Doxorubicin addition test

Doxorubicin addition test#

using ProgressLogging
using OrdinaryDiffEq
using ModelingToolkit
using Plots
using DisplayAs: PNG
using ECMEDox
using ECMEDox: second, mM, Hz, μM, build_stim_callbacks
Plots.default(lw=1.5, size=(600, 600))

tend = 1000.0second
bcl = 1second
@named sys = build_model(; bcl=0, tend)
@unpack DOX = sys
sts = unknowns(sys)
u0 = build_u0(sys)
alg = KenCarp47()
stim = build_stim_callbacks(sys.iStim, tend)
opts = (; reltol=1e-6, abstol=1e-6, progress=true, callback=stim)
prob = ODEProblem(sys, u0, tend)

ODEProblem with uType Vector{Float64} and tType Float64. In-place: true
Initialization status: FULLY_DETERMINED
Non-trivial mass matrix: false
timespan: (0.0, 1.0e6)
u0: 63-element Vector{Float64}:
      0.2035581785037846
    162.56309672844773
    532.1996659605478
     14.943572782390564
     48.69968107803388
      0.9117090226602712
      0.1940860288439055
   1205.7933694003293
   1209.9516385500046
 144752.08717647262
      ⋮
     98.34143985940155
     98.37940028159827
   1834.4350814204734
    133.6477723249107
      0.7232603119926468
     16.99573535574641
      0.8261803348922151
      0.0002891017177402435
      0.0003791207507588391

The collapse of MMP is between 290uM and 300uM of DOX

doxrange = 290μM:1μM:300μM
prob_func = (prob, i, repeat) -> begin
    prob.ps[DOX] = doxrange[i]
    prob
end

eprob = EnsembleProblem(prob; prob_func)
@time sim = solve(eprob, alg; trajectories=length(doxrange), opts...)

431.011003 seconds (57.61 M allocations: 9.657 GiB, 2.45% gc time, 4.97% compilation time)

