(* Generated by JWS Online *)

(* This is an experimental feature of JWS Online. Please report any mistakes.*)

(* Note that the following notable SBML entities or features are not supported in notebook outputyet: *)
    (* Events *)
    (* Constraints *)
    (* Units and UnitDefinitions *)
    (* AlgebraicRules *)
    (* conversionFactors *)

variables = {
ADP[t], ADPi[t], ATP[t], ATPi[t], Cr[t], Cri[t], P[t], PCr[t], PCri[t], Pi[t]
};

initialValues = {
ADP[0] == 0.0, ADPi[0] == 0.0, ATP[0] == 9700.0, ATPi[0] == 0.0, Cr[0] == 26000.0, Cri[0] == 0.0, P[0] == 0.0, PCr[0] == 0.0, PCri[0] == 0.0, Pi[0] == 32000.0
};

rates = {
ADP\[LetterSpace]diffusion, ATP\[LetterSpace]diffusion, ATPase, Cr\[LetterSpace]diffusion, MMCK, MiCK, OxPhos, PCr\[LetterSpace]diffusion, Pi\[LetterSpace]diffusion
};

rateEquations = {
ADP\[LetterSpace]diffusion -> -(ADP\[LetterSpace]diffusion\[LetterSpace]k1\[LetterSpace]7*CYT*ADP[t]) + ADP\[LetterSpace]diffusion\[LetterSpace]k1\[LetterSpace]7*IMS*ADPi[t], ATP\[LetterSpace]diffusion -> -(ATP\[LetterSpace]diffusion\[LetterSpace]k1\[LetterSpace]9*CYT*ATP[t]) + ATP\[LetterSpace]diffusion\[LetterSpace]k1\[LetterSpace]9*IMS*ATPi[t], ATPase -> ATPase\[LetterSpace]v\[LetterSpace]4*CYT*ATP[t], Cr\[LetterSpace]diffusion -> -(Cr\[LetterSpace]diffusion\[LetterSpace]k1\[LetterSpace]6*CYT*Cr[t]) + Cr\[LetterSpace]diffusion\[LetterSpace]k1\[LetterSpace]6*IMS*Cri[t], MMCK -> (CYT*((MMCK\[LetterSpace]Vf\[LetterSpace]3*ATP[t]*Cr[t])/(MMCK\[LetterSpace]Kb\[LetterSpace]3*MMCK\[LetterSpace]Kia\[LetterSpace]3) - (MMCK\[LetterSpace]Vb\[LetterSpace]3*ADP[t]*PCr[t])/(MMCK\[LetterSpace]Kd\[LetterSpace]3*MMCK\[LetterSpace]Kic\[LetterSpace]3)))/(1 + Cr[t]/MMCK\[LetterSpace]Kib\[LetterSpace]3 + ATP[t]*(MMCK\[LetterSpace]Kia\[LetterSpace]3^(-1) + Cr[t]/(MMCK\[LetterSpace]Kb\[LetterSpace]3*MMCK\[LetterSpace]Kia\[LetterSpace]3)) + PCr[t]/MMCK\[LetterSpace]Kid\[LetterSpace]3 + ADP[t]*(MMCK\[LetterSpace]Kic\[LetterSpace]3^(-1) + Cr[t]/(MMCK\[LetterSpace]Kib\[LetterSpace]3*MMCK\[LetterSpace]Kic\[LetterSpace]3) + PCr[t]/(MMCK\[LetterSpace]Kd\[LetterSpace]3*MMCK\[LetterSpace]Kic\[LetterSpace]3))), MiCK -> (IMS*((MiCK\[LetterSpace]Vf\[LetterSpace]2*ATPi[t]*Cri[t])/(MiCK\[LetterSpace]Kb\[LetterSpace]2*MiCK\[LetterSpace]Kia\[LetterSpace]2) - (MiCK\[LetterSpace]Vb\[LetterSpace]2*ADPi[t]*PCri[t])/(MiCK\[LetterSpace]Kd\[LetterSpace]2*MiCK\[LetterSpace]Kic\[LetterSpace]2)))/(1 + Cri[t]/MiCK\[LetterSpace]Kib\[LetterSpace]2 + ATPi[t]*(MiCK\[LetterSpace]Kia\[LetterSpace]2^(-1) + Cri[t]/(MiCK\[LetterSpace]Kb\[LetterSpace]2*MiCK\[LetterSpace]Kia\[LetterSpace]2)) + PCri[t]/MiCK\[LetterSpace]Kid\[LetterSpace]2 + ADPi[t]*(MiCK\[LetterSpace]Kic\[LetterSpace]2^(-1) + Cri[t]/(MiCK\[LetterSpace]Kib\[LetterSpace]2*MiCK\[LetterSpace]Kic\[LetterSpace]2) + PCri[t]/(MiCK\[LetterSpace]Kd\[LetterSpace]2*MiCK\[LetterSpace]Kic\[LetterSpace]2))), OxPhos -> (IMS*OxPhos\[LetterSpace]V\[LetterSpace]1*ADPi[t]*Pi[t])/(OxPhos\[LetterSpace]Ka\[LetterSpace]1*OxPhos\[LetterSpace]Kb\[LetterSpace]1*(1 + ADPi[t]/OxPhos\[LetterSpace]Ka\[LetterSpace]1 + Pi[t]/OxPhos\[LetterSpace]Kb\[LetterSpace]1 + (ADPi[t]*Pi[t])/(OxPhos\[LetterSpace]Ka\[LetterSpace]1*OxPhos\[LetterSpace]Kb\[LetterSpace]1))), PCr\[LetterSpace]diffusion -> -(CYT*PCr\[LetterSpace]diffusion\[LetterSpace]k1\[LetterSpace]8*PCr[t]) + IMS*PCr\[LetterSpace]diffusion\[LetterSpace]k1\[LetterSpace]8*PCri[t], Pi\[LetterSpace]diffusion -> -(CYT*Pi\[LetterSpace]diffusion\[LetterSpace]k2\[LetterSpace]5*P[t]) + IMS*Pi\[LetterSpace]diffusion\[LetterSpace]k2\[LetterSpace]5*Pi[t]
};

