ROS effects

using ModelingToolkit
using OrdinaryDiffEq, DiffEqCallbacks
using Plots
using CSV
using DataFrames
using Dates
using CaMKIIModel
using CaMKIIModel: second, μM
Plots.default(lw=1.5)

Setup model

sys = build_neonatal_ecc_sys(simplify=true, reduce_iso=true, reduce_camk=true)
tend = 205second
prob = ODEProblem(sys, [], tend)
stimstart = 30second
stimend = 120second
@unpack Istim = sys
callback = build_stim_callbacks(Istim, stimend; period=1second, starttime=stimstart)
alg = KenCarp47()

KenCarp47(; linsolve = nothing, nlsolve = OrdinaryDiffEqNonlinearSolve.NLNewton{Rational{Int64}, Rational{Int64}, Rational{Int64}, Nothing}(1//100, 10, 1//5, 1//5, false, true, nothing), precs = DEFAULT_PRECS, smooth_est = true, extrapolant = linear, controller = PI, autodiff = ADTypes.AutoForwardDiff(),)

Comparisons

@time sol = solve(prob, alg; callback)

  4.506558 seconds (4.76 M allocations: 461.088 MiB, 2.06% gc time, 80.73% compilation time)

retcode: Success
Interpolation: 3rd order Hermite
t: 4071-element Vector{Float64}:
      0.0
      0.019333123284849308
      0.09098129546757994
      0.20735582943983855
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      1.0472562928406122
      2.0342667657223696
      3.451776641148454
      6.733792423912806
     12.450117081023194
      ⋮
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 191258.90946281631
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u: 4071-element Vector{Vector{Float64}}:
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 ⋮
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ROS 0.1uM

prob2 = remake(prob, p=[sys.ROS => 0.1μM])
@time sol2 = solve(prob2, alg; callback)

  1.399586 seconds (63.57 k allocations: 215.081 MiB, 7.71% gc time)

retcode: Success
Interpolation: 3rd order Hermite
t: 4072-element Vector{Float64}:
      0.0
      0.019333123284849367
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     12.45011708102323
      ⋮
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u: 4072-element Vector{Vector{Float64}}:
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 ⋮
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 [0.13347264327070307, 0.13347227063632128, 0.13347190362839487, 0.13347154195013364, 0.13347118532079197, 0.1334708334745993, 0.1334704861597746, 0.1334701431376185, 0.1334698041816744, 0.13346946907695378  …  1.0028808944338115, 0.6570225846036165, 0.0016307550440619785, 0.006516719020231025, 0.9997170204585021, 0.999718983927008, 0.20108876988276675, 151468.84470879182, 13324.926015454703, -69.90008938888379]

ROS 0.5uM

prob3 = remake(prob, p=[sys.ROS => 0.5μM])
@time sol3 = solve(prob3, alg; callback)

  0.880758 seconds (63.27 k allocations: 214.945 MiB, 6.51% gc time)

retcode: Success
Interpolation: 3rd order Hermite
t: 4070-element Vector{Float64}:
      0.0
      0.01933312328485172
      0.09098129546759129
      0.20735582943986441
      0.4561191027686822
      1.047256292840743
      2.0342667657226237
      3.451776641148885
      6.7337924239136475
     12.45011708102475
      ⋮
 148407.71053766683
 152963.08286658817
 157518.4551955095
 163268.1543188535
 169694.74092358912
 177941.12476481107
 186187.50860603302
 195845.675555337
 205000.0
u: 4070-element Vector{Vector{Float64}}:
 [0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113  …  0.9911, 0.61179, 0.09243, 0.00702, 0.966, 0.22156, 0.07192, 150952.75035000002, 13838.37602, -68.79268]
 [0.12112999999999999, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113  …  0.9911240298625772, 0.61179209692054, 0.09242766669618695, 0.007020208561323646, 0.9660018276402699, 0.2215639938807744, 0.07192100954852718, 150952.7504077194, 13838.375711519551, -68.79732946186226]
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 [0.1212995420290433, 0.1212778346866677, 0.12125890403747791, 0.1212425879351912, 0.12122873583441053, 0.12121721111566236, 0.12120789316717223, 0.12120067917599113, 0.12119548558727027, 0.12119224919647789  …  0.9971828595843293, 0.6201838932607651, 0.09161908329520757, 0.006355039713677761, 0.966628695781256, 0.22294828828976596, 0.07235305497134369, 150952.77598869594, 13838.2694938995, -70.35063788657448]
 [0.12145539710275362, 0.12143259661681072, 0.12141268299068811, 0.12139558631643761, 0.12138124198529934, 0.12136959056512993, 0.12136057763401649, 0.12135415355743055, 0.12135027319843647, 0.12134889555279485  …  0.9999327439121078, 0.6347673874618583, 0.09093422465365371, 0.005926150085675952, 0.967155451223036, 0.2241256030327346, 0.07284451729172246, 150952.80529264064, 13838.18882346682, -71.35304509818098]
 ⋮
 [0.13720912006533661, 0.13720991949051364, 0.13721069360180985, 0.13721144338253188, 0.13721216976279407, 0.13721287362306409, 0.13721355579742928, 0.1372142170766076, 0.13721485821072757, 0.13721547991189703  …  1.002672123678413, 0.678970311006764, 0.0014970539272432604, 0.0062588238933868855, 0.9997510563304199, 0.9992129260155501, 0.21677364954534015, 151153.32454080152, 13639.748604866636, -70.49393530669364]
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 [0.13627821790136063, 0.136277940846014, 0.13627766583705736, 0.1362773927104613, 0.13627712131106193, 0.13627685149197, 0.13627658311402632, 0.13627631604530002, 0.1362760501606249, 0.13627578534117163  …  1.00272552382619, 0.6726410744516013, 0.00153510205334041, 0.006333010877620564, 0.9997415509465565, 0.9997331350294371, 0.2120440151253054, 151244.14744399584, 13548.997291471083, -70.32065303692771]
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 [0.135227197085615, 0.13522681671395925, 0.1352264414250984, 0.13522607093386743, 0.13522570497051756, 0.1352253432796896, 0.13522498561946628, 0.1352246317605, 0.13522428148520674, 0.13522393458702192  …  1.0027840515385484, 0.6669278540971403, 0.0015697104260778518, 0.00640009917728788, 0.999732767644386, 0.9997345875789514, 0.2079517132762076, 151328.02088514855, 13465.34318461949, -70.16567912133848]
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 [0.1340359830559549, 0.13403560322338637, 0.13403522896530004, 0.1340348599834776, 0.13403449599582318, 0.13403413673528866, 0.13403378194888374, 0.13403343139676296, 0.13403308485138318, 0.13403274209672494  …  1.0028498893265507, 0.6602905482319706, 0.001610460937189975, 0.006478196508340264, 0.9997222906492309, 0.999724274568144, 0.20332321844986462, 151423.11463258122, 13370.522161909283, -69.98729455452413]
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Comparisons