EnsembleSolution Solution of length 11 with uType:
SciMLBase.ODESolution{Float64, 2, Vector{Vector{Float64}}, Nothing, Nothing, Vector{Float64}, Vector{Vector{Vector{Float64}}}, Nothing, SciMLBase.ODEProblem{Vector{Float64}, Tuple{Float64, Float64}, true, ModelingToolkit.MTKParameters{Vector{Float64}, Vector{Float64}, Tuple{}, Tuple{}, Tuple{}, Tuple{}}, SciMLBase.ODEFunction{true, SciMLBase.FullSpecialize, ModelingToolkit.GeneratedFunctionWrapper{(2, 3, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xaf19012e, 0xa760132a, 0x823e8610, 0x6ddfdc3f, 0x307103c8), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xf7101ef8, 0x133d1eac, 0x4186cb75, 0xa77c647c, 0xb12179b3), Nothing}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, ModelingToolkit.ObservedFunctionCache{ModelingToolkit.System}, Nothing, ModelingToolkit.System, SciMLBase.OverrideInitData{SciMLBase.NonlinearProblem{Nothing, true, ModelingToolkit.MTKParameters{Vector{Float64}, StaticArraysCore.SizedVector{0, Float64, Vector{Float64}}, Tuple{}, Tuple{}, Tuple{}, Tuple{}}, SciMLBase.NonlinearFunction{true, SciMLBase.FullSpecialize, ModelingToolkit.GeneratedFunctionWrapper{(2, 2, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x9a1dc1ad, 0x71defabe, 0x857c130d, 0xdfc20b1f, 0x2cf6f9a1), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x00797acb, 0x0db5e856, 0xa0aff6bc, 0xf6b12faf, 0xd9a97c31), Nothing}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, ModelingToolkit.ObservedFunctionCache{ModelingToolkit.System}, Nothing, ModelingToolkit.System, Nothing, Nothing}, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}, SciMLBase.StandardNonlinearProblem}, typeof(ModelingToolkit.update_initializeprob!), ComposedFunction{ComposedFunction{typeof(identity), typeof(ModelingToolkit.safe_float)}, SymbolicIndexingInterface.TimeIndependentObservedFunction{ModelingToolkit.GeneratedFunctionWrapper{(2, 2, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xb46c05cd, 0xa2d342ca, 0xfea8c69e, 0x86cb029c, 0xc44d325c), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x2fc0fa4a, 0xf466d035, 0x68eb4d0d, 0x0fde0448, 0x6784c992), Nothing}}}}, ModelingToolkit.var"#initprobpmap_split#900"{ModelingToolkit.var"#_getter#896"{Tuple{ComposedFunction{ModelingToolkit.PConstructorApplicator{typeof(identity)}, ModelingToolkit.ObservedWrapper{false, ModelingToolkit.GeneratedFunctionWrapper{(2, 2, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x55eb9521, 0x89126b0c, 0xec15c9e8, 0x0890e042, 0xadbd7ad2), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x3a182261, 0x73509c17, 0xf1f3e876, 0x832aa98d, 0xd4bbeb10), Nothing}}}}, ComposedFunction{ModelingToolkit.PConstructorApplicator{typeof(identity)}, ModelingToolkit.ObservedWrapper{false, ModelingToolkit.GeneratedFunctionWrapper{(2, 2, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x940a1314, 0x9e62ccde, 0x07140ed0, 0x0b66b4d1, 0x6eb512fa), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x4e2cf4f6, 0x3de85f3a, 0xfd427d96, 0x2a4331c7, 0xde99d64b), Nothing}}}}, Returns{Tuple{}}, Returns{Tuple{}}, Returns{Tuple{}}}}}, ModelingToolkit.InitializationMetadata{ModelingToolkit.ReconstructInitializeprob{ModelingToolkit.var"#_getter#896"{Tuple{ComposedFunction{ModelingToolkit.PConstructorApplicator{typeof(identity)}, ModelingToolkit.ObservedWrapper{true, ModelingToolkit.GeneratedFunctionWrapper{(2, 3, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xffb583da, 0x1b5feb97, 0xf94a7924, 0x3d7ce483, 0x3a53ae04), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x0e47c3ee, 0x9e723e14, 0xba0d90c3, 0x43cf84d1, 