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}, Rational{Int64}}(1//100, 10, 1//5, 1//5, false, true, 0//1), precs = DEFAULT_PRECS, smooth_est = true, extrapolant = linear, controller = PI, autodiff = ADTypes.AutoForwardDiff(),)

Comparisons

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

  2.559016 seconds (38.88 k allocations: 8.464 MiB)

retcode: Success
Interpolation: 3rd order Hermite
t: 4071-element Vector{Float64}:
      0.0
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      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)

  3.204666 seconds (38.89 k allocations: 8.466 MiB)

retcode: Success
Interpolation: 3rd order Hermite
t: 4072-element Vector{Float64}:
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      ⋮
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u: 4072-element Vector{Vector{Float64}}:
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 ⋮
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 [0.001764769136052643, 780.8305763558926, 781.1407513244295, 0.0065167190202318585, 0.9997170204585022, 0.9997189839270082, 0.0016307550440619464, 0.0025240432778757477, 0.0016305998246822003, 0.0012114327900504904  …  0.1334639037343722, 0.13346361208660248, 0.1334633215899144, 0.1334630321619589, 0.13346274372365063, 0.1334624561990075, 0.13346216951500056, -69.90008938888197, 13324.926015454601, 151468.84470879185]

ROS 0.5uM

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

  2.908386 seconds (40.72 k allocations: 8.490 MiB, 3.82% 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
 163268.15494025752
 169694.74223955238
 177941.12600875087
 186187.50977794937
 195845.6756684691
 205000.0
u: 4070-element Vector{Vector{Float64}}:
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 [0.002228995040224504, 829.7704141396295, 829.923524981244, 0.005926150085675958, 0.967155451223036, 0.2241256030327346, 0.09093422465365371, 0.0015688568862425737, 0.009873892913308362, 0.2610441780460306  …  0.12171274673876382, 0.12175152667167384, 0.12179171693004423, 0.12183318573340755, 0.12187579038290361, 0.12191937753328344, 0.12196378364408184, -71.35304509818098, 13838.18882346682, 150952.80529264064]
 ⋮
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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/github/actions-runner-2/_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/github/actions-runner-2/_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/github/actions-runner-2/_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/github/actions-runner-2/_work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/.cache/docs/ros-exp.png"

---

This notebook was generated using Literate.jl.