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)
6.514856 seconds (15.39 M allocations: 737.786 MiB, 1.57% gc time, 91.26% compilation time)
retcode: Success
Interpolation: 3rd order Hermite
t: 4019-element Vector{Float64}:
0.0
0.019333123284849308
0.09098129546757994
0.20735582943983855
0.45611910276862533
1.0472562928406122
2.0342667657223696
3.451776641148454
6.733792423912806
12.450117081023194
⋮
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199430.11091792677
205000.0
u: 4019-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)
0.620643 seconds (40.43 k allocations: 9.744 MiB, 8.08% gc time)
retcode: Success
Interpolation: 3rd order Hermite
t: 4019-element Vector{Float64}:
0.0
0.019333123284849367
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⋮
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u: 4019-element Vector{Vector{Float64}}:
[150952.75035000002, 13838.37602, -68.79268, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113 … 0.26081, 0.00977, 0.00188, 0.09243, 0.22156, 0.966, 0.00702, 830.0, 830.0, 0.0026]
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⋮
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ROS 0.5uM
prob3 = remake(prob, p=[sys.ROS => 0.5μM])
@time sol3 = solve(prob3, alg; callback)
0.568242 seconds (40.43 k allocations: 9.747 MiB)
retcode: Success
Interpolation: 3rd order Hermite
t: 4018-element Vector{Float64}:
0.0
0.01933312328485172
0.09098129546759129
0.20735582943986441
0.4561191027686822
1.047256292840743
2.0342667657226237
3.451776641148885
6.7337924239136475
12.45011708102475
⋮
148408.62966738208
152964.20825143054
157519.786835479
163269.67214080694
169696.5522318492
177943.5318763309
186190.5115208126
195849.1976897178
205000.0
u: 4018-element Vector{Vector{Float64}}:
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⋮
[151153.66117203393, 13639.413325041323, -70.49334025713556, 0.13722141493304396, 0.13722111372692478, 0.13722080305135947, 0.1372204826648577, 0.13722015231613355, 0.13721981174360678, 0.13721946067487198 … 0.0011048391859494729, 0.0015602453601087018, 0.0024151909057797435, 0.0014971820490073764, 0.9992130189138748, 0.9997510244003522, 0.006259077166460648, 784.2950884788013, 783.9283301565424, 0.0020423873558264175]
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[151469.08953916663, 13324.682038284704, -69.8996194736355, 0.1334591812894076, 0.13345946791944083, 0.13345975538973676, 0.13346004377328724, 0.1334603331460362, 0.13346062358702973, 0.1334609151785763 … 0.0012115349087125197, 0.0016306577856805638, 0.0025241314097101345, 0.0016308651725181304, 0.9997189548650767, 0.9997169918568466, 0.0065169271005958195, 781.1362782919936, 780.8261486449753, 0.001764519064408347]
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.