0xcdb9c002), Nothing}}}}, Returns{StaticArraysCore.SizedVector{0, Float64, Vector{Float64}}}, Returns{Tuple{}}, Returns{Tuple{}}, Returns{Tuple{}}}}, ComposedFunction{typeof(identity), SymbolicIndexingInterface.MultipleGetters{SymbolicIndexingInterface.ContinuousTimeseries, Vector{Any}}}}, ModelingToolkit.GetUpdatedU0{SymbolicIndexingInterface.MultipleGetters{SymbolicIndexingInterface.ContinuousTimeseries, Vector{SymbolicUtils.BasicSymbolic{Real}}}, SymbolicIndexingInterface.MultipleParametersGetter{SymbolicIndexingInterface.IndexerNotTimeseries, Vector{SymbolicIndexingInterface.GetParameterIndex{ModelingToolkit.ParameterIndex{SciMLStructures.Initials, Int64}}}, Nothing}}, ModelingToolkit.SetInitialUnknowns{SymbolicIndexingInterface.MultipleSetters{Vector{SymbolicIndexingInterface.ParameterHookWrapper{SymbolicIndexingInterface.SetParameterIndex{ModelingToolkit.ParameterIndex{SciMLStructures.Initials, Int64}}, SymbolicUtils.BasicSymbolic{Real}}}}}}, Val{true}}, Nothing}, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}, SciMLBase.StandardODEProblem}, OrdinaryDiffEqSDIRK.KenCarp47{0, ADTypes.AutoForwardDiff{nothing, ForwardDiff.Tag{DiffEqBase.OrdinaryDiffEqTag, Float64}}, Nothing, OrdinaryDiffEqNonlinearSolve.NLNewton{Rational{Int64}, Rational{Int64}, Rational{Int64}, Nothing}, typeof(OrdinaryDiffEqCore.DEFAULT_PRECS), Val{:forward}(), true, nothing}, OrdinaryDiffEqCore.InterpolationData{SciMLBase.ODEFunction{true, SciMLBase.FullSpecialize, ModelingToolkit.GeneratedFunctionWrapper{(2, 3, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xaf19012e, 0xa760132a, 0x823e8610, 0x6ddfdc3f, 0x307103c8), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xf7101ef8, 0x133d1eac, 0x4186cb75, 0xa77c647c, 0xb12179b3), Nothing}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, ModelingToolkit.ObservedFunctionCache{ModelingToolkit.System}, Nothing, ModelingToolkit.System, SciMLBase.OverrideInitData{SciMLBase.NonlinearProblem{Nothing, true, ModelingToolkit.MTKParameters{Vector{Float64}, StaticArraysCore.SizedVector{0, Float64, Vector{Float64}}, Tuple{}, Tuple{}, Tuple{}, Tuple{}}, SciMLBase.NonlinearFunction{true, SciMLBase.FullSpecialize, ModelingToolkit.GeneratedFunctionWrapper{(2, 2, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x9a1dc1ad, 0x71defabe, 0x857c130d, 0xdfc20b1f, 0x2cf6f9a1), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x00797acb, 0x0db5e856, 0xa0aff6bc, 0xf6b12faf, 0xd9a97c31), Nothing}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, ModelingToolkit.ObservedFunctionCache{ModelingToolkit.System}, Nothing, ModelingToolkit.System, Nothing, Nothing}, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}, SciMLBase.StandardNonlinearProblem}, typeof(ModelingToolkit.update_initializeprob!), ComposedFunction{ComposedFunction{typeof(identity), typeof(ModelingToolkit.safe_float)}, SymbolicIndexingInterface.TimeIndependentObservedFunction{ModelingToolkit.GeneratedFunctionWrapper{(2, 2, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xb46c05cd, 0xa2d342ca, 0xfea8c69e, 0x86cb029c, 0xc44d325c), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x2fc0fa4a, 0xf466d035, 0x68eb4d0d, 0x0fde0448, 0x6784c992), Nothing}}}}, ModelingToolkit.var"#initprobpmap_split#900"{ModelingToolkit.var"#_getter#896"{Tuple{ComposedFunction{ModelingToolkit.PConstructorApplicator{typeof(identity)}, ModelingToolkit.ObservedWrapper{false, ModelingToolkit.GeneratedFunctionWrapper{(2, 2, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x55eb9521, 0x89126b0c, 0xec15c9e8, 0x0890e042, 0xadbd7ad2), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x3a182261, 0x73509c17, 0xf1f3e876, 0x832aa98d, 0xd4bbeb10), Nothing}}}}, ComposedFunction{ModelingToolkit.PConstructorApplicator{typeof(identity)}, ModelingToolkit.ObservedWrapper{false, ModelingToolkit.GeneratedFunctionWrapper{(2, 2, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x940a1314, 0x9e62ccde, 0x07140ed0, 0x0b66b4d1, 0x6eb512fa), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x4e2cf4f6, 0x3de85f3a, 0xfd427d96, 0x2a4331c7, 0xde99d64b), Nothing}}}}, Returns{Tuple{}}, Returns{Tuple{}}, Returns{Tuple{}}}}}, ModelingToolkit.InitializationMetadata{ModelingToolkit.ReconstructInitializeprob{ModelingToolkit.var"#_getter#896"{Tuple{ComposedFunction{ModelingToolkit.PConstructorApplicator{typeof(identity)}, ModelingToolkit.ObservedWrapper{true, ModelingToolkit.GeneratedFunctionWrapper{(2, 3, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xffb583da, 0x1b5feb97, 0xf94a7924, 0x3d7ce483, 0x3a53ae04), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x0e47c3ee, 0x9e723e14, 0xba0d90c3, 0x43cf84d1, 