLabel->{"Time (min)","net monophosphate production (molecules per minute)"},PlotRange->{-1000,1000},PlotStyle->{Red,Green,Blue,Black}]

Plot[Evaluate[{(dTmpkforward-dTmpkreverse),(dCmpkforward-dCmpkreverse),(dAmpkforward-dAmpkreverse),(dGmpkforward-dGmpkreverse)}/.solution[1]],{t,start,end},AxesLabel->{"Time (min)","net diphosphate production (molecules per minute)"},PlotRange->{0,1000},PlotStyle->{Red,Green,Blue,Black}]

Plot[Evaluate[{(dTdpkforward-dTdpkreverse),(dCdpkforward-dCdpkreverse),(dAdpkforward-dAdpkreverse),(dGdpkforward-dGdpkreverse)}/.solution[1]],{t,start,end},AxesLabel->{"Time (min)","net triphosphate production (molecules per minute)"},PlotRange->{-1000,1000},PlotStyle->{Red,Green,Blue,Black}]

t

{dT[t],dC[t],dA[t],dG[t]}/.solution[1]

{dTMP[t],dCMP[t],dAMP[t],dGMP[t]}/.solution[1]

{dTDP[t],dCDP[t],dADP[t],dGDP[t]}/.solution[1]

{dTTP[t],dCTP[t],dATP[t],dGTP[t]}/.solution[1]

{dT'[t],dC'[t],dA'[t],dG'[t]}/.solution[1]

{dTMP'[t],dCMP'[t],dAMP'[t],dGMP'[t]}/.solution[1]

{dTDP'[t],dCDP'[t],dADP'[t],dGDP'[t]}/.solution[1]

{dTTP'[t],dCTP'[t],dATP'[t],dGTP'[t]}/.solution[1]

{HDNA[t], LDNA[t], HDNA[t] + LDNA[t]}/.solution[1]

{HDNA'[t], LDNA'[t], HDNA'[t] + LDNA'[t]}/.solution[1]

{dTnucleosidetransport,dCnucleosidetransport,dAnucleosidetransport,dGnucleosidetransport}/.solution[1]

{dTnucleosidekinase,dCnucleosidekinase,dAnucleosidekinase,dGnucleosidekinase}/.solution[1]

{dTnucleotidase,dCnucleotidase,dAnucleotidase,dGnucleotidase}/.solution[1]

{dTmpkforward,dCmpkforward,dAmpkforward,dGmpkforward}/.solution[1]

{dTmpkreverse,dCmpkreverse,dAmpkreverse,dGmpkreverse}/.solution[1]

{dTdpkforward,dCdpkforward,dAdpkforward,dGdpkforward}/.solution[1]

{dTdpkreverse,dCdpkreverse,dAdpkreverse,dGdpkreverse}/.solution[1]

{(dTnucleosidekinase-dTnucleotidase),(dCnucleosidekinase-dCnucleotidase),(dAnucleosidekinase-dAnucleotidase),(dGnucleosidekinase-dGnucleotidase)}/.solution[1]

{(dTmpkforward-dTmpkreverse),(dCmpkforward-dCmpkreverse),(dAmpkforward-dAmpkreverse),(dGmpkforward-dGmpkreverse)}/.solution[1]

{(dTdpkforward-dTdpkreverse),(dCdpkforward-dCdpkreverse),(dAdpkforward-dAdpkreverse),(dGdpkforward-dGdpkreverse)}/.solution[1]