Effects of isoproterenol

Contents

Effects of isoproterenol#

using ModelingToolkit
using OrdinaryDiffEq, SteadyStateDiffEq, 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
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(),)

Without isoproterenol#

@unpack Istim = sys
callback = build_stim_callbacks(Istim, stimend; period=1second, starttime=stimstart)
@time sol = solve(prob, alg; callback)

  0.866076 seconds (65.78 k allocations: 215.070 MiB, 6.40% gc time)

retcode: Success
Interpolation: 3rd order Hermite
t: 4071-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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 183684.1140466068
 191258.90946281631
 199427.37350661293
 205000.0
u: 4071-element Vector{Vector{Float64}}:
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 ⋮
 [0.136944495257914, 0.13694464168446063, 0.13694477927589319, 0.13694490832270664, 0.13694502909967796, 0.13694514186691303, 0.13694524687081178, 0.1369453443449584, 0.13694543451094182, 0.13694551757911558  …  1.0026877925575108, 0.6766722833255902, 0.0015108660008013646, 0.006285742961034189, 0.9997476285219717, 0.9996108819600831, 0.21502044147161872, 151185.30233112013, 13607.749833006827, -70.43082440918054]
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i = (sys.t / 1000, sys.vm)
plot(sol, idxs=i, tspan=(100second, 101second), title="Action potential", xlabel="Time (s)")

_images/b190ca3a982f55a403368609cdf6fe61a4533dca62ac65b6a50d883eda173a26.png

plot(sol, idxs=(sys.t / 1000, [sys.Cai_sub_SR, sys.Cai_sub_SL, sys.Cai_mean]), tspan=(100second, 101second), title="Calcium transient", xlabel="Time (s)", ylabel="Conc. (μM)", label=["Ca (SR)" "Ca (SL)" "Ca (avg)"])

_images/f2ae0291809546749ce7b6b2d2d27fb2c92bb674ae2856816276820116c7f0de.png

plot(sol, idxs=(sys.t / 1000, sys.CaMKAct * 100), title="Active CaMKII", label=false, ylabel="Active fraction (%)", xlabel="Time (s)")

_images/87094db655d7faa2b8cc50192c9697906db4e325dd22053b852ae79b24a361ea.png

0.1uM isoproterenol#

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

retcode: Success
Interpolation: 3rd order Hermite
t: 4138-element Vector{Float64}:
      0.0
      0.019332211071584192
      0.09097534627605569
      0.20734339686524408
      0.4561200538541287
      1.0549952720719427
      2.0687580593126613
      3.5324261824253345
      6.954473747659736
     12.881140201769806
      ⋮
 152270.482708526
 157174.07587050938
 162194.01343084572
 168138.29627423352
 174916.26987407374
 181898.84288967986
 189304.81198883272
 197588.1225791665
 205000.0
u: 4138-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]
 [0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113  …  0.9911240291173739, 0.611792089769367, 0.0924276668078433, 0.007020212947405008, 0.9660018275573545, 0.221563993694571, 0.07192100944202194, 150952.75040560117, 13838.37575462767, -68.79688468304944]
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 ⋮
 [0.1269091035059655, 0.1269091478953703, 0.12690918191057013, 0.12690920585086127, 0.12690921999936527, 0.12690922462410742, 0.1269092199790097, 0.12690920630480712, 0.12690918382989289, 0.12690915277109957  …  1.0032363778515994, 0.6825988690960976, 0.0014756873624897583, 0.006216329537690998, 0.9997563697872125, 0.9995674489205095, 0.21944855504046362, 150927.44243962396, 13855.447607237576, -70.59411328189955]
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 [0.12486970350391131, 0.12486972522617236, 0.12486973834834862, 0.12486974311265439, 0.12486973974821655, 0.12486972847194712, 0.1248697094893477, 0.12486968299524859, 0.1248696491744957, 0.12486960820257982  …  1.00334502563846, 0.6721358889083349, 0.0015379203360091655, 0.006338953528048526, 0.9997408078707524, 0.9997426766643989, 0.2117434626483751, 151082.99594042654, 13700.121315694732, -70.30685771446615]
 [0.12429671621113456, 0.12429673188974771, 0.1242967394639483, 0.12429673916010314, 0.124296731192349, 0.12429671576340796, 0.12429669306533843, 0.12429666328022775, 0.12429662658083133, 0.12429658313116347  …  1.0033753931250984, 0.6690087581447743, 0.0015568059542798941, 0.006375667093769877, 0.9997360201470835, 0.9997382835800526, 0.20950321339328734, 151127.8129868295, 13655.370303312957, -70.22192860931868]
 [0.12371550434749742, 0.1237155143770396, 0.12371551678500632, 0.12371551178249247, 0.12371549956918754, 0.1237154803341359, 0.12371545425643725, 0.12371542150589232, 0.12371538224359924, 0.12371533662250409  …  1.0034061262070648, 0.6657442675035907, 0.0015766664531285265, 0.006414030171115832, 0.9997309526599986, 0.9997332832912293, 0.2071942081934502, 151173.81666220695, 13609.434641207697, -70.13370023408375]
 [0.1230961779894367, 0.12309618224061367, 0.12309617938237978, 0.12309616960970099, 0.12309615310700832, 0.12309613004890056, 0.12309610060079097, 0.12309606491950391, 0.12309602315382545, 0.1230959754450122  …  1.0034387981044124, 0.6621575614478484, 0.0015986588419268464, 0.006456227899200938, 0.999725301014825, 0.9997276295977499, 0.20469142947864624, 151223.46657862767, 13559.85838546061, -70.03725612195733]
 [0.1225682586558789, 0.12256825834962111, 0.12256825135792374, 0.12256823786249388, 0.12256821803522021, 0.12256819203882757, 0.12256816002748001, 0.12256812214733673, 0.12256807853706504, 0.12256802932831494  …  1.0034665858860294, 0.6590065479787393, 0.0016181313950653596, 0.00649334473351526, 0.9997202628390558, 0.9997225836604193, 0.20252160788615026, 151266.33084828782, 13517.057904846399, -69.9529408320586]