0xcdb9c002), Nothing}}}}, Returns{StaticArraysCore.SizedVector{0, Float64, Vector{Float64}}}, Returns{Tuple{}}, Returns{Tuple{}}, Returns{Tuple{}}}}, ComposedFunction{typeof(identity), SymbolicIndexingInterface.MultipleGetters{SymbolicIndexingInterface.ContinuousTimeseries, Vector{Any}}}}, ModelingToolkit.GetUpdatedU0{SymbolicIndexingInterface.MultipleGetters{SymbolicIndexingInterface.ContinuousTimeseries, Vector{SymbolicUtils.BasicSymbolic{Real}}}, SymbolicIndexingInterface.MultipleParametersGetter{SymbolicIndexingInterface.IndexerNotTimeseries, Vector{SymbolicIndexingInterface.GetParameterIndex{ModelingToolkit.ParameterIndex{SciMLStructures.Initials, Int64}}}, Nothing}}, ModelingToolkit.SetInitialUnknowns{SymbolicIndexingInterface.MultipleSetters{Vector{SymbolicIndexingInterface.ParameterHookWrapper{SymbolicIndexingInterface.SetParameterIndex{ModelingToolkit.ParameterIndex{SciMLStructures.Initials, Int64}}, SymbolicUtils.BasicSymbolic{Real}}}}}}, Val{true}}, Nothing}, Vector{Vector{Float64}}, Vector{Float64}, Vector{Vector{Vector{Float64}}}, Nothing, cacheType, Nothing}, SciMLBase.DEStats, Nothing, Nothing, Nothing, Nothing} where cacheType<:(OrdinaryDiffEqSDIRK.KenCarp47Cache{Vector{Float64}, Vector{Float64}, Vector{Float64}, N, OrdinaryDiffEqSDIRK.KenCarp47Tableau{Float64, Float64}, Nothing} where N<:(OrdinaryDiffEqNonlinearSolve.NLSolver{OrdinaryDiffEqNonlinearSolve.NLNewton{Rational{Int64}, Rational{Int64}, Rational{Int64}, Nothing}, true, Vector{Float64}, Float64, Nothing, Float64, OrdinaryDiffEqNonlinearSolve.NLNewtonCache{Vector{Float64}, Float64, Float64, Vector{Float64}, Matrix{Float64}, Matrix{Float64}, SciMLBase.UJacobianWrapper{true, SciMLBase.ODEFunction{true, SciMLBase.FullSpecialize, ModelingToolkit.GeneratedFunctionWrapper{(2, 3, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xaf19012e, 0xa760132a, 0x823e8610, 0x6ddfdc3f, 0x307103c8), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xf7101ef8, 0x133d1eac, 0x4186cb75, 0xa77c647c, 0xb12179b3), Nothing}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, ModelingToolkit.ObservedFunctionCache{ModelingToolkit.System}, Nothing, ModelingToolkit.System, SciMLBase.OverrideInitData{SciMLBase.NonlinearProblem{Nothing, true, ModelingToolkit.MTKParameters{Vector{Float64}, StaticArraysCore.SizedVector{0, Float64, Vector{Float64}}, Tuple{}, Tuple{}, Tuple{}, Tuple{}}, SciMLBase.NonlinearFunction{true, SciMLBase.FullSpecialize, ModelingToolkit.GeneratedFunctionWrapper{(2, 2, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x9a1dc1ad, 0x71defabe, 0x857c130d, 0xdfc20b1f, 0x2cf6f9a1), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x00797acb, 0x0db5e856, 0xa0aff6bc, 0xf6b12faf, 0xd9a97c31), Nothing}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, ModelingToolkit.ObservedFunctionCache{ModelingToolkit.System}, Nothing, ModelingToolkit.System, Nothing, Nothing}, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}, SciMLBase.StandardNonlinearProblem}, typeof(ModelingToolkit.update_initializeprob!), ComposedFunction{ComposedFunction{typeof(identity), typeof(ModelingToolkit.safe_float)}, SymbolicIndexingInterface.TimeIndependentObservedFunction{ModelingToolkit.GeneratedFunctionWrapper{(2, 2, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xb46c05cd, 0xa2d342ca, 0xfea8c69e, 0x86cb029c, 0xc44d325c), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x2fc0fa4a, 0xf466d035, 0x68eb4d0d, 0x0fde0448, 0x6784c992), Nothing}}}}, ModelingToolkit.var"#initprobpmap_split#900"{ModelingToolkit.var"#_getter#896"{Tuple{ComposedFunction{ModelingToolkit.PConstructorApplicator{typeof(identity)}, ModelingToolkit.ObservedWrapper{false, ModelingToolkit.GeneratedFunctionWrapper{(2, 2, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x55eb9521, 0x89126b0c, 0xec15c9e8, 0x0890e042, 0xadbd7ad2), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x3a182261, 0x73509c17, 0xf1f3e876, 0x832aa98d, 0xd4bbeb10), Nothing}}}}, ComposedFunction{ModelingToolkit.PConstructorApplicator{typeof(identity)}, ModelingToolkit.ObservedWrapper{false, ModelingToolkit.GeneratedFunctionWrapper{(2, 2, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x940a1314, 