parameters = {
OxPhos\[LetterSpace]V\[LetterSpace]1 -> 4600.0, OxPhos\[LetterSpace]Ka\[LetterSpace]1 -> 800.0, OxPhos\[LetterSpace]Kb\[LetterSpace]1 -> 20.0, MiCK\[LetterSpace]Vf\[LetterSpace]2 -> 2658.0, MiCK\[LetterSpace]Kia\[LetterSpace]2 -> 750.0, MiCK\[LetterSpace]Kb\[LetterSpace]2 -> 5200.0, MiCK\[LetterSpace]Vb\[LetterSpace]2 -> 11160.0, MiCK\[LetterSpace]Kic\[LetterSpace]2 -> 204.8, MiCK\[LetterSpace]Kd\[LetterSpace]2 -> 500.0, MiCK\[LetterSpace]Kib\[LetterSpace]2 -> 28800.0, MiCK\[LetterSpace]Kid\[LetterSpace]2 -> 1600.0, MMCK\[LetterSpace]Vf\[LetterSpace]3 -> 6966.0, MMCK\[LetterSpace]Kia\[LetterSpace]3 -> 900.0, MMCK\[LetterSpace]Kb\[LetterSpace]3 -> 15500.0, MMCK\[LetterSpace]Vb\[LetterSpace]3 -> 29250.0, MMCK\[LetterSpace]Kic\[LetterSpace]3 -> 222.4, MMCK\[LetterSpace]Kd\[LetterSpace]3 -> 1670.0, MMCK\[LetterSpace]Kib\[LetterSpace]3 -> 34900.0, MMCK\[LetterSpace]Kid\[LetterSpace]3 -> 4730.0, ATPase\[LetterSpace]v\[LetterSpace]4 -> 4600.0, Pi\[LetterSpace]diffusion\[LetterSpace]k2\[LetterSpace]5 -> 18.4, Cr\[LetterSpace]diffusion\[LetterSpace]k1\[LetterSpace]6 -> 14.6, ADP\[LetterSpace]diffusion\[LetterSpace]k1\[LetterSpace]7 -> 8.16, PCr\[LetterSpace]diffusion\[LetterSpace]k1\[LetterSpace]8 -> 14.6, ATP\[LetterSpace]diffusion\[LetterSpace]k1\[LetterSpace]9 -> 8.16, CYT -> 0.75, IMS -> 0.0625
};