i = (sys.t / 1000, sys.CaMKAct * 100)
plot(sol, idxs=i, lab="ROS (-)")
plot!(sol2, idxs=i, lab="ROS 0.1uM")
plot!(sol3, idxs=i, lab="ROS 0.5uM")
plot!(xlabel="Time (s)", ylabel="Active fraction (%)", title="Simulation")

savefig("ros-camkii.pdf")
savefig("ros-camkii.png")

"/home/runner/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/.cache/docs/ros-camkii.png"

Oxidized fraction

i = (sys.t / 1000, 100 * (sys.CaMKBOX + sys.CaMKPOX + sys.CaMKAOX + sys.CaMKOX ))
plot(sol, idxs=i, lab="ROS (-)")
plot!(sol2, idxs=i, lab="ROS 0.1uM")
plot!(sol3, idxs=i, lab="ROS 0.5uM")
plot!(xlabel="Time (s)", ylabel="Oxidized fraction (%)", title="Simulation")

savefig("ros-camkiiox.pdf")
savefig("ros-camkiiox.png")

"/home/runner/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/.cache/docs/ros-camkiiox.png"

Autophosphorylated fraction

i = (sys.t / 1000, 100 * (sys.CaMKP + sys.CaMKA + sys.CaMKA2))
plot(sol, idxs=i, lab="ROS (-)")
plot!(sol2, idxs=i, lab="ROS 0.1uM")
plot!(sol3, idxs=i, lab="ROS 0.5uM")
plot!(xlabel="Time (s)", ylabel="Phosphorylated fraction (%)", title="Simulation")

savefig("ros-camkiip.pdf")
savefig("ros-camkiip.png")

"/home/runner/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/.cache/docs/ros-camkiip.png"

Experimental data

chemicaldf = CSV.read(joinpath(@__DIR__, "data/CaMKAR-chemical.csv"), DataFrame)
ts = Dates.value.(chemicaldf[!, "Time"]) ./ 10^9
ctl = chemicaldf[!, "Ctrl Mean"]
ctl_error = chemicaldf[!, "Ctrl SD"] ./ sqrt.(chemicaldf[!, "Ctrl N"])

ros50 = chemicaldf[!, "H2O2 50uM Mean"]
ros50_error = chemicaldf[!, "H2O2 50uM SD"] ./ sqrt.(chemicaldf[!, "H2O2 50uM N"])
ros200 = chemicaldf[!, "H2O2 200uM Mean"]
ros200_error = chemicaldf[!, "H2O2 200uM SD"] ./ sqrt.(chemicaldf[!, "H2O2 200uM N"])

plot(ts, ctl, yerr=ctl_error, lab="Control", color=:blue, markerstrokecolor=:blue)
plot!(ts, ros50, yerr=ros50_error, lab="H2O2 50uM", color=:red, markerstrokecolor=:red)
plot!(ts, ros200, yerr=ros200_error, lab="H2O2 200uM", color=:green, markerstrokecolor=:green)
plot!(xlabel="Time (s)", ylabel="CaMKII activity (A.U.)", title="Experiment")

savefig("ros-exp.pdf")
savefig("ros-exp.png")

"/home/runner/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/.cache/docs/ros-exp.png"

---

This notebook was generated using Literate.jl.