0x9e62ccde, 0x07140ed0, 0x0b66b4d1, 0x6eb512fa), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x4e2cf4f6, 0x3de85f3a, 0xfd427d96, 0x2a4331c7, 0xde99d64b), Nothing}}}}, Returns{Tuple{}}, Returns{Tuple{}}, Returns{Tuple{}}}}}, ModelingToolkit.InitializationMetadata{ModelingToolkit.ReconstructInitializeprob{ModelingToolkit.var"#_getter#896"{Tuple{ComposedFunction{ModelingToolkit.PConstructorApplicator{typeof(identity)}, ModelingToolkit.ObservedWrapper{true, ModelingToolkit.GeneratedFunctionWrapper{(2, 3, true), RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:__mtk_arg_1, :___mtkparameters___, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0xffb583da, 0x1b5feb97, 0xf94a7924, 0x3d7ce483, 0x3a53ae04), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :__mtk_arg_1, :___mtkparameters___, :t), ModelingToolkit.var"#_RGF_ModTag", ModelingToolkit.var"#_RGF_ModTag", (0x0e47c3ee, 0x9e723e14, 0xba0d90c3, 0x43cf84d1, 0xcdb9c002), Nothing}}}}, Returns{StaticArraysCore.SizedVector{0, Float64, Vector{Float64}}}, Returns{Tuple{}}, Returns{Tuple{}}, Returns{Tuple{}}}}, ComposedFunction{typeof(identity), SymbolicIndexingInterface.MultipleGetters{SymbolicIndexingInterface.ContinuousTimeseries, Vector{Any}}}}, ModelingToolkit.GetUpdatedU0{SymbolicIndexingInterface.MultipleGetters{SymbolicIndexingInterface.ContinuousTimeseries, Vector{SymbolicUtils.BasicSymbolic{Real}}}, SymbolicIndexingInterface.MultipleParametersGetter{SymbolicIndexingInterface.IndexerNotTimeseries, Vector{SymbolicIndexingInterface.GetParameterIndex{ModelingToolkit.ParameterIndex{SciMLStructures.Initials, Int64}}}, Nothing}}, ModelingToolkit.SetInitialUnknowns{SymbolicIndexingInterface.MultipleSetters{Vector{SymbolicIndexingInterface.ParameterHookWrapper{SymbolicIndexingInterface.SetParameterIndex{ModelingToolkit.ParameterIndex{SciMLStructures.Initials, Int64}}, SymbolicUtils.BasicSymbolic{Real}}}}}}, Val{true}}, Nothing}, Float64, ModelingToolkit.MTKParameters{Vector{Float64}, Vector{Float64}, Tuple{}, Tuple{}, Tuple{}, Tuple{}}}, jcType, LinearSolve.LinearCache{Matrix{Float64}, Vector{Float64}, Vector{Float64}, SciMLBase.NullParameters, LinearSolve.DefaultLinearSolver, LinearSolve.DefaultLinearSolverInit{LinearAlgebra.LU{Float64, Matrix{Float64}, Vector{Int64}}, LinearAlgebra.QRCompactWY{Float64, Matrix{Float64}, Matrix{Float64}}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Tuple{LinearAlgebra.LU{Float64, Matrix{Float64}, Vector{Int64}}, Vector{Int64}}, Tuple{LinearAlgebra.LU{Float64, Matrix{Float64}, Vector{Int64}}, Vector{Int64}}, Nothing, Nothing, Nothing, LinearAlgebra.SVD{Float64, Float64, Matrix{Float64}, Vector{Float64}}, LinearAlgebra.Cholesky{Float64, Matrix{Float64}}, LinearAlgebra.Cholesky{Float64, Matrix{Float64}}, Tuple{LinearAlgebra.LU{Float64, Matrix{Float64}, Vector{Int32}}, Base.RefValue{Int32}}, Tuple{LinearAlgebra.LU{Float64, Matrix{Float64}, Vector{Int64}}, Base.RefValue{Int64}}, LinearAlgebra.QRPivoted{Float64, Matrix{Float64}, Vector{Float64}, Vector{Int64}}, Nothing, Nothing}, LinearSolve.InvPreconditioner{LinearAlgebra.Diagonal{Float64, Vector{Float64}}}, LinearAlgebra.Diagonal{Float64, Vector{Float64}}, Float64, Bool, LinearSolve.LinearSolveAdjoint{Missing}}}, Float64} where jcType<:Tuple{DifferentiationInterfaceForwardDiffExt.ForwardDiffTwoArgJacobianPrep{Nothing, C, Tuple{}} where C<:(ForwardDiff.JacobianConfig{ForwardDiff.Tag{DiffEqBase.OrdinaryDiffEqTag, Float64}, Float64, _A, <:Tuple{Array{ForwardDiff.Dual{ForwardDiff.Tag{DiffEqBase.OrdinaryDiffEqTag, Float64}, Float64, _A}, 1} where _A, Array{ForwardDiff.Dual{ForwardDiff.Tag{DiffEqBase.OrdinaryDiffEqTag, Float64}, Float64, _A}, 1} where _A}} where _A), DifferentiationInterfaceForwardDiffExt.ForwardDiffTwoArgJacobianPrep{Nothing, C, Tuple{}} where C<:(ForwardDiff.JacobianConfig{ForwardDiff.Tag{DiffEqBase.OrdinaryDiffEqTag, Float64}, Float64, _A, <:Tuple{Array{ForwardDiff.Dual{ForwardDiff.Tag{DiffEqBase.OrdinaryDiffEqTag, Float64}, Float64, _A}, 1} where _A, Array{ForwardDiff.Dual{ForwardDiff.Tag{DiffEqBase.OrdinaryDiffEqTag, Float64}, Float64, _A}, 1} where _A}} where _A)}))

