(* 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 = {
CC[t], Cn[t], Mp[t], Mt[t], P0[t], P1[t], P2[t], T0[t], T1[t], T2[t]
};

initialValues = {
CC[0] == 0.0, Cn[0] == 0.0, Mp[0] == 0.0, Mt[0] == 0.0, P0[0] == 0.0, P1[0] == 0.0, P2[0] == 0.0, T0[0] == 0.0, T1[0] == 0.0, T2[0] == 0.0
};

rates = {
Mp\[LetterSpace]degradation, Mp\[LetterSpace]production, Mt\[LetterSpace]degradation, Mt\[LetterSpace]production, P0\[LetterSpace]degradation, P0\[LetterSpace]production, P0\[LetterSpace]to\[LetterSpace]P1, P1\[LetterSpace]degradation, P1\[LetterSpace]to\[LetterSpace]P0, P1\[LetterSpace]to\[LetterSpace]P2, P2\[LetterSpace]degradation, P2\[LetterSpace]to\[LetterSpace]P1, PT\[LetterSpace]complex\[LetterSpace]degradation, PT\[LetterSpace]complex\[LetterSpace]formation, PT\[LetterSpace]complex\[LetterSpace]nucleation, PTnucl\[LetterSpace]complex\[LetterSpace]degradation, T0\[LetterSpace]degradation, T0\[LetterSpace]production, T0\[LetterSpace]to\[LetterSpace]T1, T1\[LetterSpace]degradation, T1\[LetterSpace]to\[LetterSpace]T0, T1\[LetterSpace]to\[LetterSpace]T2, T2\[LetterSpace]degradation, T2\[LetterSpace]to\[LetterSpace]T1
};

rateEquations = {
Mp\[LetterSpace]degradation -> Cell*Mp\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d*Mp[t] + (Cell*Mp\[LetterSpace]degradation\[LetterSpace]V\[LetterSpace]mP*Mp[t])/(Mp\[LetterSpace]degradation\[LetterSpace]K\[LetterSpace]mP + Mp[t]), Mp\[LetterSpace]production -> (Cell*Mp\[LetterSpace]production\[LetterSpace]K\[LetterSpace]IP^Mp\[LetterSpace]production\[LetterSpace]n*Mp\[LetterSpace]production\[LetterSpace]v\[LetterSpace]sP)/(Mp\[LetterSpace]production\[LetterSpace]K\[LetterSpace]IP^Mp\[LetterSpace]production\[LetterSpace]n + Cn[t]^Mp\[LetterSpace]production\[LetterSpace]n), Mt\[LetterSpace]degradation -> Cell*Mt\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d*Mt[t] + (Cell*V\[LetterSpace]mT*Mt[t])/(Mt\[LetterSpace]degradation\[LetterSpace]K\[LetterSpace]mT + Mt[t]), Mt\[LetterSpace]production -> (Cell*Mt\[LetterSpace]production\[LetterSpace]K\[LetterSpace]IT^Mt\[LetterSpace]production\[LetterSpace]n*Mt\[LetterSpace]production\[LetterSpace]V\[LetterSpace]sT)/(Mt\[LetterSpace]production\[LetterSpace]K\[LetterSpace]IT^Mt\[LetterSpace]production\[LetterSpace]n + Cn[t]^Mt\[LetterSpace]production\[LetterSpace]n), P0\[LetterSpace]degradation -> Cell*P0\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d*P0[t], P0\[LetterSpace]production -> Cell*P0\[LetterSpace]production\[LetterSpace]k\[LetterSpace]sP*Mp[t], P0\[LetterSpace]to\[LetterSpace]P1 -> (Cell*P0\[LetterSpace]to\[LetterSpace]P1\[LetterSpace]V\[LetterSpace]1P*P0[t])/(P0\[LetterSpace]to\[LetterSpace]P1\[LetterSpace]K1\[LetterSpace]P + P0[t]), P1\[LetterSpace]degradation -> Cell*P1\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d*P1[t], P1\[LetterSpace]to\[LetterSpace]P0 -> (Cell*P1\[LetterSpace]to\[LetterSpace]P0\[LetterSpace]V\[LetterSpace]2P*P1[t])/(P1\[LetterSpace]to\[LetterSpace]P0\[LetterSpace]K\[LetterSpace]2P + P1[t]), P1\[LetterSpace]to\[LetterSpace]P2 -> (Cell*P1\[LetterSpace]to\[LetterSpace]P2\[LetterSpace]V\[LetterSpace]3P*P1[t])/(P1\[LetterSpace]to\[LetterSpace]P2\[LetterSpace]K\[LetterSpace]3P + P1[t]), P2\[LetterSpace]degradation -> Cell*P2\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d*P2[t] + (Cell*P2\[LetterSpace]degradation\[LetterSpace]V\[LetterSpace]dP*P2[t])/(P2\[LetterSpace]degradation\[LetterSpace]K\[LetterSpace]dP + P2[t]), P2\[LetterSpace]to\[LetterSpace]P1 -> (Cell*P2\[LetterSpace]to\[LetterSpace]P1\[LetterSpace]V\[LetterSpace]4P*P2[t])/(P2\[LetterSpace]to\[LetterSpace]P1\[LetterSpace]K\[LetterSpace]4P + P2[t]), PT\[LetterSpace]complex\[LetterSpace]degradation -> Cell*PT\[LetterSpace]complex\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]dC*CC[t], PT\[LetterSpace]complex\[LetterSpace]formation -> -(Cell*PT\[LetterSpace]complex\[LetterSpace]formation\[LetterSpace]k4*CC[t]) + Cell*PT\[LetterSpace]complex\[LetterSpace]formation\[LetterSpace]k3*P2[t]*T2[t], PT\[LetterSpace]complex\[LetterSpace]nucleation -> Cell*PT\[LetterSpace]complex\[LetterSpace]nucleation\[LetterSpace]k1*CC[t] - compartment\[LetterSpace]0000002*PT\[LetterSpace]complex\[LetterSpace]nucleation\[LetterSpace]k2*Cn[t], PTnucl\[LetterSpace]complex\[LetterSpace]degradation -> compartment\[LetterSpace]0000002*PTnucl\[LetterSpace]complex\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]dN*Cn[t], T0\[LetterSpace]degradation -> Cell*T0\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d*T0[t], T0\[LetterSpace]production -> Cell*T0\[LetterSpace]production\[LetterSpace]k\[LetterSpace]sT*Mt[t], T0\[LetterSpace]to\[LetterSpace]T1 -> (Cell*T0\[LetterSpace]to\[LetterSpace]T1\[LetterSpace]V\[LetterSpace]1T*T0[t])/(T0\[LetterSpace]to\[LetterSpace]T1\[LetterSpace]K\[LetterSpace]1T + T0[t]), T1\[LetterSpace]degradation -> Cell*T1\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d*T1[t], T1\[LetterSpace]to\[LetterSpace]T0 -> (Cell*T1\[LetterSpace]to\[LetterSpace]T0\[LetterSpace]V\[LetterSpace]2T*T1[t])/(T1\[LetterSpace]to\[LetterSpace]T0\[LetterSpace]K\[LetterSpace]2T + T1[t]), T1\[LetterSpace]to\[LetterSpace]T2 -> (Cell*T1\[LetterSpace]to\[LetterSpace]T2\[LetterSpace]V\[LetterSpace]3T*T1[t])/(T1\[LetterSpace]to\[LetterSpace]T2\[LetterSpace]K\[LetterSpace]3T + T1[t]), T2\[LetterSpace]degradation -> Cell*T2\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d*T2[t] + (Cell*V\[LetterSpace]dT*T2[t])/(T2\[LetterSpace]degradation\[LetterSpace]K\[LetterSpace]dT + T2[t]), T2\[LetterSpace]to\[LetterSpace]T1 -> (Cell*T2\[LetterSpace]to\[LetterSpace]T1\[LetterSpace]V\[LetterSpace]4T*T2[t])/(T2\[LetterSpace]to\[LetterSpace]T1\[LetterSpace]K\[LetterSpace]4T + T2[t])
};