plot(sol2, idxs=(sys.t / 1000, sys.vm), tspan=(100second, 101second), title="Action potential", xlabel="Time (s)")

_images/82abf60cd4110d279b8c0bea881452ff9428320206a2edecd1ed933f435d6b66.png

plot(sol2, idxs=(sys.t / 1000, [sys.Cai_sub_SR, sys.Cai_sub_SL, sys.Cai_mean]), tspan=(100second, 101second), title="Calcium transcient", xlabel="Time (s)", ylabel="Conc. (μM)", label=["Ca (SR)" "Ca (SL)" "Ca (avg)"])

_images/8396ed7435d858b7c06d74d688d3d40555e92d49bc1951be46750f3b184ffc34.png

plot(sol2, idxs=(sys.t / 1000, sys.CaMKAct * 100), title="Active CaMKII", label=false, ylabel="Active fraction (%)", xlabel="Time (s)")

_images/c0592c7164c01edbb39075d389ad1b9dcc7cd0912071d1c3ecf4d3a1c344c52f.png

Comparison#

i = (sys.t / 1000, sys.Cai_mean)
tspan = (100second, 101second)
plot(sol, idxs=i, title="Calcium transcient", lab="ISO (-)"; tspan)
plot!(sol2, idxs=i, lab="ISO (0.1uM)", xlabel="Time (s)", ylabel="Concentration (μM)"; tspan)

_images/f8881b20b73c069d36d29de5badc77a116d6f333379ba08b50ec45bf33dd92fc.png

Compare the numbers

ca_ctl = sol(tspan[1]:1:tspan[2], idxs=sys.Cai_mean)
println(extrema(ca_ctl))

(0.23505056446792236, 0.5781214777886924)

ca_iso = sol2(tspan[1]:1:tspan[2], idxs=sys.Cai_mean)
println(extrema(ca_iso))

(0.19033626526983535, 0.7110939450938599)

savefig("iso-caT.pdf")
savefig("iso-caT.png")

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

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

_images/4ab3bc3617e3a5bce825e65dabbea725d7cd155fffb3e30f9e506bab71e46295.png

savefig("iso-camkact.pdf")
savefig("iso-camkact.png")

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

i = (sys.t / 1000, sys.vm)
tspan = (100second, 101second)
plot(sol, idxs=i, title="Action potential", lab="ISO (-)"; tspan)
plot!(sol2, idxs=i, lab="ISO (0.1uM)", xlabel="Time (ms)", ylabel="Voltage (mV)"; tspan)

_images/7e23b9b339879ceacc079ccb7b1e589f057c05dac0c9a39fde163fa9fade18ea.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"])

iso = chemicaldf[!, "isoproterenol 100nM Mean"]
iso_error = chemicaldf[!, "isoproterenol 100nM SD"] ./ sqrt.(chemicaldf[!, "isoproterenol 100nM N"])

plot(ts, ctl, yerr=ctl_error, lab="Control", color=:blue, markerstrokecolor=:blue)
plot!(ts, iso, yerr=iso_error, lab="ISO 100nM", color=:red, markerstrokecolor=:red)
plot!(xlabel="Time (sec.)", ylabel="CaMKII activity (A.U.)")

_images/e151e9cc176acf7e0374a623a6bdf51ee537fba88b436053999e3ebc4d9d0996.png

savefig("iso-exp.pdf")

"/home/runner/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/.cache/docs/iso-exp.pdf"

This notebook was generated using Literate.jl.