assignments = {

};

events = {

};

speciesAnnotations = {
ADP[t]->"http://identifiers.org/chebi/CHEBI:16761", ADP[t]->"http://identifiers.org/kegg.compound/C00008", ADPi[t]->"http://identifiers.org/chebi/CHEBI:16761", ADPi[t]->"http://identifiers.org/kegg.compound/C00008", ATP[t]->"http://identifiers.org/chebi/CHEBI:15422", ATP[t]->"http://identifiers.org/kegg.compound/C00002", ATPi[t]->"http://identifiers.org/chebi/CHEBI:15422", ATPi[t]->"http://identifiers.org/kegg.compound/C00002", Cr[t]->"http://identifiers.org/chebi/CHEBI:16919", Cr[t]->"http://identifiers.org/kegg.compound/C00300", Cri[t]->"http://identifiers.org/chebi/CHEBI:16919", Cri[t]->"http://identifiers.org/kegg.compound/C00300", P[t]->"http://identifiers.org/chebi/CHEBI:18367", P[t]->"http://identifiers.org/kegg.compound/C00009", PCr[t]->"http://identifiers.org/chebi/CHEBI:17287", PCr[t]->"http://identifiers.org/kegg.compound/C02305", PCri[t]->"http://identifiers.org/chebi/CHEBI:17287", PCri[t]->"http://identifiers.org/kegg.compound/C02305", Pi[t]->"http://identifiers.org/chebi/CHEBI:18367", Pi[t]->"http://identifiers.org/kegg.compound/C00009"
};

reactionAnnotations = {

};

units = {
{"time" -> "", "metabolite" -> "", "extent" -> ""}
};

(* Time evolution *)
odes = {
ADP'[t] == 1.0*MMCK +1.0*ATPase +1.0*ADP\[LetterSpace]diffusion , ADPi'[t] == 1.0*MiCK -1.0*OxPhos -1.0*ADP\[LetterSpace]diffusion, ATP'[t] == 1.0*ATP\[LetterSpace]diffusion -1.0*MMCK -1.0*ATPase, ATPi'[t] == 1.0*OxPhos -1.0*MiCK -1.0*ATP\[LetterSpace]diffusion, Cr'[t] == 1.0*Cr\[LetterSpace]diffusion -1.0*MMCK, Cri'[t] ==  -1.0*MiCK -1.0*Cr\[LetterSpace]diffusion, P'[t] == 1.0*ATPase +1.0*Pi\[LetterSpace]diffusion , PCr'[t] == 1.0*MMCK +1.0*PCr\[LetterSpace]diffusion , PCri'[t] == 1.0*MiCK -1.0*PCr\[LetterSpace]diffusion, Pi'[t] ==  -1.0*OxPhos -1.0*Pi\[LetterSpace]diffusion
};
timeCourse = NDSolve[Join[odes, initialValues]//.rateEquations//.assignments//.parameters, variables, {t, 0, 100}];

(* Steady-state solution initialized with result of time evolution *)
findRootEquations = odes /.D[_[t],t]->0;
findRootVariables = Partition[Flatten[{#, #/.timeCourse/.t->100} &/@variables],2];
steadyStateVariables = FindRoot[findRootEquations//.rateEquations//.assignments//.parameters, findRootVariables, MaxIterations->100]
fluxes = #//.assignments//.parameters/.steadyStateVariables&/@rateEquations

(* Plot the time evolution of the variables *)
plotTable=Table[Plot[variables[[i]]/.parameters/.timeCourse,{t,0,100},PlotLegends->variables[[i]],PlotRange->Full],{i,Length[variables]}]