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)
0.718820 seconds (40.85 k allocations: 9.849 MiB)
retcode: Success
Interpolation: 3rd order Hermite
t: 4071-element Vector{Float64}:
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3.451776641148454
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⋮
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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)
0.722934 seconds (40.86 k allocations: 9.851 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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[151468.8447087918, 13324.926015454625, -69.90008938888471, 0.1334621695149899, 0.13346245619899683, 0.13346274372363987, 0.1334630321619481, 0.13346332158990354, 0.1334636120865917, 0.13346390373436137 … 0.0012114327900542181, 0.0016305998246802294, 0.002524043277874933, 0.001630755044061683, 0.9997189839270083, 0.9997170204585021, 0.006516719020230605, 781.1407513244196, 780.8305763558827, 0.001764769136052052]
ROS 0.5uM
prob3 = remake(prob, p=[sys.ROS => 0.5μM])
@time sol3 = solve(prob3, alg; callback)
0.737171 seconds (40.85 k allocations: 9.850 MiB)
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
195845.67664289946
205000.0
u: 4070-element Vector{Vector{Float64}}:
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⋮
[151153.32454080152, 13639.74860486667, -70.4939353066943, 0.1372259364390038, 0.1372256354237224, 0.1372253249405459, 0.1372250047480518, 0.13722467459502546, 0.13722433421996044, 0.1372239833505281 … 0.0011047375624288485, 0.0015601763447898012, 0.0024150840865671745, 0.0014970539272432578, 0.99921292601555, 0.99975105633042, 0.006258823893386615, 784.3009800191994, 783.9341478970665, 0.0020427963561337474]
[151181.82102815833, 13611.229537457637, -70.4375201658915, 0.13698081196259732, 0.13698083013879692, 0.13698084375477984, 0.13698085272639532, 0.1369808569660735, 0.13698085638265087, 0.1369808508811849 … 0.001114601014499355, 0.0015667421524987377, 0.002425231738647423, 0.0015093993782630463, 0.9995887201790881, 0.9997479938239395, 0.00628288154268653, 784.902763300997, 784.5385372411637, 0.00204399406960069]
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[151423.11463812715, 13370.522156379518, -69.98729454400751, 0.1340252387456469, 0.13402553474183596, 0.13402583150380076, 0.13402612910491674, 0.13402642762152647, 0.1340267271330907, 0.1340270277223492 … 0.0011951806403485644, 0.001620067490472732, 0.0025077437013566683, 0.0016104609396225319, 0.9997242745675123, 0.9997222906486013, 0.006478196512972268, 781.9572018355344, 781.6384048976417, 0.0018118185740146633]
[151468.83532423564, 13324.93516364507, -69.90010637574454, 0.13346228447944836, 0.1334625711544277, 0.13346285866984853, 0.1334631470987181, 0.13346343651699616, 0.13346372700374579, 0.13346401864129295 … 0.0012114429563905495, 0.0016305987410686934, 0.002524040119170661, 0.0016307509259011616, 0.999718984794436, 0.9997170216065125, 0.006516711396670767, 781.140889736983, 780.8307127894604, 0.0017647781670401413]
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.