parameters = {
V\[LetterSpace]dT -> 2.0, V\[LetterSpace]mT -> 0.7, P1\[LetterSpace]to\[LetterSpace]P2\[LetterSpace]K\[LetterSpace]3P -> 2.0, P0\[LetterSpace]to\[LetterSpace]P1\[LetterSpace]K1\[LetterSpace]P -> 2.0, P0\[LetterSpace]to\[LetterSpace]P1\[LetterSpace]V\[LetterSpace]1P -> 8.0, T0\[LetterSpace]to\[LetterSpace]T1\[LetterSpace]K\[LetterSpace]1T -> 2.0, T0\[LetterSpace]to\[LetterSpace]T1\[LetterSpace]V\[LetterSpace]1T -> 8.0, P1\[LetterSpace]to\[LetterSpace]P0\[LetterSpace]K\[LetterSpace]2P -> 2.0, P1\[LetterSpace]to\[LetterSpace]P0\[LetterSpace]V\[LetterSpace]2P -> 1.0, T1\[LetterSpace]to\[LetterSpace]T0\[LetterSpace]K\[LetterSpace]2T -> 2.0, T1\[LetterSpace]to\[LetterSpace]T0\[LetterSpace]V\[LetterSpace]2T -> 1.0, P1\[LetterSpace]to\[LetterSpace]P2\[LetterSpace]V\[LetterSpace]3P -> 8.0, T1\[LetterSpace]to\[LetterSpace]T2\[LetterSpace]K\[LetterSpace]3T -> 2.0, T1\[LetterSpace]to\[LetterSpace]T2\[LetterSpace]V\[LetterSpace]3T -> 8.0, P2\[LetterSpace]to\[LetterSpace]P1\[LetterSpace]K\[LetterSpace]4P -> 2.0, P2\[LetterSpace]to\[LetterSpace]P1\[LetterSpace]V\[LetterSpace]4P -> 1.0, T2\[LetterSpace]to\[LetterSpace]T1\[LetterSpace]K\[LetterSpace]4T -> 2.0, T2\[LetterSpace]to\[LetterSpace]T1\[LetterSpace]V\[LetterSpace]4T -> 1.0, P0\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d -> 0.01, T0\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d -> 0.01, P1\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d -> 0.01, T1\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d -> 0.01, P2\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d -> 0.01, P2\[LetterSpace]degradation\[LetterSpace]V\[LetterSpace]dP -> 2.0, P2\[LetterSpace]degradation\[LetterSpace]K\[LetterSpace]dP -> 0.2, T2\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d -> 0.01, T2\[LetterSpace]degradation\[LetterSpace]K\[LetterSpace]dT -> 0.2, PT\[LetterSpace]complex\[LetterSpace]formation\[LetterSpace]k3 -> 1.2, PT\[LetterSpace]complex\[LetterSpace]formation\[LetterSpace]k4 -> 0.6, PT\[LetterSpace]complex\[LetterSpace]nucleation\[LetterSpace]k1 -> 0.6, PT\[LetterSpace]complex\[LetterSpace]nucleation\[LetterSpace]k2 -> 0.2, PT\[LetterSpace]complex\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]dC -> 0.01, PTnucl\[LetterSpace]complex\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]dN -> 0.01, Mp\[LetterSpace]production\[LetterSpace]v\[LetterSpace]sP -> 1.0, Mp\[LetterSpace]production\[LetterSpace]K\[LetterSpace]IP -> 1.0, Mp\[LetterSpace]production\[LetterSpace]n -> 4.0, Mt\[LetterSpace]production\[LetterSpace]V\[LetterSpace]sT -> 1.0, Mt\[LetterSpace]production\[LetterSpace]K\[LetterSpace]IT -> 1.0, Mt\[LetterSpace]production\[LetterSpace]n -> 4.0, P0\[LetterSpace]production\[LetterSpace]k\[LetterSpace]sP -> 0.9, T0\[LetterSpace]production\[LetterSpace]k\[LetterSpace]sT -> 0.9, Mp\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d -> 0.01, Mp\[LetterSpace]degradation\[LetterSpace]V\[LetterSpace]mP -> 0.7, Mp\[LetterSpace]degradation\[LetterSpace]K\[LetterSpace]mP -> 0.2, Mt\[LetterSpace]degradation\[LetterSpace]k\[LetterSpace]d -> 0.01, Mt\[LetterSpace]degradation\[LetterSpace]K\[LetterSpace]mT -> 0.2, Cell -> 1.0, compartment\[LetterSpace]0000002 -> 1.0
};