fig = plot(title="MMP")
for (i, dox) in enumerate(doxrange)
    plot!(fig, sim[i], idxs=(sys.t/1000, sys.dpsi), lab="DOX = $(dox) μM")
end
plot!(fig, ylabel="mV", xlabel="Time (s)") |> PNG
_images/52bc374bd8580ee0d14ff76dad17eac57a222f1a77deedd852d3fa1d545647c9.png 
fig = plot(title="ATP")
for (i, dox) in enumerate(doxrange)
    plot!(fig, sim[i], idxs=(sys.t/1000, sys.atp_i), lab="DOX = $(dox) μM")
end
plot!(fig, ylabel="Conc. (μM)", xlabel="Time (s)", legend=:bottomright, ylim=(0, 8mM)) |> PNG
_images/db6914345bd1db11b9a149fb38917c3fd753c2dc0b526a0beed7a973ac855836.png 
fig = plot(title="Cytosolic superoxide")
for (i, dox) in enumerate(doxrange)
    plot!(fig, sim[i], idxs=(sys.t/1000, sys.sox_i), lab="DOX = $(dox) μM")
end
plot!(fig, ylabel="Conc. (μM)", xlabel="Time (s)", legend=:right) |> PNG
_images/345012532523aeb6c29537439e26a1d7573c942f86b8938dded6ea34829f3298.png 
fig = plot(title="Mitochondrial superoxide")
for (i, dox) in enumerate(doxrange)
    plot!(fig, sim[i], idxs=(sys.t/1000, sys.sox_m), lab="DOX = $(dox) μM")
end
plot!(fig, ylabel="Conc. (μM)", xlabel="Time (s)", legend=:topright) |> PNG
_images/98f415412d238798d73edcb1d7ce34bf7d0e0c652832abe0f0be5ff2c14069b9.png 
fig = plot(title="Superoxide production")
for (i, dox) in enumerate(doxrange)
    plot!(fig, sim[i], idxs=(sys.t/1000, sys.vROS), lab="DOX = $(dox) μM")
end
plot!(fig, ylabel="Rate (μM/ms)", xlabel="Time (s)", legend=:right) |> PNG
_images/a41d0969fa2b0e7e8f6bfd1049a99b289859ab8c77467500d2e50641f098dd0d.png 
fig = plot(title="O2 shunt")
for (i, dox) in enumerate(doxrange)
    plot!(fig, sim[i], idxs=(sys.t/1000, 100*sys.vROS / (sys.vO2 + sys.vROS)), lab="DOX = $(dox) μM")
end
plot!(fig, ylabel="Percentage (%)", xlabel="Time (s)", legend=:right) |> PNG
_images/b4bd72cee0e0ed1837f9b02dc39c9a73af9c21253039d21a82cd57cff3404b4c.png 
@unpack Q_n, SQn, QH2_n, QH2_p, Q_p, fes_ox, fes_rd, cytc_ox, cytc_rd = sys
plot(sim[end], idxs=[Q_n + Q_p, SQn, QH2_n+QH2_p], title="Q cycle ", legend=:right) |> PNG
_images/cc86876137d98d60c524428b21de301d3e3f443abfcf6e1f3ab989daddf141fa.png 
plot(sim[end], idxs=[fes_ox, fes_rd, cytc_ox, cytc_rd], title="Q cycle (downstream)", legend=:right) |> PNG
_images/51ed75b7069d38cfd2ce2e1d705a56bcebf191283dbd55446047180b3986cb6a.png 
@unpack cit, isoc, oaa, akg, scoa, suc, fum, mal, nadh_m = sys
plot(sim[end], idxs=[cit, isoc, oaa, akg, scoa, suc, fum, mal, nadh_m], title="TCA cycle ", legend=:right) |> PNG
_images/3ac148e22506715e9247b4c039a3f29c971514e203b57744e9836e2794a7c83b.png

This notebook was generated using Literate.jl.