assignments = {
Tt -> CC[t] + Cn[t] + T0[t] + T1[t] + T2[t], Pt -> CC[t] + Cn[t] + P0[t] + P1[t] + P2[t]
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
CC'[t] == 1.0*PT\[LetterSpace]complex\[LetterSpace]formation -1.0*PT\[LetterSpace]complex\[LetterSpace]nucleation -1.0*PT\[LetterSpace]complex\[LetterSpace]degradation, Cn'[t] == 1.0*PT\[LetterSpace]complex\[LetterSpace]nucleation -1.0*PTnucl\[LetterSpace]complex\[LetterSpace]degradation, Mp'[t] == 1.0*Mp\[LetterSpace]production -1.0*Mp\[LetterSpace]degradation, Mt'[t] == 1.0*Mt\[LetterSpace]production -1.0*Mt\[LetterSpace]degradation, P0'[t] == 1.0*P1\[LetterSpace]to\[LetterSpace]P0 +1.0*P0\[LetterSpace]production -1.0*P0\[LetterSpace]to\[LetterSpace]P1 -1.0*P0\[LetterSpace]degradation, P1'[t] == 1.0*P0\[LetterSpace]to\[LetterSpace]P1 +1.0*P2\[LetterSpace]to\[LetterSpace]P1 -1.0*P1\[LetterSpace]to\[LetterSpace]P0 -1.0*P1\[LetterSpace]to\[LetterSpace]P2 -1.0*P1\[LetterSpace]degradation, P2'[t] == 1.0*P1\[LetterSpace]to\[LetterSpace]P2 -1.0*P2\[LetterSpace]to\[LetterSpace]P1 -1.0*P2\[LetterSpace]degradation -1.0*PT\[LetterSpace]complex\[LetterSpace]formation, T0'[t] == 1.0*T1\[LetterSpace]to\[LetterSpace]T0 +1.0*T0\[LetterSpace]production -1.0*T0\[LetterSpace]to\[LetterSpace]T1 -1.0*T0\[LetterSpace]degradation, T1'[t] == 1.0*T0\[LetterSpace]to\[LetterSpace]T1 +1.0*T2\[LetterSpace]to\[LetterSpace]T1 -1.0*T1\[LetterSpace]to\[LetterSpace]T0 -1.0*T1\[LetterSpace]to\[LetterSpace]T2 -1.0*T1\[LetterSpace]degradation, T2'[t] == 1.0*T1\[LetterSpace]to\[LetterSpace]T2 -1.0*T2\[LetterSpace]to\[LetterSpace]T1 -1.0*T2\[LetterSpace]degradation -1.0*PT\[LetterSpace]complex\[LetterSpace]formation
};
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]}]